Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008033.1 Hibiscus syriacus cultivar Beakdansim tig00110515_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3048429
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 14
Found at i:1551128 original size:59 final size:59
Alignment explanation
Indices: 1550990--1551273 Score: 356
Period size: 59 Copynumber: 4.8 Consensus size: 59
1550980 TATATTTCCC
* * * * * ** * *
1550990 ATACAGAAATTCATACACTTAGTATGAGTTCCTTATC-TTTTTGCGCATAAAGTCCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACCAAGTGCCTA
* * * * *
1551048 ATACGAAAATTCATACGCTTAGTATGAATTTCTTAACATTTTTTCACACCGAGTGACTA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACCAAGTGCCTA
* * * *
1551107 ATACAGAAATTCACACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACCAAGTGCCTA
*
1551166 ATACGGAAATTCATACACTTAGTATGAATTCCTTAACATTTTTGCACA-CAAGGTGCCTA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACCAA-GTGCCTA
* *
1551225 ATACGGAAATTCATACACTCAGTATGAATTTCTTAACTTTTTTGCACAC
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACAC
1551274 TTAGTGTCAT
Statistics
Matches: 192, Mismatches: 31, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
58 33 0.17
59 159 0.83
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.34
Consensus pattern (59 bp):
ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACCAAGTGCCTA
Found at i:1551176 original size:118 final size:117
Alignment explanation
Indices: 1550990--1551273 Score: 399
Period size: 118 Copynumber: 2.4 Consensus size: 117
1550980 TATATTTCCC
* * * * *
1550990 ATACAGAAATTCATACACTTAGTATGAGTTCCTTATCTTTTTGCGCATAAAGTCCCCAATACGAA
1 ATACAGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTCCCCAATACGAA
* * * *
1551055 AATTCATACGCTTAGTATGAATTTCTTAACATTTTTTCACAC-CGAGTGACTA
66 AATTCATACACTTAGTATGAATTCCTTAACATTTTTGCACACAAG-GTGACTA
* * *
1551107 ATACAGAAATTCACACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCCCAATACGG
1 ATACAGAAATTCATACACTTAGTATGAATTTCTTAAC-TTTTTGCACACAAAGTCCCCAATACGA
*
1551172 AAATTCATACACTTAGTATGAATTCCTTAACATTTTTGCACACAAGGTGCCTA
65 AAATTCATACACTTAGTATGAATTCCTTAACATTTTTGCACACAAGGTGACTA
* *
1551225 ATACGGAAATTCATACACTCAGTATGAATTTCTTAACTTTTTTGCACAC
1 ATACAGAAATTCATACACTTAGTATGAATTTCTTAAC-TTTTTGCACAC
1551274 TTAGTGTCAT
Statistics
Matches: 148, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
117 33 0.22
118 114 0.77
119 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.34
Consensus pattern (117 bp):
ATACAGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTCCCCAATACGAA
AATTCATACACTTAGTATGAATTCCTTAACATTTTTGCACACAAGGTGACTA
Found at i:1551632 original size:20 final size:19
Alignment explanation
Indices: 1551607--1551649 Score: 63
Period size: 17 Copynumber: 2.3 Consensus size: 19
1551597 TCCATAGTAT
1551607 CGATACTACTACCCTGGTAC
1 CGATA-TACTACCCTGGTAC
1551627 CG--ATACTACCCTGGTAC
1 CGATATACTACCCTGGTAC
1551644 CGATAT
1 CGATAT
1551650 CCCCTTTCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 16 0.76
18 1 0.05
19 2 0.10
20 2 0.10
ACGTcount: A:0.26, C:0.33, G:0.16, T:0.26
Consensus pattern (19 bp):
CGATATACTACCCTGGTAC
Found at i:1551635 original size:17 final size:17
Alignment explanation
Indices: 1551613--1551648 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1551603 GTATCGATAC
1551613 TACTACCCTGGTACCGA
1 TACTACCCTGGTACCGA
1551630 TACTACCCTGGTACCGA
1 TACTACCCTGGTACCGA
1551647 TA
1 TA
1551649 TCCCCTTTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (17 bp):
TACTACCCTGGTACCGA
Found at i:1559284 original size:31 final size:32
Alignment explanation
Indices: 1559216--1559284 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 32
1559206 TTCATTCGTA
* * *
1559216 GTCACTTTCATTTCGTTTTAAATTAAGATGCG
1 GTCACTTTCATTTAGTTTTAAATTAAAATACG
* * *
1559248 ATCACTTTCGTTTAGTTTT-AATTAAAATATG
1 GTCACTTTCATTTAGTTTTAAATTAAAATACG
1559279 GTCACT
1 GTCACT
1559285 ACTCAGTTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
31 14 0.47
32 16 0.53
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.45
Consensus pattern (32 bp):
GTCACTTTCATTTAGTTTTAAATTAAAATACG
Found at i:1560270 original size:22 final size:22
Alignment explanation
Indices: 1560245--1560303 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
1560235 AATTCAGCTG
*
1560245 TTTGTAACTCATGCAATAAAGC
1 TTTGTAACTCTTGCAATAAAGC
* * *
1560267 TTTGTAACTCTTGTATTAATGC
1 TTTGTAACTCTTGCAATAAAGC
1560289 TTTGTAACTCTTGCA
1 TTTGTAACTCTTGCA
1560304 TTCATTATGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (22 bp):
TTTGTAACTCTTGCAATAAAGC
Found at i:1560606 original size:30 final size:30
Alignment explanation
Indices: 1560572--1560634 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
1560562 CCTAATTTTT
* *
1560572 TTTAAAAAAAATTTGAGGACTAAATTGAAA
1 TTTAAAAAAAATTTGAGGACCAAAGTGAAA
** *
1560602 TTTAAATTAAATTTGATGACCAAAGTGAAA
1 TTTAAAAAAAATTTGAGGACCAAAGTGAAA
1560632 TTT
1 TTT
1560635 TGATTAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.48, C:0.05, G:0.13, T:0.35
Consensus pattern (30 bp):
TTTAAAAAAAATTTGAGGACCAAAGTGAAA
Found at i:1560641 original size:30 final size:30
Alignment explanation
Indices: 1560580--1560644 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
1560570 TTTTTAAAAA
* *
1560580 AAATTTGAGGACTAAATTGAAATTTAAATT
1 AAATTTGAGGACCAAAGTGAAATTTAAATT
* **
1560610 AAATTTGATGACCAAAGTGAAATTTTGATT
1 AAATTTGAGGACCAAAGTGAAATTTAAATT
1560640 AAATT
1 AAATT
1560645 CGGATCCAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.45, C:0.05, G:0.14, T:0.37
Consensus pattern (30 bp):
AAATTTGAGGACCAAAGTGAAATTTAAATT
Found at i:1566223 original size:47 final size:47
Alignment explanation
Indices: 1566167--1566325 Score: 207
Period size: 47 Copynumber: 3.4 Consensus size: 47
1566157 AGAATCCTTC
*
1566167 CATGTATTTTTAGTTATGGCATCCTTTCATGCCTTAAT-AATTCCGTT
1 CATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGAATT-CGTT
* * * *
1566214 CATGCATTTTTAGTTTTGGCATCCGTTCATACCATAATGAA-TCTGTT
1 CATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGAATTC-GTT
*
1566261 CATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGCATAT-GTT
1 CATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGAAT-TCGTT
*
1566308 TATGCATTTTTAGTTATG
1 CATGCATTTTTAGTTATG
1566326 AATTCAGTTT
Statistics
Matches: 97, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
46 1 0.01
47 93 0.96
48 2 0.02
49 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.14, T:0.46
Consensus pattern (47 bp):
CATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGAATTCGTT
Found at i:1573037 original size:47 final size:47
Alignment explanation
Indices: 1572982--1573132 Score: 216
Period size: 47 Copynumber: 3.2 Consensus size: 47
1572972 GTTCCTTTCA
* * *
1572982 TTTT-GTTATGGCATCCTTTCATGCCTTTATGCATCCATTCATGTAT
1 TTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCAT
**
1573028 TTTTAGTTATAACATCCGTTT-ATGCCTTAATGCATCCGTTCATGCAT
1 TTTTAGTTATGGCATCC-TTTCATGCCTTAATGCATCCGTTCATGCAT
* *
1573075 TTTTAGTTATGGCGTCCTTTCATGCCTTAATGAATCCGTTCATGCAT
1 TTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCAT
1573122 TTTTAGTTATG
1 TTTTAGTTATG
1573133 AATTCGGTTT
Statistics
Matches: 93, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
46 7 0.08
47 83 0.89
48 3 0.03
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.46
Consensus pattern (47 bp):
TTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCAT
Found at i:1573709 original size:94 final size:94
Alignment explanation
Indices: 1573541--1573716 Score: 223
Period size: 94 Copynumber: 1.9 Consensus size: 94
1573531 TACTAACCTG
* * *
1573541 GTATCGATACTTCTATACTATGGTACCGATATCCCCTTTCAATATCGATACCATTTCTATATTTG
1 GTATCGATACTACTATACTATGGTACCGAAATCCCCTTTCAATATCGATACCATTTCTACATTTG
* * *
1573606 TGTTGCATGGTATCGATGCCCTTCTCTCA
66 AGATCCATGGTATCGATGCCCTTCTCTCA
* **
1573635 GTATCGATTCTACTATACTATGGTACCGAAA-CTCCCTTTCGGTATCGATACCATTT-TGACATT
1 GTATCGATACTACTATACTATGGTACCGAAATC-CCCTTTCAATATCGATACCATTTCT-ACATT
1573698 CT-AGATCCATGGTATCGAT
64 -TGAGATCCATGGTATCGAT
1573717 ACTTCCCCTT
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
93 2 0.03
94 67 0.96
95 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.38
Consensus pattern (94 bp):
GTATCGATACTACTATACTATGGTACCGAAATCCCCTTTCAATATCGATACCATTTCTACATTTG
AGATCCATGGTATCGATGCCCTTCTCTCA
Found at i:1573835 original size:14 final size:14
Alignment explanation
Indices: 1573813--1573851 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1573803 ACACCTTTAG
* *
1573813 TATCGGTACTGTTC
1 TATCAGTACCGTTC
1573827 TATCAGTACCGTTC
1 TATCAGTACCGTTC
*
1573841 TATCAATACCG
1 TATCAGTACCG
1573852 ATACCATTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (14 bp):
TATCAGTACCGTTC
Found at i:1576398 original size:21 final size:21
Alignment explanation
Indices: 1576374--1576422 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
1576364 TATTTTTAAG
1576374 ACACAATACTTGATTTTCTTA
1 ACACAATACTTGATTTTCTTA
1576395 ACACAATACTTGATTTTCTTA
1 ACACAATACTTGATTTTCTTA
1576416 ACACAAT
1 ACACAAT
1576423 TTATCTGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.37, C:0.20, G:0.04, T:0.39
Consensus pattern (21 bp):
ACACAATACTTGATTTTCTTA
Found at i:1577993 original size:36 final size:31
Alignment explanation
Indices: 1577903--1578004 Score: 159
Period size: 31 Copynumber: 3.3 Consensus size: 31
1577893 CGTTTAGGAT
* * *
1577903 AAGTGATCATATCTTAATTAAAACGAAATGA
1 AAGTGACCACATCTTAATTAAAACGAAACGA
1577934 AAGTGACCACATCTTAATTAAAACGAAACGA
1 AAGTGACCACATCTTAATTAAAACGAAACGA
*
1577965 AAGTGACCACATCTTAATTAAAACAAAACGA
1 AAGTGACCACATCTTAATTAAAACGAAACGA
*
1577996 AAATGACCA
1 AAGTGACCA
1578005 TAAATTAAAC
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 66 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.22
Consensus pattern (31 bp):
AAGTGACCACATCTTAATTAAAACGAAACGA
Found at i:1578238 original size:47 final size:47
Alignment explanation
Indices: 1578165--1578258 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
1578155 ACATTTTATA
*
1578165 ACATTTCATCATAGAACTTGGCTTGAGCTTAATTAAATGTAATTGTG
1 ACATTTCATCATAGAACTTGGATTGAGCTTAATTAAATGTAATTGTG
*
1578212 ACATTTCATCTTAGAACTTGGATTGAGCTTAATTAAATGTAATTGTG
1 ACATTTCATCATAGAACTTGGATTGAGCTTAATTAAATGTAATTGTG
1578259 GCTTTTATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (47 bp):
ACATTTCATCATAGAACTTGGATTGAGCTTAATTAAATGTAATTGTG
Found at i:1581723 original size:21 final size:19
Alignment explanation
Indices: 1581706--1581761 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 19
1581696 CATACATACT
1581706 AAAATATAAATATTACATA
1 AAAATATAAATATTACATA
**
1581725 ATTATATAATATATATACATA
1 AAAATATAA-ATAT-TACATA
1581746 AAAATATATAATATTA
1 AAAATATA-AATATTA
1581762 AAATATAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
19 7 0.23
20 6 0.20
21 16 0.53
22 1 0.03
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATATAAATATTACATA
Found at i:1582883 original size:811 final size:808
Alignment explanation
Indices: 1581315--1583659 Score: 3497
Period size: 812 Copynumber: 2.9 Consensus size: 808
1581305 TTATGAAATT
* * * *
1581315 TAAAAATAAATTAGGCATTTTAACTCGGGACTTAAAAGCATCAAGAGTCAAACTTCAAAACTACT
1 TAAAAATAAATTAGACATTTTAACTCGGGACTTGAAGGCATCAAAAGTCAAACTTCAAAACTACT
* *
1581380 TCACTTGTTAAAGCCATTTGTTTTATGGTTAAGAATTAGTTTTATTTATCTTATAACTGTGTTAA
66 TCACTTGTCAAAGCCATTTGTTTTATGGTTAAGAATTAATTTTATTTATCTTATAACTGTGTTAA
* * *
1581445 TTTTAATCATAAATTAATTTTGATTGTATATTAATTTATTTTAGTATTATAAATATTGTGAACAA
131 GTTTAATCATAAATTAATTTTGATTTTATATTAATTTATTTTAGTATTATAAATACTGTGAACAA
* * * *
1581510 TATGGTAAAGTCCATTTTTTT-AAGAAATTCCAAATATTATTAACTTGTTATGATGTACTCAACA
196 TATGGTAAAATCCATTTTTTTAAAGAAATTCCAAATATTATTAACTTGTTATGGTATAATCAACA
* * * *
1581574 ATTATTTGCCAAATACAATAGGGACAGTCATATTCAAAATATAAAGAACCAAAAGACAGCTCCAA
261 ATTATTTGCCAAATACAATAGGGACAATCATATTCAAAATATAAAGAACCAAAAGAGAGCGCCCA
* * *
1581639 AACAGCTAAAGTGTGTGATAAAAATAAAATTA-TTTTTAATAAATAACTAATTCTTTGCATACAT
326 AACA-CTAAAGTGTGTAATAAAAACAAAATTATTTTTTAATCAATAACTAATTCTTTGCATACAT
* *
1581703 ACTAAAATATAAATATTACATAATTATATAATATATATACATA-AAAATATATAATATTAAAATA
390 ACTAAAATATAAATATTACATAATTATATAATATATATACATACAACATATATAATATTAAAATT
* * * * *
1581767 TAAG-AAAATTTACAATGCTCGACGAGTACTGATGCGCACTAATAATTTAATTTATAAAAATTTA
455 TAAGAAAAATTTACAATGATTGACGAGTACAGATGAGCACTATTAATTTAATTTATAAAAATTTA
* *
1581831 AAATTCTAAAGGGCTCAGCGTATAATTATAAATTAGTTAAAAATTTGAAGGTAAATTATTTAAAA
520 AAATTATAAA-GGCTCAACGTATAATTATAAATTAGTTAAAAATTTGAAGGTAAATTATTTAAAA
* * * *
1581896 TAAAGAGTAAATTATATCA-TTGACCACCTAACTATTGCTCATTTTCATTTTGACCACCATTTTT
584 TAAAGAGTAAAATATATCAGTT-ACCACCTAACTATTGCCCATTTTCATTTTGGCC-TCATTTTT
* **
1581960 GAAATTTCATCAATCAGGTCACTCAACTATTTAGATGCATTCAATTAAGTCACTTGCTTTTAATA
647 GAAATTTCATCAATCAGGTCACTCAACTATTTAAATGCATTCAATTAAGTCACTTGCCATTAATA
* * **
1582025 TTTAACAGAGAAGCTGATGTGGCAATTAAAATATTTAGTACAATTACACATTTGGTCACTGTTAC
712 TTTAACGGAGAAACTGATGTGGCAATTAAAATATTTAGTACAATTACACATTTAATCACTGTTAC
*
1582090 TTATATATTATATT-AATTTATTCCTAATTTTA
777 TTATATATTAT-TTCAATTTAGTCCTAATTTTA
* *
1582122 GTAAAAATAAATTAGATATTTAAACTCGGGACTTGAAGGCATCAAAAGTCAAACTTCAAAACTAC
1 -TAAAAATAAATTAGACATTTTAACTCGGGACTTGAAGGCATCAAAAGTCAAACTTCAAAACTAC
* *
1582187 TTCACTTGTCAAAGCCACTTGTTTTATGGTTAAGAATTAATTTTATTTATCTTATAACTGCGTTA
65 TTCACTTGTCAAAGCCATTTGTTTTATGGTTAAGAATTAATTTTATTTATCTTATAACTGTGTTA
* * *
1582252 AGTTTAATCATAAATTAATTTTGATTTTATACTAATTTATTTTAGTATTGTAAATACTGTTAACA
130 AGTTTAATCATAAATTAATTTTGATTTTATATTAATTTATTTTAGTATTATAAATACTGTGAACA
*
1582317 ACATGGTAAAATCCATTTTTTTAAAGAAATTCCAAATATTATTAACTTGTTATGGTATAATCAAC
195 ATATGGTAAAATCCATTTTTTTAAAGAAATTCCAAATATTATTAACTTGTTATGGTATAATCAAC
** *
1582382 AATTATTTGCCAAATACAATATAGACAATCATATACAAAATATAAAGAACCAAAAGAGAGCGCCC
260 AATTATTTGCCAAATACAATAGGGACAATCATATTCAAAATATAAAGAACCAAAAGAGAGCGCCC
* *
1582447 AAACACTAAAGTGTGTTATAAAAACAAAATTATTTTTTAATCAATAACTAATTGTTTGCATACAT
325 AAACACTAAAGTGTGTAATAAAAACAAAATTATTTTTTAATCAATAACTAATTCTTTGCATACAT
1582512 ACTAAAATATAAATATTACATAATTATATAATATATATACATACAACATATATAATATTAAAATT
390 ACTAAAATATAAATATTACATAATTATATAATATATATACATACAACATATATAATATTAAAATT
* * * *
1582577 TAAGAAAAATTTACAATGTTTGACAAATACAGATGAGCACTATTAATTTAATTTATAAAAATTTT
455 TAAGAAAAATTTACAATGATTGACGAGTACAGATGAGCACTATTAATTTAATTTATAAAAATTTA
* * *
1582642 AAAGTATAAAGGACTCAATGTATATTTATAAATTAGTTAAAAATTTGAAGGTAAATTATTTAAAA
520 AAATTATAAAGG-CTCAACGTATAATTATAAATTAGTTAAAAATTTGAAGGTAAATTATTTAAAA
* *
1582707 TAAACAGTAAAATATATAAGTTACCACCTAACTATTGCCCATTTTCATTTTGGCCTCAATTTTTG
584 TAAAGAGTAAAATATATCAGTTACCACCTAACTATTGCCCATTTTCATTTTGGCCTC-ATTTTTG
* *
1582772 AAATTTCATCAATCAGGTCACTAAACTATTTAAATGCATTCAATTAAGTCACTTGCCGTTAATAT
648 AAATTTCATCAATCAGGTCACTCAACTATTTAAATGCATTCAATTAAGTCACTTGCCATTAATAT
* * * *
1582837 TTAACGGAGAAACTGATGTGGCAGTTAAAATATTTTGTATAATTACACATTTAATCATTGTTACT
713 TTAACGGAGAAACTGATGTGGCAATTAAAATATTTAGTACAATTACACATTTAATCACTGTTACT
* *
1582902 TATATATTCTTTCAATTTGGTCCTAATTTTA
778 TATATATTATTTCAATTTAGTCCTAATTTTA
*
1582933 -AATAAATAAATTATACATTTTAACTCGGGACTTGAAGGCATCAAAAGTCAAACTTCAAAACTAC
1 TAA-AAATAAATTAGACATTTTAACTCGGGACTTGAAGGCATCAAAAGTCAAACTTCAAAACTAC
* * *
1582997 TTCACTTATCAAAGCCATTTGTTTTATGGTTAAGAATTCATTTTATTTATCTTATAACTATGTTA
65 TTCACTTGTCAAAGCCATTTGTTTTATGGTTAAGAATTAATTTTATTTATCTTATAACTGTGTTA
1583062 AGTTTAATCATAAATTAATTTTGATTTTATATTAATTTATTTTAGTATTATAAATACTGTGAACA
130 AGTTTAATCATAAATTAATTTTGATTTTATATTAATTTATTTTAGTATTATAAATACTGTGAACA
* * * *
1583127 ATATGGTAAAATCCA-TTTTTTAAAGAAATTCCAAATATTATTATCCTGTTATGGCATCATCAAC
195 ATATGGTAAAATCCATTTTTTTAAAGAAATTCCAAATATTATTAACTTGTTATGGTATAATCAAC
* * * * **
1583191 AACTATTTGCCAAATACAATAGGGAAAATCATATTCAAAACATAAAAAAAATGAAAAGAGAGCGC
260 AATTATTTGCCAAATACAATAGGGACAATCATATTC-AAA-ATATAAAGAACCAAAAGAGAGCGC
*
1583256 CCAAACAACTAAAGTGTGCAATAAAAACAAAATTATTTTTTAATCAATAACTAATTCTTTGCATA
323 CCAAAC-ACTAAAGTGTGTAATAAAAACAAAATTATTTTTTAATCAATAACTAATTCTTTGCATA
* * *
1583321 CATACTAAAATATAAATATTGCATAATTATATAATATATATTCATACAACATATATAATAATAAA
387 CATACTAAAATATAAATATTACATAATTATATAATATATATACATACAACATATATAATATTAAA
* * * * * * *
1583386 ATTTAAGAAAATTTTACAA-CATTCAGTGAGTACCGATGAACACTATTAATTTAGTTTATAAAAA
452 ATTTAAGAAAAATTTACAATGATTGA-CGAGTACAGATGAGCACTATTAATTTAATTTATAAAAA
* * *
1583450 TTTAAAATTTTAAAAGGTTCAACGTATAATTATAAATTAGTTAAAAATTTGAAGGTAAATTACTT
516 TTTAAAATTAT-AAAGGCTCAACGTATAATTATAAATTAGTTAAAAATTTGAAGGTAAATTATTT
* * *
1583515 AAAATAAAGAGTAAACTATATCAGTGGA-CACCTAA-TGATTGCCCATTTTCATTTTGGACATCA
580 AAAATAAAGAGTAAAATATATCAGT-TACCACCTAACT-ATTGCCCATTTTCATTTTGG-CCTCA
* ** * *
1583578 TTTTTTAAATTTTGTCAATCAAGTCACTCAACTATTTAAATGCATCCAATTAAGTCACTTGCCAT
642 TTTTTGAAATTTCATCAATCAGGTCACTCAACTATTTAAATGCATTCAATTAAGTCACTTGCCAT
1583643 TAATATTTAACGGAGAA
707 TAATATTTAACGGAGAA
1583660 GTTGATAGAG
Statistics
Matches: 1392, Mismatches: 128, Indels: 30
0.90 0.08 0.02
Matches are distributed among these distances:
808 223 0.16
809 253 0.18
810 225 0.16
811 336 0.24
812 346 0.25
813 9 0.01
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (808 bp):
TAAAAATAAATTAGACATTTTAACTCGGGACTTGAAGGCATCAAAAGTCAAACTTCAAAACTACT
TCACTTGTCAAAGCCATTTGTTTTATGGTTAAGAATTAATTTTATTTATCTTATAACTGTGTTAA
GTTTAATCATAAATTAATTTTGATTTTATATTAATTTATTTTAGTATTATAAATACTGTGAACAA
TATGGTAAAATCCATTTTTTTAAAGAAATTCCAAATATTATTAACTTGTTATGGTATAATCAACA
ATTATTTGCCAAATACAATAGGGACAATCATATTCAAAATATAAAGAACCAAAAGAGAGCGCCCA
AACACTAAAGTGTGTAATAAAAACAAAATTATTTTTTAATCAATAACTAATTCTTTGCATACATA
CTAAAATATAAATATTACATAATTATATAATATATATACATACAACATATATAATATTAAAATTT
AAGAAAAATTTACAATGATTGACGAGTACAGATGAGCACTATTAATTTAATTTATAAAAATTTAA
AATTATAAAGGCTCAACGTATAATTATAAATTAGTTAAAAATTTGAAGGTAAATTATTTAAAATA
AAGAGTAAAATATATCAGTTACCACCTAACTATTGCCCATTTTCATTTTGGCCTCATTTTTGAAA
TTTCATCAATCAGGTCACTCAACTATTTAAATGCATTCAATTAAGTCACTTGCCATTAATATTTA
ACGGAGAAACTGATGTGGCAATTAAAATATTTAGTACAATTACACATTTAATCACTGTTACTTAT
ATATTATTTCAATTTAGTCCTAATTTTA
Found at i:1584835 original size:18 final size:18
Alignment explanation
Indices: 1584812--1584860 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
1584802 AAATCAAGCA
1584812 ATTTTCCTTTCAATATTC
1 ATTTTCCTTTCAATATTC
1584830 ATTTTCCTTTCAATATTC
1 ATTTTCCTTTCAATATTC
*
1584848 ATTTTGCTTTCAA
1 ATTTTCCTTTCAA
1584861 AGAACACCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.22, C:0.20, G:0.02, T:0.55
Consensus pattern (18 bp):
ATTTTCCTTTCAATATTC
Found at i:1589776 original size:23 final size:23
Alignment explanation
Indices: 1589744--1589805 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
1589734 CCCCCCATGA
*
1589744 GGGAATCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
*
1589767 GGGAACCGATTCCCCATTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
1589790 GGGAACCGATTCCCCC
1 GGGAACCGATTCCCCC
1589806 CACAGGGGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.23, C:0.31, G:0.26, T:0.21
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:1605701 original size:122 final size:122
Alignment explanation
Indices: 1605561--1605806 Score: 492
Period size: 122 Copynumber: 2.0 Consensus size: 122
1605551 GGTTAATATG
1605561 ATTTTTTGTAAACAAATAATAATAATAATTGAAGGATCTTATTTATAAATTTTCCTTTTTTAGTT
1 ATTTTTTGTAAACAAATAATAATAATAATTGAAGGATCTTATTTATAAATTTTCCTTTTTTAGTT
1605626 TTGGGATATTATAGAGTTCATGTGAAAGTGCATTAATTGATTTATTTGAATTATTTT
66 TTGGGATATTATAGAGTTCATGTGAAAGTGCATTAATTGATTTATTTGAATTATTTT
1605683 ATTTTTTGTAAACAAATAATAATAATAATTGAAGGATCTTATTTATAAATTTTCCTTTTTTAGTT
1 ATTTTTTGTAAACAAATAATAATAATAATTGAAGGATCTTATTTATAAATTTTCCTTTTTTAGTT
1605748 TTGGGATATTATAGAGTTCATGTGAAAGTGCATTAATTGATTTATTTGAATTATTTT
66 TTGGGATATTATAGAGTTCATGTGAAAGTGCATTAATTGATTTATTTGAATTATTTT
1605805 AT
1 AT
1605807 AATAATTATT
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
122 124 1.00
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.48
Consensus pattern (122 bp):
ATTTTTTGTAAACAAATAATAATAATAATTGAAGGATCTTATTTATAAATTTTCCTTTTTTAGTT
TTGGGATATTATAGAGTTCATGTGAAAGTGCATTAATTGATTTATTTGAATTATTTT
Found at i:1608195 original size:26 final size:26
Alignment explanation
Indices: 1608160--1608209 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1608150 TGATTCAAGA
1608160 ATATCATCAAG-TTCAGAAATGAATAG
1 ATATCATCAAGCTT-AGAAATGAATAG
* *
1608186 ATATCCTCAAGCTTTGAAATGAAT
1 ATATCATCAAGCTTAGAAATGAAT
1608210 GGAAAAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 19 0.90
27 2 0.10
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (26 bp):
ATATCATCAAGCTTAGAAATGAATAG
Found at i:1618275 original size:3 final size:3
Alignment explanation
Indices: 1618267--1618296 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
1618257 TAAATATAAA
1618267 TAT TAT TAT TAT TAT TACT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TA
1618297 CATATTTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1618290 original size:13 final size:13
Alignment explanation
Indices: 1618267--1618302 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1618257 TAAATATAAA
1618267 TATTA-TTATTAT
1 TATTACTTATTAT
1618279 TATTACTTATTAT
1 TATTACTTATTAT
*
1618292 TATTACATATT
1 TATTACTTATT
1618303 TTGCAGCACC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTACTTATTAT
Found at i:1620885 original size:17 final size:18
Alignment explanation
Indices: 1620863--1620897 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1620853 TGTCTTTTAA
*
1620863 ATTAAAATTA-ATATTTT
1 ATTAAAATGACATATTTT
1620880 ATTAAAATGACATATTTT
1 ATTAAAATGACATATTTT
1620898 TATAGTGCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (18 bp):
ATTAAAATGACATATTTT
Found at i:1624560 original size:955 final size:944
Alignment explanation
Indices: 1622712--1624613 Score: 3612
Period size: 955 Copynumber: 2.0 Consensus size: 944
1622702 CATTTTTCCG
1622712 AGAGTTCTCAGACATATTGATGTATCAGTGGTTGACATATTTGAAAGACTGGATAGACATGTGGA
1 AGAGTTCTCAGACATATTGATGTATCAGTGGTTGACATATTTGAAAGACTGGATAGACATGTGGA
1622777 TCCTGTTCCAGTTATTCTGGTAGAAACATTTCGTTCCCTGAGCTCTTGCCGAAGAGAAGGGGAAG
66 TCCTGTTCCAGTTATTCTGGTAGAAACATTTCGTTCCCTGAGCTCTTGCCGAAGAGAAGGGGAAG
1622842 GACGATTCATAGGTTGCACCATTATGCTAACATGGATCCTTAGTCATTTCAAACACTTCGAGAGA
131 GACGATTCATAGGTTGCACCATTATGCTAACATGGATCCTTAGTCATTTCAAACACTTCGAGAGA
1622907 GCACCTGGTCGGGTCTCTTAGATGGTTTTTCACTGTTGAAGGATTTCATTTCTCGACAGTGGCTG
196 GCACCTGGTCGGGTCTCTTAGATGGTTTTTCACTGTTGAAGGATTTCATTTCTCGACAGTGGCTG
1622972 GGTTTTACTGAGGAAAAGTGGATGGTCCTTTTCAAAAGTATCCGAGACAGTAACATTCTATGGCG
261 GGTTTTACTGAGGAAAAGTGGATGGTCCTTTTCAAAAGTATCCGAGACAGTAACATTCTATGGCG
1623037 TACCTCATGGAATGTCTCATCCGACATATTGTATCGATGTGGAGACAGAGATTGGGTTCCATTAC
326 TACCTCATGGAATGTCTCATCCGACATATTGTATCGATGTGGAGACAGAGATTGGGTTCCATTAC
1623102 CTGGTATTTGGGGATCTGTAGGGTATGCCCCATTACTGGTTTCCCGACAATTTGGGTCGAGACAA
391 CTGGTATTTGGGGATCTGTAGGGTATGCCCCATTACTGGTTTCCCGACAATTTGGGTCGAGACAA
1623167 TTTATTCCAACAACAAAGGAGTTATCTAAGTCAGGTTCTCATTCAAGGGAGAATGTATAAGAATA
456 TTTATTCCAACAACAAAGGAGTTATCTAAGTCAGGTTCTCATTCAAGGGAGAATGTATAAGAATA
1623232 AGTTAAAGGGGTCACTGATGCTGGAGACACACCCATCGGGTAAATCTCTTTACTTTTGAGTCAAT
521 AGTTAAAGGGGTCACTGATGCTGGAGACACACCCATCGGGTAAATCTCTTTACTTTTGAGTCAAT
1623297 GCTATCTCGAGGATACGAGAAGTGGATAAGCAACCGAGTCAATGATAATATTCCAATAGGCAATC
586 GCTATCTCGAGGATACGAGAAGTGGATAAGCAACCGAGTCAATGATAATATTCCAATAGGCAATC
*
1623362 AAGAGAATATCCATCTATGGAAGAACACCTCAGCGTGATCCCGTCTTCGCTCGAAACAAGCCAGA
651 AAGAGAATATCCATCTATGGAAGAACACCTCAGCGTGATCCCGTCTCCGCTCGAAACAAGCCAGA
*
1623427 TTGATTTTGAGGTAGAGATGAAACAATGGAGAGTAACTTTGCAAAAGCTAGAAGATGAAGTGTAT
716 TTGATTTTGAGGTAGAAATGAAACAATGGAGAGTAACTTTGCAAAAGCTAGAAGATGAAGTGTAT
1623492 CAGAAAGGGTTGGAGATTGACATCTAAAAGAGTCGGGCTGATCGGATTGAAAAAGTGGAGAAGCA
781 CAGAAAGGGTTGGAGATTGACATCTAAAAGAGTCGGGCTGATCGGATTGAAAAAGTGGAGAAGCA
1623557 ACTTAGATTGGATTTCGATGACCTCCATTTATCACACCAACGAATGATC-AAGATCCGGCATCTG
846 ACTTAGATTGGATTTCGATGACCTCCATTTATCACACCAACGAATGATCAAAGATCCGGCATCTG
1623621 CTAGCTCTAGTAAGTCTTCTACTGAATGGAGGCA
911 CTAGCTCTAGTAAGTCTTCTACTGAATGGAGGCA
*
1623655 AGAGTGTCTCGGACATATTGATGTATCAGTGGTTGACATATTTGAAAGACTGGATAGACATGTGG
1 AGAGT-TCTCAGACATATTGATGTATCAGTGGTTGACATATTTGAAAGACTGGATAGACATGTGG
1623720 ATCCTGTTCCAGTTATTCTGGTAGAAACATTTCGTTCCCTGAGCTCTTGCCGAAGAGAAGGGGAA
65 ATCCTGTTCCAGTTATTCTGGTAGAAACATTTCGTTCCCTGAGCTCTTGCCGAAGAGAAGGGGAA
1623785 GGACGATTCATAGGTTGTGCACCATTATTGCTAACATGGATCCTTAGTCATTTCAAACACTTCGA
130 GGACGATTCATAGG-T-TGCACCATTA-TGCTAACATGGATCCTTAGTCATTTCAAACACTTCGA
1623850 GAGAGCACCTGGTCGGGTCTTCTTAGATGGTTTTTCACTGTTGAAGGATTTCATTTCTCGACAGT
192 GAGAGCACCTGGTCGGGTC-TCTTAGATGGTTTTTCACTGTTGAAGGATTTCATTTCTCGACAGT
1623915 GGCCTGGGGGTTTTACTGAGGAAAAGTGGATGGTCCTTTTCAAAAGTATCCGAGACAGTAACATT
256 GG-CT--GGGTTTTACTGAGGAAAAGTGGATGGTCCTTTTCAAAAGTATCCGAGACAGTAACATT
1623980 CTATGGCGTACCTCATGGAATGTCTCATCCGACATATTGTATCGATGTGGAGACAGAGATTGGGT
318 CTATGGCGTACCTCATGGAATGTCTCATCCGACATATTGTATCGATGTGGAGACAGAGATTGGGT
*
1624045 TCCATTACCTGGTATTTGGGGATCTGTAGGGTATGCCCCATTACTGGTTTCCCGATAATTTGGGT
383 TCCATTACCTGGTATTTGGGGATCTGTAGGGTATGCCCCATTACTGGTTTCCCGACAATTTGGGT
*
1624110 CGAGACAATTTATTCCAACAACAAAGGAGTTATCTAAGTCCGAGTTCTCATTCAAGGGAGAATTG
448 CGAGACAATTTATTCCAACAACAAAGGAGTTATCTAAGTCAG-GTTCTCATTCAAGGGAGAA-TG
1624175 TATAAGAATAAAGTTAAAGGGGTCACTGATGCTTGGAGACACACCCATCGGGTAAATCTCTTTAC
511 TATAAGAAT-AAGTTAAAGGGGTCACTGATGC-TGGAGACACACCCATCGGGTAAATCTCTTTAC
1624240 TTTTGAGTCAATGCTATCTCGAGGATACGAGAAGTGGATAAGCAACCGAGTCAATGATAATATTC
574 TTTTGAGTCAATGCTATCTCGAGGATACGAGAAGTGGATAAGCAACCGAGTCAATGATAATATTC
1624305 CAATAGGCAATCAAGAGAATATCCAATCTATGGAAGAACACCTCAGCGTGATCCCGTCTCCGCTC
639 CAATAGGCAATCAAGAGAATATCC-ATCTATGGAAGAACACCTCAGCGTGATCCCGTCTCCGCTC
1624370 G-AACAAGCCAGACTTGATTTTGAGGTAGAAATGAAACAATGGAGAGTAACTTTGCAAAAGCTAG
703 GAAACAAGCCAGA-TTGATTTTGAGGTAGAAATGAAACAATGGAGAGTAACTTTGCAAAAGCTAG
1624434 AAGATGAAGTGTATCA-AAAGGGTTGGAGATTGACATCTAAAAGAGTCGGGCTGATCGGATTGAA
767 AAGATGAAGTGTATCAGAAAGGGTTGGAGATTGACATCTAAAAGAGTCGGGCTGATCGGATTGAA
1624498 AAAGTGGAGAAGCAACTTAGATTGGATTTCGATGACCTCCATTTATCACACCAACGAATGATCAA
832 AAAGTGGAGAAGCAACTTAGATTGGATTTCGATGACCTCCATTTATCACACCAACGAATGATCAA
1624563 AGATCCGGCATCTGCTAGCTCTAGTAAGTCTTCTACTGAATGGAGGCA
897 AGATCCGGCATCTGCTAGCTCTAGTAAGTCTTCTACTGAATGGAGGCA
1624611 AGA
1 AGA
1624614 AGTGGCAGGA
Statistics
Matches: 939, Mismatches: 5, Indels: 17
0.98 0.01 0.02
Matches are distributed among these distances:
943 5 0.01
944 137 0.15
945 1 0.00
946 10 0.01
947 56 0.06
948 47 0.05
949 2 0.00
951 228 0.24
952 19 0.02
953 11 0.01
954 22 0.02
955 243 0.26
956 158 0.17
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (944 bp):
AGAGTTCTCAGACATATTGATGTATCAGTGGTTGACATATTTGAAAGACTGGATAGACATGTGGA
TCCTGTTCCAGTTATTCTGGTAGAAACATTTCGTTCCCTGAGCTCTTGCCGAAGAGAAGGGGAAG
GACGATTCATAGGTTGCACCATTATGCTAACATGGATCCTTAGTCATTTCAAACACTTCGAGAGA
GCACCTGGTCGGGTCTCTTAGATGGTTTTTCACTGTTGAAGGATTTCATTTCTCGACAGTGGCTG
GGTTTTACTGAGGAAAAGTGGATGGTCCTTTTCAAAAGTATCCGAGACAGTAACATTCTATGGCG
TACCTCATGGAATGTCTCATCCGACATATTGTATCGATGTGGAGACAGAGATTGGGTTCCATTAC
CTGGTATTTGGGGATCTGTAGGGTATGCCCCATTACTGGTTTCCCGACAATTTGGGTCGAGACAA
TTTATTCCAACAACAAAGGAGTTATCTAAGTCAGGTTCTCATTCAAGGGAGAATGTATAAGAATA
AGTTAAAGGGGTCACTGATGCTGGAGACACACCCATCGGGTAAATCTCTTTACTTTTGAGTCAAT
GCTATCTCGAGGATACGAGAAGTGGATAAGCAACCGAGTCAATGATAATATTCCAATAGGCAATC
AAGAGAATATCCATCTATGGAAGAACACCTCAGCGTGATCCCGTCTCCGCTCGAAACAAGCCAGA
TTGATTTTGAGGTAGAAATGAAACAATGGAGAGTAACTTTGCAAAAGCTAGAAGATGAAGTGTAT
CAGAAAGGGTTGGAGATTGACATCTAAAAGAGTCGGGCTGATCGGATTGAAAAAGTGGAGAAGCA
ACTTAGATTGGATTTCGATGACCTCCATTTATCACACCAACGAATGATCAAAGATCCGGCATCTG
CTAGCTCTAGTAAGTCTTCTACTGAATGGAGGCA
Found at i:1632465 original size:24 final size:24
Alignment explanation
Indices: 1632438--1632489 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
1632428 GACAAAAATG
*
1632438 AAAAATGAAAGAAAAAGGAAAGAAA
1 AAAAATGAAA-AAAAAGAAAAGAAA
* *
1632463 AAAAATGAGAAAAAATAAAAGAAA
1 AAAAATGAAAAAAAAGAAAAGAAA
1632487 AAA
1 AAA
1632490 TAAAAGGAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (24 bp):
AAAAATGAAAAAAAAGAAAAGAAA
Found at i:1632485 original size:12 final size:12
Alignment explanation
Indices: 1632438--1632495 Score: 57
Period size: 12 Copynumber: 4.9 Consensus size: 12
1632428 GACAAAAATG
*
1632438 AAAAATGAAAG-
1 AAAAATAAAAGA
**
1632449 AAAAAGGAAAGA
1 AAAAATAAAAGA
*
1632461 AAAAA-AATGAGA
1 AAAAATAA-AAGA
1632473 AAAAATAAAAGA
1 AAAAATAAAAGA
1632485 AAAAATAAAAG
1 AAAAATAAAAG
1632496 GAGGGTTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
11 11 0.28
12 27 0.68
13 2 0.05
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.07
Consensus pattern (12 bp):
AAAAATAAAAGA
Found at i:1633762 original size:113 final size:113
Alignment explanation
Indices: 1633563--1634106 Score: 799
Period size: 113 Copynumber: 4.8 Consensus size: 113
1633553 GGTTCGATCC
* * *
1633563 CGATTCAATGGATCAATTCCTCC-TGATCTGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTC
1 CGATTCAATGGATCAACTCCCCCAT-ATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTC
* *
1633627 TTATCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTACC-
65 TTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTTCCT
* * *
1633675 CTGATTCAATGGATTAACTCCCCCATATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTTTT
1 C-GATTCAATGGATCAACTCCCCCATATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTC
*
1633740 TTTTCTAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTATCCT
65 TTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCT-TCCT
* *
1633790 -GATTCAATGGATCAACTCCCCCATACATGATATTCCCTTCAGAGTAAGCGAAACATGTCTCT-T
1 CGATTCAATGGATCAACTCCCCCATATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCT
* * *
1633853 TCTTCTAAGGTTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTTCTT
66 T-TTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTTCCT
* *
1633902 CGATTCAATGGATTAACTCCCCCAGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCT
1 CGATTCAATGGATCAACTCCCCCATATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCT
* * *
1633967 TTTCCAAGATTTGATATTCCATTCAGAGTAAGTGGAACAAGTCTGCTT
66 TTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTTCCT
* * * *
1634015 CGATTCAATGGATCAACTTCCCCAAATCTGATAGTCCCTTCAGAGTAAGCGGAACATGTCTCTCT
1 CGATTCAATGGATCAACTCCCCCATATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCT
* *
1634080 TCTCAAAGATTTGATATTCCCTTCAGA
66 TTTCCAAGATTTGATATTCCCTTCAGA
1634107 TGGAATAGAT
Statistics
Matches: 394, Mismatches: 31, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
112 6 0.02
113 383 0.97
114 5 0.01
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (113 bp):
CGATTCAATGGATCAACTCCCCCATATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCT
TTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTTCCT
Found at i:1636115 original size:12 final size:12
Alignment explanation
Indices: 1636098--1636123 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1636088 TGGTATGATT
1636098 TATAATTTATAG
1 TATAATTTATAG
1636110 TATAATTTATAG
1 TATAATTTATAG
1636122 TA
1 TA
1636124 AACTTTCTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TATAATTTATAG
Found at i:1638981 original size:22 final size:21
Alignment explanation
Indices: 1638935--1639006 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 21
1638925 TTCGCCTGAA
*
1638935 AAAAATGAAAAAGACAA-AAATG
1 AAAAATGAAAAA-A-AAGAAAAG
*
1638957 AAAAATGAAAGAAAAAGGAAAGAA
1 AAAAATGAAA-AAAAA-GAAA-AG
*
1638981 AAAAATGAGAAAAAAGAAAAG
1 AAAAATGAAAAAAAAGAAAAG
1639002 AAAAA
1 AAAAA
1639007 ATAAAAGGAG
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
21 8 0.19
22 15 0.36
23 10 0.24
24 9 0.21
ACGTcount: A:0.76, C:0.01, G:0.17, T:0.06
Consensus pattern (21 bp):
AAAAATGAAAAAAAAGAAAAG
Found at i:1638992 original size:15 final size:15
Alignment explanation
Indices: 1638932--1639006 Score: 66
Period size: 15 Copynumber: 5.0 Consensus size: 15
1638922 TATTTCGCCT
1638932 GAAAAAAATGAAAAA
1 GAAAAAAATGAAAAA
*
1638947 GACAAAAATGAAAAA
1 GAAAAAAATGAAAAA
* *
1638962 TGAAAGAAAAAG-GAAA
1 -GAAA-AAAATGAAAAA
1638978 GAAAAAAATGAGAAAA
1 GAAAAAAATGA-AAAA
*
1638994 -AAGAAAA-GAAAAA
1 GAAAAAAATGAAAAA
1639007 ATAAAAGGAG
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
13 4 0.08
14 7 0.14
15 24 0.49
16 9 0.18
17 5 0.10
ACGTcount: A:0.76, C:0.01, G:0.17, T:0.05
Consensus pattern (15 bp):
GAAAAAAATGAAAAA
Found at i:1639008 original size:22 final size:24
Alignment explanation
Indices: 1638957--1639007 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
1638947 GACAAAAATG
*
1638957 AAAAATGAAAGAAAAAGGAAAGAA
1 AAAAATGAAAGAAAAAGAAAAGAA
*
1638981 AAAAATGAGA-AAAAAGAAAAGAA
1 AAAAATGAAAGAAAAAGAAAAGAA
1639004 AAAA
1 AAAA
1639008 TAAAAGGAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (24 bp):
AAAAATGAAAGAAAAAGAAAAGAA
Found at i:1639012 original size:12 final size:12
Alignment explanation
Indices: 1638951--1639013 Score: 51
Period size: 12 Copynumber: 5.4 Consensus size: 12
1638941 GAAAAAGACA
*
1638951 AAAATGAAAAATG
1 AAAA-GAAAAAAG
1638964 -AAAG-AAAAAG
1 AAAAGAAAAAAG
*
1638974 GAAAGAAAAAA-
1 AAAAGAAAAAAG
**
1638985 ATGAGAAAAAAG
1 AAAAGAAAAAAG
*
1638997 AAAAGAAAAAAT
1 AAAAGAAAAAAG
1639009 AAAAG
1 AAAAG
1639014 GAGGGTTCAA
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
10 5 0.12
11 13 0.32
12 22 0.55
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.06
Consensus pattern (12 bp):
AAAAGAAAAAAG
Found at i:1640192 original size:48 final size:48
Alignment explanation
Indices: 1640136--1640264 Score: 231
Period size: 48 Copynumber: 2.7 Consensus size: 48
1640126 CCTCCTGATC
* *
1640136 TGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCTTATCCAAGATT
1 TGATATTCCCTTCAGAGTAAGTGGAACATGTCTCTATTATCCAAGATT
1640184 TGATATTCCCTTCAGAGTAAGTGGAACATGTCTCTATTATCCAAGATT
1 TGATATTCCCTTCAGAGTAAGTGGAACATGTCTCTATTATCCAAGATT
*
1640232 TGATATTCCCTTCAGAGTAAGTGGAACAAGTCT
1 TGATATTCCCTTCAGAGTAAGTGGAACATGTCT
1640265 ACCTTGATTC
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 78 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (48 bp):
TGATATTCCCTTCAGAGTAAGTGGAACATGTCTCTATTATCCAAGATT
Found at i:1640343 original size:113 final size:113
Alignment explanation
Indices: 1640179--1640699 Score: 715
Period size: 113 Copynumber: 4.6 Consensus size: 113
1640169 CTCTTATCCA
* * * *
1640179 AGATTTGATATTCCCTTCAGAGTAAGTGGAACATGTCTCTATTATCCAAGATTTGATATTCCCTT
1 AGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCTTTTCCAAGATTTGATATTCCCTT
* *
1640244 CAGAGTAAGTGGAACAAGTCTACCTT-GATTCAATGGATTAACTCCCCC
66 CAGAGTAAGTGGAACAAGTCT-GCTTCGATTCAATGGATCAACTCCCCC
* *
1640292 AGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTTTTTTCTAAGATTTGATATTCCCTT
1 AGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCTTTTCCAAGATTTGATATTCCCTT
* * *
1640357 CAGAGTAGGTGGAACAAGTCTATCAT-GATTCAATGGATCAACTCCCCC
66 CAGAGTAAGTGGAACAAGTCT-GCTTCGATTCAATGGATCAACTCCCCC
* * * * *
1640405 AGACATGATATTCCCTTCAGAGTAAGCGAAACATGTCTCT-TTCTTCTAAGGTTTGATATTCCCC
1 AGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCTT-TTCCAAGATTTGATATTCCCT
*
1640469 TCAGAGTAAGTGGAACAAGTCTGCTTCGATTCAATGGATTAACTCCCCC
65 TCAGAGTAAGTGGAACAAGTCTGCTTCGATTCAATGGATCAACTCCCCC
* * *
1640518 AGATATGATATTCCCTTCAGAGTAAGCAGAACATGTCTCTCTTTTCCAAGATTTGATATTTCATT
1 AGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCTTTTCCAAGATTTGATATTCCCTT
* *
1640583 CAGAGTAAATGGAACAAGTCTGCTTCGATTCAATGGATCAACTTCCCC
66 CAGAGTAAGTGGAACAAGTCTGCTTCGATTCAATGGATCAACTCCCCC
* * * * * * * **
1640631 AAATCTGATAGTCCCTTCAGAGTAAGCAGAACAGGTCTCTCTTCTCAAAGATTTTTTATTCCCTT
1 AGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCTTTTCCAAGATTTGATATTCCCTT
1640696 CAGA
66 CAGA
1640700 TGGAATAGAT
Statistics
Matches: 367, Mismatches: 38, Indels: 6
0.89 0.09 0.01
Matches are distributed among these distances:
112 4 0.01
113 361 0.98
114 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (113 bp):
AGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCTTTTCCAAGATTTGATATTCCCTT
CAGAGTAAGTGGAACAAGTCTGCTTCGATTCAATGGATCAACTCCCCC
Found at i:1640903 original size:3 final size:3
Alignment explanation
Indices: 1640895--1640924 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
1640885 TAAATATAAA
1640895 TAT TAT TAT TAT TAT TACT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TA
1640925 CATATTTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1640918 original size:13 final size:13
Alignment explanation
Indices: 1640895--1640930 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1640885 TAAATATAAA
1640895 TATTA-TTATTAT
1 TATTACTTATTAT
1640907 TATTACTTATTAT
1 TATTACTTATTAT
*
1640920 TATTACATATT
1 TATTACTTATT
1640931 TTGCAGCACC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTACTTATTAT
Found at i:1644126 original size:15 final size:15
Alignment explanation
Indices: 1644066--1644127 Score: 63
Period size: 15 Copynumber: 4.0 Consensus size: 15
1644056 TATTTCGCCT
1644066 GAAAAAAATGAAAAA
1 GAAAAAAATGAAAAA
*
1644081 GACAAAAATGAAAAA
1 GAAAAAAATGAAAAA
* *
1644096 TGAAAGAAAAAG-GAAA
1 -GAAA-AAAATGAAAAA
1644112 GAAAAAAATGAGAAAA
1 GAAAAAAATGA-AAAA
1644128 AATAAAAGGA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
14 5 0.14
15 18 0.49
16 9 0.24
17 5 0.14
ACGTcount: A:0.74, C:0.02, G:0.18, T:0.06
Consensus pattern (15 bp):
GAAAAAAATGAAAAA
Found at i:1645437 original size:113 final size:114
Alignment explanation
Indices: 1645238--1645781 Score: 729
Period size: 113 Copynumber: 4.8 Consensus size: 114
1645228 GGTTCGATCC
* ** * *
1645238 CGATTCAATGGATCAATTCATCCTGATCTGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCT
1 CGATTCAATGGATCAACTCCCCCAGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCT
* * *
1645303 TATCCAAGATTTGATATTCCCTTCAGAGTTAGTGGAACAAGTCTACCCT
66 TTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTAGCCT
* * * *
1645352 -GATTCAATGGATTAACTCCCCCAGATATGATATTCCCTTCAGAGTAAGCAGAAAATGTCTCTTT
1 CGATTCAATGGATCAACTCCCCCAGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCT
* *
1645416 TTTCTAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTATCCT
66 TTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTAGCCT
* * * * *
1645465 -GATTCAATGGATCAACTCCCCTAGACATGATATTCCCTTCACAGTAAGTGGAACATGCCTCT-T
1 CGATTCAATGGATCAACTCCCCCAGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCT
* * * * *
1645528 TCTTCTAAGGTTTGATATTCCCTTCAAAGTAAGTGGAACAAGTC-GGCTT
66 T-TTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTAGCCT
*
1645577 CGATTCAATGGATTAACTCCCCCAGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCT
1 CGATTCAATGGATCAACTCCCCCAGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCT
* *
1645642 TTTCCAAGATTTGATATTCCATTCAGAGTAAGTGGAACAAGTCT-GCTT
66 TTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTAGCCT
* * * * * *
1645690 CGATTCAATGGATCAAATTCCCCAAATCTGATAGTCCCTTCAGAGTAAGCGGAACAGGTCTCTCT
1 CGATTCAATGGATCAACTCCCCCAGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCT
* *
1645755 TCTCAAAGATTTGATATTCCCTTCAGA
66 TTTCCAAGATTTGATATTCCCTTCAGA
1645782 TGGAATAGAT
Statistics
Matches: 380, Mismatches: 46, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
112 4 0.01
113 374 0.98
114 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (114 bp):
CGATTCAATGGATCAACTCCCCCAGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCT
TTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTAGCCT
Found at i:1645985 original size:3 final size:3
Alignment explanation
Indices: 1645977--1646006 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
1645967 TAAATATAAA
1645977 TAT TAT TAT TAT TAT TACT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TA
1646007 CATATTTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1646000 original size:13 final size:13
Alignment explanation
Indices: 1645977--1646012 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1645967 TAAATATAAA
1645977 TATTA-TTATTAT
1 TATTACTTATTAT
1645989 TATTACTTATTAT
1 TATTACTTATTAT
*
1646002 TATTACATATT
1 TATTACTTATT
1646013 TTGCAGCACC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTACTTATTAT
Found at i:1650587 original size:11 final size:11
Alignment explanation
Indices: 1650571--1650621 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
1650561 AGACAAAAAT
1650571 GAAAAATGAAA
1 GAAAAATGAAA
*
1650582 GAAAAAGGAAA
1 GAAAAATGAAA
*
1650593 GAAAAAAATGAGA
1 G--AAAAATGAAA
*
1650606 -AAAAATAAAA
1 GAAAAATGAAA
1650616 GAAAAA
1 GAAAAA
1650622 ATTAAATGAG
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
10 8 0.25
11 16 0.50
13 8 0.25
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (11 bp):
GAAAAATGAAA
Found at i:1650600 original size:31 final size:33
Alignment explanation
Indices: 1650545--1650608 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
1650535 ATATTTCGCC
*
1650545 TGAAAAAAAAAGAAAAAGACAAAAATGA-AAAA
1 TGAAAAAAAAAGAAAAAGAAAAAAATGAGAAAA
* *
1650577 TGAAAGAAAAAG-GAAAGAAAAAAATGAGAAAA
1 TGAAAAAAAAAGAAAAAGAAAAAAATGAGAAAA
1650609 AATAAAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 13 0.46
32 15 0.54
ACGTcount: A:0.75, C:0.02, G:0.17, T:0.06
Consensus pattern (33 bp):
TGAAAAAAAAAGAAAAAGAAAAAAATGAGAAAA
Found at i:1650623 original size:22 final size:24
Alignment explanation
Indices: 1650553--1650622 Score: 72
Period size: 23 Copynumber: 2.9 Consensus size: 24
1650543 CCTGAAAAAA
1650553 AAAGAAAAAGACAAA-AATGAAAAATG
1 AAAGAAAAAGA-AAAGAA--AAAAATG
*
1650579 AAAGAAAAAGGAAAGAAAAAAATG
1 AAAGAAAAAGAAAAGAAAAAAATG
* *
1650603 AGA-AAAAATAAAAGAAAAAA
1 AAAGAAAAAGAAAAGAAAAAA
1650623 TTAAATGAGG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
23 15 0.38
24 9 0.23
25 3 0.08
26 12 0.31
ACGTcount: A:0.77, C:0.01, G:0.16, T:0.06
Consensus pattern (24 bp):
AAAGAAAAAGAAAAGAAAAAAATG
Found at i:1651835 original size:44 final size:43
Alignment explanation
Indices: 1651763--1651878 Score: 141
Period size: 44 Copynumber: 2.7 Consensus size: 43
1651753 CTTGATCTGA
*
1651763 TATTCCCTTCAGAGT-AGC-GAACATGTCTCTCTTATCCAAGATT
1 TATTCCCTTCAGAGTAATCGGAACATGTCTCT-TTAT-CAAGATT
1651806 TATT-CCTTCAGAGTAATCGGAACATGTCTCTTTATCAAGATT
1 TATTCCCTTCAGAGTAATCGGAACATGTCTCTTTATCAAGATT
* *
1651848 GATTTCCCTTCAGAGTAAGT-GGAACAAGTCT
1 TA-TTCCCTTCAGAGTAA-TCGGAACATGTCT
1651879 ACCCTGATTC
Statistics
Matches: 65, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
42 18 0.28
43 12 0.18
44 34 0.52
45 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (43 bp):
TATTCCCTTCAGAGTAATCGGAACATGTCTCTTTATCAAGATT
Found at i:1652004 original size:113 final size:113
Alignment explanation
Indices: 1651806--1652307 Score: 707
Period size: 113 Copynumber: 4.5 Consensus size: 113
1651796 ATCCAAGATT
* *
1651806 TATT-CCTTCAGAGTAATCGGAACATGTCTC-TTTATC-AAGA-TTGAT-TTCCCTTCAGAGTAA
1 TATTCCCTTCAGAGTAAGCGGAACATGTCTCTTTTTTCTAAGATTTGATATTCCCTTCAGAGTAA
* *
1651866 GTGGAACAAGTCTACC-CTGATTCAATGGATTAACTCCCCCAGATATGA
66 GTGGAACAAGTCTTCCTC-GATTCAATGGATCAACTCCCCCAGATATGA
1651914 TATTCCCTTCAGAGTAAGCGGAACATGTCTCTTTTTTCTAAGATTTGATATTCCCTTCAGAGTAA
1 TATTCCCTTCAGAGTAAGCGGAACATGTCTCTTTTTTCTAAGATTTGATATTCCCTTCAGAGTAA
*
1651979 GTGGAACAAGTCTATCCT-GATTCAATGGATCAACTCCCCCAGACATGA
66 GTGGAACAAGTCT-TCCTCGATTCAATGGATCAACTCCCCCAGATATGA
* * * *
1652027 TATTCCCTTCAGAGTAAGTGGAACATGTCTCTTTCTTCTAAGGTTTGATATTCCCTTCAGATTAA
1 TATTCCCTTCAGAGTAAGCGGAACATGTCTCTTTTTTCTAAGATTTGATATTCCCTTCAGAGTAA
* *
1652092 GTGGAACAAGTCTTCTTCGATTCAATGGATTAACTCCCCCAGATATGA
66 GTGGAACAAGTCTTCCTCGATTCAATGGATCAACTCCCCCAGATATGA
* * *
1652140 TATTCCCTTCAGAGTAAGCGGAACATGTCTC--TTTTCCAAGATTTGATATTCCCTTCATAGTGA
1 TATTCCCTTCAGAGTAAGCGGAACATGTCTCTTTTTTCTAAGATTTGATATTCCCTTCAGAGTAA
* * * * *
1652203 GTGGAACAAGTCTGCTTCGATTCAATGGATCAACTTCCCCAAATCTGA
66 GTGGAACAAGTCTTCCTCGATTCAATGGATCAACTCCCCCAGATATGA
* * * * *
1652251 TAGTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAAAGATTTGATATTCCCTT
1 TATTCCCTTCAGAGTAAGCGGAACATGTCTCTTTTTTCTAAGATTTGATATTCCCTT
1652308 TAGATGGAAT
Statistics
Matches: 356, Mismatches: 28, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
108 4 0.01
109 25 0.07
110 5 0.01
111 102 0.29
112 8 0.02
113 210 0.59
114 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (113 bp):
TATTCCCTTCAGAGTAAGCGGAACATGTCTCTTTTTTCTAAGATTTGATATTCCCTTCAGAGTAA
GTGGAACAAGTCTTCCTCGATTCAATGGATCAACTCCCCCAGATATGA
Found at i:1652515 original size:3 final size:3
Alignment explanation
Indices: 1652507--1652536 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
1652497 TAAATATAAA
1652507 TAT TAT TAT TAT TAT TACT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TA
1652537 CATATTTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1652530 original size:13 final size:13
Alignment explanation
Indices: 1652507--1652542 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1652497 TAAATATAAA
1652507 TATTA-TTATTAT
1 TATTACTTATTAT
1652519 TATTACTTATTAT
1 TATTACTTATTAT
*
1652532 TATTACATATT
1 TATTACTTATT
1652543 TTGCAGCACC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTACTTATTAT
Found at i:1654357 original size:12 final size:12
Alignment explanation
Indices: 1654340--1654365 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1654330 ATATCTAATT
1654340 TATAATTTATAG
1 TATAATTTATAG
1654352 TATAATTTATAG
1 TATAATTTATAG
1654364 TA
1 TA
1654366 CACTTTCTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TATAATTTATAG
Found at i:1657033 original size:11 final size:11
Alignment explanation
Indices: 1657017--1657068 Score: 61
Period size: 11 Copynumber: 4.6 Consensus size: 11
1657007 AGACAAAATT
*
1657017 GAAAAATGAAA
1 GAAAAAAGAAA
1657028 GAAAAAAGAAA
1 GAAAAAAGAAA
*
1657039 GAAAAAA-AAT
1 GAAAAAAGAAA
1657049 GAGAAAAAGAAAA
1 GA-AAAAAG-AAA
1657062 GAAAAAA
1 GAAAAAA
1657069 TAAAAGGAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
10 4 0.11
11 22 0.63
12 5 0.14
13 4 0.11
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:1657044 original size:23 final size:24
Alignment explanation
Indices: 1657018--1657072 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
1657008 GACAAAATTG
1657018 AAAAATGAAAGA-AAAAAG-AAAGA
1 AAAAAT-AAAGAGAAAAAGAAAAGA
*
1657041 AAAAA-AATGAGAAAAAGAAAAGA
1 AAAAATAAAGAGAAAAAGAAAAGA
1657064 AAAAATAAA
1 AAAAATAAA
1657073 AGGAGGGTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 4 0.15
22 6 0.22
23 15 0.56
24 2 0.07
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (24 bp):
AAAAATAAAGAGAAAAAGAAAAGA
Found at i:1657073 original size:12 final size:11
Alignment explanation
Indices: 1657025--1657074 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
1657015 TTGAAAAATG
*
1657025 AAAGAAAAAAG
1 AAAGAAAAAAA
1657036 AAAGAAAAAAA
1 AAAGAAAAAAA
* *
1657047 ATGAGAAAAAGA
1 A-AAGAAAAAAA
1657059 AAAGAAAAAATA
1 AAAGAAAAAA-A
1657071 AAAG
1 AAAG
1657075 GAGGGTTCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
11 18 0.56
12 14 0.44
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:1658260 original size:48 final size:48
Alignment explanation
Indices: 1658204--1658332 Score: 222
Period size: 48 Copynumber: 2.7 Consensus size: 48
1658194 CCTCCTGATC
1658204 TGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCTTATCCAAGATT
1 TGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCTTATCCAAGATT
1658252 TGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCTTATCCAAGATT
1 TGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCTTATCCAAGATT
** * *
1658300 TGATATTCATTTCAGAGTAAGTGGAACAAGTCT
1 TGATATTCCCTTCAGAGTAAGCGGAACATGTCT
1658333 ACCCTGATTC
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 77 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (48 bp):
TGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCTTATCCAAGATT
Found at i:1658452 original size:113 final size:113
Alignment explanation
Indices: 1658247--1658767 Score: 726
Period size: 113 Copynumber: 4.6 Consensus size: 113
1658237 CTCTTATCCA
* * **
1658247 AGATTTGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCTTATCCAAGATTTGATATTCATTT
1 AGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCTTTTCCAAGATTTGATATTCCCTT
*
1658312 CAGAGTAAGTGGAACAAGTCTACC-CTGATTCAAAT-GATTAACTCCCCC
66 CAGAGTAAGTGGAACAAGTCTACCTC-GATTC-AATGGATCAACTCCCCC
* *
1658360 AGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTTTTTTCTAAGATTTGATATTCCCTT
1 AGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCTTTTCCAAGATTTGATATTCCCTT
1658425 CAGAGTAAGTGGAACAAGTCTATCCT-GATTCAATGGATCAACTCCCCC
66 CAGAGTAAGTGGAACAAGTCTA-CCTCGATTCAATGGATCAACTCCCCC
* * * *
1658473 AGACATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCT-TTCTTCTAAGGTTTTATATTCCCT
1 AGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCTT-TTCCAAGATTTGATATTCCCT
* * * *
1658537 TCAGAGTAAGTGGAACAAGTCTGCTTCGATTCAATGGATTAATTCCCCC
65 TCAGAGTAAGTGGAACAAGTCTACCTCGATTCAATGGATCAACTCCCCC
* * *
1658586 AGATATGATATTCCCTTCAGAGTAAGTGGAACATGTCTCTCTTTTCCAAGATTAGATATTCCATT
1 AGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCTTTTCCAAGATTTGATATTCCCTT
* *
1658651 CAGAGTAAGTGGAACAAGTCTACTTCGATTCAATGGATCAACTTCCCC
66 CAGAGTAAGTGGAACAAGTCTACCTCGATTCAATGGATCAACTCCCCC
* * * * * * * *
1658699 AAATCTGATAGTCCCTTCAGAGTAAGCGAAACAGGTCTCTCTTCTCAAAAATTTGATATTCCCTT
1 AGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCTTTTCCAAGATTTGATATTCCCTT
1658764 CAGA
66 CAGA
1658768 TGGAATAGAT
Statistics
Matches: 366, Mismatches: 36, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
112 7 0.02
113 355 0.97
114 4 0.01
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (113 bp):
AGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCTTTTCCAAGATTTGATATTCCCTT
CAGAGTAAGTGGAACAAGTCTACCTCGATTCAATGGATCAACTCCCCC
Found at i:1658971 original size:3 final size:3
Alignment explanation
Indices: 1658963--1659007 Score: 72
Period size: 3 Copynumber: 14.7 Consensus size: 3
1658953 TAAATATAAA
*
1658963 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TACT TGT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TA
1659008 CATATTTTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 37 0.95
4 2 0.05
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1665943 original size:84 final size:84
Alignment explanation
Indices: 1665782--1665944 Score: 227
Period size: 84 Copynumber: 1.9 Consensus size: 84
1665772 AACTCGTCAG
* * *
1665782 GTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTG
1 GTCTTTGGTTGACAAATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGACTTGGAGCTG
**
1665847 AGCGTAGTCGAACTCGAAC
66 AGCGTAACCGAACTCGAAC
* * * * *
1665866 GTCTTTGGTTGACAAATAGCCCTTCTTGCCTTGAGTTATGTTGCAAATGATGTGACTTGGAGCTG
1 GTCTTTGGTTGACAAATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGACTTGGAGCTG
*
1665931 AGTGTAACCGAACT
66 AGCGTAACCGAACT
1665945 TGAAAGTTTG
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
84 68 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.31
Consensus pattern (84 bp):
GTCTTTGGTTGACAAATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGACTTGGAGCTG
AGCGTAACCGAACTCGAAC
Found at i:1666039 original size:37 final size:37
Alignment explanation
Indices: 1665994--1666328 Score: 168
Period size: 36 Copynumber: 8.6 Consensus size: 37
1665984 TTATTTTTTG
1665994 TGTTTCAAGAGAAACTGTCTCAAGAAAGATAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAAAGATAAAACTT
* * *
1666031 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGAGAAACTGTCTCAAGAAAGATAAAACTT
*
1666067 TGTTTCAAGAGAGACAAAACTTAGT-TC-CGAAAG---AAAC--
1 TGTTTC-A-AGAG---AAAC-T-GTCTCAAGAAAGATAAAACTT
* * * * *
1666104 TGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAAGATTT
1 TGTTTC-A---AGA-GAAA-CTGTCTC-AAG-AAAGATA---AAA-CT-T
*
1666154 TGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAA-TT
1 TGTTTCAAGAGAAACTGTCTCAAGAAAGATAAAACTT
* * *
1666190 TGTTTCAAGGGAAATTGTCTCAAGAAACATAAAA-TT
1 TGTTTCAAGAGAAACTGTCTCAAGAAAGATAAAACTT
* * *
1666226 TGTTTCAAGAGAAACTGTCTAAAGATAGACAAAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAAAGATAAA-AC----TT
* * *
1666268 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAAAGATAAAACTT
* * * *
1666305 AGTTCCAAAAGAAATTGTCTCAAG
1 TGTTTCAAGAGAAACTGTCTCAAG
1666329 GGAGACGAAA
Statistics
Matches: 234, Mismatches: 32, Indels: 64
0.71 0.10 0.19
Matches are distributed among these distances:
36 70 0.30
37 70 0.30
38 6 0.03
39 8 0.03
40 4 0.02
41 10 0.04
42 40 0.17
43 5 0.02
44 5 0.02
45 4 0.02
46 6 0.03
49 1 0.00
50 5 0.02
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTGTCTCAAGAAAGATAAAACTT
Found at i:1666087 original size:58 final size:58
Alignment explanation
Indices: 1666013--1666198 Score: 203
Period size: 58 Copynumber: 3.1 Consensus size: 58
1666003 AGAAACTGTC
* *
1666013 TCAAGAAAGATAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTT
1 TCAAGAAAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTT
* * * * *
1666071 TCAAGAGAGACAAAACTTAGTTCCGAA-AGAAACTGTCTCAAGGGAGACGAAATTTGTT
1 TCAAGAAAGACAAAACTTTGTTTC-AAGAGAAACTGTCTCAAGAGAGACAAAATTTGTT
* * *
1666129 TCAAAGAAAACATATTCAAAGATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAATTTGTT
1 TC-AAG--AA-AGA--CAAA-ACTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTT
1666194 TCAAG
1 TCAAG
1666199 GGAAATTGTC
Statistics
Matches: 104, Mismatches: 15, Indels: 12
0.79 0.11 0.09
Matches are distributed among these distances:
58 50 0.48
59 5 0.05
61 1 0.01
62 2 0.02
64 9 0.09
65 37 0.36
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (58 bp):
TCAAGAAAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTT
Found at i:1666209 original size:36 final size:36
Alignment explanation
Indices: 1666152--1666345 Score: 208
Period size: 36 Copynumber: 5.2 Consensus size: 36
1666142 ATTCAAAGAT
* *
1666152 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAA
1 TTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAA
* * * *
1666188 TTTGTTTCAAGGGAAATTGTCTCAAGAAACATAAAA
1 TTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAA
* *
1666224 TTTGTTTCAAGAGAAACTGTCTAAAGATAGACAAAGACAAAA
1 TTTGTTTCAAGAGAAATTGTCTCAAG--AG----AGACAAAA
1666266 TTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAA
* * * * *
1666302 CTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAA
1 -TTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAA
1666339 TTTGTTT
1 TTTGTTT
1666346 AACGTAAAAC
Statistics
Matches: 132, Mismatches: 19, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
36 68 0.52
37 31 0.23
38 1 0.01
40 2 0.02
42 30 0.23
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAA
Found at i:1666276 original size:78 final size:72
Alignment explanation
Indices: 1666152--1666345 Score: 210
Period size: 78 Copynumber: 2.6 Consensus size: 72
1666142 ATTCAAAGAT
* * *
1666152 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGGGAAATTGTCTCAAGAAA
1 TTTGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAATTTGTTTCAAGAGAAATTGTCTCAAGAAA
1666217 CATAAAA
66 CATAAAA
1666224 TTTGTTTCAAGAGAAACTGTCTAAAGATAGACAAAGACAAAATTTGTTTCAAGAGAAATTGTCTC
1 TTTGTTTCAAGAGAAACTGTCTAAAG--AG----AGACAAAATTTGTTTCAAGAGAAATTGTCTC
*
1666289 AAGAGAGACA-AAAC
60 AAGA-A-ACATAAAA
* * * * * * *
1666303 TTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAATTTGTTT
1 TTTGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAATTTGTTT
1666346 AACGTAAAAC
Statistics
Matches: 103, Mismatches: 11, Indels: 15
0.80 0.09 0.12
Matches are distributed among these distances:
72 25 0.24
73 14 0.14
74 2 0.02
77 1 0.01
78 33 0.32
79 25 0.24
80 3 0.03
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (72 bp):
TTTGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAATTTGTTTCAAGAGAAATTGTCTCAAGAAA
CATAAAA
Found at i:1666279 original size:42 final size:42
Alignment explanation
Indices: 1666220--1666300 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
1666210 CAAGAAACAT
*
1666220 AAAATTTGTTTCAAGAGAAACTGTCTAAAGATAGACAAAGAC
1 AAAATTTGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAGAC
* *
1666262 AAAATTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAA
1 AAAATTTGTTTCAAGAGAAACTGTCTAAAGAGAGACAAA
1666301 ACTTAGTTCC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.25
Consensus pattern (42 bp):
AAAATTTGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAGAC
Found at i:1666431 original size:36 final size:37
Alignment explanation
Indices: 1666363--1666432 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 37
1666353 AACATATTCA
* *
1666363 AAGATTTTGTTTCAAGGTAAATTGTCTCAAGAGATAT
1 AAGATTTTGTTTCAAGGTAAACTATCTCAAGAGATAT
*
1666400 AAGA-TTTGTTTCAAGAG-AAACTATCTTAAGAGA
1 AAGATTTTGTTTCAAG-GTAAACTATCTCAAGAGA
1666433 GACAAAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 24 0.83
37 5 0.17
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.34
Consensus pattern (37 bp):
AAGATTTTGTTTCAAGGTAAACTATCTCAAGAGATAT
Found at i:1668369 original size:14 final size:13
Alignment explanation
Indices: 1668346--1668391 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
1668336 TTTTCCTTTG
*
1668346 TTTTTGTTTCTCT
1 TTTTTTTTTCTCT
1668359 TTTTTATTTTCTCT
1 TTTTT-TTTTCTCT
*
1668373 TTGTTTTTTCTCT
1 TTTTTTTTTCTCT
1668386 TTTTTT
1 TTTTTT
1668392 CCTTTTTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 18 0.62
14 11 0.38
ACGTcount: A:0.02, C:0.13, G:0.04, T:0.80
Consensus pattern (13 bp):
TTTTTTTTTCTCT
Found at i:1668399 original size:24 final size:26
Alignment explanation
Indices: 1668335--1668401 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 26
1668325 TTTTCTTCAC
1668335 TTTTTCCTTTGTT-TTTGTTTCTCTTTT
1 TTTTTCCTTT-TTGTTTGTTTCTC-TTT
* *
1668362 TTATTTTCTCTTTGTTT-TTTCTC-TT
1 TT-TTTCCTTTTTGTTTGTTTCTCTTT
1668387 TTTTTCCTTTTTGTT
1 TTTTTCCTTTTTGTT
1668402 ATGATTGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
24 11 0.32
25 4 0.12
27 10 0.29
28 9 0.26
ACGTcount: A:0.01, C:0.15, G:0.06, T:0.78
Consensus pattern (26 bp):
TTTTTCCTTTTTGTTTGTTTCTCTTT
Found at i:1670453 original size:13 final size:14
Alignment explanation
Indices: 1670435--1670465 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1670425 GAATCAAACG
1670435 AAAAATAA-AATAA
1 AAAAATAATAATAA
1670448 AAAAATAATAATAA
1 AAAAATAATAATAA
1670462 AAAA
1 AAAA
1670466 TTTAACAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (14 bp):
AAAAATAATAATAA
Found at i:1672566 original size:21 final size:21
Alignment explanation
Indices: 1672528--1672567 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1672518 TTTAATCATA
*
1672528 AATTAATTTTTATTTTATATT
1 AATTAATTTTTATATTATATT
* *
1672549 AATTTATTTTTGTATTATA
1 AATTAATTTTTATATTATA
1672568 AATACTGTGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (21 bp):
AATTAATTTTTATATTATATT
Found at i:1673183 original size:752 final size:755
Alignment explanation
Indices: 1671952--1674266 Score: 2549
Period size: 810 Copynumber: 3.0 Consensus size: 755
1671942 TTATATTTAA
*
1671952 TCAATAACTAATTTTTTGCATACGGGCTAAAATAAAAATATTCAATAATTAAATAATATATATAT
1 TCAATAACTAATTTTTTGCATACGGACTAAAATAAAAATATTCAATAATTAAATAATATATATAT
* *
1672017 ATACAACATATATAATATTAAAATTTAAGAAAATTTTACAACACTCGACGAATACTGATGAGCAC
66 AAACAACATATATAATATTAAAATTTAAGAAAATTTTACAACACTCGACGAATACTGATGAACAC
* * * *
1672082 TGTTAATTTAATTTATAAAAATTTAAAATTCTAAAGGCCTCAACGTATAATTGTAAATTAGTTAA
131 TATTAAATTAATTTATAAAAATTTAAAATTCTAAAGGCCTAAACGTATAATTATAAATTAGTTAA
*
1672147 AAATTGAAGGTAAATTATTTAAAATAAAAGTAAACTATATCAGTAACACCTAACTATTGACCATT
196 AAATTAAAGGTAAATTATTTAAAATAAAAGTAAACTATATCAGTAACACCTAACTATTGACCATT
*** * * * *
1672212 TTCATTTTGACCGTTATTTTTGAAAATTTCGTCAATCATGTCACTCAATTATTTAAATATATTCA
261 TTCATTTTGACCACCATTTTTGAAAATTTAGTCAATCAGGTCACTCAACTATTTAAATACATTCA
* * * * *
1672277 ATTAAATTATTTTCCGTTAATATTTAACAGAGAAGATGATGTGGTAGTTAAAATATTTGGTTATA
326 ATTAAATCACTTGCCGTTAATATTTAACAGAGAAGATGAAGTGGTAGTTAAAATATTAGGTTATA
* * * * *
1672342 ATTACACATTTGATTATTGTTACTTATATTTTTTTATCAATTTGATCCTTATTTTAATAAAATAA
391 ACTACACATTTGATCACTGTTACTTATATTATTCTATCAATTTGATCCTTATTTTAATAAAATAA
* *
1672407 ATTAGGCATTTTAACTCGGGACTCGAAGGCAGCAAAAG-TC-AA-ACTTCACTTGTCAAAGCTAT
456 ATTAGGCATTTTAACTCAGGACTCGAAGGCAGCAAAAGATCAAACACTTCACTTGTCAAAGCCAT
** *
1672469 TTGTTTTATGGTTA-ATAATTAATTTTATTTATCTTATAATTGTGTTAAGTTTAATCATAAATTA
521 TTGTTTTATGGTTACA-AATTAATTTTATTTATCTTATAATTGCCTTAAGTTTAATCATAAATAA
* * *
1672533 ATTTTTATTTTATATTAATTTATTTTTGTATTATAAATACTGTGAACAATATGGAAAAATCCAAT
585 ATTTTCATTTCATATTAATTTATTTTAGTATTATAAATACTGTGAACAATATGGAAAAATCCAA-
* * * *
1672598 TTTTTAAAGAAATTCCAAATATTATTAACCTGTTATGGCATCATCAACAACTATTTGCTAGATAC
649 TTTTTAAACAAACTCCAAATATTATTAACCTGTTATGGCATCATCAACAACGATTTGCTAAATAC
1672663 AATAGGGACAGTCATATTCAAA-ATAAAAAAGTTATTTTTCG
714 AATAGGGACAGTCATATTCAAATATAAAAAAGTTATTTTTCG
* *
1672704 TCAATAACTAATTCTTTT-CATACGTACTAAAATAAAAATATT-ACATAATTATATAATATATAT
1 TCAATAACTAATT-TTTTGCATACGGACTAAAATAAAAATATTCA-ATAATTAAATAATATATAT
* ** *
1672767 TTAAACAACATATATAATATTAAAATTTAAGAAAATTTTACAATGCTCGACGATTA-TCGATGAA
64 ATAAACAACATATATAATATTAAAATTTAAGAAAATTTTACAACACTCGACGAATACT-GATGAA
* * *
1672831 TACTATTAAATTAATTTATGAAAATTTAAGATTCTAAATGG-CTAAACGTATAATTATAAATTAG
128 CACTATTAAATTAATTTATAAAAATTTAAAATTCTAAA-GGCCTAAACGTATAATTATAAATTAG
*
1672895 TTAAAAATTTAAAGGTAAATTATTTAAAATAAAGAGTAAACTATATCAGTGACAACCTAACTATT
192 TTAAAAA-TTAAAGGTAAATTATTTAAAATAAA-AGTAAACTATATCAGTAAC-ACCTAACTATT
*
1672960 GACCATTTTCATTTTGACCACCATTTTTG-AAATTTAGTCTATCAGGTCACTCAACTATTTAAAT
254 GACCATTTTCATTTTGACCACCATTTTTGAAAATTTAGTCAATCAGGTCACTCAACTATTTAAAT
* * * * * *
1673024 GCATTTAATTAAGTCACTTGCCGTTAATATTTAACGGTGAAGCTGAAGTGGTAGTTAAAATATTA
319 ACATTCAATTAAATCACTTGCCGTTAATATTTAACAGAGAAGATGAAGTGGTAGTTAAAATATTA
* * * *
1673089 GG-TCTAACTATACATTTTG-TCACTGTTAGTTATA-TATTCTATCAATTTGGT-CTTAATTTTA
384 GGTTATAACTACACA-TTTGATCACTGTTACTTATATTATTCTATCAATTTGATCCTT-ATTTTA
*
1673150 ATAAAATAAATTAGGCATTTTAACTCAGGACTCGAAGGCATCAAAAGTCAAACTTCAAAACTACT
447 ATAAAATAAATTAGGCATTTTAACTCAGGACTCGAAGGCAGCAAAAG----A--TC-AAAC-ACT
* *
1673215 TCACTTGTCATAGCCATTTGTTTTATGGTTACAAATTAATTTTATTTTTCTTATAATTGCCTTAA
504 TCACTTGTCAAAGCCATTTGTTTTATGGTTACAAATTAATTTTATTTATCTTATAATTGCCTTAA
1673280 GTTTAATCATAAATAAATTTTCATTTCATATTAATTTATTTTAGTATTATAAATACTGTGAACAA
569 GTTTAATCATAAATAAATTTTCATTTCATATTAATTTATTTTAGTATTATAAATACTGTGAACAA
* *
1673345 TATGGTAAAATTCAATTTTTAAACAAACTCCAAATATTATTAACCTGTTATGGCATCATCAACAA
634 TATGGAAAAATCCAATTTTTAAACAAACTCCAAATATTATTAACCTGTTATGGCATCATCAACAA
*
1673410 CGATTTGCTAAATACAATAGGGATAGTCATATTCAAATTATAAAAAAAAAAACCAAAAGAGAGCG
699 CGATTTGCTAAATACAATAGGGACAGTCATATTCAAA-TAT------------------------
*
1673475 CCCAAACAGCTAAAGTGTGCGATAAAAAAATATTTTTCA
739 ----AA-A---AAA------G-T-------TATTTTTCG
* * * *
1673514 TCAATAACTAGTTCTTTGCATACGTACTAAAATAAAAATATTTC-ATAATTATATAATATATATA
1 TCAATAACTAATTTTTTGCATACGGACTAAAATAAAAATA-TTCAATAATTAAATAATATATATA
* * * * * ** * *
1673578 CATAA-AACATATATAATATTAAAATTTAAGAAAATTTTATATCGCTCGATGTGTACCGATGAGC
65 TA-AACAACATATATAATATTAAAATTTAAGAAAATTTTACAACACTCGACGAATACTGATGAAC
* * * ** *
1673642 ACTATCAATTTAATTTATAAAAATTTAAAATTCTAAAGGACTCTACGTATGATTATTAAA-TAGT
129 ACTATTAAATTAATTTATAAAAATTTAAAATTCTAAAGGCCTAAACGTATAATTA-TAAATTAGT
* * * * * *
1673706 TAAAATTTTGAAGGTAAATTATTTAAAATAAGGAGTAAATTATATTAGTGACCACCTAACTATTG
193 TAAAA-ATTAAAGGTAAATTATTTAAAATAA-AAGTAAACTATATCAGT-AACACCTAACTATTG
* * *
1673771 CCCATTTTCATTTTGACTACCATTTTT-AAAATTTCA-TCAATCAGGTCACTCAACTATTTTAAT
255 ACCATTTTCATTTTGACCACCATTTTTGAAAATTT-AGTCAATCAGGTCACTCAACTATTTAAAT
* * * * * *
1673834 GCATTTAATTAAGTCACTTGCCGTTAATATTTAA-ATAAGAAGTTGATGTGGTAGTTAAAATATT
319 ACATTCAATTAAATCACTTGCCGTTAATATTTAACA-GAGAAGATGAAGTGGTAGTTAAAATATT
* * * * * * * *
1673898 AAG-TATAATTACATATTTGGTCACTATTAGTTATA-TATTATATCAATTT-AGTCCTAATTTTA
383 AGGTTATAACTACACATTTGATCACTGTTACTTATATTATTCTATCAATTTGA-TCCTTATTTTA
* * *
1673960 ATAAAATAAATTAGACATTTATAACTCGGGACTCGAAGGCATCAAAAGTTAAACATCAAAACTAC
447 ATAAAATAAATTAGGCATTT-TAACTCAGGACTCGAAGGCAGCAAAAG------ATC-AAAC-AC
* * * *
1674025 TTCACTAGTCAAAGCCTTTTGTTTTACGGTTA-AGAATTAATTTTATTTATCTTATAATTGCGTT
503 TTCACTTGTCAAAGCCATTTGTTTTATGGTTACA-AATTAATTTTATTTATCTTATAATTGCCTT
* * *
1674089 AAGTTTAATCATAAATTAATTTTTAATTT-ATATTAATTTATTTTAGTATTATAAATAATGTGAA
567 AAGTTTAATCATAAA-TAAATTTTCATTTCATATTAATTTATTTTAGTATTATAAATACTGTGAA
* * * * *
1674153 CAATATGGTAAAATCCAATTTTTAAAGAAATTCAAAATATTATTAACCTGTTATGGCATAATCAA
631 CAATATGGAAAAATCCAATTTTTAAACAAACTCCAAATATTATTAACCTGTTATGGCATCATCAA
* *
1674218 CAACGATTTGCCAAATACAATA-GGATAGTCATATTCAAAATATAAAAAA
696 CAACGATTTGCTAAATACAATAGGGACAGTCATATTC-AAATATAAAAAA
1674267 CCAAAAGAGA
Statistics
Matches: 1342, Mismatches: 130, Indels: 156
0.82 0.08 0.10
Matches are distributed among these distances:
751 5 0.00
752 235 0.18
753 51 0.04
754 108 0.08
755 37 0.03
759 2 0.00
761 2 0.00
762 82 0.06
763 135 0.10
764 3 0.00
778 3 0.00
781 1 0.00
782 2 0.00
792 2 0.00
793 1 0.00
796 3 0.00
802 1 0.00
803 1 0.00
809 9 0.01
810 409 0.30
811 237 0.18
812 11 0.01
813 2 0.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (755 bp):
TCAATAACTAATTTTTTGCATACGGACTAAAATAAAAATATTCAATAATTAAATAATATATATAT
AAACAACATATATAATATTAAAATTTAAGAAAATTTTACAACACTCGACGAATACTGATGAACAC
TATTAAATTAATTTATAAAAATTTAAAATTCTAAAGGCCTAAACGTATAATTATAAATTAGTTAA
AAATTAAAGGTAAATTATTTAAAATAAAAGTAAACTATATCAGTAACACCTAACTATTGACCATT
TTCATTTTGACCACCATTTTTGAAAATTTAGTCAATCAGGTCACTCAACTATTTAAATACATTCA
ATTAAATCACTTGCCGTTAATATTTAACAGAGAAGATGAAGTGGTAGTTAAAATATTAGGTTATA
ACTACACATTTGATCACTGTTACTTATATTATTCTATCAATTTGATCCTTATTTTAATAAAATAA
ATTAGGCATTTTAACTCAGGACTCGAAGGCAGCAAAAGATCAAACACTTCACTTGTCAAAGCCAT
TTGTTTTATGGTTACAAATTAATTTTATTTATCTTATAATTGCCTTAAGTTTAATCATAAATAAA
TTTTCATTTCATATTAATTTATTTTAGTATTATAAATACTGTGAACAATATGGAAAAATCCAATT
TTTAAACAAACTCCAAATATTATTAACCTGTTATGGCATCATCAACAACGATTTGCTAAATACAA
TAGGGACAGTCATATTCAAATATAAAAAAGTTATTTTTCG
Found at i:1675236 original size:21 final size:21
Alignment explanation
Indices: 1675198--1675237 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1675188 TTTAATCATA
*
1675198 AATTAATTTTTATTTTATATT
1 AATTAATTTTTATATTATATT
* *
1675219 AATTTATTTTTGTATTATA
1 AATTAATTTTTATATTATA
1675238 AATACTGTGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (21 bp):
AATTAATTTTTATATTATATT
Found at i:1677552 original size:21 final size:21
Alignment explanation
Indices: 1677528--1677567 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1677518 TTTAATCATA
* *
1677528 AATTAATTTTGATTTTATATT
1 AATTAATTTTAATATTATATT
*
1677549 AATTTATTTTAATATTATA
1 AATTAATTTTAATATTATA
1677568 AATACTGTGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (21 bp):
AATTAATTTTAATATTATATT
Found at i:1677565 original size:16 final size:17
Alignment explanation
Indices: 1677529--1677565 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
1677519 TTAATCATAA
1677529 ATTAATTTTGATTTTAT
1 ATTAATTTTGATTTTAT
1677546 ATTAA-TTT-ATTTTAAT
1 ATTAATTTTGATTTT-AT
1677562 ATTA
1 ATTA
1677566 TAAATACTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 5 0.26
16 9 0.47
17 5 0.26
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
ATTAATTTTGATTTTAT
Found at i:1678591 original size:21 final size:21
Alignment explanation
Indices: 1678562--1678601 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1678552 TTTAATAACA
1678562 AATTAATTTT-GATATTATATT
1 AATTAATTTTAG-TATTATATT
*
1678583 AATTCATTTTAGTATTATA
1 AATTAATTTTAGTATTATA
1678602 AATACTGTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (21 bp):
AATTAATTTTAGTATTATATT
Found at i:1683359 original size:18 final size:19
Alignment explanation
Indices: 1683336--1683379 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1683326 CCAGTAATCC
*
1683336 TATTCC-CTGATAATCTTT
1 TATTCCACTGATAATCTTA
*
1683354 TATTCCCACTGGTAATCTTA
1 TATT-CCACTGATAATCTTA
1683374 TATTCC
1 TATTCC
1683380 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 4 0.18
19 4 0.18
20 14 0.64
ACGTcount: A:0.23, C:0.25, G:0.07, T:0.45
Consensus pattern (19 bp):
TATTCCACTGATAATCTTA
Found at i:1685373 original size:31 final size:31
Alignment explanation
Indices: 1685337--1685411 Score: 132
Period size: 31 Copynumber: 2.4 Consensus size: 31
1685327 TCAAAAAACA
**
1685337 TAAGTTTTGGTCACTTACGTTATTGTTTTAT
1 TAAGTTTTGGTCACTTACGTTATCATTTTAT
1685368 TAAGTTTTGGTCACTTACGTTATCATTTTAT
1 TAAGTTTTGGTCACTTACGTTATCATTTTAT
1685399 TAAGTTTTGGTCA
1 TAAGTTTTGGTCA
1685412 TACGAATGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.21, C:0.11, G:0.16, T:0.52
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTACGTTATCATTTTAT
Found at i:1686962 original size:20 final size:21
Alignment explanation
Indices: 1686915--1686966 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
1686905 TCGGATGATC
*
1686915 AGTACCGATACTGATGTAGGT
1 AGTATCGATACTGATGTAGGT
1686936 AGTATCGATACTGATGT-GG-
1 AGTATCGATACTGATGTAGGT
1686955 AGGTATCGATAC
1 A-GTATCGATAC
1686967 CATGAGTAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 1 0.03
20 12 0.41
21 16 0.55
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.29
Consensus pattern (21 bp):
AGTATCGATACTGATGTAGGT
Found at i:1687673 original size:23 final size:23
Alignment explanation
Indices: 1687640--1687742 Score: 89
Period size: 23 Copynumber: 4.4 Consensus size: 23
1687630 AGTCAAGGGT
*
1687640 TCTACGCGGTCCTTCGGGACAAA
1 TCTACGTGGTCCTTCGGGACAAA
* * *
1687663 TCTATGTGGTCTTTCGGGACAAT
1 TCTACGTGGTCCTTCGGGACAAA
* * *
1687686 TCTACGTGGTCATTTGGGAAAAA
1 TCTACGTGGTCCTTCGGGACAAA
* * **
1687709 TTCTACGCGGTCATTCAAGACAAA
1 -TCTACGTGGTCCTTCGGGACAAA
1687733 TTCTACGTGG
1 -TCTACGTGG
1687743 CACTTCGATG
Statistics
Matches: 64, Mismatches: 15, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
23 37 0.58
24 27 0.42
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (23 bp):
TCTACGTGGTCCTTCGGGACAAA
Found at i:1687715 original size:24 final size:24
Alignment explanation
Indices: 1687639--1687742 Score: 95
Period size: 24 Copynumber: 4.4 Consensus size: 24
1687629 GAGTCAAGGG
* * *
1687639 TTCTACGCGGTCCTTCGGGACAAA
1 TTCTACGTGGTCATTCGGGAAAAA
* * *
1687663 -TCTATGTGGTCTTTCGGG-ACAA
1 TTCTACGTGGTCATTCGGGAAAAA
*
1687685 TTCTACGTGGTCATTTGGGAAAAA
1 TTCTACGTGGTCATTCGGGAAAAA
* ** *
1687709 TTCTACGCGGTCATTCAAGACAAA
1 TTCTACGTGGTCATTCGGGAAAAA
1687733 TTCTACGTGG
1 TTCTACGTGG
1687743 CACTTCGATG
Statistics
Matches: 63, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
22 2 0.03
23 30 0.48
24 31 0.49
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (24 bp):
TTCTACGTGGTCATTCGGGAAAAA
Found at i:1694594 original size:24 final size:24
Alignment explanation
Indices: 1694562--1694617 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
1694552 TCATTTGGGA
**
1694562 AAATTCTACTTGGTCCTTCGAGAC
1 AAATTCTACACGGTCCTTCGAGAC
*
1694586 AAATTCTACACGGTCCTTCGGGAC
1 AAATTCTACACGGTCCTTCGAGAC
1694610 AAATTCTA
1 AAATTCTA
1694618 AGTGGCACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (24 bp):
AAATTCTACACGGTCCTTCGAGAC
Found at i:1700981 original size:23 final size:23
Alignment explanation
Indices: 1700941--1701032 Score: 121
Period size: 23 Copynumber: 4.0 Consensus size: 23
1700931 CACCACAGCT
* * *
1700941 CGTATAAATACACTGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
1700964 TGTAGAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
1700987 CGTAGAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
1701010 CGTAGAAATGCACCTAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
1701033 TATAAGATGT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.34, C:0.24, G:0.25, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:1703479 original size:69 final size:68
Alignment explanation
Indices: 1703321--1703515 Score: 248
Period size: 69 Copynumber: 2.8 Consensus size: 68
1703311 GGGATGTTAC
* * * * *
1703321 ATAACATATAGTTTTAAAAACCTATTTTGAAAATATATATAATGTATAGTTTTTAAAACATCTTG
1 ATAATATATAGTTTTTAAAA-C-ATTTTG-AAA-ACATATAATATATAATTTTTAAAACATCTTG
1703386 AAAATAT
62 AAAATAT
* * * *
1703393 ATAATATATAGTTTTTAAAACATTTTGAAAACATATAATATATAATTTTGAAAATATTTTTTACA
1 ATAATATATAGTTTTTAAAACATTTTGAAAACATATAATATATAATTTTTAAAACA-TCTTGA-A
1703458 AA-AT
64 AATAT
1703462 ATAATATATAGTTTTTAAAACATTTTGAAAACATATAATATATAATTTTTAAAA
1 ATAATATATAGTTTTTAAAACATTTTGAAAACATATAATATATAATTTTTAAAA
1703516 ACGATTTTTG
Statistics
Matches: 111, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
68 21 0.19
69 62 0.56
70 9 0.08
71 1 0.01
72 18 0.16
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (68 bp):
ATAATATATAGTTTTTAAAACATTTTGAAAACATATAATATATAATTTTTAAAACATCTTGAAAA
TAT
Found at i:1703523 original size:36 final size:34
Alignment explanation
Indices: 1703321--1703534 Score: 234
Period size: 34 Copynumber: 6.1 Consensus size: 34
1703311 GGGATGTTAC
* * *
1703321 ATAACATATAGTTTTAAAAACCTATTTTGAAAATATAT
1 ATAATATATAGTTTTTAAAA-C-ATTTTG-AAA-ACAT
* * *
1703359 ATAATGTATAGTTTTTAAAACATCTTGAAAATAT
1 ATAATATATAGTTTTTAAAACATTTTGAAAACAT
1703393 ATAATATATAGTTTTTAAAACATTTTGAAAACAT
1 ATAATATATAGTTTTTAAAACATTTTGAAAACAT
* * * *
1703427 ATAATATATAATTTTGAAAATATTTTTTACAAA-AT
1 ATAATATATAGTTTTTAAAACA-TTTTGA-AAACAT
1703462 ATAATATATAGTTTTTAAAACATTTTGAAAACAT
1 ATAATATATAGTTTTTAAAACATTTTGAAAACAT
*
1703496 ATAATATATAATTTTTAAAAACGATTTTTG-AAACAT
1 ATAATATATAGTTTTT-AAAAC-A-TTTTGAAAACAT
1703532 ATA
1 ATA
1703535 CTTTTTGAAA
Statistics
Matches: 154, Mismatches: 16, Indels: 14
0.84 0.09 0.08
Matches are distributed among these distances:
33 3 0.02
34 76 0.49
35 34 0.22
36 18 0.12
37 6 0.04
38 17 0.11
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (34 bp):
ATAATATATAGTTTTTAAAACATTTTGAAAACAT
Found at i:1703605 original size:9 final size:9
Alignment explanation
Indices: 1703589--1703665 Score: 62
Period size: 9 Copynumber: 9.2 Consensus size: 9
1703579 AGTTACATTA
1703589 TATTTATTT
1 TATTTATTT
1703598 CT-TTTATTT
1 -TATTTATTT
1703607 TATTTATTT
1 TATTTATTT
1703616 TATTTATTT
1 TATTTATTT
*
1703625 TGTTT-TATT
1 TATTTAT-TT
*
1703634 TA-TT-CTT
1 TATTTATTT
1703641 TA-TT-TTT
1 TATTTATTT
1703648 TATTT-TTT
1 TATTTATTT
1703656 T-TTTATTT
1 TATTTATTT
1703664 TA
1 TA
1703666 GGCTCAAAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 11
0.79 0.05 0.15
Matches are distributed among these distances:
7 13 0.22
8 14 0.24
9 30 0.52
10 1 0.02
ACGTcount: A:0.17, C:0.03, G:0.01, T:0.79
Consensus pattern (9 bp):
TATTTATTT
Found at i:1703608 original size:14 final size:14
Alignment explanation
Indices: 1703586--1703656 Score: 60
Period size: 14 Copynumber: 5.1 Consensus size: 14
1703576 TTTAGTTACA
1703586 TTATATTTATTTCTT
1 TTAT-TTTATTTCTT
*
1703601 TTATTTTATTTATT
1 TTATTTTATTTCTT
*
1703615 TTA-TTTATTTTGTT
1 TTATTTTA-TTTCTT
1703629 TTA-TTTA-TTCTT
1 TTATTTTATTTCTT
*
1703641 TATTTTTTATTT-TT
1 T-TATTTTATTTCTT
1703655 TT
1 TT
1703657 TTTATTTTAG
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
12 5 0.10
13 6 0.12
14 31 0.65
15 6 0.12
ACGTcount: A:0.17, C:0.03, G:0.01, T:0.79
Consensus pattern (14 bp):
TTATTTTATTTCTT
Found at i:1703612 original size:4 final size:4
Alignment explanation
Indices: 1703589--1703663 Score: 52
Period size: 4 Copynumber: 19.2 Consensus size: 4
1703579 AGTTACATTA
* *
1703589 TATT TATT TCTTT TATTT TATT TATTT TATT TATT T-TG T-TT TATT TA-T
1 TATT TATT T-ATT TA-TT TATT TA-TT TATT TATT TATT TATT TATT TATT
* *
1703637 TCTT TATT T-TT TATT T-TT TTTT TATT T
1 TATT TATT TATT TATT TATT TATT TATT T
1703664 TAGGCTCAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
3 12 0.21
4 34 0.60
5 11 0.19
ACGTcount: A:0.16, C:0.03, G:0.01, T:0.80
Consensus pattern (4 bp):
TATT
Found at i:1705657 original size:45 final size:42
Alignment explanation
Indices: 1705606--1705961 Score: 218
Period size: 34 Copynumber: 8.9 Consensus size: 42
1705596 ATAAAAGAAT
1705606 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GATGCCATAG-T-A
***
1705651 AATGCATATGGGTGCATTAGCAGCAT-AAA-A-G--A-A-T-
1 AATGCATATGGGTGCATTATTGGCATGAAAGATGCCATAGTA
*
1705685 AATGCATATGGGTGCATTATTGGCATGAAAAGATGCCTTAGTTGA
1 AATGCATATGGGTGCATTATTGGCATG-AAAGATGCCATAG-T-A
* ***
1705730 AATGCATATGGATGCATTATCAACAT-AAA-A-G--A-A-T-
1 AATGCATATGGGTGCATTATTGGCATGAAAGATGCCATAGTA
*
1705764 AATGCATATAGGTGCATTATTGGCATGAAAGGATGCCATAGCTTA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GATGCCATAG--TA
* **
1705809 AATGCATATGAGTGCATTATCAGCAT-AAA-A-G--A-A-T-
1 AATGCATATGGGTGCATTATTGGCATGAAAGATGCCATAGTA
1705843 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GATGCCATAG-T-A
** **
1705888 AATGCATATGAATGCATTATCAGCAT-AAA-A-G--A-A-T-
1 AATGCATATGGGTGCATTATTGGCATGAAAGATGCCATAGTA
*
1705922 AATGCATATGGGTGCATTATTGGCATGAAAAAATGCCATA
1 AATGCATATGGGTGCATTATTGGCATG-AAAGATGCCATA
1705962 ACTAAAAATG
Statistics
Matches: 239, Mismatches: 32, Indels: 84
0.67 0.09 0.24
Matches are distributed among these distances:
34 89 0.37
35 7 0.03
36 9 0.04
37 4 0.02
38 8 0.03
39 3 0.01
40 3 0.01
41 8 0.03
42 4 0.02
43 5 0.02
44 10 0.04
45 89 0.37
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.27
Consensus pattern (42 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGATGCCATAGTA
Found at i:1705731 original size:79 final size:79
Alignment explanation
Indices: 1705596--1705988 Score: 615
Period size: 79 Copynumber: 4.9 Consensus size: 79
1705586 GAATGAATAA
1705596 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
** *
1705661 GGTGCATTAGCAGC
66 AATGCATTATCAGC
* * *
1705675 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAAGATGCCTTAGTTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
* *
1705740 GATGCATTATCAAC
66 AATGCATTATCAGC
* *
1705754 ATAAAAGAATAATGCATATAGGTGCATTATTGGCATGAAAGGATGCCATAGCTTAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
*
1705819 AGTGCATTATCAGC
66 AATGCATTATCAGC
1705833 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
1705898 AATGCATTATCAGC
66 AATGCATTATCAGC
** * *
1705912 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAAAATGCCATAACTAAAAATGCATGA
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCT-GAAATGCAT--
*
1705977 AAGAATGCATTA
63 ATGAATGCATTA
1705989 AGGCATAAAA
Statistics
Matches: 289, Mismatches: 22, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
79 270 0.93
80 8 0.03
82 11 0.04
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.27
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
AATGCATTATCAGC
Found at i:1706397 original size:29 final size:29
Alignment explanation
Indices: 1706355--1706415 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
1706345 TATGCCAGTT
*
1706355 AGATAAACGGTTAAACACTGTTGAGTAAA
1 AGATAAACGATTAAACACTGTTGAGTAAA
*
1706384 AGATGAACGATTAAACACTGTTGAGTAAA
1 AGATAAACGATTAAACACTGTTGAGTAAA
1706413 AGA
1 AGA
1706416 ATAAGGGACT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.23
Consensus pattern (29 bp):
AGATAAACGATTAAACACTGTTGAGTAAA
Found at i:1708719 original size:20 final size:19
Alignment explanation
Indices: 1708694--1708743 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
1708684 TGATTCAATC
* *
1708694 AGTATCGATACTGAAGAGGG
1 AGTATCGATACCGAAG-GGA
1708714 AGTATCGATACCGAAGGGA
1 AGTATCGATACCGAAGGGA
1708733 AGGTATCGATA
1 A-GTATCGATA
1708744 TATTTCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 3 0.11
20 24 0.89
ACGTcount: A:0.36, C:0.12, G:0.32, T:0.20
Consensus pattern (19 bp):
AGTATCGATACCGAAGGGA
Found at i:1709138 original size:22 final size:22
Alignment explanation
Indices: 1709113--1709155 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1709103 TATGTTGTAC
1709113 TAATCATATATGT-ATGATTACT
1 TAAT-ATATATGTGATGATTACT
* *
1709135 TAATATGTATGTGGTGATTAC
1 TAATATATATGTGATGATTAC
1709156 CAAATAGGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (22 bp):
TAATATATATGTGATGATTACT
Found at i:1709220 original size:54 final size:54
Alignment explanation
Indices: 1709162--1709956 Score: 1091
Period size: 54 Copynumber: 14.8 Consensus size: 54
1709152 TTACCAAATA
* *
1709162 GGCACTAAAGTGTGTATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTT-
1 GGCACT-AAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
*
1709216 GGCACTAAGTGTGCA-TTCA-GAGAATTCATCCTATGTGGATGAATAACTGTTTC
1 GGCACTAAGTGTGCATTTCACG-GAATTCATCCTATGTGGATGAATAACCGTTTC
1709269 GGCACTAAGTGTGCATTTCACGGAATTCA-CTCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATC-CTATGTGGATGAATAACCGTTTC
* * * *
1709323 GACACTAAGTGTGCATTTCACAGAATTCATCCT-GGTGGATGAATAACTGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
1709376 GACACTAAGTGTGTATTTCAGGGAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * * **
1709430 GACATTAAGTGTGTATTTCACGGAATTCATCCTATGCGGATG-ATAATAGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * * *
1709483 GACATTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAAAAATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * **
1709537 GGCACTAACTGTGTATTTCAAAGAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * * *
1709591 AGCACTAAGTGTGCATTTCCCAGAATTTATCCTATGTGGATGAATAACCGTTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
** * *
1709645 GGCACTTGGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * *
1709699 GACACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGAATGAATAACTGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* *
1709753 GGCACTAAGTGTTCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
1709807 GGCACTAAGTGTGCTTTTCACGGAATACATCCTATGTGGATGAATAACCGGTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
1709861 GTCACTAAGTGTGCATTTCACGGAATTCATCCTACGTGGATGAATAACCATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
*
1709915 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGT-GATGA
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGA
1709957 TTAATTGTAC
Statistics
Matches: 661, Mismatches: 72, Indels: 17
0.88 0.10 0.02
Matches are distributed among these distances:
51 1 0.00
52 33 0.05
53 125 0.19
54 500 0.76
55 2 0.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
Found at i:1710019 original size:54 final size:55
Alignment explanation
Indices: 1709933--1710066 Score: 184
Period size: 55 Copynumber: 2.5 Consensus size: 55
1709923 GTGTGCATTT
* *
1709933 CACAGAATTCATCCT-A-TGTGATGATTAATTGTACAGACACTATGT-TGCAAATC
1 CACAGAATTCATCATGAGT-TGATGAATAATTGTACAGACACTATGTGTGCAAATC
* * *
1709986 TACGGAATTCATCATGAGTTGATGAATAATTGTACAGGCACTATGTGTGCAAATC
1 CACAGAATTCATCATGAGTTGATGAATAATTGTACAGACACTATGTGTGCAAATC
*
1710041 CACATAATTCATCATGAGTTGATGAA
1 CACAGAATTCATCATGAGTTGATGAA
1710067 CTACCGTATA
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
53 12 0.17
54 26 0.37
55 32 0.46
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31
Consensus pattern (55 bp):
CACAGAATTCATCATGAGTTGATGAATAATTGTACAGACACTATGTGTGCAAATC
Found at i:1710080 original size:55 final size:54
Alignment explanation
Indices: 1709933--1710083 Score: 155
Period size: 55 Copynumber: 2.8 Consensus size: 54
1709923 GTGTGCATTT
* * ** *
1709933 CACAGAATTCATCCT-A-TGTGATGATTAATTGTACAGACACTATGTTGCAAATC
1 CACAGAATTCATCATGAGT-TGATGAATAACCGTACAGGCACTATGTTGCAAATC
* * **
1709986 TACGGAATTCATCATGAGTTGATGAATAATTGTACAGGCACTATGTGTGCAAATC
1 CACAGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGT-TGCAAATC
* *
1710041 CACATAATTCATCATGAGTTGATGAACT-ACCGTATAGGCACTA
1 CACAGAATTCATCATGAGTTGATGAA-TAACCGTACAGGCACTA
1710084 CATGTGCATA
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
53 12 0.14
54 26 0.31
55 44 0.53
56 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (54 bp):
CACAGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTTGCAAATC
Found at i:1710522 original size:46 final size:46
Alignment explanation
Indices: 1710448--1710585 Score: 195
Period size: 46 Copynumber: 3.0 Consensus size: 46
1710438 TGTCACAATA
* * *
1710448 TATAATAACGTTTAGAAGGGCATGAAAGGATGCCATAAATGAAATG
1 TATAATAGCGTATAGAAGGGCATGAAAGGATGTCATAAATGAAATG
* *
1710494 TGTAATAGCGTATAGAAGGGCATTAAAGGATGTCATAAATGAAATG
1 TATAATAGCGTATAGAAGGGCATGAAAGGATGTCATAAATGAAATG
* * * *
1710540 TATAATAGCTTATAAAAGCGCATGAAAGGATGTCATAAATAAAATG
1 TATAATAGCGTATAGAAGGGCATGAAAGGATGTCATAAATGAAATG
1710586 CATATGGTGC
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 81 1.00
ACGTcount: A:0.44, C:0.08, G:0.22, T:0.25
Consensus pattern (46 bp):
TATAATAGCGTATAGAAGGGCATGAAAGGATGTCATAAATGAAATG
Found at i:1710641 original size:32 final size:31
Alignment explanation
Indices: 1710580--1710641 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 31
1710570 TGTCATAAAT
* **
1710580 AAAATGCATATGGTGCATTATCGGCATGAAA
1 AAAATGCATATCGTGCATTATAAGCATGAAA
*
1710611 AAAATGCATAATCGTGCATTATAAGTATGAA
1 AAAATGCAT-ATCGTGCATTATAAGCATGAA
1710642 TGGATGCTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 9 0.35
32 17 0.65
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.27
Consensus pattern (31 bp):
AAAATGCATATCGTGCATTATAAGCATGAAA
Found at i:1714565 original size:20 final size:19
Alignment explanation
Indices: 1714540--1714590 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
1714530 TGATTCAATC
*
1714540 AGTATCGATACCGAAGAGGG
1 AGTATCGATACCGAAG-GGA
*
1714560 AGTATCGATACCTAAGGGA
1 AGTATCGATACCGAAGGGA
1714579 AGGTATCGATAC
1 A-GTATCGATAC
1714591 TATTTCGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 3 0.11
20 25 0.89
ACGTcount: A:0.35, C:0.16, G:0.29, T:0.20
Consensus pattern (19 bp):
AGTATCGATACCGAAGGGA
Found at i:1715076 original size:54 final size:54
Alignment explanation
Indices: 1715008--1715903 Score: 1221
Period size: 54 Copynumber: 16.9 Consensus size: 54
1714998 TTACCAAATA
* ** *
1715008 GGCACTAAAGTGTGCATTTCACGTAATTCATCCTATGTGGATGAATAAATGTTTT
1 GGCACT-AAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * *
1715063 GGCACTAAGTGTGCATTTCAGGGAATTCATCATATGTGGATGAATAACTGTTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
1715117 GGCACTAAGTGTGCATTTCATGGAATTCATCATATGTGGATGAATAATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* *
1715171 GGCACTAAGTGTGCATTTCACGGAATTCATCTTATGTAGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* *
1715225 GGCACTAAGTGTGCGTTTCACGGAATTCATCCTATGTGGATGAATAATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
*
1715279 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGGGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
1715333 GACACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATGACTGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
1715387 GGCACTAAGTGTGTATTTCATGGAATTTATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
*
1715441 GACACTAAGTGTGCATTTCACGGAATTCATCC--------T-AATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * *
1715486 GACACTAAGTGTACATTTCACGGAATTCATCATATGTGGATGAATAACTGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* ** * *
1715540 GTCACTAAGTGTGCATTTCACAAAATTCATCCTAGGTGGATGAATAACCATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * *
1715594 GGCACTATGTGTGCATTTCACAGAATTCATCCTAGGTGGATGAATAACCATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * ** *
1715648 GGGACTAAGTTTGCATTTCACGGAATTCATCCTACATGGTTGAATAA---TTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * **
1715699 GGCACTAAGTGTGCATTTCACGGAATTTATCCTATATGGATGAATAACTATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
*
1715753 AGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
1715807 GGTACTAAGTGTGCATTTCACAGAATTCATCCTACGTGGATGAATAACCG-TT-
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
*
1715859 -GCACTAAGTGTGCATTTCACGAAATTCATCCTATGT-GATGAATAA
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAA
1715904 TCGTACATGT
Statistics
Matches: 757, Mismatches: 72, Indels: 29
0.88 0.08 0.03
Matches are distributed among these distances:
45 42 0.06
46 1 0.00
50 9 0.01
51 78 0.10
53 3 0.00
54 618 0.82
55 6 0.01
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
Found at i:1715493 original size:45 final size:45
Alignment explanation
Indices: 1715429--1715516 Score: 167
Period size: 45 Copynumber: 2.0 Consensus size: 45
1715419 TATGTGGATG
*
1715429 AATAACCGTTTCGACACTAAGTGTGCATTTCACGGAATTCATCCT
1 AATAACCGTTTCGACACTAAGTGTACATTTCACGGAATTCATCCT
1715474 AATAACCGTTTCGACACTAAGTGTACATTTCACGGAATTCATC
1 AATAACCGTTTCGACACTAAGTGTACATTTCACGGAATTCATC
1715517 ATATGTGGAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (45 bp):
AATAACCGTTTCGACACTAAGTGTACATTTCACGGAATTCATCCT
Found at i:1715942 original size:54 final size:53
Alignment explanation
Indices: 1715509--1715997 Score: 281
Period size: 54 Copynumber: 9.2 Consensus size: 53
1715499 CATTTCACGG
* * * * *
1715509 AATTCATCATATGTGGATGAATAACTGT-TTCGTCACTAAGTGTGCATTTCACAA
1 AATTCATCCTATGTGGATGAATAACCGTACT-G-CACTAAGTGTGCAATCCACAA
* * * * * * * *
1715563 AATTCATCCTAGGTGGATGAATAACCATTTCGGCACTATGTGTGCATTTCACAG
1 AATTCATCCTATGTGGATGAATAACC-GTACTGCACTAAGTGTGCAATCCACAA
* * * * * * * * **
1715617 AATTCATCCTAGGTGGATGAATAACCATTTCGGGACTAAGTTTGCATTTCACGG
1 AATTCATCCTATGTGGATGAATAACC-GTACTGCACTAAGTGTGCAATCCACAA
** * * * * * * **
1715671 AATTCATCCTACATGGTTGAATAA--TTTCGGCACTAAGTGTGCATTTCACGG
1 AATTCATCCTATGTGGATGAATAACCGTACTGCACTAAGTGTGCAATCCACAA
* * ** * * * * **
1715722 AATTTATCCTATATGGATGAATAACTATTTCAGCACTAAGTGTGCATTTCACGG
1 AATTCATCCTATGTGGATGAATAAC-CGTACTGCACTAAGTGTGCAATCCACAA
* * * * * *
1715776 AATTCATCCTATGTGGATGAATAACCGTTTCGGTACTAAGTGTGCATTTCACAG
1 AATTCATCCTATGTGGATGAATAACCG-TACTGCACTAAGTGTGCAATCCACAA
* * * *
1715830 AATTCATCCTACGTGGATGAATAACCGT--TGCACTAAGTGTGCATTTCACGA
1 AATTCATCCTATGTGGATGAATAACCGTACTGCACTAAGTGTGCAATCCACAA
* * *
1715881 AATTCATCCTATGT-GATGAATAATCGTACATGTACTATGTGTGCAAATCCACAA
1 AATTCATCCTATGTGGATGAATAACCGTAC-TGCACTAAGTGTGC-AATCCACAA
* * * * *
1715935 AATTCATCATGA-GTTGATGAATAACCGTACAAGCACTATGTGTGCAAATCCACAG
1 AATTCATCCT-ATGTGGATGAATAACCGTAC-TGCACTAAGTGTGC-AATCCACAA
1715990 AATTCATC
1 AATTCATC
1715998 ATGAGTTGAT
Statistics
Matches: 378, Mismatches: 45, Indels: 23
0.85 0.10 0.05
Matches are distributed among these distances:
50 12 0.03
51 78 0.21
53 13 0.03
54 228 0.60
55 47 0.12
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (53 bp):
AATTCATCCTATGTGGATGAATAACCGTACTGCACTAAGTGTGCAATCCACAA
Found at i:1715957 original size:55 final size:55
Alignment explanation
Indices: 1715894--1716010 Score: 198
Period size: 55 Copynumber: 2.1 Consensus size: 55
1715884 TCATCCTATG
* * *
1715894 TGATGAATAATCGTACATGTACTATGTGTGCAAATCCACAAAATTCATCATGAGT
1 TGATGAATAACCGTACAAGCACTATGTGTGCAAATCCACAAAATTCATCATGAGT
*
1715949 TGATGAATAACCGTACAAGCACTATGTGTGCAAATCCACAGAATTCATCATGAGT
1 TGATGAATAACCGTACAAGCACTATGTGTGCAAATCCACAAAATTCATCATGAGT
1716004 TGATGAA
1 TGATGAA
1716011 CTACTGTATA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (55 bp):
TGATGAATAACCGTACAAGCACTATGTGTGCAAATCCACAAAATTCATCATGAGT
Found at i:1716521 original size:46 final size:46
Alignment explanation
Indices: 1716381--1716527 Score: 195
Period size: 46 Copynumber: 3.2 Consensus size: 46
1716371 GTCTAGTGGT
* * **
1716381 ATGACAATGTATAACAGCTTATATAAGGGTGTGAAAGGATGCCATAA
1 ATGA-AATGTATAATAGCTTATAAAAGGGAATGAAAGGATGCCATAA
* * * *
1716428 ACGAAATGTATAATAGCGTATAGAAGGGCATGAAAGGATGCCATAA
1 ATGAAATGTATAATAGCTTATAAAAGGGAATGAAAGGATGCCATAA
*
1716474 ATGAAATGTATAATAGCTTATAAAAGGGAATGAAAGGATGTCATAA
1 ATGAAATGTATAATAGCTTATAAAAGGGAATGAAAGGATGCCATAA
*
1716520 ATAAAATG
1 ATGAAATG
1716528 CATATGGGTG
Statistics
Matches: 88, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
46 85 0.97
47 3 0.03
ACGTcount: A:0.45, C:0.08, G:0.23, T:0.24
Consensus pattern (46 bp):
ATGAAATGTATAATAGCTTATAAAAGGGAATGAAAGGATGCCATAA
Found at i:1716572 original size:45 final size:46
Alignment explanation
Indices: 1716522--1716634 Score: 151
Period size: 45 Copynumber: 2.5 Consensus size: 46
1716512 TGTCATAAAT
*
1716522 AAAATGCATATGGGTGCATTATCGACATGAAA-AGATACCATA-ATT
1 AAAATGCATATGGGTGCATTATCGACATGAAAGA-ATACCATATATA
* * *
1716567 GAAATGCATATGGGTGCATTATTGGCATGAAAGAATACCATATATA
1 AAAATGCATATGGGTGCATTATCGACATGAAAGAATACCATATATA
1716613 AAAATGCATAAT-GGTGCATTAT
1 AAAATGCAT-ATGGGTGCATTAT
1716635 AAGTATGAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
45 37 0.62
46 21 0.35
47 2 0.03
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (46 bp):
AAAATGCATATGGGTGCATTATCGACATGAAAGAATACCATATATA
Found at i:1726748 original size:81 final size:80
Alignment explanation
Indices: 1726665--1727199 Score: 615
Period size: 81 Copynumber: 6.6 Consensus size: 80
1726655 AGTGTAGCTA
* * * *
1726665 TGCATTTGGCAGAAAAGTGTCAATTATGCCAATTAAATGAAAAGTTAAATACCTTTGAGTAAAAG
1 TGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
*
1726730 ATTAATGTCCTAGTTA
66 ATTAATG-CCTAGTTG
* * *
1726746 TGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGGTTAAATACCTTTCAGTAAAAG
1 TGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
** * *
1726811 ATTAATG-GAATTTATA
66 ATTAATGCCTA-GT-TG
* * *
1726827 TACATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGATAAATACCTTTGAGTAAAAG
1 TGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
*
1726892 ATTAATGGCCTAGCTG
66 ATTAAT-GCCTAGTTG
* ** * *
1726908 TACATTTAACATAAAGGTGTTAATTATGCCAGTTAGATGAAAGGTTAAA-ACCTTTGAGTAAAAG
1 TGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
*
1726972 ATTAATGGTCTAGTTG
66 ATTAAT-GCCTAGTTG
* * * * * * *
1726988 TGCATTTGGTAGAAATGTGTTAATCATGCCAGTTAGATGAAAGGTTAAATGCCTTTTAGTAAAAT
1 TGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
* * *
1727053 ACTAAAAGCCTAGCTG
66 A-TTAATGCCTAGTTG
* * * * *
1727069 TGCATTTGGTATAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATGCCTTTTAGTAAAAG
1 TGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
* * *
1727134 ACTAAAAGCCTAGATG
66 A-TTAATGCCTAGTTG
* *
1727150 TGCATTTGGCATAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAAT
1 TGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAAT
1727200 GCTCTAGATG
Statistics
Matches: 403, Mismatches: 45, Indels: 12
0.88 0.10 0.03
Matches are distributed among these distances:
79 1 0.00
80 72 0.18
81 325 0.81
82 4 0.01
83 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (80 bp):
TGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
ATTAATGCCTAGTTG
Found at i:1727165 original size:242 final size:243
Alignment explanation
Indices: 1726641--1727199 Score: 690
Period size: 242 Copynumber: 2.3 Consensus size: 243
1726631 ACTGTTCTGA
* ** * * * * *
1726641 AGTAAAAGACTAAGAGTGTAGCTATGCATTTGGCAGAAAAGTGTCAATTATGCCAATTAAATGAA
1 AGTAAAAGACTAAAAGCCTAGCTGTGCATTTGGCATAAAGGTGTCAATTATGCCAGTTAGATGAA
* *
1726706 AAGTTAAATACCTTTGAGTAAAAGATTAATGTCCTAGTTATGCATTTGACAGAAAGGTGTCAATT
66 AGGTTAAATACCTTTGAGTAAAAGATTAATGTCCTAGTTATGCATTTGACAGAAAGGTGTCAATC
* * ** **
1726771 ATGCTAGTTAGATGAAAGGTTAAATACCTTTCAGTAAAAGATTAATGGAATTTATATACATTTGA
131 ATGCCAGTTAGATGAAAGGTTAAATACCTTTCAGTAAAAGACTAAAAGAATAGATATACATTTGA
*
1726836 CAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGATAAATACCTTTG
196 CAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGATAAATACCTTTG
* ** * ** *
1726884 AGTAAAAGATTAATGGCCTAGCTGTACATTTAACATAAAGGTGTTAATTATGCCAGTTAGATGAA
1 AGTAAAAGACTAAAAGCCTAGCTGTGCATTTGGCATAAAGGTGTCAATTATGCCAGTTAGATGAA
* ** * *
1726949 AGGTTAAA-ACCTTTGAGTAAAAGATTAATGGT-CTAGTTGTGCATTTGGTAGAAATGTGTTAAT
66 AGGTTAAATACCTTTGAGTAAAAGATTAAT-GTCCTAGTTATGCATTTGACAGAAAGGTGTCAAT
* * * ** * * *
1727012 CATGCCAGTTAGATGAAAGGTTAAATGCCTTTTAGTAAAATACTAAAAGCCTAGCTGTGCATTTG
130 CATGCCAGTTAGATGAAAGGTTAAATACCTTTCAGTAAAAGACTAAAAGAATAGATATACATTTG
** * * * *
1727077 GTATAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATGCCTTTT
195 ACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGATAAATACCTTTG
* *
1727126 AGTAAAAGACTAAAAGCCTAGATGTGCATTTGGCATAAAGGTGTCAATCATGCCAGTTAGATGAA
1 AGTAAAAGACTAAAAGCCTAGCTGTGCATTTGGCATAAAGGTGTCAATTATGCCAGTTAGATGAA
1727191 AGGTTAAAT
66 AGGTTAAAT
1727200 GCTCTAGATG
Statistics
Matches: 263, Mismatches: 51, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
242 203 0.77
243 60 0.23
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (243 bp):
AGTAAAAGACTAAAAGCCTAGCTGTGCATTTGGCATAAAGGTGTCAATTATGCCAGTTAGATGAA
AGGTTAAATACCTTTGAGTAAAAGATTAATGTCCTAGTTATGCATTTGACAGAAAGGTGTCAATC
ATGCCAGTTAGATGAAAGGTTAAATACCTTTCAGTAAAAGACTAAAAGAATAGATATACATTTGA
CAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGATAAATACCTTTG
Found at i:1729118 original size:2 final size:2
Alignment explanation
Indices: 1729111--1729135 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1729101 GATTTCAGAA
1729111 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
1729136 TATAACTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1732015 original size:20 final size:21
Alignment explanation
Indices: 1731966--1732019 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
1731956 ATACAGAAAG
1731966 GGGTATCGATACCATAGTATA
1 GGGTATCGATACCATAGTATA
* * *
1731987 GAAGTATCGATACCCTGGTAT-
1 G-GGTATCGATACCATAGTATA
1732008 GGGTATCGATAC
1 GGGTATCGATAC
1732020 TATTGAGCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 10 0.36
21 2 0.07
22 16 0.57
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGTATCGATACCATAGTATA
Found at i:1733014 original size:81 final size:81
Alignment explanation
Indices: 1732536--1733012 Score: 600
Period size: 81 Copynumber: 5.9 Consensus size: 81
1732526 CTTGTTCTAA
* ** * ** *
1732536 AGTAAAAGACTAAAAGCCTAGTTGTGCATTTTG-CAGAAATTTGTCAATTATGCCAGTTAGATTA
1 AGTAAAAGATTAATGGCCTAGCTGTGCA-TTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGA
1732600 AAGGTTAAATACCTTTG
65 AAGGTTAAATACCTTTG
* * * * * *
1732617 ATTAAAAGATTAATGGCCTAGTTGTTCATTTGACAGAAA--TGTCAATTATGACAATTAGATTAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1732680 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * * * *
1732696 AGTAAAATATTAATGGCCTAGCTTTGCATTTGACGGAAAGGTGTCAATTATACTAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1732761 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
*
1732777 AGTAAAAGATTAATGGCCTAGCTGTGCATTTAACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
* *
1732842 AAGTTAAATAACTTTG
66 AGGTTAAATACCTTTG
* * * * *
1732858 AGTAAAAGATTAATGGCCTAGCTGTACATTTAACAGAAAGGTGTCAATCATGCTAGTTAGATGCA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
* *
1732923 AGGTTAAATGCGTTTG
66 AGGTTAAATACCTTTG
* ** * * * * *
1732939 AGTAAAAGACTAAAAGCCTAGCTGTGCATATGGCAGAAAGGTGCCAATCATTCCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1733004 AGGTTAAAT
66 AGGTTAAAT
1733013 GCTCTAGATG
Statistics
Matches: 348, Mismatches: 45, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
79 71 0.20
80 4 0.01
81 273 0.78
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.31
Consensus pattern (81 bp):
AGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
AGGTTAAATACCTTTG
Found at i:1733099 original size:11 final size:11
Alignment explanation
Indices: 1733083--1733111 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1733073 TGAAAATACA
1733083 TAACGGTGTAT
1 TAACGGTGTAT
1733094 TAACGGTGTAT
1 TAACGGTGTAT
1733105 TAACGGT
1 TAACGGT
1733112 ATATAAGGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.28, T:0.34
Consensus pattern (11 bp):
TAACGGTGTAT
Found at i:1736566 original size:11 final size:11
Alignment explanation
Indices: 1736550--1736574 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1736540 CCCTAAATTG
1736550 AAAAAAAAGAA
1 AAAAAAAAGAA
1736561 AAAAAAAAGAA
1 AAAAAAAAGAA
1736572 AAA
1 AAA
1736575 TAAGGTAGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:1738259 original size:36 final size:39
Alignment explanation
Indices: 1738218--1738305 Score: 114
Period size: 34 Copynumber: 2.4 Consensus size: 39
1738208 CTTCGAATTT
*
1738218 TTTTTGAAAATATATATAATATATAGTTTTT-AAAA-CA
1 TTTTTGAAAATATATATAATATATAATTTTTAAAAACCA
*
1738255 -TTTTG-AAA-ACATATAATATATAATTTTTAAAAACCA
1 TTTTTGAAAATATATATAATATATAATTTTTAAAAACCA
1738291 TTTTTGAAACATATA
1 TTTTTGAAA-ATATA
1738306 ATTTTTAGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
34 18 0.43
35 7 0.17
36 7 0.17
37 5 0.12
38 2 0.05
39 1 0.02
40 2 0.05
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.43
Consensus pattern (39 bp):
TTTTTGAAAATATATATAATATATAATTTTTAAAAACCA
Found at i:1738274 original size:34 final size:36
Alignment explanation
Indices: 1738231--1738307 Score: 115
Period size: 34 Copynumber: 2.2 Consensus size: 36
1738221 TTGAAAATAT
*
1738231 ATATAATATATAGTTTTT-AAAA-CA-TTTTGAAAAC
1 ATATAATATATAATTTTTAAAAACCATTTTTG-AAAC
1738265 ATATAATATATAATTTTTAAAAACCATTTTTGAAAC
1 ATATAATATATAATTTTTAAAAACCATTTTTGAAAC
1738301 ATATAAT
1 ATATAAT
1738308 TTTTAGAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
34 17 0.44
35 4 0.10
36 13 0.33
37 5 0.13
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (36 bp):
ATATAATATATAATTTTTAAAAACCATTTTTGAAAC
Found at i:1738399 original size:14 final size:13
Alignment explanation
Indices: 1738379--1738419 Score: 57
Period size: 14 Copynumber: 3.2 Consensus size: 13
1738369 ATTTATTTTG
1738379 TTTATTCTTTATT
1 TTTATTCTTTATT
1738392 TCTTATTCTTTATT
1 T-TTATTCTTTATT
*
1738406 TTTCTT-TTTATT
1 TTTATTCTTTATT
1738418 TT
1 TT
1738420 AGGCCCAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 8 0.31
13 5 0.19
14 13 0.50
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTATTCTTTATT
Found at i:1738413 original size:6 final size:6
Alignment explanation
Indices: 1738356--1738419 Score: 51
Period size: 6 Copynumber: 10.2 Consensus size: 6
1738346 TTTAGTTACA
*
1738356 TTATAT TTA-TT TTATTT ATT-TTGT TTATTCT TTATTT CTTATTCT TTATTT
1 TTATTT TTATTT TTATTT -TTATT-T TTATT-T TTATTT -TTATT-T TTATTT
*
1738407 TTCTTT TTATTT T
1 TTATTT TTATTT T
1738420 AGGCCCAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
5 4 0.08
6 22 0.46
7 21 0.44
8 1 0.02
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.77
Consensus pattern (6 bp):
TTATTT
Found at i:1745828 original size:26 final size:26
Alignment explanation
Indices: 1745793--1745849 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
1745783 TATCCCAATA
*
1745793 AAAGAGCTATTAAATCTCTTTTAATT
1 AAAGAGCTATTAAATCTATTTTAATT
1745819 AAAGAGCTATTAAATCTATTTTAATT
1 AAAGAGCTATTAAATCTATTTTAATT
1745845 AAAGA
1 AAAGA
1745850 AATAAATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.39
Consensus pattern (26 bp):
AAAGAGCTATTAAATCTATTTTAATT
Found at i:1745861 original size:23 final size:24
Alignment explanation
Indices: 1745811--1745864 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
1745801 ATTAAATCTC
* *
1745811 TTTTAATTAAAGAGCTATTAAATCTA
1 TTTTAATTAAAGA-C-AATAAATATA
1745837 TTTTAATTAAAGA-AATAAATATA
1 TTTTAATTAAAGACAATAAATATA
1745860 TTTTA
1 TTTTA
1745865 TTTTTATCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 13 0.50
26 13 0.50
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (24 bp):
TTTTAATTAAAGACAATAAATATA
Found at i:1746674 original size:21 final size:21
Alignment explanation
Indices: 1746635--1746674 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1746625 TTAGCATCAT
1746635 AGTAAAATCCTAAATATTATC
1 AGTAAAATCCTAAATATTATC
1746656 AGTACAAATCCTAAA-ATTA
1 AGTA-AAATCCTAAATATTA
1746675 AAGGTTCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.50, C:0.15, G:0.05, T:0.30
Consensus pattern (21 bp):
AGTAAAATCCTAAATATTATC
Found at i:1747080 original size:16 final size:18
Alignment explanation
Indices: 1747045--1747081 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
1747035 ATGCAAAACA
*
1747045 AAAGTAGAAATATTAAAT
1 AAAGTAGAAATATAAAAT
1747063 AAAG-AGAAA-ATAAAAT
1 AAAGTAGAAATATAAAAT
1747079 AAA
1 AAA
1747082 TAAATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 9 0.50
17 5 0.28
18 4 0.22
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.19
Consensus pattern (18 bp):
AAAGTAGAAATATAAAAT
Found at i:1748824 original size:11 final size:11
Alignment explanation
Indices: 1748808--1748832 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1748798 TGAAGCTCAT
1748808 TTATCATGGTG
1 TTATCATGGTG
1748819 TTATCATGGTG
1 TTATCATGGTG
1748830 TTA
1 TTA
1748833 CGTTGAACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.08, G:0.24, T:0.48
Consensus pattern (11 bp):
TTATCATGGTG
Found at i:1750327 original size:19 final size:22
Alignment explanation
Indices: 1750283--1750328 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 22
1750273 CCTACAGTAT
*
1750283 CGATACTTTCCTTAAAGGGTAT
1 CGATACTTTCCTTAAAGGGTAC
1750305 CGATAC-TTCCTT-AA-GGTAC
1 CGATACTTTCCTTAAAGGGTAC
1750324 CGATA
1 CGATA
1750329 ACAATTTGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 9 0.39
20 2 0.09
21 6 0.26
22 6 0.26
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (22 bp):
CGATACTTTCCTTAAAGGGTAC
Found at i:1755187 original size:21 final size:21
Alignment explanation
Indices: 1755163--1755211 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1755153 ACCGAAGTGT
* *
1755163 CACATATTTAACCCGAATGAC
1 CACATAATTAACCCGAAGGAC
**
1755184 CACATAATTGTCCCGAAGGAC
1 CACATAATTAACCCGAAGGAC
1755205 CACATAA
1 CACATAA
1755212 AACCCTCGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.39, C:0.29, G:0.12, T:0.20
Consensus pattern (21 bp):
CACATAATTAACCCGAAGGAC
Found at i:1757996 original size:23 final size:23
Alignment explanation
Indices: 1757948--1758020 Score: 101
Period size: 23 Copynumber: 3.0 Consensus size: 23
1757938 TTTTTATCCC
*
1757948 AATAAAAGAATTATTAAATCTCTTTT
1 AATAAAAGAA--A-TAAATCTATTTT
1757974 AATAAAAGAAATAAATCTATTTT
1 AATAAAAGAAATAAATCTATTTT
*
1757997 AATAAAAGAAATAAATTTATTTT
1 AATAAAAGAAATAAATCTATTTT
1758020 A
1 A
1758021 TTTTTATCCT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
23 34 0.76
24 1 0.02
26 10 0.22
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (23 bp):
AATAAAAGAAATAAATCTATTTT
Found at i:1760510 original size:21 final size:21
Alignment explanation
Indices: 1760466--1760510 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1760456 AAATTATATA
* *
1760466 TTTAGTACATAAATTATCAGT
1 TTTAATACATAAATTATCAAT
1760487 TTTAATACATAAACTT-TCAAT
1 TTTAATACATAAA-TTATCAAT
1760508 TTT
1 TTT
1760511 TTAAAACAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47
Consensus pattern (21 bp):
TTTAATACATAAATTATCAAT
Done.