Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008724.1 Hibiscus syriacus cultivar Beakdansim tig00111783_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: 5289199
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 23
Found at i:1517281 original size:21 final size:21
Alignment explanation
Indices: 1517256--1517302 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
1517246 AGTTGACTTT
1517256 GGTCAGA-GTTAACCATTGACC
1 GGTCAGACGTTAA-CATTGACC
*
1517277 GGTCAGACCGTTAACTTTGACC
1 GGTCAGA-CGTTAACATTGACC
1517299 GGTC
1 GGTC
1517303 TGACCATTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 7 0.30
22 11 0.48
23 5 0.22
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (21 bp):
GGTCAGACGTTAACATTGACC
Found at i:1524722 original size:41 final size:40
Alignment explanation
Indices: 1524674--1524957 Score: 218
Period size: 41 Copynumber: 7.0 Consensus size: 40
1524664 CGATCTTGGC
*
1524674 AGCATGCAATATTTCATCATTCAACTTGATTAGATCATGGT
1 AGCATGCAATAATTCATCATTCAACTTGATTA-ATCATGGT
* * * *
1524715 AGTATGCAATAATTCACCATTTC-A-TTCAATTCAATCAT-GA
1 AGCATGCAATAATTCATCA-TTCAACTT-GATT-AATCATGGT
* *
1524755 AGCATACAATAGTTCATCATTCAACTTGATTCAATCATGGT
1 AGCATGCAATAATTCATCATTCAACTTGATT-AATCATGGT
* * * *
1524796 AGCATGCAATAATTCACCATTCAA-TTCAACTCAATCATGGC
1 AGCATGCAATAATTCATCATTCAACTT-GA-TTAATCATGGT
** * *
1524837 AGCATAAAATAGTTCATCATTCAACTTGATTCGATCATGGT
1 AGCATGCAATAATTCATCATTCAACTTGATT-AATCATGGT
* * * * *
1524878 AGCATGCAATAATTCACCATTCGA-TTCAATTCAATCAAGGC
1 AGCATGCAATAATTCATCATTCAACTT-GATT-AATCATGGT
** * *
1524919 AGCATATAGTAGTTCATCATTCAACTTGATTAGATCATG
1 AGCATGCAATAATTCATCATTCAACTTGATTA-ATCATG
1524958 TTAGTATACA
Statistics
Matches: 188, Mismatches: 42, Indels: 26
0.73 0.16 0.10
Matches are distributed among these distances:
39 3 0.02
40 35 0.19
41 141 0.75
42 9 0.05
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (40 bp):
AGCATGCAATAATTCATCATTCAACTTGATTAATCATGGT
Found at i:1524878 original size:82 final size:81
Alignment explanation
Indices: 1524670--1524957 Score: 436
Period size: 82 Copynumber: 3.5 Consensus size: 81
1524660 AGTTCGATCT
* * *
1524670 TGGCAGCATGCAATATTTCATCATTCAACTTGATTAGATCATGGTAGTATGCAATAATTCACCAT
1 TGGCAGCATACAATAGTTCATCATTCAACTTGATTAGATCATGGTAGCATGCAATAATTCACCA-
1524735 TTCATTCAATTCAATCA
65 TTCATTCAATTCAATCA
*
1524752 T-GAAGCATACAATAGTTCATCATTCAACTTGATTCA-ATCATGGTAGCATGCAATAATTCACCA
1 TGGCAGCATACAATAGTTCATCATTCAACTTGATT-AGATCATGGTAGCATGCAATAATTCACCA
*
1524815 TTCAATTCAACTCAATCA
65 TTC-ATTCAATTCAATCA
* *
1524833 TGGCAGCATAAAATAGTTCATCATTCAACTTGATTCGATCATGGTAGCATGCAATAATTCACCAT
1 TGGCAGCATACAATAGTTCATCATTCAACTTGATTAGATCATGGTAGCATGCAATAATTCACCAT
1524898 TCGATTCAATTCAATCA
66 TC-ATTCAATTCAATCA
* * *
1524915 AGGCAGCATATAGTAGTTCATCATTCAACTTGATTAGATCATG
1 TGGCAGCATACAATAGTTCATCATTCAACTTGATTAGATCATG
1524958 TTAGTATACA
Statistics
Matches: 188, Mismatches: 14, Indels: 8
0.90 0.07 0.04
Matches are distributed among these distances:
80 3 0.02
81 70 0.37
82 115 0.61
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (81 bp):
TGGCAGCATACAATAGTTCATCATTCAACTTGATTAGATCATGGTAGCATGCAATAATTCACCAT
TCATTCAATTCAATCA
Found at i:1524987 original size:82 final size:82
Alignment explanation
Indices: 1524671--1524990 Score: 394
Period size: 82 Copynumber: 3.9 Consensus size: 82
1524661 GTTCGATCTT
** * * *
1524671 GGCAGCATGCAATATTTCATCATTCAACTTGATTAGATCATGGTAGTATGCAATAATTCACCATT
1 GGCAGCATAAAATAGTTCATCATTCAACTTGATTAGATCATGGTAGCATGCAATAATTCA-CAAT
1524736 TC-ATTCAATTCAATC-A
65 TCAATTCAATTCAATCAA
* * * *
1524752 TGAAGCATACAATAGTTCATCATTCAACTTGATTCA-ATCATGGTAGCATGCAATAATTCACCAT
1 GGCAGCATAAAATAGTTCATCATTCAACTTGATT-AGATCATGGTAGCATGCAATAATTCACAAT
* *
1524816 TCAATTCAACTCAATCAT
65 TCAATTCAATTCAATCAA
* *
1524834 GGCAGCATAAAATAGTTCATCATTCAACTTGATTCGATCATGGTAGCATGCAATAATTCACCATT
1 GGCAGCATAAAATAGTTCATCATTCAACTTGATTAGATCATGGTAGCATGCAATAATTCACAATT
*
1524899 CGATTCAATTCAATCAA
66 CAATTCAATTCAATCAA
* * * * * * * **
1524916 GGCAGCATATAGTAGTTCATCATTCAACTTGATTAGATCATGTTAGTATACATTTATTCACAAAC
1 GGCAGCATAAAATAGTTCATCATTCAACTTGATTAGATCATGGTAGCATGCAATAATTCACAATT
1524981 CAATTCAATT
66 CAATTCAATT
1524991 AGATCATGAT
Statistics
Matches: 207, Mismatches: 28, Indels: 7
0.86 0.12 0.03
Matches are distributed among these distances:
80 4 0.02
81 65 0.31
82 138 0.67
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (82 bp):
GGCAGCATAAAATAGTTCATCATTCAACTTGATTAGATCATGGTAGCATGCAATAATTCACAATT
CAATTCAATTCAATCAA
Found at i:1527095 original size:29 final size:29
Alignment explanation
Indices: 1527051--1527166 Score: 205
Period size: 29 Copynumber: 4.0 Consensus size: 29
1527041 TGATTCACGT
*
1527051 ACCATGCATTCTCATTTGTTATACATTGA
1 ACCATGCATTCTCATTTGTTATACATTGG
*
1527080 ATCATGCATTCTCATTTGTTATACATTGG
1 ACCATGCATTCTCATTTGTTATACATTGG
1527109 ACCATGCATTCTCATTTGTTATACATTGG
1 ACCATGCATTCTCATTTGTTATACATTGG
*
1527138 ACCATGCATTCTCATTTGTTAAACATTGG
1 ACCATGCATTCTCATTTGTTATACATTGG
1527167 GCTGTTAGTT
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 83 1.00
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (29 bp):
ACCATGCATTCTCATTTGTTATACATTGG
Found at i:1532984 original size:21 final size:19
Alignment explanation
Indices: 1532950--1532988 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
1532940 TTTAAATTTT
*
1532950 AAATAATTATATTATAAATA
1 AAATAATAATATTA-AAATA
1532970 AAATAAATAATATTAAAAT
1 AAAT-AATAATATTAAAAT
1532989 TATTATCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATAATAATATTAAAATA
Found at i:1533917 original size:38 final size:38
Alignment explanation
Indices: 1533866--1533941 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
1533856 ATAACATCAT
1533866 TGATGTCTAAATGATATTATAGGCTGGTATGTTTCCTA
1 TGATGTCTAAATGATATTATAGGCTGGTATGTTTCCTA
1533904 TGATGTCTAAATGATATTATAGGCTGGTATGTTTCCTA
1 TGATGTCTAAATGATATTATAGGCTGGTATGTTTCCTA
1533942 AAAAGATGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (38 bp):
TGATGTCTAAATGATATTATAGGCTGGTATGTTTCCTA
Found at i:1539521 original size:15 final size:16
Alignment explanation
Indices: 1539501--1539530 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1539491 AAGTGGTAAT
1539501 TTCCAAAAAA-AATTA
1 TTCCAAAAAAGAATTA
1539516 TTCCAAAAAAGAATT
1 TTCCAAAAAAGAATT
1539531 TTATTTCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (16 bp):
TTCCAAAAAAGAATTA
Found at i:1545718 original size:34 final size:34
Alignment explanation
Indices: 1545675--1545743 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
1545665 TAACAACTTC
1545675 AACCTTTCCAAAATAACTCTTTAATTCTATAAAT
1 AACCTTTCCAAAATAACTCTTTAATTCTATAAAT
* * *
1545709 AACCTTTCCAAAATGACTTTTTAATTTTATAAAT
1 AACCTTTCCAAAATAACTCTTTAATTCTATAAAT
1545743 A
1 A
1545744 TTCTGTCAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.41, C:0.17, G:0.01, T:0.41
Consensus pattern (34 bp):
AACCTTTCCAAAATAACTCTTTAATTCTATAAAT
Found at i:1551296 original size:12 final size:12
Alignment explanation
Indices: 1551269--1551309 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1551259 CCATTTGTAA
1551269 TAATA-ATAT-T
1 TAATATATATAT
1551279 TAAATATATATAT
1 T-AATATATATAT
*
1551292 TAATATATATAA
1 TAATATATATAT
1551304 TAATAT
1 TAATAT
1551310 TTAATAACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 1 0.04
11 4 0.15
12 20 0.74
13 2 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TAATATATATAT
Found at i:1551316 original size:10 final size:10
Alignment explanation
Indices: 1551269--1551316 Score: 53
Period size: 10 Copynumber: 4.6 Consensus size: 10
1551259 CCATTTGTAA
1551269 TAATAATATT
1 TAATAATATT
1551279 TAAATATATATAT
1 T-AATA-ATAT-T
*
1551292 TAAT-ATATA
1 TAATAATATT
1551301 TAATAATATT
1 TAATAATATT
1551311 TAATAA
1 TAATAA
1551317 CATAACACTC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
9 4 0.12
10 15 0.47
11 4 0.12
12 7 0.22
13 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
TAATAATATT
Found at i:1551552 original size:47 final size:47
Alignment explanation
Indices: 1551492--1551618 Score: 157
Period size: 47 Copynumber: 2.7 Consensus size: 47
1551482 ATCGTGCTCA
* * **
1551492 TGCTT-ACTACTCTTATGTGAAGGTTGAGGATGACTTGCAAACAATT
1 TGCTTCACTACTCTTACGTGAAGGCTGAGGATGACTCACAAACAATT
* * *
1551538 TGCTTCACTACTCTTCCGTGAAGGCTGATGATGACTCACAAACGATT
1 TGCTTCACTACTCTTACGTGAAGGCTGAGGATGACTCACAAACAATT
* * *
1551585 TGCTTCACTACTCTTCCGTGATGGCTGAGAATGA
1 TGCTTCACTACTCTTACGTGAAGGCTGAGGATGA
1551619 TTAACTTCAT
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
46 5 0.07
47 65 0.93
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.32
Consensus pattern (47 bp):
TGCTTCACTACTCTTACGTGAAGGCTGAGGATGACTCACAAACAATT
Found at i:1551774 original size:20 final size:20
Alignment explanation
Indices: 1551749--1551828 Score: 108
Period size: 20 Copynumber: 4.0 Consensus size: 20
1551739 CTGAAAGATG
*
1551749 ACCCAAAGGATTTACAAATT
1 ACCCAAAGGCTTTACAAATT
1551769 ACCCAAAAGGCTTTACAAA-T
1 ACCC-AAAGGCTTTACAAATT
** *
1551789 AATCAAAGGCTTTACAAATG
1 ACCCAAAGGCTTTACAAATT
1551809 ACCCAAAGGCTTTACAAATT
1 ACCCAAAGGCTTTACAAATT
1551829 CATGAAAAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
19 14 0.27
20 24 0.47
21 13 0.25
ACGTcount: A:0.44, C:0.21, G:0.11, T:0.24
Consensus pattern (20 bp):
ACCCAAAGGCTTTACAAATT
Found at i:1551807 original size:40 final size:39
Alignment explanation
Indices: 1551752--1551827 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 39
1551742 AAAGATGACC
*
1551752 CAAAGGATTTACAAATTACCCAAAAGGCTTTACAAATAAT
1 CAAAGGATTTACAAATGACCC-AAAGGCTTTACAAATAAT
*
1551792 CAAAGGCTTTACAAATGACCCAAAGGCTTTACAAAT
1 CAAAGGATTTACAAATGACCCAAAGGCTTTACAAAT
1551828 TCATGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 15 0.44
40 19 0.56
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.24
Consensus pattern (39 bp):
CAAAGGATTTACAAATGACCCAAAGGCTTTACAAATAAT
Found at i:1552438 original size:22 final size:22
Alignment explanation
Indices: 1552410--1552456 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1552400 GCTTTCGTCT
* * *
1552410 TTGAAAAAATAATCTATCATTC
1 TTGAAAAAAGAATATATCATCC
*
1552432 TTGAAAAGAGAATATATCATCC
1 TTGAAAAAAGAATATATCATCC
1552454 TTG
1 TTG
1552457 TAGAATGTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.34
Consensus pattern (22 bp):
TTGAAAAAAGAATATATCATCC
Found at i:1560394 original size:12 final size:12
Alignment explanation
Indices: 1560366--1560407 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
1560356 CCATTTGTAA
1560366 TAATA-ATAT-T
1 TAATATATATAT
1560376 TAA-ATATATAT
1 TAATATATATAT
*
1560387 TAATATATATAA
1 TAATATATATAT
1560399 TAATATATA
1 TAATATATA
1560408 ATAACATAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 1 0.04
10 7 0.25
11 4 0.14
12 16 0.57
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAATATATATAT
Found at i:1560411 original size:10 final size:10
Alignment explanation
Indices: 1560365--1560411 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
1560355 TCCATTTGTA
1560365 ATAATAATAT
1 ATAATAATAT
*
1560375 TTAA-ATATAT
1 ATAATA-ATAT
1560385 ATTAAT-ATAT
1 A-TAATAATAT
1560395 ATAATAATAT
1 ATAATAATAT
1560405 ATAATAA
1 ATAATAA
1560412 CATAACACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
9 5 0.16
10 23 0.74
11 3 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
ATAATAATAT
Found at i:1562366 original size:9 final size:9
Alignment explanation
Indices: 1562303--1562382 Score: 61
Period size: 10 Copynumber: 8.4 Consensus size: 9
1562293 CCGGTTTTCA
1562303 ACCGGTTCTG
1 ACCGGTT-TG
*
1562313 ACCGATTTG
1 ACCGGTTTG
* *
1562322 ACTGGTTTCA
1 ACCGGTTT-G
*
1562332 ACCGGTTCG
1 ACCGGTTTG
*
1562341 AACCGGTTCG
1 -ACCGGTTTG
1562351 AACCGGTTTG
1 -ACCGGTTTG
*
1562361 ACCGGTCTG
1 ACCGGTTTG
*
1562370 ACCGGTCTG
1 ACCGGTTTG
1562379 ACCG
1 ACCG
1562383 ACCAACCCGA
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
9 29 0.49
10 30 0.51
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:1562446 original size:13 final size:14
Alignment explanation
Indices: 1562418--1562447 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1562408 GACCCGACCC
1562418 GACCGTTGATCGTT
1 GACCGTTGATCGTT
1562432 GACCGTTGA-CGTT
1 GACCGTTGATCGTT
1562445 GAC
1 GAC
1562448 TTTCTTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.17, C:0.23, G:0.30, T:0.30
Consensus pattern (14 bp):
GACCGTTGATCGTT
Found at i:1566410 original size:46 final size:46
Alignment explanation
Indices: 1566348--1566451 Score: 163
Period size: 46 Copynumber: 2.3 Consensus size: 46
1566338 ATGTCAGAAC
* *
1566348 AAATACTATAATCCTTACATCATATCTAAACTTTAAAGAAATAAAA
1 AAATCCTACAATCCTTACATCATATCTAAACTTTAAAGAAATAAAA
*
1566394 AAATCCTACAATCCTTACATCATATCTAAACTTTAAAGAAATCAAA
1 AAATCCTACAATCCTTACATCATATCTAAACTTTAAAGAAATAAAA
* *
1566440 GAAGCCTACAAT
1 AAATCCTACAAT
1566452 GGTTATTGAC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 53 1.00
ACGTcount: A:0.49, C:0.19, G:0.04, T:0.28
Consensus pattern (46 bp):
AAATCCTACAATCCTTACATCATATCTAAACTTTAAAGAAATAAAA
Found at i:1567860 original size:61 final size:61
Alignment explanation
Indices: 1567785--1567908 Score: 196
Period size: 61 Copynumber: 2.0 Consensus size: 61
1567775 TATCTCATTT
* *
1567785 TCCAAAGTTTAATTT-ATTTTACAACTTTAGCATACTTTTTCACTTTACTTAATTTCGTACC
1 TCCAAAGTTTAATTTCATTTTACAACTTTAGCATAATTTTGCA-TTTACTTAATTTCGTACC
* *
1567846 TCCAAAGTTTAATTTCTTTTTACAACTTTAGCATAATTTTGCATTTACTTAATTTCTTACC
1 TCCAAAGTTTAATTTCATTTTACAACTTTAGCATAATTTTGCATTTACTTAATTTCGTACC
1567907 TC
1 TC
1567909 GACACACTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
61 34 0.59
62 24 0.41
ACGTcount: A:0.27, C:0.19, G:0.05, T:0.48
Consensus pattern (61 bp):
TCCAAAGTTTAATTTCATTTTACAACTTTAGCATAATTTTGCATTTACTTAATTTCGTACC
Found at i:1567933 original size:62 final size:62
Alignment explanation
Indices: 1567805--1567936 Score: 142
Period size: 62 Copynumber: 2.1 Consensus size: 62
1567795 AATTTATTTT
* * * * ***
1567805 ACAACTTTAGCATACTTTTTCACTTTACTTAATTTCGTACCTCCAAAGTTTAATTTCTTTTT
1 ACAACTTTAGCATAATTTTGCACTTTACTTAATTTCGTACCTCCAAACTTTAATATCTTCCA
* * *
1567867 ACAACTTTAGCATAATTTTGCA-TTTACTTAATTTCTTACCTCGACACACTTTTATAT-TTCCA
1 ACAACTTTAGCATAATTTTGCACTTTACTTAATTTCGTACCTC--CAAACTTTAATATCTTCCA
1567929 ACAACTTT
1 ACAACTTT
1567937 CACTATAGCA
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
61 19 0.33
62 30 0.52
63 9 0.16
ACGTcount: A:0.28, C:0.22, G:0.05, T:0.45
Consensus pattern (62 bp):
ACAACTTTAGCATAATTTTGCACTTTACTTAATTTCGTACCTCCAAACTTTAATATCTTCCA
Found at i:1568320 original size:18 final size:18
Alignment explanation
Indices: 1568281--1568314 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1568271 TTATTAATTG
1568281 TTGTTTTAGTTTTATTTA
1 TTGTTTTAGTTTTATTTA
*
1568299 TTGTTTTTG-TTTATTT
1 TTGTTTTAGTTTTATTT
1568315 CTTTGTCAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (18 bp):
TTGTTTTAGTTTTATTTA
Found at i:1571050 original size:46 final size:46
Alignment explanation
Indices: 1570986--1571474 Score: 827
Period size: 46 Copynumber: 10.7 Consensus size: 46
1570976 AGTTAAATTT
* * *
1570986 CATTTTATTTATGACATCCTTTCATGCCTTAATGTATCATTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
**
1571032 CATTTTATTTATTCCATCCTTTCATGCCTTAATGCATCCTTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
* *
1571078 CATTTTATTTATGACATCCTTTCATGCCTTAACGCATCCTTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
*
1571124 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATT
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
* * *
1571170 CATTTTATTTATGGCATCCTTTCATGCGTTAATGCATCGTTTCATT
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
1571216 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
*
1571262 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCAAG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
* *
1571308 CATTTTATTTATGGCATCCTTTCATGCCTTAAGGCATCCTTTCAAG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
1571354 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
**
1571400 CATTTTATTTATTACATCCTTTCATGCCTTAATGCATCC-TTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
1571445 CATTTTATTTATGGCATCCTTTCATGCCTT
1 CATTTTATTTATGGCATCCTTTCATGCCTT
1571475 TTATTTATGT
Statistics
Matches: 420, Mismatches: 23, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
45 34 0.08
46 386 0.92
ACGTcount: A:0.21, C:0.24, G:0.10, T:0.46
Consensus pattern (46 bp):
CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
Found at i:1573611 original size:241 final size:242
Alignment explanation
Indices: 1573313--1573797 Score: 954
Period size: 241 Copynumber: 2.0 Consensus size: 242
1573303 CCATGTGCCT
*
1573313 TGTTCCTCGAGCTCTCGGATCGAAAAGTAAAAAATCTGAAAAGTATTAAACAAGGAGTGTGAGAT
1 TGTTCCTCGAGCTCTCAGATCGAAAAGTAAAAAATCTGAAAAGTATTAAACAAGGAGTGTGAGAT
1573378 ATAAAGCCCAGTGAATGACTAAACATTCAAATATGATATACATGTCAATACTAAAGG-AAGCATA
66 ATAAAGCCCAGTGAATGACTAAACATTCAAATATGATATACATGTCAATACTAAAGGAAAGCATA
1573442 CCTAAATGCCATGCAACCTTACTTGTTTTTAGCTCAATGATCATACCTTAATGTCATGCTACAAT
131 CCTAAATGCCATGCAACCTTACTTGTTTTTAGCTCAATGATCATACCTTAATGTCATGCTACAAT
1573507 GTTCACTTAATGCATAATAAATGCACACAAAATCCAGATTATAATCA
196 GTTCACTTAATGCATAATAAATGCACACAAAATCCAGATTATAATCA
1573554 TGTTCCTCGAGCTCTCAGATCGAAAAGTAAAAAATCTGAAAAGTATTAAACAAGGAGTGTGAGAT
1 TGTTCCTCGAGCTCTCAGATCGAAAAGTAAAAAATCTGAAAAGTATTAAACAAGGAGTGTGAGAT
1573619 ATAAAGCCCAGTGAATGACTAAACATTCAAATATGATATACATGTCAATACTAAAGGAAAGCATA
66 ATAAAGCCCAGTGAATGACTAAACATTCAAATATGATATACATGTCAATACTAAAGGAAAGCATA
1573684 CCTAAATGCCATGCAACCTTACTTGTTTTTAGCTCAATGATCATACCTTAATGTCATGCTACAAT
131 CCTAAATGCCATGCAACCTTACTTGTTTTTAGCTCAATGATCATACCTTAATGTCATGCTACAAT
1573749 GTTCACTTAATGCATAATAAATGCACACAAAATCCAGATTATAATCA
196 GTTCACTTAATGCATAATAAATGCACACAAAATCCAGATTATAATCA
1573796 TG
1 TG
1573798 CTTTACATAA
Statistics
Matches: 242, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
241 121 0.50
242 121 0.50
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (242 bp):
TGTTCCTCGAGCTCTCAGATCGAAAAGTAAAAAATCTGAAAAGTATTAAACAAGGAGTGTGAGAT
ATAAAGCCCAGTGAATGACTAAACATTCAAATATGATATACATGTCAATACTAAAGGAAAGCATA
CCTAAATGCCATGCAACCTTACTTGTTTTTAGCTCAATGATCATACCTTAATGTCATGCTACAAT
GTTCACTTAATGCATAATAAATGCACACAAAATCCAGATTATAATCA
Found at i:1601002 original size:32 final size:32
Alignment explanation
Indices: 1600943--1601014 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
1600933 CTAACGTTGT
* * * *
1600943 TGTGCATTATCTAAATGCAAAATTGACATTAA
1 TGTGCATTATCAAAATACAAAACTGACACTAA
* * *
1600975 TGTGCATTATCAAAATATAACACTGACACTGA
1 TGTGCATTATCAAAATACAAAACTGACACTAA
1601007 TGTGCATT
1 TGTGCATT
1601015 CTCTAATACA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (32 bp):
TGTGCATTATCAAAATACAAAACTGACACTAA
Found at i:1616896 original size:20 final size:18
Alignment explanation
Indices: 1616871--1616907 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
1616861 AATAATCAAT
1616871 TTATTATATTTTTATTTTAA
1 TTATTAT-TTTTT-TTTTAA
1616891 TTATTATTTTTTTTTTA
1 TTATTATTTTTTTTTTA
1616908 CAAAATCATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 5 0.29
20 7 0.41
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
TTATTATTTTTTTTTTAA
Found at i:1616905 original size:17 final size:17
Alignment explanation
Indices: 1616873--1616907 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1616863 TAATCAATTT
1616873 ATTATATTTTTATTTTA
1 ATTATATTTTTATTTTA
*
1616890 ATTATTATTTTTTTTTTA
1 ATTA-TATTTTTATTTTA
1616908 CAAAATCATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
ATTATATTTTTATTTTA
Found at i:1617268 original size:29 final size:29
Alignment explanation
Indices: 1617185--1617260 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
1617175 TTTTCTTGGT
1617185 GTAGGTCGCCATGCA-GTCTCGGCGACATG
1 GTAGGTCGCCATGCACG-CTCGGCGACATG
* * *
1617214 GTAGGTCACCGTGCACGCTGGGCGACATG
1 GTAGGTCGCCATGCACGCTCGGCGACATG
*
1617243 GTAGGTCGCCATGTACGC
1 GTAGGTCGCCATGCACGC
1617261 CCGACGACCA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 39 0.98
30 1 0.03
ACGTcount: A:0.17, C:0.28, G:0.36, T:0.20
Consensus pattern (29 bp):
GTAGGTCGCCATGCACGCTCGGCGACATG
Found at i:1617793 original size:28 final size:30
Alignment explanation
Indices: 1617753--1617814 Score: 101
Period size: 28 Copynumber: 2.1 Consensus size: 30
1617743 AATTTAGTTA
*
1617753 ATTAGTTTGTTAGTTTAAG-T-TATATTAT
1 ATTAGTTTGTTAGATTAAGTTATATATTAT
1617781 ATTAGTTTGTTAGATTAAGTTATATATTAT
1 ATTAGTTTGTTAGATTAAGTTATATATTAT
1617811 ATTA
1 ATTA
1617815 TATAAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 18 0.58
29 1 0.03
30 12 0.39
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (30 bp):
ATTAGTTTGTTAGATTAAGTTATATATTAT
Found at i:1618662 original size:8 final size:8
Alignment explanation
Indices: 1618634--1618689 Score: 51
Period size: 8 Copynumber: 6.9 Consensus size: 8
1618624 AAATCATATT
1618634 ATTATTAA
1 ATTATTAA
*
1618642 ATTGTTAA
1 ATTATTAA
1618650 A-TATTAA
1 ATTATTAA
*
1618657 ATTATTAG
1 ATTATTAA
*
1618665 ATTAATAATA
1 ATT-ATTA-A
1618675 ATTATTAA
1 ATTATTAA
*
1618683 ATCATTA
1 ATTATTA
1618690 TTAGTAATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
7 6 0.16
8 23 0.61
9 6 0.16
10 3 0.08
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (8 bp):
ATTATTAA
Found at i:1622236 original size:20 final size:20
Alignment explanation
Indices: 1622211--1622252 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1622201 TCAAAAATTA
1622211 TCGCCTCTCTACCATTATTG
1 TCGCCTCTCTACCATTATTG
* *
1622231 TCGCCTCTCTGCCATTGTTG
1 TCGCCTCTCTACCATTATTG
1622251 TC
1 TC
1622253 AGGAACGACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.36, G:0.14, T:0.40
Consensus pattern (20 bp):
TCGCCTCTCTACCATTATTG
Found at i:1624524 original size:26 final size:26
Alignment explanation
Indices: 1624486--1624543 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
1624476 CTCTTTCTTT
1624486 CTTTC-TCGACTGCAATATCTTCTCC
1 CTTTCTTCGACTGCAATATCTTCTCC
* *
1624511 CTTTCTTCGGCTGCAATCTCTTCTCC
1 CTTTCTTCGACTGCAATATCTTCTCC
1624537 CTTTCTT
1 CTTTCTT
1624544 TCTTTTATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 5 0.17
26 25 0.83
ACGTcount: A:0.10, C:0.36, G:0.09, T:0.45
Consensus pattern (26 bp):
CTTTCTTCGACTGCAATATCTTCTCC
Found at i:1629836 original size:14 final size:13
Alignment explanation
Indices: 1629813--1629852 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
1629803 ATTTATTTTT
1629813 TTTAATTATAATG
1 TTTAATTATAATG
*
1629826 TTTATATTATAAATT
1 TTTA-ATTAT-AATG
1629841 TTTAATTATAAT
1 TTTAATTATAAT
1629853 CATTAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 7 0.29
14 10 0.42
15 7 0.29
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (13 bp):
TTTAATTATAATG
Found at i:1630293 original size:2 final size:2
Alignment explanation
Indices: 1630288--1630348 Score: 51
Period size: 2 Copynumber: 33.0 Consensus size: 2
1630278 TTTGTGTGTG
* *
1630288 TA TA TA TA TA TA TA TA T- TA TA AA TA TA -A TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1630328 -A GA -A TA TA TT TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
1630349 CATACATCAT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
1 5 0.10
2 43 0.90
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1630333 original size:21 final size:21
Alignment explanation
Indices: 1630288--1630348 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 21
1630278 TTTGTGTGTG
1630288 TATATATATATATATATTATA-AA
1 TATATATAT-TATATA-TA-AGAA
1630311 TATAATATATT-TATATAAGAA
1 TAT-ATATATTATATATAAGAA
*
1630332 TATATTTATTATATATA
1 TATATATATTATATATA
1630349 CATACATCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
20 7 0.21
21 13 0.38
22 4 0.12
23 4 0.12
24 6 0.18
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
TATATATATTATATATAAGAA
Found at i:1630363 original size:20 final size:19
Alignment explanation
Indices: 1630338--1630380 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
1630328 AGAATATATT
1630338 TATTAT-ATATACATACATCA
1 TATTATCATA-ACATACAT-A
*
1630358 TATTATCATAACATTCATA
1 TATTATCATAACATACATA
1630377 TATT
1 TATT
1630381 TAATTACATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 13 0.62
21 3 0.14
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (19 bp):
TATTATCATAACATACATA
Found at i:1632029 original size:2 final size:2
Alignment explanation
Indices: 1632022--1632046 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1632012 TGAAACTTTA
1632022 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1632047 ACATATGAGT
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1632402 original size:18 final size:18
Alignment explanation
Indices: 1632375--1632409 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1632365 TTGCAGGTTA
*
1632375 TGGAAGAAGAAGAAGAAT
1 TGGAAGAAGAAAAAGAAT
*
1632393 TGGAATAAGAAAAAGAA
1 TGGAAGAAGAAAAAGAA
1632410 GAAGAGAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.29, T:0.11
Consensus pattern (18 bp):
TGGAAGAAGAAAAAGAAT
Found at i:1641801 original size:36 final size:36
Alignment explanation
Indices: 1641761--1641867 Score: 84
Period size: 36 Copynumber: 3.0 Consensus size: 36
1641751 TTAGTTGTGA
1641761 TGTTCTTCTATGTTTCTTAGCCATGTGAGATTGTTT
1 TGTTCTTCTATGTTTCTTAGCCATGTGAGATTGTTT
* *
1641797 TGTTC-TC-ATATTT-TTA-CTC-T-TTAGACTT-TTGT
1 TGTTCTTCTATGTTTCTTAGC-CATGTGAGA-TTGTT-T
* *
1641829 GATGCTCTTCTATGTTTCTTAGTCATGTGAGATTGTTT
1 --TGTTCTTCTATGTTTCTTAGCCATGTGAGATTGTTT
1641867 T
1 T
1641868 TTTAAAAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 24
0.64 0.07 0.29
Matches are distributed among these distances:
31 6 0.11
32 5 0.09
33 4 0.08
34 9 0.17
35 4 0.08
36 11 0.21
37 4 0.08
38 4 0.08
39 6 0.11
ACGTcount: A:0.15, C:0.14, G:0.17, T:0.54
Consensus pattern (36 bp):
TGTTCTTCTATGTTTCTTAGCCATGTGAGATTGTTT
Found at i:1657362 original size:23 final size:23
Alignment explanation
Indices: 1657331--1657391 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
1657321 TTAATATTTG
1657331 GTTTGGATTGTTTTTGTTTTGAA-T
1 GTTT-GATTGTTTTTG-TTTGAATT
*
1657355 GTTTGATTGTGGTTTGTTTGAATT
1 GTTTGATTGT-TTTTGTTTGAATT
*
1657379 GTTATGAATGTTT
1 GTT-TGATTGTTT
1657392 ATTAGTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
23 12 0.39
24 13 0.42
25 6 0.19
ACGTcount: A:0.15, C:0.00, G:0.26, T:0.59
Consensus pattern (23 bp):
GTTTGATTGTTTTTGTTTGAATT
Found at i:1657663 original size:22 final size:21
Alignment explanation
Indices: 1657620--1657664 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1657610 ATTTAACAAA
*
1657620 AAGGGGGAGAAATGTTATAGT
1 AAGGGGGAGAAATGTTAAAGT
* *
1657641 AAGGGGGAGTAATTTTCAAAGT
1 AAGGGGGAGAAATGTT-AAAGT
1657663 AA
1 AA
1657665 TTTTTTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.40, C:0.02, G:0.33, T:0.24
Consensus pattern (21 bp):
AAGGGGGAGAAATGTTAAAGT
Found at i:1657790 original size:13 final size:13
Alignment explanation
Indices: 1657772--1657798 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1657762 AAAGTAATAA
1657772 TGAATTTTAAGAT
1 TGAATTTTAAGAT
1657785 TGAATTTTAAGAT
1 TGAATTTTAAGAT
1657798 T
1 T
1657799 TTATATTCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (13 bp):
TGAATTTTAAGAT
Found at i:1657834 original size:17 final size:18
Alignment explanation
Indices: 1657800--1657836 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
1657790 TTTAAGATTT
1657800 TATATTCGATTCAAAATTA
1 TATATTCGATTC-AAATTA
1657819 TATATTCGATTC-AATTA
1 TATATTCGATTCAAATTA
1657836 T
1 T
1657837 TCGAATATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (18 bp):
TATATTCGATTCAAATTA
Found at i:1663644 original size:18 final size:18
Alignment explanation
Indices: 1663621--1663666 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1663611 ATTCATGCAT
1663621 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
* *
1663639 TTAGTTTATTGAATAATG
1 TTAGTTCATTGAATAAAG
*
1663657 TTATTTCATT
1 TTAGTTCATT
1663667 AATCAAACTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:1665243 original size:28 final size:28
Alignment explanation
Indices: 1665204--1665259 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1665194 GAATAGTAGA
1665204 AGAAGTGTAAACCTCGATCGTGTGCAAT
1 AGAAGTGTAAACCTCGATCGTGTGCAAT
1665232 AGAAGTGTAAACCTCGATCGTGTGCAAT
1 AGAAGTGTAAACCTCGATCGTGTGCAAT
1665260 GTCCATCGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (28 bp):
AGAAGTGTAAACCTCGATCGTGTGCAAT
Found at i:1669295 original size:180 final size:180
Alignment explanation
Indices: 1669092--1669561 Score: 712
Period size: 180 Copynumber: 2.6 Consensus size: 180
1669082 GATCCAAATT
* * * **
1669092 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAA-CGGTATTGAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * * *
1669156 AAACCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCTACACTTC
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTC
*
1669221 GTGAATTTAAAAGAGAAGCAGTTTTAAATCCTTTAA-GTGTCGATACTTTTA
130 GTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAATGTGTCGATAC-TTTA
*
1669272 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
*
1669337 AAACCGGTAAAAC-ATTACCGGATATATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTT
66 AAACCGGTAAAACGA-TACCGGATATATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTC
**
1669401 GTGAATTTAAAAGAGAAGCAGTTTTAGCTCCTATAATGTGTCGATACTTTA
130 GTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAATGTGTCGATACTTTA
* *
1669452 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* *
1669517 AAACCGGTAAAATGATACCGGATATATTGAAAGTGTTGATACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
1669562 CGTAAGTACG
Statistics
Matches: 265, Mismatches: 21, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
180 201 0.76
181 64 0.24
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.28
Consensus pattern (180 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTCG
TGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAATGTGTCGATACTTTA
Found at i:1669325 original size:20 final size:19
Alignment explanation
Indices: 1669302--1669348 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1669292 CGATATACCA
1669302 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
1669322 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
1669342 GGTAAAA
1 GGTAAAA
1669349 CATTACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1669505 original size:20 final size:19
Alignment explanation
Indices: 1669482--1669528 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1669472 CGATATAACA
1669482 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
1669502 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
1669522 GGTAAAA
1 GGTAAAA
1669529 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1669530 original size:17 final size:19
Alignment explanation
Indices: 1669491--1669533 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1669481 AGGTAAAAAT
1669491 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
1669511 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
1669528 ATGATA
1 ATGATA
1669534 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:1671783 original size:21 final size:21
Alignment explanation
Indices: 1671757--1671821 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
1671747 AAGACAATCA
*
1671757 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
1671778 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
1671799 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
1671820 AG
1 AG
1671822 GCATAAGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:1671897 original size:33 final size:33
Alignment explanation
Indices: 1671855--1671920 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1671845 AAATAGATGG
* *
1671855 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGAGGTGA
* *
1671888 AGTGGTGAAAGAAGTTGGGGTGTTAAGAGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGAGGTGA
1671921 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGAGGTGA
Found at i:1673731 original size:19 final size:19
Alignment explanation
Indices: 1673707--1673755 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1673697 AATGTAGGGT
*
1673707 TAATTTTGTATAATATTTA
1 TAATTTTGTATAAGATTTA
*
1673726 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
1673745 TAATTTTGTAT
1 TAATTTTGTAT
1673756 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1674211 original size:200 final size:200
Alignment explanation
Indices: 1673868--1674638 Score: 1343
Period size: 200 Copynumber: 3.9 Consensus size: 200
1673858 AATTTACAAT
* *
1673868 ATGGCAAATAGGGTGCAACCATAACGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
1673933 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
1673998 ATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGATTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
1674063 AATGA
196 AATGA
*
1674068 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGTTCCCAAAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
1674133 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
1674198 ATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATAGTTTTGGTCCAG
131 ATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
1674263 AATGA
196 AATGA
1674268 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
1674333 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
1674398 AT--GAG---A-G----AAT-A--TGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
1674450 AATGA
196 AATGA
* *
1674455 ATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
* * *
1674520 TGAAACCCAAAAGTCTAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGG-TTT
*
1674585 TATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATA
130 TATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATA
1674639 CTAATTTAAA
Statistics
Matches: 545, Mismatches: 12, Indels: 27
0.93 0.02 0.05
Matches are distributed among these distances:
187 166 0.30
188 6 0.01
189 1 0.00
190 6 0.01
193 1 0.00
194 2 0.00
195 1 0.00
198 6 0.01
199 1 0.00
200 326 0.60
201 29 0.05
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
AATGA
Found at i:1674541 original size:187 final size:188
Alignment explanation
Indices: 1674222--1674596 Score: 689
Period size: 187 Copynumber: 2.0 Consensus size: 188
1674212 CTAAATAATG
1674222 TGTCGACACTTTTTTAGTTTGTGTCGATAGTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAAC
1 TGTCGACACTTTTTTAGTTTGTGTCGATAGTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAAC
1674287 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAAT
1674352 GTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGG-TTTTATGAGAGAATA
131 GTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTTATGAGAGAATA
*
1674409 TGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAAC
1 TGTCGACACTTTTTTAGTTTGTGTCGATAGTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAAC
* * * * *
1674474 CGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATTGAAACCCAAAAGTCTAAT
66 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAAT
1674539 GTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTTATGAGAGAATA
131 GTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTTATGAGAGAATA
1674597 GGTCTAAATA
Statistics
Matches: 181, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
187 166 0.92
188 15 0.08
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.31
Consensus pattern (188 bp):
TGTCGACACTTTTTTAGTTTGTGTCGATAGTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAAC
CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAAT
GTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTTATGAGAGAATA
Found at i:1676135 original size:12 final size:12
Alignment explanation
Indices: 1676113--1676194 Score: 110
Period size: 12 Copynumber: 6.8 Consensus size: 12
1676103 CAAGTGGTCA
*
1676113 ATGAAGATGAAG
1 ATGACGATGAAG
*
1676125 CTGACGATGAAG
1 ATGACGATGAAG
*
1676137 ATGACGATGATG
1 ATGACGATGAAG
*
1676149 ATGGCGATGAAG
1 ATGACGATGAAG
*
1676161 CTGACGATGAAG
1 ATGACGATGAAG
1676173 ATGACGATGAAG
1 ATGACGATGAAG
*
1676185 ATGATGATGA
1 ATGACGATGA
1676195 TGATCCAAAC
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 60 1.00
ACGTcount: A:0.38, C:0.09, G:0.34, T:0.20
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:1676136 original size:18 final size:18
Alignment explanation
Indices: 1676113--1676176 Score: 83
Period size: 18 Copynumber: 3.6 Consensus size: 18
1676103 CAAGTGGTCA
1676113 ATGAAGATGAAGCTGACG
1 ATGAAGATGAAGCTGACG
* * *
1676131 ATGAAGATGACGATGATG
1 ATGAAGATGAAGCTGACG
**
1676149 ATGGCGATGAAGCTGACG
1 ATGAAGATGAAGCTGACG
1676167 ATGAAGATGA
1 ATGAAGATGA
1676177 CGATGAAGAT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.38, C:0.09, G:0.34, T:0.19
Consensus pattern (18 bp):
ATGAAGATGAAGCTGACG
Found at i:1676165 original size:36 final size:36
Alignment explanation
Indices: 1676118--1676187 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
1676108 GGTCAATGAA
*
1676118 GATGAAGCTGACGATGAAGATGACGATGATGATGGC
1 GATGAAGCTGACGATGAAGATGACGATGAAGATGGC
1676154 GATGAAGCTGACGATGAAGATGACGATGAAGATG
1 GATGAAGCTGACGATGAAGATGACGATGAAGATG
1676188 ATGATGATGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.36, C:0.10, G:0.36, T:0.19
Consensus pattern (36 bp):
GATGAAGCTGACGATGAAGATGACGATGAAGATGGC
Found at i:1676198 original size:6 final size:6
Alignment explanation
Indices: 1676113--1676194 Score: 74
Period size: 6 Copynumber: 13.7 Consensus size: 6
1676103 CAAGTGGTCA
* * * * **
1676113 ATGAAG ATGAAG CTGACG ATGAAG ATGACG ATGATG ATGGCG ATGAAG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
* * * *
1676161 CTGACG ATGAAG ATGACG ATGAAG ATGATG ATGA
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGA
1676195 TGATCCAAAC
Statistics
Matches: 59, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.38, C:0.09, G:0.34, T:0.20
Consensus pattern (6 bp):
ATGAAG
Found at i:1677716 original size:183 final size:183
Alignment explanation
Indices: 1677408--1678350 Score: 1744
Period size: 183 Copynumber: 5.2 Consensus size: 183
1677398 CAAAGTTTTC
* * * *
1677408 ACACTTTTTAATATTGTGTCTGTACTTTATGTCCAGAATGAAAGAAAAATATGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
*
1677473 CAAAAAGTGTCGACATTTACACATCGAAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
*
1677538 AACCGGTATAAATATACCGATTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
1677591 ACACTTTTTAATATTGTGTCGGTACTTTATGTTCAGATTGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
1677656 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
1677721 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
1677774 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
1677839 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
*
1677904 AACCGGTATAAATATACCGGTTTTATAAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
1677957 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
* *
1678022 CAAAAAGTGTCGATATTTACACATCGAAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
* * **
1678087 AACTGGCATAAATATACCAATTTTATGAGCGAATA-GTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
1678139 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
1678204 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
1678269 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
1678322 ATACTTTTTAATATTGTGTCGGTACTTTA
1 ACACTTTTTAATATTGTGTCGGTACTTTA
1678351 CAATAGGAGT
Statistics
Matches: 736, Mismatches: 23, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
182 176 0.24
183 560 0.76
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (183 bp):
ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:1681125 original size:23 final size:23
Alignment explanation
Indices: 1681094--1681143 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
1681084 ATAGGTAAAA
*
1681094 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
1681117 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
1681140 ATAT
1 ATAT
1681144 TGTAAAGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1681569 original size:23 final size:23
Alignment explanation
Indices: 1681506--1681578 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
1681496 ATAGGTAAAA
* * *
1681506 ATATGATGTAATAGGTAACACTT
1 ATATAATGTAATAGGTAGCGCTT
*
1681529 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
1681552 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
1681575 ATAT
1 ATAT
1681579 TGTAAAATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1683010 original size:35 final size:35
Alignment explanation
Indices: 1682959--1683034 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 35
1682949 AACACAATCC
* *
1682959 TCAATTTCATTCTAAAC-CCTAAATTCCAAAATAAT
1 TCAATTGCATTCTAAACTAC-AAATTCCAAAATAAT
* * *
1682994 TCAATTGCATTTTAAACTACAAATTCTAAAATACT
1 TCAATTGCATTCTAAACTACAAATTCCAAAATAAT
1683029 TCAATT
1 TCAATT
1683035 TAGGGTTTAG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
35 34 0.97
36 1 0.03
ACGTcount: A:0.42, C:0.20, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTGCATTCTAAACTACAAATTCCAAAATAAT
Found at i:1683079 original size:35 final size:35
Alignment explanation
Indices: 1683031--1683105 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
1683021 AAAATACTTC
*
1683031 AATTTAGGGTTTAGAATGTAATTAAAGTATTTTAG
1 AATTTAGGATTTAGAATGTAATTAAAGTATTTTAG
* * *
1683066 AATTTAGGATTTAGAATGTAATTGAAGTGTTTTGG
1 AATTTAGGATTTAGAATGTAATTAAAGTATTTTAG
1683101 AATTT
1 AATTT
1683106 TGAACATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (35 bp):
AATTTAGGATTTAGAATGTAATTAAAGTATTTTAG
Found at i:1685895 original size:13 final size:13
Alignment explanation
Indices: 1685879--1685903 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1685869 CAAATTATGT
1685879 AATTTAAAAATAA
1 AATTTAAAAATAA
1685892 AATTTAAAAATA
1 AATTTAAAAATA
1685904 TAAAAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AATTTAAAAATAA
Found at i:1692075 original size:87 final size:88
Alignment explanation
Indices: 1691925--1692143 Score: 280
Period size: 87 Copynumber: 2.5 Consensus size: 88
1691915 TTTTATAGCG
* * *
1691925 GTTAACCCATTAACGGATATATTACTTGAGAATTAATTTATTTTTTAAAAATAACTCACGTGCAT
1 GTTAACCCATTAACGGATGTATTACGTGACAATTAATTTATTTTTTAAAAATAACTCACGTGCAT
* * * *
1691990 CTATTTTGTTCTTCTT-TTATAT
66 CCATGTTCTTCTTCTTCTTACAT
* * ** * *
1692012 GTTAACTCATTAACGAATGTATTACGTGACAATTTTTTTTTTTTTTAAAAATAACTCATGTGCAT
1 GTTAACCCATTAACGGATGTATTACGTGACAATTAATTTATTTTTTAAAAATAACTCACGTGCAT
1692077 CCATGTTCTTCTTCTTCTTACAT
66 CCATGTTCTTCTTCTTCTTACAT
* **
1692100 GTTAACCCTTTAACGGATGTATTACGTGGTAATTAATTT-TTTTT
1 GTTAACCCATTAACGGATGTATTACGTGACAATTAATTTATTTTT
1692144 AAATCACGTG
Statistics
Matches: 111, Mismatches: 20, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
87 74 0.67
88 37 0.33
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.47
Consensus pattern (88 bp):
GTTAACCCATTAACGGATGTATTACGTGACAATTAATTTATTTTTTAAAAATAACTCACGTGCAT
CCATGTTCTTCTTCTTCTTACAT
Found at i:1692721 original size:39 final size:39
Alignment explanation
Indices: 1692667--1692745 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
1692657 CCTTGCCCTG
1692667 AGATCACTTCTGGTGCCAAGTACTCGTGGGTTCCGACAA
1 AGATCACTTCTGGTGCCAAGTACTCGTGGGTTCCGACAA
*
1692706 AGATCACTTCTGGTGCCAAGTACTTGTGGGTTCCGACAA
1 AGATCACTTCTGGTGCCAAGTACTCGTGGGTTCCGACAA
1692745 A
1 A
1692746 CGACTTGAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (39 bp):
AGATCACTTCTGGTGCCAAGTACTCGTGGGTTCCGACAA
Found at i:1695606 original size:20 final size:20
Alignment explanation
Indices: 1695596--1695633 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1695586 GAATAGTACC
1695596 AATACTGTATGAACAATACA
1 AATACTGTATGAACAATACA
*
1695616 AATACTGTGTGAACAATA
1 AATACTGTATGAACAATA
1695634 ATGAACAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.26
Consensus pattern (20 bp):
AATACTGTATGAACAATACA
Found at i:1697328 original size:20 final size:20
Alignment explanation
Indices: 1697296--1697343 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1697286 AACGATTTTC
1697296 TTTT-AAAAGCAAAAATAAA
1 TTTTGAAAAGCAAAAATAAA
* *
1697315 TTTTGAAAATCAAAATTAAA
1 TTTTGAAAAGCAAAAATAAA
*
1697335 TGTTGAAAA
1 TTTTGAAAA
1697344 AAAGATTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.31
Consensus pattern (20 bp):
TTTTGAAAAGCAAAAATAAA
Found at i:1698763 original size:20 final size:20
Alignment explanation
Indices: 1698715--1698763 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1698705 CTGTAGGAAT
1698715 AGTACCGATAATGTATGAAC
1 AGTACCGATAATGTATGAAC
* * * *
1698735 AATATCGATATTGTGTGAAC
1 AGTACCGATAATGTATGAAC
1698755 AGTACCGAT
1 AGTACCGAT
1698764 GCTATAAAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (20 bp):
AGTACCGATAATGTATGAAC
Found at i:1698828 original size:20 final size:20
Alignment explanation
Indices: 1698791--1698828 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1698781 TGCAAAATGG
*
1698791 GTATCGATATCTCTACAGTA
1 GTATCGATATCTCGACAGTA
1698811 GTATCGATA-CTTCGACAG
1 GTATCGATATC-TCGACAG
1698829 CAAAATCAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATATCTCGACAGTA
Found at i:1702013 original size:18 final size:19
Alignment explanation
Indices: 1701986--1702039 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 19
1701976 AATTGGTAAG
* *
1701986 AATTGATATCTTTTT-AAT
1 AATTGGTATCTTTTTAAAA
1702004 AATTGGTATCCTTTTGTAAAA
1 AATTGGTAT-CTTTT-TAAAA
1702025 AATTGGTATCTTTTT
1 AATTGGTATCTTTTT
1702040 TCATTAAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 8 0.26
19 6 0.19
20 6 0.19
21 11 0.35
ACGTcount: A:0.30, C:0.07, G:0.11, T:0.52
Consensus pattern (19 bp):
AATTGGTATCTTTTTAAAA
Found at i:1702375 original size:22 final size:22
Alignment explanation
Indices: 1702259--1702378 Score: 89
Period size: 22 Copynumber: 5.3 Consensus size: 22
1702249 AGAGGTACTG
*
1702259 ATACCCCTATAAATGGGTATCA
1 ATACCCCTATGAATGGGTATCA
* * *
1702281 ATACCTCTATGAATGGGTACCG
1 ATACCCCTATGAATGGGTATCA
* *** *
1702303 ATACCCCTATCAATACCCCTGTCA
1 ATACCCCTATGAAT--GGGTATCA
* * *
1702327 ATACCTCTTATGAACGGGTA-CGG
1 ATACC-CCTATGAATGGGTATC-A
1702350 ATACCCCTATGAATGGGTATCA
1 ATACCCCTATGAATGGGTATCA
1702372 ATACCCC
1 ATACCCC
1702379 ATTAAGGCTC
Statistics
Matches: 70, Mismatches: 23, Indels: 10
0.68 0.22 0.10
Matches are distributed among these distances:
22 50 0.71
23 7 0.10
24 7 0.10
25 6 0.09
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (22 bp):
ATACCCCTATGAATGGGTATCA
Found at i:1702834 original size:33 final size:33
Alignment explanation
Indices: 1702797--1702866 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
1702787 TTTTATAAAG
* * * *
1702797 GGGAAAGGTTCTAGCTGATCCCGTGAAAAGCTA
1 GGGAAAGATTCTAGCTGAGCCCATGAAAAACTA
* *
1702830 GGGAAAGATTCTAGTTTAGCCCATGAAAAACTA
1 GGGAAAGATTCTAGCTGAGCCCATGAAAAACTA
1702863 GGGA
1 GGGA
1702867 GTTTGTAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.21
Consensus pattern (33 bp):
GGGAAAGATTCTAGCTGAGCCCATGAAAAACTA
Found at i:1706710 original size:21 final size:21
Alignment explanation
Indices: 1706684--1706737 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
1706674 TGGGCAGAGT
1706684 GTATCGATACACATTCAACAG
1 GTATCGATACACATTCAACAG
1706705 GTATCGATACACATTCAACAG
1 GTATCGATACACATTCAACAG
1706726 GTATCGATACAC
1 GTATCGATACAC
1706738 TCTTGAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (21 bp):
GTATCGATACACATTCAACAG
Found at i:1707433 original size:18 final size:18
Alignment explanation
Indices: 1707410--1707462 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
1707400 AGGGATTATC
*
1707410 AGTGGTCCTTCGGGACCT
1 AGTGGTCCTTCGGGACAT
*
1707428 AGTGGTCATTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
1707446 AGTGGTCCTCCGGGACA
1 AGTGGTCCTTCGGGACA
1707463 AATATTCAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.17, C:0.25, G:0.34, T:0.25
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1713608 original size:19 final size:19
Alignment explanation
Indices: 1713584--1713632 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
1713574 GAATGCAATA
1713584 AGTGTATCGATACACAGTT
1 AGTGTATCGATACACAGTT
1713603 AGTGTATCGATACACAGTT
1 AGTGTATCGATACACAGTT
1713622 AGTGTATCGAT
1 AGTGTATCGAT
1713633 GCACCCCCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (19 bp):
AGTGTATCGATACACAGTT
Found at i:1714175 original size:24 final size:24
Alignment explanation
Indices: 1714134--1714187 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
1714124 TGAAATAATG
1714134 GAAGTG-ATCATGTATATGCATGT
1 GAAGTGAATCATGTATATGCATGT
* *
1714157 GAAGTGAATTATGTGTATGCATGT
1 GAAGTGAATCATGTATATGCATGT
1714181 GAAGTGA
1 GAAGTGA
1714188 TAGAAGAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
23 6 0.21
24 22 0.79
ACGTcount: A:0.31, C:0.06, G:0.30, T:0.33
Consensus pattern (24 bp):
GAAGTGAATCATGTATATGCATGT
Found at i:1714313 original size:18 final size:18
Alignment explanation
Indices: 1714290--1714324 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1714280 AGGGATTATC
* *
1714290 AGTGGTCCTTCGGGACAT
1 AGTGGTCATCCGGGACAT
1714308 AGTGGTCATCCGGGACA
1 AGTGGTCATCCGGGACA
1714325 AATATTCAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.23, G:0.34, T:0.23
Consensus pattern (18 bp):
AGTGGTCATCCGGGACAT
Found at i:1717028 original size:21 final size:24
Alignment explanation
Indices: 1716975--1717034 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 24
1716965 TACCATATAC
1716975 GGTATCGATACTACTTAGTATAGT
1 GGTATCGATACTACTTAGTATAGT
* * *
1716999 AGTACCGATACT-CTTTGT-TA-T
1 GGTATCGATACTACTTAGTATAGT
1717020 GGTATCGATACTACT
1 GGTATCGATACTACT
1717035 CCTTTTGGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 11 0.37
22 4 0.13
23 5 0.17
24 10 0.33
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (24 bp):
GGTATCGATACTACTTAGTATAGT
Found at i:1722580 original size:20 final size:20
Alignment explanation
Indices: 1722538--1722580 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1722528 ATTTCTTTGA
* *
1722538 AGTATTGATACTCCCGTTGG
1 AGTATCGATACTCCCGTTCG
1722558 AGTATCGATACTACCCG-TCG
1 AGTATCGATACT-CCCGTTCG
1722578 AGT
1 AGT
1722581 TCAACTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (20 bp):
AGTATCGATACTCCCGTTCG
Found at i:1723631 original size:15 final size:15
Alignment explanation
Indices: 1723613--1723643 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1723603 AAAGAAGGAG
1723613 AAGATCAAGAAAAGA
1 AAGATCAAGAAAAGA
*
1723628 AAGATGAAGAAAAGA
1 AAGATCAAGAAAAGA
1723643 A
1 A
1723644 GGAAATAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.03, G:0.23, T:0.06
Consensus pattern (15 bp):
AAGATCAAGAAAAGA
Found at i:1727605 original size:20 final size:20
Alignment explanation
Indices: 1727563--1727605 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1727553 ATTTCTTTGA
* *
1727563 AGTATTGATACTCCCGTTGG
1 AGTATCGATACTCCCGTTCG
1727583 AGTATCGATACTACCCG-TCG
1 AGTATCGATACT-CCCGTTCG
1727603 AGT
1 AGT
1727606 TCAACTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (20 bp):
AGTATCGATACTCCCGTTCG
Found at i:1729750 original size:26 final size:25
Alignment explanation
Indices: 1729720--1729772 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 25
1729710 TGATTTAAAA
1729720 AAGGGGGAGGGGAGAAATGTTAAAGT
1 AAGGGGG-GGGGAGAAATGTTAAAGT
1729746 AA----GGGGGAGAAATGTTAAAGT
1 AAGGGGGGGGGAGAAATGTTAAAGT
1729767 AAGGGG
1 AAGGGG
1729773 AGTAATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 9
0.72 0.00 0.28
Matches are distributed among these distances:
21 20 0.87
22 1 0.04
26 2 0.09
ACGTcount: A:0.40, C:0.00, G:0.45, T:0.15
Consensus pattern (25 bp):
AAGGGGGGGGGAGAAATGTTAAAGT
Found at i:1729790 original size:22 final size:21
Alignment explanation
Indices: 1729728--1729772 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
1729718 AAAAGGGGGA
1729728 GGGGAGAAATGTTAAAGTAAG
1 GGGGAGAAATGTTAAAGTAAG
1729749 GGGGAGAAATGTTAAAGTAAG
1 GGGGAGAAATGTTAAAGTAAG
1729770 GGG
1 GGG
1729773 AGTAATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.42, T:0.18
Consensus pattern (21 bp):
GGGGAGAAATGTTAAAGTAAG
Found at i:1734247 original size:78 final size:78
Alignment explanation
Indices: 1734118--1734273 Score: 276
Period size: 78 Copynumber: 2.0 Consensus size: 78
1734108 GGCTGTAGAG
* *
1734118 AGATCCTCCGGATTACTCGTTGAATCCTCTATGTTTATATATGATCCCTCCAAGCGTAGAGAAGA
1 AGATCCTCCAGATTACTCGTTGAATCCTCTATGTTTACATATGATCCCTCCAAGCGTAGAGAAGA
*
1734183 AACTTTCATGCCA
66 AACTTACATGCCA
*
1734196 AGATCCTCCAGATTACTCGTTGAATCCTCTATGTTTACATATGATCCCTCCAAGCTTAGAGAAGA
1 AGATCCTCCAGATTACTCGTTGAATCCTCTATGTTTACATATGATCCCTCCAAGCGTAGAGAAGA
1734261 AACTTACATGCCA
66 AACTTACATGCCA
1734274 CAATTGCAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 74 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.30
Consensus pattern (78 bp):
AGATCCTCCAGATTACTCGTTGAATCCTCTATGTTTACATATGATCCCTCCAAGCGTAGAGAAGA
AACTTACATGCCA
Found at i:1735464 original size:12 final size:12
Alignment explanation
Indices: 1735447--1735473 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1735437 GATTACCCGA
1735447 ATACCCGGCCTG
1 ATACCCGGCCTG
1735459 ATACCCGGCCTG
1 ATACCCGGCCTG
1735471 ATA
1 ATA
1735474 AATATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.37, G:0.22, T:0.19
Consensus pattern (12 bp):
ATACCCGGCCTG
Found at i:1737298 original size:18 final size:18
Alignment explanation
Indices: 1737277--1737315 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1737267 CTTTAACCTT
1737277 ACAACACTTACCACGACA
1 ACAACACTTACCACGACA
* *
1737295 ACAACATTTGCCACGACA
1 ACAACACTTACCACGACA
1737313 ACA
1 ACA
1737316 CCATTCATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.44, C:0.36, G:0.08, T:0.13
Consensus pattern (18 bp):
ACAACACTTACCACGACA
Found at i:1738774 original size:12 final size:12
Alignment explanation
Indices: 1738754--1738786 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1738744 TACTCTATCG
*
1738754 GAATAAATCAAT
1 GAATTAATCAAT
1738766 GAATTAATCAAT
1 GAATTAATCAAT
1738778 GAATTAATC
1 GAATTAATC
1738787 GGATATGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (12 bp):
GAATTAATCAAT
Found at i:1739841 original size:31 final size:31
Alignment explanation
Indices: 1739803--1739864 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
1739793 TTTATTTGTA
1739803 TTTCAGTTTGATTTTGTTGTGAGCGGTTTTT
1 TTTCAGTTTGATTTTGTTGTGAGCGGTTTTT
1739834 TTTCAGTTTGATTTTGTTGTGAGCGGTTTTT
1 TTTCAGTTTGATTTTGTTGTGAGCGGTTTTT
1739865 GTTAACCGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.10, C:0.06, G:0.26, T:0.58
Consensus pattern (31 bp):
TTTCAGTTTGATTTTGTTGTGAGCGGTTTTT
Found at i:1741996 original size:159 final size:159
Alignment explanation
Indices: 1741703--1742024 Score: 619
Period size: 159 Copynumber: 2.0 Consensus size: 159
1741693 CATCAATAAG
*
1741703 ATGT-GAGATTTAGTAGCTTGACTTAGAGCATTGGAGGTTGAAATATCTGATTCTTTCCTAGTGC
1 ATGTGGAGATTTAGTAGCTTGACTTAGAGCATTGGAGGTTGAAATATCTGATTCTTTCCTAATGC
1741767 ACTTTATACTGAACAATCTTTCACTCAGTATGGGTCATTTAAGATCGCCTATAACACACATAAGG
66 ACTTTATACTGAACAATCTTTCACTCAGTATGGGTCATTTAAGATCGCCTATAACACACATAAGG
1741832 ATAAGTGGTCTATTGAGGAACGTTTGACC
131 ATAAGTGGTCTATTGAGGAACGTTTGACC
1741861 ATGTGGAGATTTAGTAGCTTGACTTAGAGCATTGGAGGTTGAAATATCTGATTCTTTCCTAATGC
1 ATGTGGAGATTTAGTAGCTTGACTTAGAGCATTGGAGGTTGAAATATCTGATTCTTTCCTAATGC
1741926 ACTTTATACTGAACAATCTTTCACTCAGTATGGGTCATTTAAGATCGCCTATAACACACATAAGG
66 ACTTTATACTGAACAATCTTTCACTCAGTATGGGTCATTTAAGATCGCCTATAACACACATAAGG
*
1741991 ATAAGTGGTCTATTGATGAACGTTTGACC
131 ATAAGTGGTCTATTGAGGAACGTTTGACC
1742020 ATGTG
1 ATGTG
1742025 TGATCAAGAG
Statistics
Matches: 161, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
158 4 0.02
159 157 0.98
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (159 bp):
ATGTGGAGATTTAGTAGCTTGACTTAGAGCATTGGAGGTTGAAATATCTGATTCTTTCCTAATGC
ACTTTATACTGAACAATCTTTCACTCAGTATGGGTCATTTAAGATCGCCTATAACACACATAAGG
ATAAGTGGTCTATTGAGGAACGTTTGACC
Found at i:1743851 original size:2 final size:2
Alignment explanation
Indices: 1743846--1743894 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
1743836 TTTGTGTTAT
1743846 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1743887 TA TA TA TA
1 TA TA TA TA
1743895 ATAGTTGAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1743933 original size:20 final size:19
Alignment explanation
Indices: 1743908--1743972 Score: 64
Period size: 18 Copynumber: 3.4 Consensus size: 19
1743898 GTTGAAGTCA
1743908 TTTTAAAATTATAATATAGT
1 TTTTAAAA-TATAATATAGT
*
1743928 TTTTAAAA-ATAAAATA--
1 TTTTAAAATATAATATAGT
*
1743944 TTTTGAAATATAATATATAGT
1 TTTTAAAATAT-A-ATATAGT
1743965 TTTTAAAA
1 TTTTAAAA
1743973 CATTTTGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
16 7 0.19
17 2 0.06
18 8 0.22
19 4 0.11
20 8 0.22
21 7 0.19
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (19 bp):
TTTTAAAATATAATATAGT
Found at i:1744088 original size:33 final size:32
Alignment explanation
Indices: 1743937--1744127 Score: 160
Period size: 33 Copynumber: 5.8 Consensus size: 32
1743927 TTTTTAAAAA
*
1743937 TAAAATATTTTG-AAATATAATATATAGTTTT
1 TAAAACATTTTGAAAATATAATATATAGTTTT
1743968 TAAAACATTTTGAAAACT-TATATAATATAGTTTT
1 TAAAACATTTTGAAAA-TATA-AT-ATATAGTTTT
*
1744002 AAAAAACATTTTGAAAACTTATAATAT-T--TTTT
1 -TAAAACATTTTGAAAA--TATAATATATAGTTTT
* *
1744034 TAAATCATTTTTGAAACTATAATATATAGTTTT
1 TAAAACA-TTTTGAAAATATAATATATAGTTTT
* * *
1744067 GAAAACTTTTTTTAAAATATAATATATAG-TTT
1 TAAAAC-ATTTTGAAAATATAATATATAGTTTT
* *
1744099 AAAAATATTTTTGAAATATATATATATAT
1 TAAAACA-TTTTGAAA-ATATA-ATATAT
1744128 TATATAGTTT
Statistics
Matches: 130, Mismatches: 15, Indels: 27
0.76 0.09 0.16
Matches are distributed among these distances:
30 8 0.06
31 17 0.13
32 31 0.24
33 35 0.27
34 17 0.13
35 17 0.13
36 3 0.02
37 2 0.02
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (32 bp):
TAAAACATTTTGAAAATATAATATATAGTTTT
Found at i:1744111 original size:65 final size:66
Alignment explanation
Indices: 1743975--1744126 Score: 156
Period size: 65 Copynumber: 2.3 Consensus size: 66
1743965 TTTTAAAACA
* *
1743975 TTTTGAAAACT-TATATAATATAGTTTTAAAAAACATTTTGAAAACTTATAATAT-T--TTTTTA
1 TTTTG-AAACTATATAT-ATATAGTTTTAAAAAACATTTTTAAAA--TATAATATATAGTTTTAA
1744036 AATCAT
62 AAT-AT
* * *
1744042 TTTTGAAACTATA-ATATATAGTTTT-GAAAACTTTTTTTAAAATATAATATATAGTTTAAAAAT
1 TTTTGAAACTATATATATATAGTTTTAAAAAAC-ATTTTTAAAATATAATATATAGTTTTAAAAT
1744105 AT
65 AT
1744107 TTTTGAAA-TATATATATATA
1 TTTTGAAACTATATATATATA
1744127 TTATATAGTT
Statistics
Matches: 74, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
63 8 0.11
64 10 0.14
65 35 0.47
66 14 0.19
67 7 0.09
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (66 bp):
TTTTGAAACTATATATATATAGTTTTAAAAAACATTTTTAAAATATAATATATAGTTTTAAAATA
T
Found at i:1744141 original size:22 final size:21
Alignment explanation
Indices: 1744114--1744190 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 21
1744104 TATTTTTGAA
1744114 ATATATATATATATTATATAGTTT
1 ATAT-TATAT-TATTAT-TAGTTT
1744138 ATATTATATTATTATTAG--T
1 ATATTATATTATTATTAGTTT
* *
1744157 ATATTATTATT-TTTTTATTTT
1 ATATTA-TATTATTATTAGTTT
* *
1744178 ATTTTATTTTATT
1 ATATTATATTATT
1744191 TTATTCATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
19 12 0.27
20 7 0.16
21 11 0.24
22 6 0.13
23 5 0.11
24 4 0.09
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (21 bp):
ATATTATATTATTATTAGTTT
Found at i:1744175 original size:14 final size:13
Alignment explanation
Indices: 1744158--1744227 Score: 67
Period size: 14 Copynumber: 5.5 Consensus size: 13
1744148 ATTATTAGTA
1744158 TATTATTATTTTTT
1 TATT-TTATTTTTT
1744172 TATTTTA---TTT
1 TATTTTATTTTTT
1744182 TATTTTATTTTATT
1 TATTTTATTTT-TT
*
1744196 CATTTTATTTTATT
1 TATTTTATTTT-TT
*
1744210 TATCTT-TTTTTT
1 TATTTTATTTTTT
1744222 TATTTT
1 TATTTT
1744228 TCTGGTCCAG
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
10 10 0.21
12 7 0.15
13 8 0.17
14 23 0.48
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.79
Consensus pattern (13 bp):
TATTTTATTTTTT
Found at i:1744179 original size:5 final size:5
Alignment explanation
Indices: 1744169--1744227 Score: 75
Period size: 5 Copynumber: 11.8 Consensus size: 5
1744159 ATTATTATTT
* * *
1744169 TTTTA TTTTA TTTTA TTTTA TTTTA -TTCA TTTTA TTTTA TTTATC TTTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT-TA TTTTA
1744219 TTTTA TTTT
1 TTTTA TTTT
1744228 TCTGGTCCAG
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
4 3 0.06
5 40 0.85
6 4 0.09
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:1744180 original size:19 final size:20
Alignment explanation
Indices: 1744158--1744227 Score: 74
Period size: 19 Copynumber: 3.5 Consensus size: 20
1744148 ATTATTAGTA
1744158 TATTATTATTTT-TTTAT-TT
1 TATT-TTATTTTATTTATATT
1744177 TATTTTATTTTATTT-TATT
1 TATTTTATTTTATTTATATT
* *
1744196 CATTTTATTTTATTTATCTTT
1 TATTTTATTTTATTTAT-ATT
*
1744217 TTTTTTATTTT
1 TATTTTATTTT
1744228 TCTGGTCCAG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
18 8 0.19
19 23 0.53
20 1 0.02
21 11 0.26
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.79
Consensus pattern (20 bp):
TATTTTATTTTATTTATATT
Found at i:1744189 original size:15 final size:15
Alignment explanation
Indices: 1744169--1744227 Score: 75
Period size: 14 Copynumber: 3.9 Consensus size: 15
1744159 ATTATTATTT
1744169 TTTTATTTTATTTTA
1 TTTTATTTTATTTTA
*
1744184 TTTTATTTTA-TTCA
1 TTTTATTTTATTTTA
*
1744198 TTTTATTTTATTTATC
1 TTTTATTTTATTT-TA
*
1744214 TTTTTTTTTATTTT
1 TTTTATTTTATTTT
1744228 TCTGGTCCAG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
14 13 0.34
15 13 0.34
16 12 0.32
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTATTTTATTTTA
Found at i:1744195 original size:45 final size:45
Alignment explanation
Indices: 1744135--1744227 Score: 109
Period size: 45 Copynumber: 2.1 Consensus size: 45
1744125 TATTATATAG
*
1744135 TTTATATTATATTATT-ATTAGTATATTA-TTATTTTTTTATTTTAT
1 TTTATATTATATTATTCATT-GTATATTATTTATCTTTTT-TTTTAT
* * * *
1744180 TTTATTTTATTTTATTCATTTTATTTTATTTATCTTTTTTTTTAT
1 TTTATATTATATTATTCATTGTATATTATTTATCTTTTTTTTTAT
1744225 TTT
1 TTT
1744228 TCTGGTCCAG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
45 29 0.71
46 12 0.29
ACGTcount: A:0.23, C:0.02, G:0.01, T:0.74
Consensus pattern (45 bp):
TTTATATTATATTATTCATTGTATATTATTTATCTTTTTTTTTAT
Found at i:1744228 original size:10 final size:10
Alignment explanation
Indices: 1744160--1744228 Score: 59
Period size: 10 Copynumber: 6.8 Consensus size: 10
1744150 TATTAGTATA
1744160 TTATTATTTTT
1 TTATT-TTTTT
*
1744171 TTATTTTATT
1 TTATTTTTTT
*
1744181 TTATTTTATT
1 TTATTTTTTT
**
1744191 TTA-TTCATT
1 TTATTTTTTT
1744200 TTATTTTATTT
1 TTATTTT-TTT
* *
1744211 ATCTTTTTTT
1 TTATTTTTTT
1744221 TTATTTTT
1 TTATTTTT
1744229 CTGGTCCAGG
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
9 8 0.17
10 28 0.58
11 12 0.25
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (10 bp):
TTATTTTTTT
Found at i:1745517 original size:37 final size:36
Alignment explanation
Indices: 1745476--1745558 Score: 114
Period size: 37 Copynumber: 2.2 Consensus size: 36
1745466 TTTTCTTGAC
1745476 CTTTGATTTATTTT-TTATTTTTTTATCTCATCTTTTT
1 CTTTGATTTATTTTCTTATTTTTTTATCT-AT-TTTTT
* *
1745513 CTTTGATTTATTTTCTTTTTTTTTTTTCTATTTTTT
1 CTTTGATTTATTTTCTTATTTTTTTATCTATTTTTT
1745549 CTTTTGATTT
1 C-TTTGATTT
1745559 TATTATTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
36 6 0.14
37 24 0.57
38 12 0.29
ACGTcount: A:0.11, C:0.10, G:0.04, T:0.76
Consensus pattern (36 bp):
CTTTGATTTATTTTCTTATTTTTTTATCTATTTTTT
Found at i:1745566 original size:3 final size:3
Alignment explanation
Indices: 1745558--1745605 Score: 73
Period size: 3 Copynumber: 16.7 Consensus size: 3
1745548 TCTTTTGATT
*
1745558 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TT- TTA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1745604 TT
1 TT
1745606 TTTTTCTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 4 0.10
3 38 0.90
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
TTA
Found at i:1745606 original size:6 final size:6
Alignment explanation
Indices: 1745519--1745608 Score: 58
Period size: 6 Copynumber: 14.5 Consensus size: 6
1745509 TTTTCTTTGA
* * *
1745519 TTTATT TTCTTTT TTTTTT TTCTATT TTT-TCT TTTGA-T TTTATT ATTATT
1 TTTATT TT-TATT TTTATT TT-TATT TTTAT-T TTT-ATT TTTATT TTTATT
* * * *
1745569 ATTATT ATTATT ATTATT ATTATTT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTA-TT TTTATT TTTATT TTT
1745609 TTCTTTTGAT
Statistics
Matches: 73, Mismatches: 4, Indels: 14
0.80 0.04 0.15
Matches are distributed among these distances:
5 2 0.03
6 56 0.77
7 15 0.21
ACGTcount: A:0.18, C:0.03, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:1745724 original size:6 final size:6
Alignment explanation
Indices: 1745708--1745737 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
1745698 TGAATCGAAT
1745708 TTTTAAA TTTTAA TTTTAA TTTTAA TTTTA
1 TTTT-AA TTTTAA TTTTAA TTTTAA TTTTA
1745738 CAATTAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTTAA
Found at i:1749480 original size:64 final size:64
Alignment explanation
Indices: 1749242--1749726 Score: 735
Period size: 64 Copynumber: 7.6 Consensus size: 64
1749232 TACATCTTTT
* *
1749242 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAATAA--TTCCAGTTTCATTT
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
*
1749304 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCATTTTCATTC
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
*
1749368 AGAGTCAATTT-AACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTT
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* * *
1749431 AGAGTTAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAGCAACTTTCCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* * * * * *
1749495 AGAGTCAATTTCAACTTCACAGTGAAGGACATTGGACTCAATAAATAACGTTCCAGTTTTATTC
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* * *
1749559 AGAGTCAATTTCAACTTCACATCGAAGGATATTGGACTCAACAAATAACTTTCCACTTTCATTC
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* * * * * *
1749623 AGAATCAATTTTAACTTCACAACGATGTATATTGGACTCAAC-AACAACTTTCCAGTTTCAATC
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
*
1749686 AGAGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCAA
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAA
1749727 AACAATGCAA
Statistics
Matches: 381, Mismatches: 39, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
62 47 0.12
63 113 0.30
64 221 0.58
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (64 bp):
AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
Found at i:1749561 original size:191 final size:191
Alignment explanation
Indices: 1749239--1749726 Score: 759
Period size: 191 Copynumber: 2.6 Consensus size: 191
1749229 TTTTACATCT
* *
1749239 TTTAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAA-ATA-ATTCCAGTTTCAT
1 TTTAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAACA-ACTTTCCAGTTTCAT
* * *
1749302 TTAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCATTTTCATT
65 TCAGAGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCAACAAACAACGTTCCATTTTCATT
*
1749367 CAGAGTCAATTT-AACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCA
130 CAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCACTTTCA
*
1749428 TTTAGAGTTAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAGCAACTTTCCAGTTTCAT
1 TTTAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAA-CAACTTTCCAGTTTCAT
* * *
1749493 TCAGAGTCAATTTCAACTTCACAGTGAAGGACATTGGACTCAATAAATAACGTTCCAGTTTT-AT
65 TCAGAGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCAACAAACAACGTTCCA-TTTTCAT
* *
1749557 TCAGAGTCAATTTCAACTTCACATCGAAGGATATTGGACTCAACAAATAACTTTCCACTTTCA
129 TCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCACTTTCA
* * * * * *
1749620 TTCAGAATCAATTTTAACTTCACAACGATGTATATTGGACTCAACAACAACTTTCCAGTTTCAAT
1 TTTAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAACAACTTTCCAGTTTCATT
1749685 CAGAGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCAA
66 CAGAGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCAA
1749727 AACAATGCAA
Statistics
Matches: 274, Mismatches: 20, Indels: 8
0.91 0.07 0.03
Matches are distributed among these distances:
189 45 0.16
190 1 0.00
191 137 0.50
192 91 0.33
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.31
Consensus pattern (191 bp):
TTTAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAACAACTTTCCAGTTTCATT
CAGAGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCAACAAACAACGTTCCATTTTCATTC
AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCACTTTCA
Found at i:1749698 original size:255 final size:253
Alignment explanation
Indices: 1749242--1749726 Score: 783
Period size: 255 Copynumber: 1.9 Consensus size: 253
1749232 TACATCTTTT
* *
1749242 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAATAATTCCAGTTTCATTTAGA
1 AGAGTCAATTTCAACTTCACAGCGAAGGACATTGGACTCAACAAATAATTCCAGTTTCATTCAGA
* *
1749307 GTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCATTTTCATTCAGAG
66 GTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCACTTTCATTCAGAA
* * * *
1749372 TCAATTTAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTTAGAGTT
131 TCAATTTAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCAATCAGAGTC
1749437 AATTTCAACTTCACAACGAAGGATATTGGACTCAACAAGCAACTTTCCAGTTTCATTC
196 AATTTCAACTTCACAACGAAGGATATTGGACTCAACAAGCAACTTTCCAGTTTCATTC
* * *
1749495 AGAGTCAATTTCAACTTCACAGTGAAGGACATTGGACTCAATAAATAACGTTCCAGTTTTATTCA
1 AGAGTCAATTTCAACTTCACAGCGAAGGACATTGGACTCAACAAATAA--TTCCAGTTTCATTCA
* *
1749560 GAGTCAATTTCAACTTCACATCGAAGGATATTGGACTCAACAAATAACTTTCCACTTTCATTCAG
64 GAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCACTTTCATTCAG
* *
1749625 AATCAATTTTAACTTCACAACGATGTATATTGGACTCAAC-AACAACTTTCCAGTTTCAATCAGA
129 AATCAA-TTTAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCAATCAGA
**
1749689 GTCAATTTCAACTTCACAGTGAAGGATATTGGACTCAA
193 GTCAATTTCAACTTCACAACGAAGGATATTGGACTCAA
1749727 AACAATGCAA
Statistics
Matches: 212, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
253 45 0.21
255 137 0.65
256 30 0.14
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (253 bp):
AGAGTCAATTTCAACTTCACAGCGAAGGACATTGGACTCAACAAATAATTCCAGTTTCATTCAGA
GTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCACTTTCATTCAGAA
TCAATTTAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCAATCAGAGTC
AATTTCAACTTCACAACGAAGGATATTGGACTCAACAAGCAACTTTCCAGTTTCATTC
Found at i:1749904 original size:123 final size:121
Alignment explanation
Indices: 1749729--1750031 Score: 448
Period size: 123 Copynumber: 2.5 Consensus size: 121
1749719 GGACTCAAAA
* *
1749729 CAATGCAACCCTTGGATTTCAACTTGACGACGAAGGATATCCAATTCAAAGCTCAAATTCAAAAC
1 CAATGCAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCAAAAC
*
1749794 AAATGAGCTATCCACAATTTTAACTTAACGACAAAGGATATATCATGCCCACAAGCAG
66 AAATGAGCCATCCACAATTTTAACTTAACGACAAAGG--ATATCATGCCCACAAGCAG
* * *
1749852 CAATGCAACCCTTGGATTTCAACTTCACGATGGAGGATATCCAATTCAAAGCTCAACTTCACAAC
1 CAATGCAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCAAAAC
* * * * * *
1749917 GAATGAGCCATCCACGATTTTAACTTCACGACGAAGGATATCGTTCCCACAAGCAG
66 AAATGAGCCATCCACAATTTTAACTTAACGACAAAGGATATCATGCCCACAAGCAG
* *
1749973 TAATGCAACCCTTGGATTTCAA-TTCACG-CGAAAGATATCCAATTCAAAGCTCAACTTCA
1 CAATGCAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCA
1750032 CAACGAAGGA
Statistics
Matches: 164, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
119 28 0.17
120 6 0.04
121 38 0.23
123 92 0.56
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (121 bp):
CAATGCAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCAAAAC
AAATGAGCCATCCACAATTTTAACTTAACGACAAAGGATATCATGCCCACAAGCAG
Found at i:1750352 original size:82 final size:85
Alignment explanation
Indices: 1750140--1750359 Score: 268
Period size: 82 Copynumber: 2.6 Consensus size: 85
1750130 CAAGTGCAGT
* *
1750140 ATAACTCAAGGCGATAAGGGTTATCTGTCAACAAAAGACCTCCGAGTTCGATTACACTCAACTCA
1 ATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAA-ACCTTCGAGTTCGATTACACTCAACTCA
* *
1750205 AAGGCACATCCAATTTACAGC
65 AAGACACATCAAATTTACAGC
* * * * * * *
1750226 ATAACTCAAGGCGAGAAGGGTTATATGTTAACCAAGACCTTCGAGGTCGATTACACTTAGCT-AA
1 ATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTACACTCAACTCAA
*
1750290 A-ATACAT-AAATTTACAGC
66 AGACACATCAAATTTACAGC
* *
1750308 ATAACTCAAGGCGAGAAGGGCTATCTGTCAA-AAAAAACTGTCGAGTTCGATT
1 ATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCT-TCGAGTTCGATT
1750360 CCATTCAGCT
Statistics
Matches: 114, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
81 5 0.04
82 49 0.43
83 4 0.04
84 3 0.03
85 22 0.19
86 31 0.27
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.24
Consensus pattern (85 bp):
ATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTACACTCAACTCAA
AGACACATCAAATTTACAGC
Found at i:1751049 original size:40 final size:40
Alignment explanation
Indices: 1750993--1751105 Score: 130
Period size: 36 Copynumber: 2.9 Consensus size: 40
1750983 AGTTTGAAGT
*
1750993 CATTCTGAAAATTATATAATATATAGTTTTTAAAAATAAAA
1 CATTTTGAAAATTATATAATATATAG-TTTTAAAAATAAAA
* * *
1751034 CATTTT-AAAAATATATAATAAATGGTTTT-----TAAAA
1 CATTTTGAAAATTATATAATATATAGTTTTAAAAATAAAA
1751068 CATTTTGAAAACTTATATAATATATAGTTTTAAAAATA
1 CATTTTGAAAA-TTATATAATATATAGTTTTAAAAATA
1751106 TTTTTTGAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
34 11 0.19
35 4 0.07
36 16 0.28
39 4 0.07
40 16 0.28
41 7 0.12
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (40 bp):
CATTTTGAAAATTATATAATATATAGTTTTAAAAATAAAA
Found at i:1751070 original size:34 final size:36
Alignment explanation
Indices: 1751029--1751173 Score: 126
Period size: 36 Copynumber: 4.2 Consensus size: 36
1751019 TTTTTAAAAA
*
1751029 TAAAACATTTT-AAAA-ATATATAATAAATGGTTTT
1 TAAAACATTTTGAAAACATATATAATAAATAGTTTT
* *
1751063 TAAAACATTTTGAAAACTTATATAATATATAGTTTT
1 TAAAACATTTTGAAAACATATATAATAAATAGTTTT
* *
1751099 AAAAATATTTTTTGAAAAC-T-TAT-AT-AATA-TTTT
1 TAAAACA--TTTTGAAAACATATATAATAAATAGTTTT
* * *
1751132 TAAATCATTTTTTAAAAC-TATATAATATATAGTTTT
1 TAAAACA-TTTTGAAAACATATATAATAAATAGTTTT
*
1751168 GAAAAC
1 TAAAAC
1751174 TTTATTTTAA
Statistics
Matches: 90, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
32 11 0.12
33 11 0.12
34 16 0.18
35 9 0.10
36 32 0.36
37 1 0.01
38 10 0.11
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (36 bp):
TAAAACATTTTGAAAACATATATAATAAATAGTTTT
Found at i:1751133 original size:69 final size:73
Alignment explanation
Indices: 1750993--1751172 Score: 194
Period size: 69 Copynumber: 2.5 Consensus size: 73
1750983 AGTTTGAAGT
*
1750993 CATTCTGAAAA-TTATATAATATATAGTTTTTAAAAATAAAACATTTTAAAAATATATAATAAAT
1 CATTTTGAAAACTTATATAATATATAG-TTTTAAAAAT--AACATTTTAAAAATATATAATAAAT
*
1751057 GGTTTTTAAAA
63 GATTTTTAAAA
** *
1751068 CATTTTGAAAACTTATATAATATATAGTTTTAAAAAT-ATTTTTTGAAAACT-TAT-AT-AAT-A
1 CATTTTGAAAACTTATATAATATATAGTTTTAAAAATAACATTTT-AAAAATATATAATAAATGA
*
1751128 TTTTTAAAT
65 TTTTTAAAA
* *
1751137 CATTTTTTAAAAC-TATATAATATATAGTTTTGAAAA
1 CA-TTTTGAAAACTTATATAATATATAGTTTTAAAAA
1751173 CTTTATTTTA
Statistics
Matches: 94, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
69 32 0.34
70 12 0.13
71 2 0.02
72 8 0.09
73 5 0.05
75 20 0.21
76 15 0.16
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (73 bp):
CATTTTGAAAACTTATATAATATATAGTTTTAAAAATAACATTTTAAAAATATATAATAAATGAT
TTTTAAAA
Found at i:1751142 original size:33 final size:34
Alignment explanation
Indices: 1751070--1751161 Score: 111
Period size: 38 Copynumber: 2.7 Consensus size: 34
1751060 TTTTAAAACA
1751070 TTTTGAAAACTTATATAATATATAGTTTTAAAAATATT
1 TTTTGAAAACTTATAT-A-ATATA-TTTT-AAAATATT
1751108 TTTTGAAAACTTATATAATAT-TTTT-AAATCATT
1 TTTTGAAAACTTATATAATATATTTTAAAAT-ATT
1751141 TTTT-AAAAC-TATATAATATAT
1 TTTTGAAAACTTATATAATATAT
1751162 AGTTTTGAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
31 10 0.19
32 10 0.19
33 7 0.13
34 4 0.08
36 4 0.08
37 1 0.02
38 16 0.31
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.49
Consensus pattern (34 bp):
TTTTGAAAACTTATATAATATATTTTAAAATATT
Found at i:1751211 original size:69 final size:69
Alignment explanation
Indices: 1751070--1751235 Score: 182
Period size: 69 Copynumber: 2.4 Consensus size: 69
1751060 TTTTAAAACA
**
1751070 TTTTGAAAACTTATATAATATATAGTTTTAAAAATATTTTTTGAAAACTTATATAATATTTTTAA
1 TTTTGAAAAC-TATATAATATATAGTTTTAAAAATATTTTTTGAAAACTTATATAATATTTAAAA
1751135 ATCAT
65 ATCAT
* *
1751140 TTTTTAAAACTATATAATATATAGTTTTGAAAACT-TTATTTT-AAAA--TATAATATATAGTTT
1 TTTTGAAAACTATATAATATATAGTTTT-AAAAATATT-TTTTGAAAACTTAT-ATA-ATA-TTT
1751201 AAAAAT-AT
61 AAAAATCAT
*
1751209 TTTTGAAATA-TATATATTATATAGTTT
1 TTTTGAAA-ACTATATAATATATAGTTT
1751236 CTATTATATT
Statistics
Matches: 84, Mismatches: 6, Indels: 13
0.82 0.06 0.13
Matches are distributed among these distances:
67 3 0.04
68 3 0.04
69 52 0.62
70 26 0.31
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (69 bp):
TTTTGAAAACTATATAATATATAGTTTTAAAAATATTTTTTGAAAACTTATATAATATTTAAAAA
TCAT
Found at i:1751230 original size:11 final size:10
Alignment explanation
Indices: 1751219--1751274 Score: 51
Period size: 11 Copynumber: 5.3 Consensus size: 10
1751209 TTTTGAAATA
1751219 TATATATTA-
1 TATATATTAT
*
1751228 TATAGTTTCTAT
1 TATA-TAT-TAT
1751240 TATATTATTAT
1 TATA-TATTAT
1751251 TAGTATATTAT
1 TA-TATATTAT
*
1751262 TATTTATTAT
1 TATATATTAT
1751272 TAT
1 TAT
1751275 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
9 4 0.10
10 12 0.31
11 15 0.38
12 8 0.21
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.61
Consensus pattern (10 bp):
TATATATTAT
Found at i:1751244 original size:21 final size:21
Alignment explanation
Indices: 1751219--1751273 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
1751209 TTTTGAAATA
1751219 TATATATTATATAGT-T-TCTAT
1 TATATATTAT-TAGTATAT-TAT
1751240 TATATTATTATTAGTATATTAT
1 TATA-TATTATTAGTATATTAT
*
1751262 TATTTATTATTA
1 TATATATTATTA
1751274 TTTTATTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
21 16 0.53
22 13 0.43
23 1 0.03
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (21 bp):
TATATATTATTAGTATATTAT
Found at i:1751250 original size:3 final size:3
Alignment explanation
Indices: 1751237--1751285 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
1751227 ATATAGTTTC
*
1751237 TAT TA- TAT TAT TAT TAG TA- TAT TAT TATT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
1751280 T-T TAT T
1 TAT TAT T
1751286 TACTTTATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
2 8 0.20
3 29 0.73
4 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1751285 original size:5 final size:5
Alignment explanation
Indices: 1751264--1751306 Score: 61
Period size: 5 Copynumber: 8.6 Consensus size: 5
1751254 TATATTATTA
*
1751264 TTTAT TATTAT TTTAT TTTA- TTTAC TTTAT TTTAT TTTAT TTT
1 TTTAT T-TTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1751307 TCTGGTCCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
4 4 0.11
5 26 0.74
6 5 0.14
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTAT
Done.