Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005680.1 Hibiscus syriacus cultivar Beakdansim tig00013285_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: 1821426
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 6 of 6
Found at i:1455671 original size:61 final size:60
Alignment explanation
Indices: 1455570--1455748 Score: 164
Period size: 61 Copynumber: 3.0 Consensus size: 60
1455560 AAATAACCAA
* * * * * *
1455570 CAAATTCGCAACGCGAACTCTAATTTCGCAAC-ACAGTTTCCAAATTCGCAACGCGATTCT
1 CAAATTCGCAACGCAAACTCCAAATTCGCGACGAGA-TTTCCAAATTCGCGACGCGATTCT
* * *
1455630 CTAAATTCGCAACGCAAACTCCAAATTCGCGACGTGATTTCCGAATTCGCGACGCGATTTT
1 C-AAATTCGCAACGCAAACTCCAAATTCGCGACGAGATTTCCAAATTCGCGACGCGATTCT
* * * * * * * *
1455691 CGAATTCGCGACGCTAATTCC-GATTCGCGACGCGATTCTCCAGATTCTCGACGCGATT
1 CAAATTCGCAACGCAAACTCCAAATTCGCGACGAGATT-TCCAAATTCGCGACGCGATT
1455749 ACCCAGATTA
Statistics
Matches: 98, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
59 14 0.14
60 34 0.35
61 49 0.50
62 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.26
Consensus pattern (60 bp):
CAAATTCGCAACGCAAACTCCAAATTCGCGACGAGATTTCCAAATTCGCGACGCGATTCT
Found at i:1455676 original size:20 final size:20
Alignment explanation
Indices: 1455606--1455769 Score: 125
Period size: 20 Copynumber: 8.1 Consensus size: 20
1455596 CGCAACACAG
* *
1455606 TTTCCAAATTCGCAACGCGA
1 TTTCCGAATTCGCGACGCGA
** * *
1455626 TTCTCTAAATTCGCAACGCAA
1 TT-TCCGAATTCGCGACGCGA
** * *
1455647 ACTCCAAATTCGCGACGTGA
1 TTTCCGAATTCGCGACGCGA
1455667 TTTCCGAATTCGCGACGCGA
1 TTTCCGAATTCGCGACGCGA
* *
1455687 TTTTCGAATTCGCGACGCTA
1 TTTCCGAATTCGCGACGCGA
*
1455707 ATTCCG-ATTCGCGACGCGA
1 TTTCCGAATTCGCGACGCGA
*
1455726 TTCTCC-AGATTCTCGACGCGA
1 TT-TCCGA-ATTCGCGACGCGA
* * *
1455747 TTACCCAGATTAGCGACGCGA
1 TTTCCGA-ATTCGCGACGCGA
1455768 TT
1 TT
1455770 CTCTAGATTT
Statistics
Matches: 117, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
19 13 0.11
20 59 0.50
21 45 0.38
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (20 bp):
TTTCCGAATTCGCGACGCGA
Found at i:1455742 original size:21 final size:21
Alignment explanation
Indices: 1455608--1455804 Score: 131
Period size: 21 Copynumber: 9.7 Consensus size: 21
1455598 CAACACAGTT
* *
1455608 TCCAAATTCGCAACGCGATTC
1 TCCAGATTCGCGACGCGATTC
* * * **
1455629 TCTAAATTCGCAACGC-AAAC
1 TCCAGATTCGCGACGCGATTC
* *
1455649 TCCAAATTCGCGACGTGATT-
1 TCCAGATTCGCGACGCGATTC
*
1455669 TCC-GAATTCGCGACGCGATTT
1 TCCAG-ATTCGCGACGCGATTC
* * *
1455690 TCGA-ATTCGCGACGCTAAT-
1 TCCAGATTCGCGACGCGATTC
1455709 TCC-GATTCGCGACGCGATTC
1 TCCAGATTCGCGACGCGATTC
*
1455729 TCCAGATTCTCGACGCGATTAC
1 TCCAGATTCGCGACGCGATT-C
*
1455751 -CCAGATTAGCGACGCGATTC
1 TCCAGATTCGCGACGCGATTC
* * * * *
1455771 TCTAGATTTGTGACTCGA-AC
1 TCCAGATTCGCGACGCGATTC
*
1455791 TCCAAATTCGCGAC
1 TCCAGATTCGCGAC
1455805 ACTAATTCCG
Statistics
Matches: 139, Mismatches: 28, Indels: 19
0.75 0.15 0.10
Matches are distributed among these distances:
19 15 0.11
20 60 0.43
21 63 0.45
22 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.26
Consensus pattern (21 bp):
TCCAGATTCGCGACGCGATTC
Found at i:1456163 original size:20 final size:20
Alignment explanation
Indices: 1456138--1456209 Score: 99
Period size: 20 Copynumber: 3.6 Consensus size: 20
1456128 CTGGGTAATC
*
1456138 GCGTCGCGAATTCAGAATTA
1 GCGTCGCGAATTCAAAATTA
1456158 GCGTCGCGAATTCAAAATTA
1 GCGTCGCGAATTCAAAATTA
* * *
1456178 ACGTCGCGAATTCAAAAATC
1 GCGTCGCGAATTCAAAATTA
*
1456198 GCGTTGCGAATT
1 GCGTCGCGAATT
1456210 TGGAAATTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (20 bp):
GCGTCGCGAATTCAAAATTA
Found at i:1456216 original size:20 final size:20
Alignment explanation
Indices: 1456193--1456251 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
1456183 GCGAATTCAA
1456193 AAATCGCGTTGCGAATTTGG
1 AAATCGCGTTGCGAATTTGG
*** *
1456213 AAATTATGTTGCGAAATTGG
1 AAATCGCGTTGCGAATTTGG
**
1456233 AGTTCGCGTTGCGAATTTG
1 AAATCGCGTTGCGAATTTG
1456252 TTGGTTATTT
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.25, C:0.12, G:0.29, T:0.34
Consensus pattern (20 bp):
AAATCGCGTTGCGAATTTGG
Found at i:1476218 original size:13 final size:13
Alignment explanation
Indices: 1476200--1476225 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1476190 AGATAAGCTC
1476200 ATTAATGTCTAGT
1 ATTAATGTCTAGT
1476213 ATTAATGTCTAGT
1 ATTAATGTCTAGT
1476226 GTGAACGCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
ATTAATGTCTAGT
Found at i:1484744 original size:18 final size:18
Alignment explanation
Indices: 1484723--1484774 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
1484713 AATATTATTA
* *
1484723 ATATTTTAATTTAAATTT
1 ATATATTAATTTAAATTC
* *
1484741 ATATACTAAATTAAATTC
1 ATATATTAATTTAAATTC
*
1484759 ATATCTTAATATTAAA
1 ATATATTAAT-TTAAA
1484775 AATAAATAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 21 0.81
19 5 0.19
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (18 bp):
ATATATTAATTTAAATTC
Found at i:1484796 original size:26 final size:26
Alignment explanation
Indices: 1484767--1484901 Score: 75
Period size: 27 Copynumber: 5.1 Consensus size: 26
1484757 TCATATCTTA
1484767 ATATTAAAAATAAATAAAAATAAAAT
1 ATATTAAAAATAAATAAAAATAAAAT
1484793 ATATTTAAATAAGTTAAGATAAAAATAAAAT
1 ATA-TTAAA-AA--TAA-ATAAAAATAAAAT
* ** * *
1484824 AT-TTTAAGCTAAAATAAGACT-AAAT
1 ATATTAAAAAT-AAATAAAAATAAAAT
**
1484849 ATACTT---TTTAAATAAAAATAAAAT
1 ATA-TTAAAAATAAATAAAAATAAAAT
*
1484873 AT-TTAATAATTAAGATAAAAATAAAAT
1 ATATTAA-AAATAA-ATAAAAATAAAAT
1484900 AT
1 AT
1484902 TTTTAATGTT
Statistics
Matches: 85, Mismatches: 10, Indels: 27
0.70 0.08 0.22
Matches are distributed among these distances:
22 2 0.02
23 8 0.09
24 7 0.08
25 6 0.07
26 14 0.16
27 24 0.28
28 2 0.02
29 4 0.05
30 3 0.04
31 15 0.18
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (26 bp):
ATATTAAAAATAAATAAAAATAAAAT
Found at i:1484842 original size:31 final size:31
Alignment explanation
Indices: 1484773--1484847 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 31
1484763 CTTAATATTA
1484773 AAAATAA-ATAAAAATAAAATATATTTAAAT
1 AAAATAAGATAAAAATAAAATATATTTAAAT
** *
1484803 AAGTTAAGATAAAAATAAAATAT-TTTAAGCT
1 AAAATAAGATAAAAATAAAATATATTTAA-AT
1484834 AAAATAAGACTAAA
1 AAAATAAGA-TAAA
1484848 TATACTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 10 0.27
31 23 0.62
32 4 0.11
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (31 bp):
AAAATAAGATAAAAATAAAATATATTTAAAT
Found at i:1484908 original size:26 final size:26
Alignment explanation
Indices: 1484780--1484908 Score: 97
Period size: 26 Copynumber: 4.8 Consensus size: 26
1484770 TTAAAAATAA
1484780 ATAAAAATAAAATATATTTAAATAAGTTAAG
1 ATAAAAATAAAATAT-TTT---TAA-TTAAG
* *
1484811 ATAAAAATAAAATA-TTTTAAGCTAAA
1 ATAAAAATAAAATATTTTTAA-TTAAG
* * *
1484837 ATAAGACT-AAATATACTTT--TTAA-
1 ATAAAAATAAAATAT-TTTTAATTAAG
*
1484860 ATAAAAATAAAATATTTAATAATTAAG
1 ATAAAAATAAAATATTT-TTAATTAAG
1484887 ATAAAAATAAAATATTTTTAAT
1 ATAAAAATAAAATATTTTTAAT
1484909 GTTAAGATGT
Statistics
Matches: 80, Mismatches: 11, Indels: 19
0.73 0.10 0.17
Matches are distributed among these distances:
23 7 0.09
24 10 0.12
25 5 0.06
26 21 0.26
27 20 0.25
29 3 0.04
31 14 0.17
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (26 bp):
ATAAAAATAAAATATTTTTAATTAAG
Found at i:1489703 original size:2 final size:2
Alignment explanation
Indices: 1489696--1489722 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1489686 CTTTACGTTG
1489696 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1489723 GAGATAGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1500688 original size:2 final size:2
Alignment explanation
Indices: 1500681--1500725 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1500671 TGAAATATTG
*
1500681 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1500723 AT A
1 AT A
1500726 AACACCCCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1501438 original size:14 final size:13
Alignment explanation
Indices: 1501418--1501450 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
1501408 TCTGTATGAT
1501418 ATATGAAAATCAC
1 ATATGAAAATCAC
1501431 ATTATGAAAATCAC
1 A-TATGAAAATCAC
1501445 ATATGA
1 ATATGA
1501451 GAAAAATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.52, C:0.12, G:0.09, T:0.27
Consensus pattern (13 bp):
ATATGAAAATCAC
Found at i:1503682 original size:11 final size:10
Alignment explanation
Indices: 1503633--1503683 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
1503623 ACGAACTTAT
1503633 AAAATTATAA
1 AAAATTATAA
1503643 ACAAATTATAA
1 A-AAATTATAA
* **
1503654 AAAAATATTT
1 AAAATTATAA
1503664 AAAA-TATATA
1 AAAATTATA-A
1503674 AAAATTATAA
1 AAAATTATAA
1503684 TTTTAAAAGG
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
9 3 0.09
10 16 0.48
11 14 0.42
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAATTATAA
Found at i:1510010 original size:29 final size:29
Alignment explanation
Indices: 1509976--1510034 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1509966 CCTAAATTAA
1509976 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1510005 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1510034 T
1 T
1510035 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1511548 original size:176 final size:176
Alignment explanation
Indices: 1511256--1511608 Score: 674
Period size: 176 Copynumber: 2.0 Consensus size: 176
1511246 GATGGCAAGT
1511256 GTTACAATTGTGGGAAGATGGGCCACATGGCAAAAGACTGTTGGACCAAGAAAGCCTGTTGAAAG
1 GTTACAATTGTGGGAAGATGGGCCACATGGCAAAAGACTGTTGGACCAAGAAAGCCTGTTGAAAG
1511321 TAATACTGCTACTTCTTGTTCGAAGGAGAATAGTGAAGATGGTTGGGATGCTGAAGCGTTATTTG
66 TAATACTGCTACTTCTTGTTCGAAGGAGAATAGTGAAGATGGTTGGGATGCTGAAGCGTTATTTG
1511386 CTACGGAGGAAGAAG-ATTAGCTCTCACGGT-ACAACACCAGAACG
131 CTACGGAGGAAGAAGAATTAGCTCTCACGGTAACAACACCAGAACG
1511430 GTTACAATTGTGGGAAGATGGGCCACATGGCAAAAGACTGTTGGACCAAGAAAAAGCCTGTTGAA
1 GTTACAATTGTGGGAAGATGGGCCACATGGCAAAAGACTGTTGGACCAAG--AAAGCCTGTTGAA
1511495 AGTAATACTGCTACTTCTTGTTCGAAGGAGAATAGTGAAGATGGTTGGGATGCTGAAGCGTTATT
64 AGTAATACTGCTACTTCTTGTTCGAAGGAGAATAGTGAAGATGGTTGGGATGCTGAAGCGTTATT
1511560 TGCTACGGAGGAAGAAGAATTAGCTCTCACGGTAACAACACCAGAACG
129 TGCTACGGAGGAAGAAGAATTAGCTCTCACGGTAACAACACCAGAACG
1511608 G
1 G
1511609 ATTGACTACA
Statistics
Matches: 175, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
174 50 0.29
176 95 0.54
177 15 0.09
178 15 0.09
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (176 bp):
GTTACAATTGTGGGAAGATGGGCCACATGGCAAAAGACTGTTGGACCAAGAAAGCCTGTTGAAAG
TAATACTGCTACTTCTTGTTCGAAGGAGAATAGTGAAGATGGTTGGGATGCTGAAGCGTTATTTG
CTACGGAGGAAGAAGAATTAGCTCTCACGGTAACAACACCAGAACG
Found at i:1514818 original size:29 final size:29
Alignment explanation
Indices: 1514784--1514842 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1514774 CCTAAATTAA
1514784 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1514813 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1514842 T
1 T
1514843 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1518845 original size:32 final size:32
Alignment explanation
Indices: 1518809--1518871 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
1518799 ATATCTATTT
* *
1518809 TAAGTATAAATG-GTTAAATTATATCATATATC
1 TAAGT-TAAATGTGATAAATTATATAATATATC
**
1518841 TAAGTTTTATGTGATAAATTATATAATATAT
1 TAAGTTAAATGTGATAAATTATATAATATAT
1518872 TATAATTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 4 0.15
32 22 0.85
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (32 bp):
TAAGTTAAATGTGATAAATTATATAATATATC
Found at i:1520961 original size:58 final size:57
Alignment explanation
Indices: 1520897--1521011 Score: 221
Period size: 58 Copynumber: 2.0 Consensus size: 57
1520887 GCATTCGAAT
1520897 GTAAAGTACCACCAGCAAGCAAATGATGCTAACAACAGCCTTTTCTTGAAATGAAATC
1 GTAAAGTACCACCAGCAAGCAAATGATGCTAACAACAGCC-TTTCTTGAAATGAAATC
1520955 GTAAAGTACCACCAGCAAGCAAATGATGCTAACAACAGCCTTTCTTGAAATGAAATC
1 GTAAAGTACCACCAGCAAGCAAATGATGCTAACAACAGCCTTTCTTGAAATGAAATC
1521012 CATTAAATTT
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
57 17 0.30
58 40 0.70
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.22
Consensus pattern (57 bp):
GTAAAGTACCACCAGCAAGCAAATGATGCTAACAACAGCCTTTCTTGAAATGAAATC
Found at i:1522092 original size:3 final size:3
Alignment explanation
Indices: 1522086--1522136 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
1522076 TTTCATAATA
* * *
1522086 ATT ATT ATA ATT ATT ATT AAT ATA ATAT ATT ATT ATT ATT ATTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT A-TT ATT
1522133 ATT A
1 ATT A
1522137 AATATATATA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 35 0.88
4 5 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:1522119 original size:28 final size:29
Alignment explanation
Indices: 1522080--1522157 Score: 90
Period size: 28 Copynumber: 2.7 Consensus size: 29
1522070 GTAGACTTTC
1522080 ATAATA-ATTATTATAATTA-TTATTAAT
1 ATAATATATTATTATAATTATTTATTAAT
* *
1522107 ATAATATATTATTATTATTATTTATTATT
1 ATAATATATTATTATAATTATTTATTAAT
1522136 A-AATATATATATATATATATTA
1 ATAATATAT-TAT-TATA-ATTA
1522158 CAAATTACAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
27 6 0.14
28 19 0.44
29 11 0.26
30 3 0.07
31 4 0.09
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
ATAATATATTATTATAATTATTTATTAAT
Found at i:1523356 original size:11 final size:11
Alignment explanation
Indices: 1523323--1523382 Score: 52
Period size: 11 Copynumber: 5.4 Consensus size: 11
1523313 TATTATTACT
1523323 TTTTAATCATTA
1 TTTT-ATCATTA
*
1523335 -TTTATTTATTA
1 TTTTA-TCATTA
*
1523346 TTTTGTCATTA
1 TTTTATCATTA
1523357 CTTTTAT-ATTA
1 -TTTTATCATTA
*
1523368 TTTTATTATTA
1 TTTTATCATTA
1523379 TTTT
1 TTTT
1523383 CATATTAGTC
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
10 7 0.17
11 25 0.62
12 8 0.20
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (11 bp):
TTTTATCATTA
Found at i:1523366 original size:22 final size:22
Alignment explanation
Indices: 1523323--1523389 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
1523313 TATTATTACT
*
1523323 TTTTAATCATTATTTAT-TTATTA
1 TTTT-ATCATTATTT-TCATATTA
*
1523346 TTTTGTCATTACTTTT-ATATTA
1 TTTTATCATTA-TTTTCATATTA
*
1523368 TTTTATTATTATTTTCATATTA
1 TTTTATCATTATTTTCATATTA
1523390 GTCGCATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
21 4 0.11
22 27 0.71
23 7 0.18
ACGTcount: A:0.27, C:0.06, G:0.01, T:0.66
Consensus pattern (22 bp):
TTTTATCATTATTTTCATATTA
Found at i:1523377 original size:33 final size:36
Alignment explanation
Indices: 1523317--1523382 Score: 95
Period size: 33 Copynumber: 1.9 Consensus size: 36
1523307 ATTTAATATT
1523317 ATTACTTTTTAATCATTATTTATTTATTATTTTGTC
1 ATTACTTTTTAATCATTATTTATTTATTATTTTGTC
1523353 ATTAC-TTTT-AT-ATTATTT-TATTATTATTTT
1 ATTACTTTTTAATCATTATTTAT-TTATTATTTT
1523383 CATATTAGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
32 1 0.03
33 17 0.59
34 2 0.07
35 4 0.14
36 5 0.17
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.67
Consensus pattern (36 bp):
ATTACTTTTTAATCATTATTTATTTATTATTTTGTC
Found at i:1523388 original size:11 final size:10
Alignment explanation
Indices: 1523331--1523389 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 10
1523321 CTTTTTAATC
*
1523331 ATTATTTATTT
1 ATTATTT-TAT
*
1523342 ATTATTTTGT
1 ATTATTTTAT
1523352 CATTACTTTTAT
1 -ATTA-TTTTAT
1523364 ATTATTTTATT
1 ATTATTTTA-T
1523375 ATTATTTTCAT
1 ATTATTTT-AT
1523386 ATTA
1 ATTA
1523390 GTCGCATAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
10 7 0.17
11 29 0.69
12 6 0.14
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (10 bp):
ATTATTTTAT
Found at i:1523426 original size:14 final size:16
Alignment explanation
Indices: 1523396--1523427 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
1523386 ATTAGTCGCA
1523396 TAAATATATATATTTT
1 TAAATATATATATTTT
1523412 TAAATA-ATA-ATTTT
1 TAAATATATATATTTT
1523426 TA
1 TA
1523428 TTTATTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 3 0.19
16 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAAATATATATATTTT
Found at i:1525939 original size:22 final size:23
Alignment explanation
Indices: 1525913--1525957 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1525903 AAAGAAAAAA
1525913 TGACA-CCTCTTT-AAAAATATTT
1 TGACACCCT-TTTAAAAAATATTT
1525935 TGACACCCTTTTAAAAAATATTT
1 TGACACCCTTTTAAAAAATATTT
1525958 AATAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.38, C:0.18, G:0.04, T:0.40
Consensus pattern (23 bp):
TGACACCCTTTTAAAAAATATTT
Found at i:1525955 original size:23 final size:22
Alignment explanation
Indices: 1525913--1525957 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1525903 AAAGAAAAAA
1525913 TGACACCTCTTTAAAAATATTT
1 TGACACCTCTTTAAAAATATTT
1525935 TGACACC-CTTTTAAAAAATATTT
1 TGACACCTC-TTT-AAAAATATTT
1525958 AATAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 1 0.05
22 10 0.48
23 10 0.48
ACGTcount: A:0.38, C:0.18, G:0.04, T:0.40
Consensus pattern (22 bp):
TGACACCTCTTTAAAAATATTT
Found at i:1529608 original size:75 final size:75
Alignment explanation
Indices: 1529436--1529884 Score: 286
Period size: 75 Copynumber: 6.1 Consensus size: 75
1529426 TCAAGTTCAT
* * * * * * **
1529436 GAAATTTAGAAGTTTGATTCCCAAAAATG--G-TCCCAGTGGGTTCAGAGGGCATGGCTTGAGGA
1 GAAATTTAGAAGCTTGTTTCCCAAACATGTTGATTCCAGGGGGTTCACAGGGCATAACTTG-GGA
*
1529498 -TCAGGTTCAG
65 TTCAGGTCCAG
* * * * **
1529508 GAAATTTTGAAGAC-TGCTTT-TCGAACATGTTCATTTGAGGGGGTTCACAGGGCA-AAGCTTGG
1 GAAATTTAGAAG-CTTG-TTTCCCAAACATGTTGATTCCAGGGGGTTCACAGGGCATAA-CTTGG
1529570 GATTCAGGTCCAG
63 GATTCAGGTCCAG
* * * * *
1529583 GAAATTTAGAAGCTTGTTTCCCGAACATGTTGATTCCTA-GGGGTTCAGAAGGTATAACTTGAGA
1 GAAATTTAGAAGCTTGTTTCCCAAACATGTTGATTCC-AGGGGGTTCACAGGGCATAACTTGGGA
* *
1529647 TT-GGAGTCCTG
65 TTCAG-GTCCAG
* * *
1529658 GAAACTTAGAAGTTTGTTTCCCAAACATGTTGATTCCAGTGGGTTCACAGGGCATAACTTGGG-T
1 GAAATTTAGAAGCTTGTTTCCCAAACATGTTGATTCCAGGGGGTTCACAGGGCATAACTTGGGAT
*
1529722 TCCAGGTTCAG
66 T-CAGGTCCAG
* * * * * ** * ** *
1529733 AAAATTTAGAAGCCTGTTGCCCAAACATGTTTATTCCAGTGGGTTCACAATGCGTTGCTTGAG-T
1 GAAATTTAGAAGCTTGTTTCCCAAACATGTTGATTCCAGGGGGTTCACAGGGCATAACTTGGGAT
*
1529797 T----T-CTG
66 TCAGGTCCAG
* * * * * ** *
1529802 GAAA-TTAGAAGCCTGTTTTCCAAACATGTTGATTCCAGAGTGTTCACAAGGCATTGCTTGAGAT
1 GAAATTTAGAAGCTTGTTTCCCAAACATGTTGATTCCAGGGGGTTCACAGGGCATAACTTGGGAT
1529866 TCAGGAT-CAG
66 TCAGG-TCCAG
1529876 GAAATTTAG
1 GAAATTTAG
1529885 GGTTTTGGTC
Statistics
Matches: 296, Mismatches: 59, Indels: 41
0.75 0.15 0.10
Matches are distributed among these distances:
68 51 0.17
69 7 0.02
70 1 0.00
72 19 0.06
73 2 0.01
74 18 0.06
75 194 0.66
76 4 0.01
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (75 bp):
GAAATTTAGAAGCTTGTTTCCCAAACATGTTGATTCCAGGGGGTTCACAGGGCATAACTTGGGAT
TCAGGTCCAG
Found at i:1529881 original size:143 final size:145
Alignment explanation
Indices: 1529548--1529884 Score: 364
Period size: 150 Copynumber: 2.3 Consensus size: 145
1529538 TCATTTGAGG
* * * *
1529548 GGGTTCACAGGGCAAAGCTTGGGATTCAGGTCCAGGAAATTTAGAAGCTTGTTTCCCGAACATGT
1 GGGTTCACAGGGCATAGCTT-GGATTCAGGT-CAGGAAATTTAGAAGCCTGTTGCCCAAACATGT
* **
1529613 TGATTCCTAGGGGTTCAGAAGGTATAACTTGAGATTGGAGTCCTGGAAACTTAGAAGTTTGTTTC
64 TGATTCCTAGGGGTTCACAAGGTATAACTTGAGATT---GTCCTGGAAACTTAGAAGCCTGTTTC
*
1529678 CCAAACATGTTGATTCCAGT
126 CCAAACATGTTGATTCCAGA
* * *
1529698 GGGTTCACAGGGCATAACTTGGGTTCCAGGTTCAGAAAATTTAGAAGCCTGTTGCCCAAACATGT
1 GGGTTCACAGGGCATAGCTTGGATT-CAGG-TCAGGAAATTTAGAAGCCTGTTGCCCAAACATGT
* * *
1529763 TTATTCC-AGTGGGTTCACAATGCGT-T-GCTTGAG-TT-T-CTGGAAA-TTAGAAGCCTGTTTT
64 TGATTCCTAG-GGGTTCACAA-G-GTATAACTTGAGATTGTCCTGGAAACTTAGAAGCCTGTTTC
1529821 CCAAACATGTTGATTCCAGA
126 CCAAACATGTTGATTCCAGA
* * *
1529841 GTGTTCACAAGGCATTGCTTGAGATTCAGGATCAGGAAATTTAG
1 GGGTTCACAGGGCATAGCTTG-GATTCAGG-TCAGGAAATTTAG
1529885 GGTTTTGGTC
Statistics
Matches: 160, Mismatches: 21, Indels: 19
0.80 0.10 0.09
Matches are distributed among these distances:
143 64 0.40
144 10 0.06
145 1 0.01
149 8 0.05
150 72 0.45
151 3 0.02
152 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.31
Consensus pattern (145 bp):
GGGTTCACAGGGCATAGCTTGGATTCAGGTCAGGAAATTTAGAAGCCTGTTGCCCAAACATGTTG
ATTCCTAGGGGTTCACAAGGTATAACTTGAGATTGTCCTGGAAACTTAGAAGCCTGTTTCCCAAA
CATGTTGATTCCAGA
Found at i:1532638 original size:23 final size:22
Alignment explanation
Indices: 1532611--1532661 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
1532601 AATATTTATG
* *
1532611 GTTCTAGATTTTAAGGATTCAGA
1 GTTCTAAAATTTAA-GATTCAGA
*
1532634 GTTCTAAAATTTAAGATTTAGA
1 GTTCTAAAATTTAAGATTCAGA
1532656 G-TCTAA
1 GTTCTAA
1532662 GGCTTTATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 5 0.20
22 8 0.32
23 12 0.48
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (22 bp):
GTTCTAAAATTTAAGATTCAGA
Found at i:1546579 original size:18 final size:18
Alignment explanation
Indices: 1546544--1546614 Score: 51
Period size: 18 Copynumber: 4.1 Consensus size: 18
1546534 ACAAACCAAA
** *
1546544 CAAAATAATACAACATTC
1 CAAAATAATATTATATTC
1546562 CAAAATAATATTATATT-
1 CAAAATAATATTATATTC
* *
1546579 C-TAATAAT-TT-TAATC
1 CAAAATAATATTATATTC
*
1546594 CAAAAATAATCTTATATTC
1 C-AAAATAATATTATATTC
1546613 CA
1 CA
1546615 TGAATAAAAC
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
14 3 0.07
15 3 0.07
16 6 0.15
17 7 0.17
18 17 0.41
19 5 0.12
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.35
Consensus pattern (18 bp):
CAAAATAATATTATATTC
Found at i:1549291 original size:10 final size:10
Alignment explanation
Indices: 1549276--1549314 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1549266 TCATCACACC
1549276 AAATTCTCTA
1 AAATTCTCTA
*
1549286 AAATTCTCTC
1 AAATTCTCTA
*
1549296 AAATTCTCTT
1 AAATTCTCTA
*
1549306 AAATACTCT
1 AAATTCTCT
1549315 CTCGTTTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.36, C:0.23, G:0.00, T:0.41
Consensus pattern (10 bp):
AAATTCTCTA
Found at i:1549300 original size:20 final size:20
Alignment explanation
Indices: 1549275--1549315 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1549265 TTCATCACAC
*
1549275 CAAATTCTCTAAAATTCTCT
1 CAAATTCTCTAAAATACTCT
*
1549295 CAAATTCTCTTAAATACTCT
1 CAAATTCTCTAAAATACTCT
1549315 C
1 C
1549316 TCGTTTAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.34, C:0.27, G:0.00, T:0.39
Consensus pattern (20 bp):
CAAATTCTCTAAAATACTCT
Found at i:1549391 original size:17 final size:18
Alignment explanation
Indices: 1549356--1549396 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1549346 ATATTATGTA
*
1549356 TTTAATTTATTTAATTAT
1 TTTACTTTATTTAATTAT
1549374 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAATTAT
1549391 TTTACT
1 TTTACT
1549397 AATATAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTACTTTATTTAATTAT
Found at i:1556366 original size:3 final size:3
Alignment explanation
Indices: 1556167--1556346 Score: 326
Period size: 3 Copynumber: 60.3 Consensus size: 3
1556157 TACCCATATC
1556167 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1556215 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
1556263 ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT ATC
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
1556311 ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT AAT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1556347 AATACATAAT
Statistics
Matches: 170, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
2 2 0.01
3 168 0.99
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1557722 original size:19 final size:19
Alignment explanation
Indices: 1557656--1557722 Score: 55
Period size: 19 Copynumber: 3.3 Consensus size: 19
1557646 ATGAATTAGA
*
1557656 TTTTTAATTTAATTTTATTG
1 TTTTTCATTT-ATTTTATTG
*
1557676 TAATTTAATCAGTTATTTTATATG
1 T--TTT--TCATTTATTTTAT-TG
1557700 -TTTTCATTTATTTTATTG
1 TTTTTCATTTATTTTATTG
1557718 TTTTT
1 TTTTT
1557723 AAATATATTG
Statistics
Matches: 38, Mismatches: 3, Indels: 13
0.70 0.06 0.24
Matches are distributed among these distances:
18 2 0.05
19 16 0.42
20 1 0.03
21 3 0.08
22 3 0.08
23 7 0.18
24 6 0.16
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.67
Consensus pattern (19 bp):
TTTTTCATTTATTTTATTG
Found at i:1560193 original size:14 final size:14
Alignment explanation
Indices: 1560155--1560208 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
1560145 ATTTTAAATA
*
1560155 ATTTACATTTACAT
1 ATTTACATTTGCAT
*
1560169 TTTTACATTTGCAT
1 ATTTACATTTGCAT
1560183 ATTTACATTTGGCAT
1 ATTTACATTT-GCAT
* *
1560198 CTTTGCATTTG
1 ATTTACATTTG
1560209 TATTGCACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:1563484 original size:17 final size:16
Alignment explanation
Indices: 1563460--1563491 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1563450 AAGAAAGAAG
1563460 AAAAAAAAAGGAAAAA
1 AAAAAAAAAGGAAAAA
1563476 AAAAGAAAAAGGAAAA
1 AAAA-AAAAAGGAAAA
1563492 TTGAATCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGGAAAAA
Found at i:1565867 original size:84 final size:84
Alignment explanation
Indices: 1565726--1566231 Score: 935
Period size: 84 Copynumber: 6.0 Consensus size: 84
1565716 GAACAAATAT
*
1565726 AATGTGCTCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAA
1 AATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAA
1565791 TCATTGAATTTAGAAGATG
66 TCATTGAATTTAGAAGATG
1565810 AATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAA
1 AATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAA
1565875 TCATTGAATTTAGAAGATG
66 TCATTGAATTTAGAAGATG
1565894 AATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAA
1 AATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAA
1565959 TCATTGAATTTAGAAGATG
66 TCATTGAATTTAGAAGATG
1565978 AATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAA
1 AATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAA
1566043 TCATTGAATTTAGAAGATG
66 TCATTGAATTTAGAAGATG
*
1566062 AATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGG-CAGAACCA
1 AATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG-GTTGGACAGAACCA
1566126 ATCATTGAATTTAGAAGATG
65 ATCATTGAATTTAGAAGATG
*
1566146 AATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAACCAA
1 AATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAA
* *
1566211 TCGATGGAA-TTAAAAGATG
66 TC-ATTGAATTTAGAAGATG
1566230 AA
1 AA
1566232 CTGCATGATC
Statistics
Matches: 413, Mismatches: 6, Indels: 6
0.97 0.01 0.01
Matches are distributed among these distances:
83 4 0.01
84 400 0.97
85 9 0.02
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.34
Consensus pattern (84 bp):
AATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAA
TCATTGAATTTAGAAGATG
Found at i:1567113 original size:113 final size:113
Alignment explanation
Indices: 1566915--1567812 Score: 1449
Period size: 113 Copynumber: 8.0 Consensus size: 113
1566905 CAAAGATTCA
* *
1566915 AATCCATCACTTGATGGATAAAT-TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCATTTGATGGAT-CATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1566979 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* ****
1567028 AATCCATCATTTGGTGGATCATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
**
1567093 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATATG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* *
1567141 AATCCATCATTTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1567206 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* ****
1567254 AATCCATCATTTGGTGGATCATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
**
1567319 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATATG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* * *
1567367 AATCCATCATTTAATGGATCAGCTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1567432 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* * *
1567480 AATTCATCAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
**
1567545 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATATG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* *
1567593 AATCCATCATTTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1567658 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* * * *
1567706 AATTCATCAATTGATGGATTATCTTTTCCGGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * * *
1567770 AGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTT
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
1567813 GCATAATTCT
Statistics
Matches: 722, Mismatches: 62, Indels: 3
0.92 0.08 0.00
Matches are distributed among these distances:
112 72 0.10
113 650 0.90
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (113 bp):
AATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
Found at i:1568140 original size:3 final size:3
Alignment explanation
Indices: 1568132--1568304 Score: 310
Period size: 3 Copynumber: 57.7 Consensus size: 3
1568122 TTTTTACCCA
1568132 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1568180 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
1568228 TAT TAT CAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1568276 TAT TAT CAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1568305 AATATATTAA
Statistics
Matches: 162, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 162 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1568347 original size:21 final size:21
Alignment explanation
Indices: 1568303--1568347 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
1568293 TTATTATTAT
* *
1568303 TAAATATATTAAATACATATA
1 TAAATATATTAAAAAAATATA
1568324 TAAATATTATTAAAAAAATA-A
1 TAAATA-TATTAAAAAAATATA
1568345 TAA
1 TAA
1568348 TTACAGGCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAATATATTAAAAAAATATA
Found at i:1571433 original size:19 final size:19
Alignment explanation
Indices: 1571409--1571455 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
1571399 ACGTTTACAG
* * *
1571409 AATATATATATATATTTTT
1 AATATATATATAAATTATA
1571428 AATATACTA-ATAAATTATA
1 AATATA-TATATAAATTATA
1571447 AATATATAT
1 AATATATAT
1571456 TATCTTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 2 0.09
19 19 0.83
20 2 0.09
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
AATATATATATAAATTATA
Found at i:1574462 original size:16 final size:16
Alignment explanation
Indices: 1574441--1574474 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1574431 TTACTATTCA
*
1574441 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
1574457 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
1574473 CG
1 CG
1574475 GTCGACGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:1606018 original size:3 final size:3
Alignment explanation
Indices: 1606010--1606069 Score: 113
Period size: 3 Copynumber: 20.3 Consensus size: 3
1606000 GTTAACTCTT
1606010 TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1606057 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
1606070 CATCATCATC
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.04
3 54 0.96
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1609030 original size:2 final size:2
Alignment explanation
Indices: 1609023--1609060 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1609013 AACTCGACAA
1609023 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1609061 TTCATTTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1610483 original size:31 final size:31
Alignment explanation
Indices: 1610385--1610475 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
1610375 CAATTTAAGG
1610385 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1610416 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1610447 CAAAAT-GTTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1610476 TTCAAAATTT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 12 0.20
31 37 0.62
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:1610567 original size:19 final size:19
Alignment explanation
Indices: 1610540--1610606 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
1610530 AATGTTTTTA
* *
1610540 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
1610559 TGAACAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
* *
1610578 TGAACAGTAAATCACTGTT
1 TGAACAGTAAATTACTATT
1610597 TGAACAGTAA
1 TGAACAGTAA
1610607 CCCGAGGCTC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.36
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:1610739 original size:21 final size:21
Alignment explanation
Indices: 1610713--1610754 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1610703 ATTTGAATAT
*
1610713 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1610734 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1610755 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:1610816 original size:21 final size:21
Alignment explanation
Indices: 1610783--1610822 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1610773 TTTGAGTAGA
*
1610783 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
1610805 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
1610823 AGATACGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:1611076 original size:34 final size:32
Alignment explanation
Indices: 1611037--1611106 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1611027 TTTTGTAAAG
* *
1611037 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
1611071 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
1611103 GGGA
1 GGGA
1611107 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:1611782 original size:36 final size:36
Alignment explanation
Indices: 1611683--1611965 Score: 394
Period size: 36 Copynumber: 7.9 Consensus size: 36
1611673 TTCGTTCTAG
* *
1611683 TTGAATCGGAAGTGC-GATGCTTCTTTCCGTTCGAC
1 TTGAATCGGAAGTGCTGATGCTTCCTTCCGTTCGAT
* *
1611718 TTGAATCGGAAGTG-TGATGCTTCTTTCCGTTCAAT
1 TTGAATCGGAAGTGCTGATGCTTCCTTCCGTTCGAT
1611753 TTGAATCGGAAGTGCTGATGCTTCCTTCCGTTCGAT
1 TTGAATCGGAAGTGCTGATGCTTCCTTCCGTTCGAT
* *
1611789 TTGAATCGGAAGTGTTGATGCTTCCTTCCGTTCTAT
1 TTGAATCGGAAGTGCTGATGCTTCCTTCCGTTCGAT
* * *
1611825 TTGAATCGGAAGTGTTGATGTTTTCTTCCGTTCGAT
1 TTGAATCGGAAGTGCTGATGCTTCCTTCCGTTCGAT
*
1611861 TTGAATCGGAAGTG-TCGATGCTTCCTTCCGTTCGAC
1 TTGAATCGGAAGTGCT-GATGCTTCCTTCCGTTCGAT
* *
1611897 TTGAATCGGAAGTGCCGATGCCTT-CTTCCGTTCGAC
1 TTGAATCGGAAGTGCTGATG-CTTCCTTCCGTTCGAT
* *
1611933 TTGAATCGGAAGTGCCGATCCTTCCTTCCGTTC
1 TTGAATCGGAAGTGCTGATGCTTCCTTCCGTTC
1611966 ACTTCCATTA
Statistics
Matches: 228, Mismatches: 14, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
35 50 0.22
36 175 0.77
37 3 0.01
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (36 bp):
TTGAATCGGAAGTGCTGATGCTTCCTTCCGTTCGAT
Found at i:1613320 original size:3 final size:3
Alignment explanation
Indices: 1613312--1613413 Score: 145
Period size: 3 Copynumber: 34.7 Consensus size: 3
1613302 TTTTTATCCA
* * * *
1613312 TAT TAT TAT TAT TAT TAT TAT TAT TAA TAA TAT TAT TAT CAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1613360 TAT TAT TAT TAT TAT TAT TTT TAT T-T TAT TAT TAT TAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1613406 TAT TAT TA
1 TAT TAT TA
1613414 AATATATTAA
Statistics
Matches: 89, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
2 4 0.04
3 85 0.96
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1615009 original size:17 final size:18
Alignment explanation
Indices: 1614984--1615036 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 18
1614974 GGATATTTTT
1614984 AAATAAATATAATTTTGA
1 AAATAAATATAATTTTGA
* *
1615002 AAAT-AATAGAATTAT-A
1 AAATAAATATAATTTTGA
* *
1615018 AATTAAATATATTTTTGA
1 AAATAAATATAATTTTGA
1615036 A
1 A
1615037 TTTTTAAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
16 4 0.15
17 17 0.63
18 6 0.22
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.40
Consensus pattern (18 bp):
AAATAAATATAATTTTGA
Found at i:1626070 original size:11 final size:11
Alignment explanation
Indices: 1626054--1626102 Score: 71
Period size: 11 Copynumber: 4.4 Consensus size: 11
1626044 ATGCTTGAAG
1626054 AAAAAAAAGAA
1 AAAAAAAAGAA
*
1626065 AAAAAAAACAA
1 AAAAAAAAGAA
*
1626076 AAAAAAAAAAA
1 AAAAAAAAGAA
1626087 AAAAAAAACGAA
1 AAAAAAAA-GAA
1626099 AAAA
1 AAAA
1626103 GGGGGTCAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
11 28 0.82
12 6 0.18
ACGTcount: A:0.92, C:0.04, G:0.04, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:1626082 original size:22 final size:22
Alignment explanation
Indices: 1626054--1626102 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
1626044 ATGCTTGAAG
*
1626054 AAAAAAAAGAAAAAAAAAACAA
1 AAAAAAAAAAAAAAAAAAACAA
*
1626076 AAAAAAAAAAAAAAAAAAACGA
1 AAAAAAAAAAAAAAAAAAACAA
1626098 AAAAA
1 AAAAA
1626103 GGGGGTCAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.92, C:0.04, G:0.04, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAAAAAAAAAAACAA
Found at i:1626102 original size:1 final size:1
Alignment explanation
Indices: 1626054--1626094 Score: 64
Period size: 1 Copynumber: 41.0 Consensus size: 1
1626044 ATGCTTGAAG
* *
1626054 AAAAAAAAGAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1626095 CGAAAAAAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.95, C:0.02, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:1626459 original size:19 final size:19
Alignment explanation
Indices: 1626431--1626467 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1626421 GTTCAACTTA
*
1626431 TTGGAGATTCAATTTATTT
1 TTGGAAATTCAATTTATTT
1626450 TTGGAAATTCAATTTATT
1 TTGGAAATTCAATTTATT
1626468 CTTTTCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (19 bp):
TTGGAAATTCAATTTATTT
Found at i:1627391 original size:52 final size:52
Alignment explanation
Indices: 1627329--1627637 Score: 559
Period size: 52 Copynumber: 5.9 Consensus size: 52
1627319 TGAATGTGCT
1627329 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GATCAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAGAA
1627381 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
*
1627433 CATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1627485 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GATCAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAGAA
*
1627537 CATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGGTTGGACAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
*
1627589 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACA
1627638 AAATCAAGTA
Statistics
Matches: 249, Mismatches: 5, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
51 2 0.01
52 243 0.98
53 4 0.02
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.38
Consensus pattern (52 bp):
CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
Found at i:1627742 original size:14 final size:14
Alignment explanation
Indices: 1627723--1627750 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1627713 AGAAGAAGTA
1627723 GCATCAGCAGCCTT
1 GCATCAGCAGCCTT
1627737 GCATCAGCAGCCTT
1 GCATCAGCAGCCTT
1627751 AGTCATTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.21
Consensus pattern (14 bp):
GCATCAGCAGCCTT
Found at i:1628494 original size:119 final size:118
Alignment explanation
Indices: 1628283--1628929 Score: 1089
Period size: 119 Copynumber: 5.5 Consensus size: 118
1628273 TTAGCAAAGA
*
1628283 CTTGAATTCATCAAACTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGT
1 CTTGAATTCATCAAATTGATGGATCATCATTTCCAGA-GAAGAGTTCATAATGAGAAGAACTCGT
1628348 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
65 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
*
1628402 CTTGAATTCATCAATTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGT
1 CTTGAATTCATCAAATTGATGGATCATCATTTCCAGA-GAAGAGTTCATAATGAGAAGAACTCGT
1628467 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
65 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
* *
1628521 CTTGAATTCATC-ACTTGATGGATCATTCTTTTCCAGAGAA-AGTTCATAATGAGAAGAA--C-T
1 CTTGAATTCATCAAATTGATGGATCA-TCATTTCCAGAGAAGAGTTCATAATGAGAAGAACTCGT
*
1628581 CATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTG
65 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
1628635 CTTGAATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGT
1 CTTGAATTCATCAAATTGATGGATCATCATTTCCAGA-GAAGAGTTCATAATGAGAAGAACTCGT
1628700 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
65 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
1628754 CTTGAATTCATCAAATTGATGGATCATCATTTCCAGAGAAGAGTTCATAATGAGAAGAACTCGTC
1 CTTGAATTCATCAAATTGATGGATCATCATTTCCAGAGAAGAGTTCATAATGAGAAGAACTCGTC
*
1628819 ATCTGAAGAA-G--GAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTG
66 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
* * **
1628869 CTTGAATTCATC-ATTTGATGGAACATCATCCCCAGCAGAA-AGTTCATAATGAGAAGAACTC
1 CTTGAATTCATCAAATTGATGGATCATCATTTCCAG-AGAAGAGTTCATAATGAGAAGAACTC
1628930 ATCTGGAGAA
Statistics
Matches: 507, Mismatches: 13, Indels: 21
0.94 0.02 0.04
Matches are distributed among these distances:
114 116 0.23
115 70 0.14
116 18 0.04
117 19 0.04
118 54 0.11
119 230 0.45
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (118 bp):
CTTGAATTCATCAAATTGATGGATCATCATTTCCAGAGAAGAGTTCATAATGAGAAGAACTCGTC
ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
Found at i:1628735 original size:233 final size:235
Alignment explanation
Indices: 1628283--1628929 Score: 1089
Period size: 233 Copynumber: 2.8 Consensus size: 235
1628273 TTAGCAAAGA
1628283 CTTGAATTCATCAAAC-TGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCG
1 CTTGAATTCATC-AACTTGATGGATCATCATTTCCAGA-GAAGAGTTCATAATGAGAAGAAC-CG
1628347 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCA
63 TCATCTGAAGAAGGAAGAAGAA-TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCA
1628412 TCAATTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGA
127 TCAATTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGA
1628477 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
192 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
*
1628521 CTTGAATTCATC-ACTTGATGGATCATTCTTTTCCAGAGAA-AGTTCATAATGAGAAGAA-C-TC
1 CTTGAATTCATCAACTTGATGGATCA-TCATTTCCAGAGAAGAGTTCATAATGAGAAGAACCGTC
1628582 ATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATC
65 ATCTGAAGAAGGAAGAAG-AATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATC
*
1628647 AAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
129 AATTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
1628712 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
194 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
*
1628754 CTTGAATTCATCAAATTGATGGATCATCATTTCCAGAGAAGAGTTCATAATGAGAAGAACTCGTC
1 CTTGAATTCATCAACTTGATGGATCATCATTTCCAGAGAAGAGTTCATAATGAGAAGAAC-CGTC
*
1628819 ATCTGAAGAAGGAAGAAG--TTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATC-
65 ATCTGAAGAAGGAAGAAGAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCA
* **
1628881 ATTTGATGGAACATCATCCCCAGCA-GAA-AGTTCATAATGAGAAGAACTC
130 ATTTGATGGATCATCATTTCCAG-AGGAAGAGTTCATAATGAGAAGAACTC
1628930 ATCTGGAGAA
Statistics
Matches: 391, Mismatches: 9, Indels: 24
0.92 0.02 0.06
Matches are distributed among these distances:
232 21 0.05
233 217 0.55
234 77 0.20
236 21 0.05
237 33 0.08
238 22 0.06
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (235 bp):
CTTGAATTCATCAACTTGATGGATCATCATTTCCAGAGAAGAGTTCATAATGAGAAGAACCGTCA
TCTGAAGAAGGAAGAAGAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAA
TTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
Found at i:1629092 original size:3 final size:3
Alignment explanation
Indices: 1629084--1629183 Score: 132
Period size: 3 Copynumber: 33.7 Consensus size: 3
1629074 TTTTTATCCA
* *
1629084 TAT TAT TAT TAT TATT TAT T-T TAT TAA TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
1629129 TAA TAT TAT TAT TAT TAT TTT TAT TTT TAT TAT TAT TAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1629176 TAT TAT TA
1 TAT TAT TA
1629184 AATATATTAA
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
2 4 0.05
3 77 0.92
4 3 0.04
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1630467 original size:18 final size:17
Alignment explanation
Indices: 1630444--1630488 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
1630434 TTAGATTTAA
1630444 TTTTATTTTTATTATAAT
1 TTTTATTTTT-TTATAAT
*
1630462 TTTTATTTATTTTATAGT
1 TTTTATTT-TTTTATAAT
*
1630480 TTTAATTTT
1 TTTTATTTT
1630489 ACTGCTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 1 0.04
18 21 0.88
19 2 0.08
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (17 bp):
TTTTATTTTTTTATAAT
Found at i:1630750 original size:17 final size:18
Alignment explanation
Indices: 1630725--1630777 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 18
1630715 GGATATTTTT
1630725 AAATAAATATAATTTTGA
1 AAATAAATATAATTTTGA
* *
1630743 AAAT-AATAGAATTAT-A
1 AAATAAATATAATTTTGA
* *
1630759 AATTAAATATATTTTTGA
1 AAATAAATATAATTTTGA
1630777 A
1 A
1630778 TTTTTAAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
16 4 0.15
17 17 0.63
18 6 0.22
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.40
Consensus pattern (18 bp):
AAATAAATATAATTTTGA
Found at i:1636092 original size:20 final size:20
Alignment explanation
Indices: 1636067--1636106 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1636057 AGTAACGGAT
1636067 TTAGAGATTTTGTTTAGGTA
1 TTAGAGATTTTGTTTAGGTA
1636087 TTAGAGATTTTGTTTAGGTA
1 TTAGAGATTTTGTTTAGGTA
1636107 GGCTTACGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (20 bp):
TTAGAGATTTTGTTTAGGTA
Found at i:1640171 original size:19 final size:19
Alignment explanation
Indices: 1640149--1640220 Score: 56
Period size: 19 Copynumber: 3.5 Consensus size: 19
1640139 TTTTGTGGAT
1640149 TGTTGCTTTGATTGTAATA
1 TGTTGCTTTGATTGTAATA
* *
1640168 TGTTACTTTGA-TGTATTTGTGGA
1 TGTTGCTTTGATTGTA---AT--A
1640191 TTGTTGCTTTGATTGTAATA
1 -TGTTGCTTTGATTGTAATA
*
1640211 TGTTGGTTTG
1 TGTTGCTTTG
1640221 GTGTATTTGT
Statistics
Matches: 41, Mismatches: 5, Indels: 14
0.68 0.08 0.23
Matches are distributed among these distances:
18 4 0.10
19 19 0.46
20 1 0.02
21 1 0.02
22 1 0.02
23 1 0.02
24 10 0.24
25 4 0.10
ACGTcount: A:0.17, C:0.04, G:0.25, T:0.54
Consensus pattern (19 bp):
TGTTGCTTTGATTGTAATA
Found at i:1640201 original size:43 final size:43
Alignment explanation
Indices: 1640112--1640281 Score: 241
Period size: 43 Copynumber: 3.9 Consensus size: 43
1640102 TTTTCACGAA
* *
1640112 TGATTATAATATGTTAGTTTGATGTTTTTTTGTGGATTGTTGCTT
1 TGATTGTAATATGTTAGTTTGATG--TATTTGTGGATTGTTGCTT
*
1640157 TGATTGTAATATGTTACTTTGATGTATTTGTGGATTGTTGCTT
1 TGATTGTAATATGTTAGTTTGATGTATTTGTGGATTGTTGCTT
* *
1640200 TGATTGTAATATGTTGGTTTGGTGTATTTGTGGATTGTTGCTT
1 TGATTGTAATATGTTAGTTTGATGTATTTGTGGATTGTTGCTT
* * * *
1640243 TGGTTGGAATATATTAGTTTGATTTATTTGTGGATTGTT
1 TGATTGTAATATGTTAGTTTGATGTATTTGTGGATTGTT
1640282 ACTCTAATGT
Statistics
Matches: 113, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
43 91 0.81
45 22 0.19
ACGTcount: A:0.18, C:0.02, G:0.25, T:0.55
Consensus pattern (43 bp):
TGATTGTAATATGTTAGTTTGATGTATTTGTGGATTGTTGCTT
Found at i:1644807 original size:63 final size:63
Alignment explanation
Indices: 1644734--1644856 Score: 158
Period size: 63 Copynumber: 2.0 Consensus size: 63
1644724 TCAGTACTCA
* * *
1644734 CACTGCCCGACTTCCTACACTTT-TTCTGCAGTTTAATGTTCATAATAGCAATATCCTCCTTAT
1 CACTGCCCGACTTCCTAC-CTTTGTTCCGCAGTTTAATGTTCATAATAGCAAAAGCCTCCTTAT
* * * * *
1644797 CACTGTCCGACTTTCTGCGTTTGTTCCGCAGTTTAATGTTCATGATAGCAAAAGCCTCCT
1 CACTGCCCGACTTCCTACCTTTGTTCCGCAGTTTAATGTTCATAATAGCAAAAGCCTCCT
1644857 CATCCCATTC
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
62 3 0.06
63 48 0.94
ACGTcount: A:0.22, C:0.28, G:0.14, T:0.37
Consensus pattern (63 bp):
CACTGCCCGACTTCCTACCTTTGTTCCGCAGTTTAATGTTCATAATAGCAAAAGCCTCCTTAT
Found at i:1659097 original size:93 final size:94
Alignment explanation
Indices: 1658962--1659157 Score: 306
Period size: 93 Copynumber: 2.1 Consensus size: 94
1658952 TCTTTAACTG
* *
1658962 TTAACCGAAGCAAATTAACCAAATTTTTTTCTTTAACATTAATCGAACTGAAATTATTTAA-TCG
1 TTAACCGAACCAAATTAACCAAATTTTTTTCTTTAACATTAATCGAACCGAAATTATTTAACT-G
* *
1659026 TTAATCGAACTGAAGTTTATTTGAAAATTA
65 TTAATCGAACCGAAATTTATTTGAAAATTA
* * *
1659056 TTAACTGAACCAAATTAACC-GATTTTTTTCTTTAACATTAATTGAACCGAAATTATTTAACTGT
1 TTAACCGAACCAAATTAACCAAATTTTTTTCTTTAACATTAATCGAACCGAAATTATTTAACTGT
1659120 TAATCGAACCGAAATTTATTTGAAAATTA
66 TAATCGAACCGAAATTTATTTGAAAATTA
1659149 TTAACCGAA
1 TTAACCGAA
1659158 TTTTTTTTTA
Statistics
Matches: 93, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
93 74 0.80
94 19 0.20
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (94 bp):
TTAACCGAACCAAATTAACCAAATTTTTTTCTTTAACATTAATCGAACCGAAATTATTTAACTGT
TAATCGAACCGAAATTTATTTGAAAATTA
Found at i:1659128 original size:26 final size:25
Alignment explanation
Indices: 1659086--1659288 Score: 108
Period size: 26 Copynumber: 7.7 Consensus size: 25
1659076 GATTTTTTTC
*
1659086 TTTAACATTAATTGAACCGAAATTA
1 TTTAACATTAATCGAACCGAAATTA
*
1659111 TTTAACTGTTAATCGAACCGAAATTTA
1 TTTAAC-ATTAATCGAACCGAAA-TTA
* * * *
1659138 TTTGAAAATT-AT-TAACCGAATTTTTT
1 TTT-AACATTAATCGAACCGAA--ATTA
1659164 TTTAACATTAATCGAACCGAAATTA
1 TTTAACATTAATCGAACCGAAATTA
* * *
1659189 TTTGACCGTTAATCGAACCAAAATTTA
1 TTT-AACATTAATCGAACCGAAA-TTA
* * * *
1659216 TTTGAAAATT-AT-TAACCGAATTTTTTTC
1 TTT-AACATTAATCGAACCGAA----ATTA
*
1659244 TTTAACCATTAATCGAACCAAAATTA
1 TTTAA-CATTAATCGAACCGAAATTA
* *
1659270 TTTGACCGTTAATCGAACC
1 TTT-AACATTAATCGAACC
1659289 CACATTTATT
Statistics
Matches: 133, Mismatches: 28, Indels: 33
0.69 0.14 0.17
Matches are distributed among these distances:
25 29 0.22
26 58 0.44
27 28 0.21
28 10 0.08
29 2 0.02
30 6 0.05
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (25 bp):
TTTAACATTAATCGAACCGAAATTA
Found at i:1659285 original size:81 final size:80
Alignment explanation
Indices: 1659069--1659313 Score: 397
Period size: 78 Copynumber: 3.1 Consensus size: 80
1659059 ACTGAACCAA
* * * *
1659069 ATTAACCG-ATTTTTTTCTTTAACATTAATTGAACCGAAATTATTTAACTGTTAATCGAACCGAA
1 ATTAACCGAATTTTTTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCAAA
1659133 ATTTATTTGAAAATT
66 ATTTATTTGAAAATT
1659148 ATTAACCGAA-TTTTTT-TTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCAAA
1 ATTAACCGAATTTTTTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCAAA
1659211 ATTTATTTGAAAATT
66 ATTTATTTGAAAATT
* *
1659226 ATTAACCGAATTTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATCGAACCCA
1 ATTAACCGAATTTTTTTCTTTAA-CATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCAA
*
1659291 CATTTATTTGAAAATT
65 AATTTATTTGAAAATT
1659307 ATTAACC
1 ATTAACC
1659314 AAATAAAATA
Statistics
Matches: 155, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
78 68 0.44
79 20 0.13
80 6 0.04
81 61 0.39
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (80 bp):
ATTAACCGAATTTTTTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCAAA
ATTTATTTGAAAATT
Found at i:1659398 original size:65 final size:65
Alignment explanation
Indices: 1659267--1659430 Score: 170
Period size: 65 Copynumber: 2.5 Consensus size: 65
1659257 CGAACCAAAA
* * * * *
1659267 TTATTTGACCGTTAATCGAACCCACATTTATTTGAAAATTATTAACCAAATAAAATAAATTA-TT
1 TTATTTAACCGTTAATCGAA-CCAAATTTATTTAAAAATTATTAACCAAACAAAATAAACTATTT
1659331 T
65 T
* * *
1659332 TTATTTAACCGTTAATCGAACCGAAATTTATTTAAAAATTATTAA-CAGAACCAAATCAACTGTT
1 TTATTTAACCGTTAATCGAACC-AAATTTATTTAAAAATTATTAACCA-AACAAAATAAACT-AT
1659396 TTT
63 TTT
* * * *
1659399 TTCTTTAACCATTAATCTAACCAAAATTATTT
1 TTATTTAACCGTTAATCGAACCAAATTTATTT
1659431 GACTGTTAAT
Statistics
Matches: 83, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
64 4 0.05
65 48 0.58
66 9 0.11
67 22 0.27
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.39
Consensus pattern (65 bp):
TTATTTAACCGTTAATCGAACCAAATTTATTTAAAAATTATTAACCAAACAAAATAAACTATTTT
Found at i:1659431 original size:158 final size:164
Alignment explanation
Indices: 1659236--1659545 Score: 461
Period size: 158 Copynumber: 1.9 Consensus size: 164
1659226 ATTAACCGAA
*
1659236 TTTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATCGAACCCACATTTATTTG
1 TTTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATCGAACCCAAATTTATTTG
1659301 AAAATTATTAACCAAA-TAA-AATAAATT-A-T-TTTTAT-TTAACCGTTAATCGAACCGAAATT
66 AAAATTATTAACCAAATTAACAATAAATTAATTATTTTATCTTAACCGTTAATCGAACCGAAATT
1659360 TATTTAAAAATTATTAACAGAACCAAATCAACTG
131 TATTTAAAAATTATTAACAGAACCAAATCAACTG
* * * *
1659394 TTTTTTTCTTTAACCATTAATCTAACCAAAATTATTTGACTGTTAATCGAATCGAAATTTATTTG
1 TTTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATCGAACCCAAATTTATTTG
* *
1659459 AAAATTATTAACCAAATTAACCGAATAAATTAAATTATTTTTTCCTTAACCGTTAATCGAACTGA
66 AAAATTATTAACCAAATTAA-C-AATAAATT-AATTATTTTAT-CTTAACCGTTAATCGAACCGA
**
1659524 AATTTATTTGGAAATTATTAAC
127 AATTTATTTAAAAATTATTAAC
1659546 CAATTGGTTA
Statistics
Matches: 133, Mismatches: 9, Indels: 10
0.88 0.06 0.07
Matches are distributed among these distances:
158 76 0.57
159 3 0.02
162 8 0.06
164 1 0.01
165 1 0.01
166 5 0.04
168 39 0.29
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.39
Consensus pattern (164 bp):
TTTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATCGAACCCAAATTTATTTG
AAAATTATTAACCAAATTAACAATAAATTAATTATTTTATCTTAACCGTTAATCGAACCGAAATT
TATTTAAAAATTATTAACAGAACCAAATCAACTG
Found at i:1660627 original size:59 final size:59
Alignment explanation
Indices: 1660529--1660660 Score: 149
Period size: 59 Copynumber: 2.2 Consensus size: 59
1660519 CATATGATCT
* * * * *
1660529 CAAAGTATGACTTTTATTTTAAATTGGTCCTTAAACTTTT-AAATATTTCAATTTAATCC
1 CAAACTATGACTATCATTCTAAATTAGTCCTTAAACTTTTCAAA-ATTTCAATTTAATCC
* * * * *
1660588 TAAATTATGACTATCATTCTAAATTAGTCCTTGATCTTTTCAAAATTTCAATTTCATCC
1 CAAACTATGACTATCATTCTAAATTAGTCCTTAAACTTTTCAAAATTTCAATTTAATCC
*
1660647 CAAACTATAACTAT
1 CAAACTATGACTAT
1660661 GTACTAATCA
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
59 57 0.95
60 3 0.05
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.43
Consensus pattern (59 bp):
CAAACTATGACTATCATTCTAAATTAGTCCTTAAACTTTTCAAAATTTCAATTTAATCC
Found at i:1661094 original size:19 final size:20
Alignment explanation
Indices: 1661055--1661105 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
1661045 CTAATTTACC
1661055 TTAA-ATATATTAGATTATT
1 TTAATATATATTAGATTATT
1661074 TTAATATATATTA-ATCT-TT
1 TTAATATATATTAGAT-TATT
1661093 TT-ATA-ATATTAGA
1 TTAATATATATTAGA
1661106 AAACATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 6 0.21
18 4 0.14
19 10 0.34
20 9 0.31
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (20 bp):
TTAATATATATTAGATTATT
Found at i:1678942 original size:21 final size:22
Alignment explanation
Indices: 1678911--1678951 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1678901 ATATATATAC
*
1678911 AATTTATAAATTATTTAAATTT
1 AATTTATAAATTATGTAAATTT
1678933 AATTT-TAAATTATGTAAAT
1 AATTTATAAATTATGTAAAT
1678952 CACTTGAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
AATTTATAAATTATGTAAATTT
Found at i:1684009 original size:31 final size:32
Alignment explanation
Indices: 1683968--1684027 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
1683958 TAATAAGAAG
*
1683968 TATTGATAATTTT-AT-TAAAATTATAAATAAT
1 TATTAATAATTTTAATATAAAATTA-AAATAAT
1683999 TATTAATAATTTTAATATAAAATTAAAAT
1 TATTAATAATTTTAATATAAAATTAAAAT
1684028 GACAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 12 0.46
32 6 0.23
33 8 0.31
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (32 bp):
TATTAATAATTTTAATATAAAATTAAAATAAT
Found at i:1684015 original size:9 final size:10
Alignment explanation
Indices: 1683979--1684015 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1683969 ATTGATAATT
1683979 TTATTAA-AA
1 TTATTAATAA
*
1683988 TTATAAATAA
1 TTATTAATAA
1683998 TTATTAATAA
1 TTATTAATAA
1684008 TT-TTAATA
1 TTATTAATA
1684016 TAAAATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 12 0.48
10 13 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
TTATTAATAA
Found at i:1684052 original size:134 final size:133
Alignment explanation
Indices: 1683902--1684171 Score: 531
Period size: 134 Copynumber: 2.0 Consensus size: 133
1683892 GTTTTCAATT
1683902 AAATATGATCTTGTTTAATTCGTTATATGATGTTCAAAATTAAAAGGTGTATTTTATAATAAGAA
1 AAATATGATCTTGTTTAATTCGTTATATGATGTTCAAAATTAAAAGGTGTATTTTATAATAAGAA
1683967 GTATTGATAATTTTATTAAAATTATAAATAATTATTAATAATTTTAATATAAAATTAAAATGACA
66 GTATTGATAATTTTATTAAAATTATAAATAATTATTAATAATTTTAATATAAAATTAAAATGACA
1684032 AAA
131 AAA
1684035 AAATAATGATCTTGTTTAATTCGTTATATGATGTTCAAAATTAAAAGGTGTATTTTATAATAAGA
1 AAAT-ATGATCTTGTTTAATTCGTTATATGATGTTCAAAATTAAAAGGTGTATTTTATAATAAGA
1684100 AGTATTGATAATTTTATTAAAATTATAAATAATTATTAATAATTTTAATATAAAATTAAAATGAC
65 AGTATTGATAATTTTATTAAAATTATAAATAATTATTAATAATTTTAATATAAAATTAAAATGAC
1684165 AAAA
130 AAAA
1684169 AAA
1 AAA
1684172 ATAAAGACTA
Statistics
Matches: 136, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
133 4 0.03
134 132 0.97
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (133 bp):
AAATATGATCTTGTTTAATTCGTTATATGATGTTCAAAATTAAAAGGTGTATTTTATAATAAGAA
GTATTGATAATTTTATTAAAATTATAAATAATTATTAATAATTTTAATATAAAATTAAAATGACA
AAA
Found at i:1684143 original size:31 final size:32
Alignment explanation
Indices: 1684102--1684161 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
1684092 TAATAAGAAG
*
1684102 TATTGATAATTTT-AT-TAAAATTATAAATAAT
1 TATTAATAATTTTAATATAAAATTA-AAATAAT
1684133 TATTAATAATTTTAATATAAAATTAAAAT
1 TATTAATAATTTTAATATAAAATTAAAAT
1684162 GACAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 12 0.46
32 6 0.23
33 8 0.31
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (32 bp):
TATTAATAATTTTAATATAAAATTAAAATAAT
Found at i:1684149 original size:9 final size:10
Alignment explanation
Indices: 1684113--1684149 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1684103 ATTGATAATT
1684113 TTATTAA-AA
1 TTATTAATAA
*
1684122 TTATAAATAA
1 TTATTAATAA
1684132 TTATTAATAA
1 TTATTAATAA
1684142 TT-TTAATA
1 TTATTAATA
1684150 TAAAATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 12 0.48
10 13 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
TTATTAATAA
Found at i:1689538 original size:35 final size:35
Alignment explanation
Indices: 1689498--1689576 Score: 149
Period size: 35 Copynumber: 2.3 Consensus size: 35
1689488 CACTAAGCTG
1689498 GGTTGAAAAACATATCACAAAGGCAAAAAAACATA
1 GGTTGAAAAACATATCACAAAGGCAAAAAAACATA
1689533 GGTTGAAAAACATATCACAAAGGCAAAAAAACATA
1 GGTTGAAAAACATATCACAAAGGCAAAAAAACATA
*
1689568 GGATGAAAA
1 GGTTGAAAA
1689577 TATTATCTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.57, C:0.13, G:0.16, T:0.14
Consensus pattern (35 bp):
GGTTGAAAAACATATCACAAAGGCAAAAAAACATA
Found at i:1701568 original size:16 final size:16
Alignment explanation
Indices: 1701544--1701580 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1701534 TAAAATATAC
1701544 ATTCCAATAATCTTTT
1 ATTCCAATAATCTTTT
*
1701560 ATTCTAATAATCTTTT
1 ATTCCAATAATCTTTT
1701576 ATTCC
1 ATTCC
1701581 TTTAACCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTCCAATAATCTTTT
Found at i:1714483 original size:14 final size:14
Alignment explanation
Indices: 1714466--1714521 Score: 51
Period size: 16 Copynumber: 3.8 Consensus size: 14
1714456 ATTTATCCAT
1714466 TTTTCATTATTTAA
1 TTTTCATTATTTAA
*
1714480 TTTTCTTTAACTTTAA
1 TTTTCATT-A-TTTAA
*
1714496 TTTATTATTATTTAAA
1 TTT-TCATTATTT-AA
1714512 TTTT-ATTATT
1 TTTTCATTATT
1714522 AATAAAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 13 0.37
15 5 0.14
16 14 0.40
17 3 0.09
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTTCATTATTTAA
Found at i:1715246 original size:6 final size:6
Alignment explanation
Indices: 1715235--1715260 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1715225 GAATAATGAG
1715235 GAGGAA GAGGAA GAGGAA GAGGAA GA
1 GAGGAA GAGGAA GAGGAA GAGGAA GA
1715261 AGACACTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
GAGGAA
Found at i:1716540 original size:29 final size:30
Alignment explanation
Indices: 1716500--1716560 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 30
1716490 ATGTCCGTTT
*
1716500 TTTCAGTTTAGTGCCTAACGTTT-ATTTCG
1 TTTCAGTTTAGTGCCTAACGTTTCATTCCG
1716529 TTTCAGTTTAGTGCCTAACGTTTCATTCCG
1 TTTCAGTTTAGTGCCTAACGTTTCATTCCG
1716559 TT
1 TT
1716561 ATTTAAAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 23 0.77
30 7 0.23
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.48
Consensus pattern (30 bp):
TTTCAGTTTAGTGCCTAACGTTTCATTCCG
Found at i:1717317 original size:6 final size:6
Alignment explanation
Indices: 1717306--1717334 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1717296 TTAAAACTTA
1717306 ATAAAT ATAAAT ATAAAT ATAAAT ATAAA
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAA
1717335 ACTCCAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
ATAAAT
Found at i:1717616 original size:22 final size:22
Alignment explanation
Indices: 1717591--1717632 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1717581 ATTAACTTTT
*
1717591 ATTTTT-TAAAACCTATAAAATG
1 ATTTTTCTAAAA-ATATAAAATG
1717613 ATTTTTCTAAAAATATAAAA
1 ATTTTTCTAAAAATATAAAA
1717633 AGATATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.40
Consensus pattern (22 bp):
ATTTTTCTAAAAATATAAAATG
Found at i:1719510 original size:19 final size:20
Alignment explanation
Indices: 1719488--1719525 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1719478 ATAAACTAAA
1719488 TTTA-ATTTTTTAAAATAAT
1 TTTATATTTTTTAAAATAAT
*
1719507 TTTATATTTTTTATAATAA
1 TTTATATTTTTTAAAATAA
1719526 AAAATTGCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTATATTTTTTAAAATAAT
Found at i:1723311 original size:19 final size:19
Alignment explanation
Indices: 1723283--1723321 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1723273 AGGTGCAATC
1723283 ACCATATAACAGT-TAAGAA
1 ACCATATAACA-TATAAGAA
*
1723302 ACCATCTAACATATAAGAA
1 ACCATATAACATATAAGAA
1723321 A
1 A
1723322 ACAATAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 17 0.94
ACGTcount: A:0.54, C:0.18, G:0.08, T:0.21
Consensus pattern (19 bp):
ACCATATAACATATAAGAA
Found at i:1744879 original size:16 final size:17
Alignment explanation
Indices: 1744860--1744893 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1744850 TTCTTTAATC
*
1744860 TTTTGTTTG-TTTATTA
1 TTTTGGTTGTTTTATTA
1744876 TTTTGGTTGTTTTATTA
1 TTTTGGTTGTTTTATTA
1744893 T
1 T
1744894 AAGTGCGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.12, C:0.00, G:0.15, T:0.74
Consensus pattern (17 bp):
TTTTGGTTGTTTTATTA
Found at i:1757516 original size:23 final size:23
Alignment explanation
Indices: 1757484--1757535 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
1757474 TTTTGCTGGT
1757484 AAAG-TAGTAAAAATAAAATCTG
1 AAAGTTAGTAAAAATAAAATCTG
1757506 AAAGTTAGTAAAAATAAAATCTG
1 AAAGTTAGTAAAAATAAAATCTG
1757529 AAAGTTA
1 AAAGTTA
1757536 TGTTTAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 4 0.14
23 25 0.86
ACGTcount: A:0.58, C:0.04, G:0.13, T:0.25
Consensus pattern (23 bp):
AAAGTTAGTAAAAATAAAATCTG
Found at i:1759559 original size:18 final size:18
Alignment explanation
Indices: 1759536--1759573 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
1759526 TTGTTGAGGT
1759536 GGTCCACCGA-AATAGCTA
1 GGTCCACC-ATAATAGCTA
1759554 GGTCCACCATAATAGCTA
1 GGTCCACCATAATAGCTA
1759572 GG
1 GG
1759574 CCCCGCACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 1 0.05
18 18 0.95
ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18
Consensus pattern (18 bp):
GGTCCACCATAATAGCTA
Found at i:1759771 original size:51 final size:51
Alignment explanation
Indices: 1759686--1759794 Score: 157
Period size: 51 Copynumber: 2.1 Consensus size: 51
1759676 CCCTTTGGGT
* * * *
1759686 TTCTCCGCTTCTTTTGGTTTGTCGACCTTTTTCTCCCCAC-CCTCTTTAGGC
1 TTCTCGGCTTCTTTTGGTTTCTCGACCTTCTTCTCCCC-CGACTCTTTAGGC
*
1759737 TTCTCGGCTTCTTTTGGTTTCTCGGCCTTCTTCTCCCCCGACTCTTTAGGC
1 TTCTCGGCTTCTTTTGGTTTCTCGACCTTCTTCTCCCCCGACTCTTTAGGC
1759788 TTCTCGG
1 TTCTCGG
1759795 GTTTCTTCTC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
50 1 0.02
51 51 0.98
ACGTcount: A:0.05, C:0.35, G:0.17, T:0.44
Consensus pattern (51 bp):
TTCTCGGCTTCTTTTGGTTTCTCGACCTTCTTCTCCCCCGACTCTTTAGGC
Found at i:1759819 original size:30 final size:30
Alignment explanation
Indices: 1759778--1759887 Score: 141
Period size: 30 Copynumber: 3.7 Consensus size: 30
1759768 TCTCCCCCGA
*
1759778 CTCTTTAGGCTTCTCGGGTTTCTTCTCAGC
1 CTCTTTAGGCTTCTCAGGTTTCTTCTCAGC
* *
1759808 CTCTTTCGGCTTCTCAGGTTTCTTCTCGGC
1 CTCTTTAGGCTTCTCAGGTTTCTTCTCAGC
* * * *
1759838 CTCTTTCGGCTTCTC-GGTCTGCTTTTCCGC
1 CTCTTTAGGCTTCTCAGGT-TTCTTCTCAGC
1759868 CTCTTTAGGCTTCTCAGGTT
1 CTCTTTAGGCTTCTCAGGTT
1759888 CCTTGGGTTT
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
29 3 0.04
30 65 0.92
31 3 0.04
ACGTcount: A:0.05, C:0.32, G:0.20, T:0.44
Consensus pattern (30 bp):
CTCTTTAGGCTTCTCAGGTTTCTTCTCAGC
Found at i:1763715 original size:122 final size:122
Alignment explanation
Indices: 1763581--1763825 Score: 490
Period size: 122 Copynumber: 2.0 Consensus size: 122
1763571 TTGGTCCCCT
1763581 TTTTTAGTATAATGATATGATTTTATAATAGTTAAAAAATAAACCATTTATAATTTAATGTGATA
1 TTTTTAGTATAATGATATGATTTTATAATAGTTAAAAAATAAACCATTTATAATTTAATGTGATA
1763646 AATTTAATTAAATGATAAGATATTCTAAAAAACTCAAATTGTTGCATCTAATACAAC
66 AATTTAATTAAATGATAAGATATTCTAAAAAACTCAAATTGTTGCATCTAATACAAC
1763703 TTTTTAGTATAATGATATGATTTTATAATAGTTAAAAAATAAACCATTTATAATTTAATGTGATA
1 TTTTTAGTATAATGATATGATTTTATAATAGTTAAAAAATAAACCATTTATAATTTAATGTGATA
1763768 AATTTAATTAAATGATAAGATATTCTAAAAAACTCAAATTGTTGCATCTAATACAAC
66 AATTTAATTAAATGATAAGATATTCTAAAAAACTCAAATTGTTGCATCTAATACAAC
1763825 T
1 T
1763826 AGGTTTCATG
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
122 123 1.00
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.40
Consensus pattern (122 bp):
TTTTTAGTATAATGATATGATTTTATAATAGTTAAAAAATAAACCATTTATAATTTAATGTGATA
AATTTAATTAAATGATAAGATATTCTAAAAAACTCAAATTGTTGCATCTAATACAAC
Found at i:1766922 original size:19 final size:18
Alignment explanation
Indices: 1766878--1766924 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
1766868 TATCAAATAG
*
1766878 TCTTAAAATAATAATATT
1 TCTTGAAATAATAATATT
1766896 TCTTGAAATAATAATATT
1 TCTTGAAATAATAATATT
*
1766914 TAGTTGAAATA
1 T-CTTGAAATA
1766925 TTCACAATGC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (18 bp):
TCTTGAAATAATAATATT
Found at i:1769369 original size:42 final size:42
Alignment explanation
Indices: 1769314--1769464 Score: 146
Period size: 42 Copynumber: 3.6 Consensus size: 42
1769304 TTTATAATGT
* * *
1769314 CGTTTTTCCAACAAACGCCGCAATAGAG-ATGTAATTTAGCGG
1 CGTTTATCAAACAAACGCCGCAATAGAGTA-ATAATTTAGCGG
* ** *
1769356 CGTTTATCAAACAAACGTCGCTGTAGAGTAATAATTTAGTGG
1 CGTTTATCAAACAAACGCCGCAATAGAGTAATAATTTAGCGG
* ** *
1769398 CGTTTGTGTAA-AAACGCCGCAATATAGTAATAATTTAGCGG
1 CGTTTATCAAACAAACGCCGCAATAGAGTAATAATTTAGCGG
*
1769439 CGTTTAT-AGTACAAAACGCCGCAATA
1 CGTTTATCA-AAC-AAACGCCGCAATA
1769465 TGTTTGTTTA
Statistics
Matches: 87, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
41 32 0.37
42 41 0.47
43 14 0.16
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.28
Consensus pattern (42 bp):
CGTTTATCAAACAAACGCCGCAATAGAGTAATAATTTAGCGG
Found at i:1769427 original size:41 final size:41
Alignment explanation
Indices: 1769326--1769502 Score: 144
Period size: 42 Copynumber: 4.3 Consensus size: 41
1769316 TTTTTCCAAC
* * * **
1769326 AAACGCCGCAATAGAG-ATGTAATTTAGCGGCGTTTATCAAA
1 AAACGCCGCAATATAGTA-ATAATTTAGTGGCGTTTATGTAA
* ** * *
1769367 CAAACGTCGCTGTAGAGTAATAATTTAGTGGCGTTTGTGTAA
1 -AAACGCCGCAATATAGTAATAATTTAGTGGCGTTTATGTAA
*
1769409 AAACGCCGCAATATAGTAATAATTTAGCGGCGTTTATAGTACA
1 AAACGCCGCAATATAGTAATAATTTAGTGGCGTTTAT-GTA-A
* ** * *
1769452 AAACGCCGCAATAT-GT-TTGTTTATAGTGGCGTTTTTATAA
1 AAACGCCGCAATATAGTAATAATT-TAGTGGCGTTTATGTAA
1769492 AAACGCCGCAA
1 AAACGCCGCAA
1769503 AAACATGTAC
Statistics
Matches: 111, Mismatches: 20, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
40 12 0.11
41 36 0.32
42 47 0.42
43 16 0.14
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.29
Consensus pattern (41 bp):
AAACGCCGCAATATAGTAATAATTTAGTGGCGTTTATGTAA
Found at i:1769935 original size:22 final size:22
Alignment explanation
Indices: 1769905--1769952 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1769895 TTGTTTTTCT
*
1769905 GCTTTCGAATA-GAAGAATAATA
1 GCTTCCGAATAGGAA-AATAATA
1769927 GCTTCCGAATAGGAAAATAATA
1 GCTTCCGAATAGGAAAATAATA
1769949 GCTT
1 GCTT
1769953 TTGAAACATG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (22 bp):
GCTTCCGAATAGGAAAATAATA
Found at i:1771083 original size:41 final size:40
Alignment explanation
Indices: 1771038--1771180 Score: 137
Period size: 41 Copynumber: 3.5 Consensus size: 40
1771028 ATCTATTGCA
1771038 GCATTTTTATACAAACGCCGCAATATAATAGAACTTTAGCG
1 GCATTTTTATACAAACGCCGCAATATAATA-AACTTTAGCG
* * * * * * *
1771079 GCATTTTTGTACAAACGCCACAGTAGATATAATCTATAGAG
1 GCATTTTTATACAAACGCCGCAATATA-ATAAACTTTAGCG
* * *
1771120 GCGTTTTTATACAAATGTCGCAATATAATATAACTTTAGCG
1 GCATTTTTATACAAACGCCGCAATATAATA-AACTTTAGCG
1771161 GCGA-TTTTATGA-AAACGCCG
1 GC-ATTTTTAT-ACAAACGCCG
1771181 ATAAATAGGC
Statistics
Matches: 78, Mismatches: 20, Indels: 8
0.74 0.19 0.08
Matches are distributed among these distances:
40 3 0.04
41 71 0.91
42 4 0.05
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (40 bp):
GCATTTTTATACAAACGCCGCAATATAATAAACTTTAGCG
Found at i:1771106 original size:82 final size:83
Alignment explanation
Indices: 1771000--1771168 Score: 218
Period size: 82 Copynumber: 2.0 Consensus size: 83
1770990 GTTGGCGGTG
* *
1771000 TTTTTATACAAACACCCCACTAGAT-TATATCTATTGCA-GCATTTTTATACAAACGCCGCAATA
1 TTTTTATACAAACACCACACTAGATATA-ATCTATAG-AGGCATTTTTATACAAACGCCGCAATA
1771063 TAATAGAACTTTAGCGGC-A
64 TAATAGAACTTTAGCGGCGA
* * * * * *
1771082 TTTTTGTACAAACGCCACAGTAGATATAATCTATAGAGGCGTTTTTATACAAATGTCGCAATATA
1 TTTTTATACAAACACCACACTAGATATAATCTATAGAGGCATTTTTATACAAACGCCGCAATATA
*
1771147 ATATAACTTTAGCGGCGA
66 ATAGAACTTTAGCGGCGA
1771165 TTTT
1 TTTT
1771169 ATGAAAACGC
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
81 1 0.01
82 67 0.89
83 7 0.09
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (83 bp):
TTTTTATACAAACACCACACTAGATATAATCTATAGAGGCATTTTTATACAAACGCCGCAATATA
ATAGAACTTTAGCGGCGA
Found at i:1771209 original size:82 final size:82
Alignment explanation
Indices: 1771041--1771193 Score: 193
Period size: 82 Copynumber: 1.8 Consensus size: 82
1771031 TATTGCAGCA
* *
1771041 TTTTTATACAAACGCCGCAATATAATAGAACTTTAGCGGCATTTTTGTACAAACGCCACAGTAGA
1 TTTTTATACAAACGCCGCAATATAATAGAACTTTAGCGGCATTTTTGTACAAACGCCAAAATAGA
*
1771106 TATAATCTATAGAGGCG
66 CATAATCTATAGAGGCG
* * *
1771123 TTTTTATACAAATGTCGCAATATAATATAACTTTAGCGGCGATTTTATG-A-AAACGCCGATAAA
1 TTTTTATACAAACGCCGCAATATAATAGAACTTTAGCGGC-ATTTT-TGTACAAACGCC-A-AAA
*
1771186 TAGGCATA
62 TAGACATA
1771194 CGTTAGTGGT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
82 44 0.73
83 7 0.12
84 9 0.15
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (82 bp):
TTTTTATACAAACGCCGCAATATAATAGAACTTTAGCGGCATTTTTGTACAAACGCCAAAATAGA
CATAATCTATAGAGGCG
Found at i:1772466 original size:50 final size:50
Alignment explanation
Indices: 1772402--1772514 Score: 208
Period size: 50 Copynumber: 2.3 Consensus size: 50
1772392 AGAATACCAA
* *
1772402 CAAATAATGGATTACTCAACTGAATTAGATTTAATGATCATTTTACCTTC
1 CAAATAAAGCATTACTCAACTGAATTAGATTTAATGATCATTTTACCTTC
1772452 CAAATAAAGCATTACTCAACTGAATTAGATTTAATGATCATTTTACCTTC
1 CAAATAAAGCATTACTCAACTGAATTAGATTTAATGATCATTTTACCTTC
1772502 CAAATAAAGCATT
1 CAAATAAAGCATT
1772515 CCATTTCATT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 61 1.00
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (50 bp):
CAAATAAAGCATTACTCAACTGAATTAGATTTAATGATCATTTTACCTTC
Found at i:1779160 original size:21 final size:21
Alignment explanation
Indices: 1779136--1779176 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1779126 AAAAATGAAG
1779136 CAAGGGAAGCAGAGAGAGCAT
1 CAAGGGAAGCAGAGAGAGCAT
1779157 CAAGGGAAGCAGAGAGAGCA
1 CAAGGGAAGCAGAGAGAGCA
1779177 GCAGCAGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.39, T:0.02
Consensus pattern (21 bp):
CAAGGGAAGCAGAGAGAGCAT
Found at i:1779186 original size:21 final size:21
Alignment explanation
Indices: 1779141--1779231 Score: 80
Period size: 21 Copynumber: 4.3 Consensus size: 21
1779131 TGAAGCAAGG
* *
1779141 GAAGCAGAGAGAGCATCAAG-G
1 GAAGCAGAGAGAGCAGC-AGCA
1779162 GAAGCAGAGAGAGCAGCAGCA
1 GAAGCAGAGAGAGCAGCAGCA
**
1779183 GAAGCAGCCAGAGCAGCAGCA
1 GAAGCAGAGAGAGCAGCAGCA
* *
1779204 -ACAGCAGAGAAAGAAGCAGCCA
1 GA-AGCAGAGAGAGCAGCAG-CA
1779226 G-AGCAG
1 GAAGCAG
1779232 CAGCGAAAGC
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
20 3 0.05
21 53 0.91
22 2 0.03
ACGTcount: A:0.43, C:0.21, G:0.35, T:0.01
Consensus pattern (21 bp):
GAAGCAGAGAGAGCAGCAGCA
Found at i:1779201 original size:33 final size:33
Alignment explanation
Indices: 1779164--1779256 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 33
1779154 CATCAAGGGA
* *
1779164 AGCAGAGAGAGCAGCAG-CAGAAGCAGCCAGAGC
1 AGCAGAGAAAGCAG-AGAAAGAAGCAGCCAGAGC
*
1779197 AGCAGCA-ACAGCAGAGAAAGAAGCAGCCAGAGC
1 AGCAG-AGAAAGCAGAGAAAGAAGCAGCCAGAGC
*
1779230 AGCAGCGAAAGCAGAGAAAGAAGCAGC
1 AGCAGAGAAAGCAGAGAAAGAAGCAGC
1779257 GGTAACACAG
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
32 2 0.04
33 50 0.94
34 1 0.02
ACGTcount: A:0.44, C:0.23, G:0.33, T:0.00
Consensus pattern (33 bp):
AGCAGAGAAAGCAGAGAAAGAAGCAGCCAGAGC
Found at i:1779221 original size:24 final size:24
Alignment explanation
Indices: 1779194--1779240 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1779184 AAGCAGCCAG
1779194 AGCAG-CAGCAACAGCAGAGAAAGA
1 AGCAGCCAG-AACAGCAGAGAAAGA
* *
1779218 AGCAGCCAGAGCAGCAGCGAAAG
1 AGCAGCCAGAACAGCAGAGAAAG
1779241 CAGAGAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.45, C:0.23, G:0.32, T:0.00
Consensus pattern (24 bp):
AGCAGCCAGAACAGCAGAGAAAGA
Found at i:1779291 original size:21 final size:21
Alignment explanation
Indices: 1779248--1779296 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1779238 AAGCAGAGAA
* *
1779248 AGAAGCAGCGGTAACACAGAG
1 AGAAGCAGCGGCAACACAAAG
**
1779269 AGAAGCAGCGGCAGTACAAAG
1 AGAAGCAGCGGCAACACAAAG
1779290 AGAAGCA
1 AGAAGCA
1779297 ACATATCAAC
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:0.45, C:0.18, G:0.33, T:0.04
Consensus pattern (21 bp):
AGAAGCAGCGGCAACACAAAG
Found at i:1779785 original size:41 final size:42
Alignment explanation
Indices: 1779728--1779837 Score: 116
Period size: 41 Copynumber: 2.6 Consensus size: 42
1779718 AAAAGACGTA
* *
1779728 AAATATCAACACCTACTGCGGCGTTTGTAAGTAAAAC-CGCT
1 AAATCTCAACACCTACTGCGGCGTTTGTAAGGAAAACGCGCT
* ** *
1779769 AAATCTCAAAACCTACTGCCACGTTTGTAGGGAAAACGTCGCT
1 AAATCTCAACACCTACTGCGGCGTTTGTAAGGAAAACG-CGCT
* *
1779812 AAA-CACCAACACCTATTGCGGCGTTT
1 AAATC-TCAACACCTACTGCGGCGTTT
1779838 TTGTGACAAA
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
41 31 0.56
42 1 0.02
43 23 0.42
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (42 bp):
AAATCTCAACACCTACTGCGGCGTTTGTAAGGAAAACGCGCT
Found at i:1782949 original size:28 final size:28
Alignment explanation
Indices: 1782918--1782976 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
1782908 TTTTATATTA
* *
1782918 GTTAATCAAGAGGAATTCAAAAATCTGG
1 GTTAATCAAAAGGAATTAAAAAATCTGG
1782946 GTTAATCAAAAGGAATTAAAAAATCTGG
1 GTTAATCAAAAGGAATTAAAAAATCTGG
1782974 GTT
1 GTT
1782977 TGAGATTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.44, C:0.08, G:0.20, T:0.27
Consensus pattern (28 bp):
GTTAATCAAAAGGAATTAAAAAATCTGG
Found at i:1794327 original size:16 final size:17
Alignment explanation
Indices: 1794306--1794338 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1794296 AAGTTAAATA
1794306 TAGAAAC-CCAAAATCT
1 TAGAAACACCAAAATCT
1794322 TAGAAACAGCCAAAATC
1 TAGAAACA-CCAAAATC
1794339 AACATAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.52, C:0.24, G:0.09, T:0.15
Consensus pattern (17 bp):
TAGAAACACCAAAATCT
Found at i:1798636 original size:21 final size:20
Alignment explanation
Indices: 1798599--1798637 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1798589 TCTCTATATT
*
1798599 ATTTTTTTCAATTAAAATTC
1 ATTTTTTTCAATAAAAATTC
*
1798619 ATTTTTATTGAATAAAAAT
1 ATTTTT-TTCAATAAAAAT
1798638 AATATTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (20 bp):
ATTTTTTTCAATAAAAATTC
Found at i:1799562 original size:20 final size:22
Alignment explanation
Indices: 1799539--1799578 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1799529 ATTTGATTTT
*
1799539 TAATTT-ATTAAAAA-TTAAAA
1 TAATTTGACTAAAAACTTAAAA
1799559 TAATTTGACTAAAAACTTAA
1 TAATTTGACTAAAAACTTAA
1799579 TTATTCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 7 0.41
22 4 0.24
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (22 bp):
TAATTTGACTAAAAACTTAAAA
Found at i:1809655 original size:15 final size:15
Alignment explanation
Indices: 1809635--1809664 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1809625 TGATCGGATC
1809635 GGATCCGGAAGGAAG
1 GGATCCGGAAGGAAG
1809650 GGATCCGGAAGGAAG
1 GGATCCGGAAGGAAG
1809665 ATTAGGCGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.47, T:0.07
Consensus pattern (15 bp):
GGATCCGGAAGGAAG
Found at i:1810731 original size:16 final size:16
Alignment explanation
Indices: 1810710--1810743 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1810700 TTACTATTCA
*
1810710 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
1810726 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
1810742 CG
1 CG
1810744 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:1817043 original size:10 final size:10
Alignment explanation
Indices: 1817025--1817058 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
1817015 GCACGTAGCT
*
1817025 TAGGCGCACC
1 TAGGTGCACC
1817035 TAGGTGCACC
1 TAGGTGCACC
1817045 TAGGTGCACC
1 TAGGTGCACC
1817055 TAGG
1 TAGG
1817059 CGCAGCGAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.21, C:0.29, G:0.32, T:0.18
Consensus pattern (10 bp):
TAGGTGCACC
Found at i:1818269 original size:33 final size:33
Alignment explanation
Indices: 1818198--1818269 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
1818188 TGACACCCAC
* *
1818198 CCTTGAATTAGTTCAAGTAACATAGCTTTTGTT
1 CCTTGAATTAGTCCAAGTAACATAGCTTTTGGT
* *
1818231 ACTTGAATTAGTCCATGTAACATAGCTTTTGGT
1 CCTTGAATTAGTCCAAGTAACATAGCTTTTGGT
1818264 CCTTGA
1 CCTTGA
1818270 GGAGAACCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (33 bp):
CCTTGAATTAGTCCAAGTAACATAGCTTTTGGT
Done.