Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 6 of 255
Found at i:1701854 original size:16 final size:16
Alignment explanation
Indices: 1701829--1701859 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1701819 TTTAACATAT
*
1701829 AAAAATTATATAAAAG
1 AAAAAATATATAAAAG
1701845 AAAAAATATATAAAA
1 AAAAAATATATAAAA
1701860 ATTAGTTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (16 bp):
AAAAAATATATAAAAG
Found at i:1706014 original size:23 final size:23
Alignment explanation
Indices: 1705988--1706032 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
1705978 TAAAGAGAAA
1705988 AAACAGATTATGAATTGAAACTT
1 AAACAGATTATGAATTGAAACTT
1706011 AAACAGATTATGAATTGAAACT
1 AAACAGATTATGAATTGAAACT
1706033 AGGAAGAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.49, C:0.09, G:0.13, T:0.29
Consensus pattern (23 bp):
AAACAGATTATGAATTGAAACTT
Found at i:1714658 original size:58 final size:58
Alignment explanation
Indices: 1714566--1714703 Score: 159
Period size: 58 Copynumber: 2.4 Consensus size: 58
1714556 TCATCTTAGT
* * * * *
1714566 CCCTTTGTGAATCCTTTGGGCTCTCGACGAAGGTGAGGCATAACTTCTACATTTGGGC
1 CCCTTCGTGAACCCTTTGAGCTCTCAACGAAGGTGAGGCATAACTTCTACATTCGGGC
* * * *
1714624 CCCTTCGTGAACCCTTTGAGCTCTCAATGGAGGTGAGGCATATCTTCTACATTCGGGT
1 CCCTTCGTGAACCCTTTGAGCTCTCAACGAAGGTGAGGCATAACTTCTACATTCGGGC
* * **
1714682 CCCTCCATGAACTTTTTGAGCT
1 CCCTTCGTGAACCCTTTGAGCT
1714704 TTCGATAGAA
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
58 67 1.00
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.32
Consensus pattern (58 bp):
CCCTTCGTGAACCCTTTGAGCTCTCAACGAAGGTGAGGCATAACTTCTACATTCGGGC
Found at i:1714718 original size:58 final size:58
Alignment explanation
Indices: 1714598--1714729 Score: 156
Period size: 58 Copynumber: 2.3 Consensus size: 58
1714588 CTCGACGAAG
* * * * * *
1714598 GTGAGGCATAACTTCTACATTTGGGCCCCTTCGTGAACCCTTTGAGCTCTCAATGGAG
1 GTGAGGCATATCTTCTACATTCGGGCCCCTCCATGAACCCTTTGAGCTCTCAATAGAA
* ** * *
1714656 GTGAGGCATATCTTCTACATTCGGGTCCCTCCATGAACTTTTTGAGCTTTCGATAGAA
1 GTGAGGCATATCTTCTACATTCGGGCCCCTCCATGAACCCTTTGAGCTCTCAATAGAA
*
1714714 GTGAGACATATCTTCT
1 GTGAGGCATATCTTCT
1714730 TCATAAAAAT
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
58 62 1.00
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.33
Consensus pattern (58 bp):
GTGAGGCATATCTTCTACATTCGGGCCCCTCCATGAACCCTTTGAGCTCTCAATAGAA
Found at i:1716165 original size:14 final size:16
Alignment explanation
Indices: 1716128--1716166 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1716118 AATTGATAAA
*
1716128 TATTTTTTTTAATATC
1 TATTATTTTTAATATC
1716144 TATTATTTTTAATAT-
1 TATTATTTTTAATATC
1716159 T-TTATTTT
1 TATTATTTT
1716167 ACACCTACAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.32
15 1 0.05
16 14 0.64
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (16 bp):
TATTATTTTTAATATC
Found at i:1716369 original size:20 final size:20
Alignment explanation
Indices: 1716346--1716384 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1716336 AAATAATAAC
1716346 AACAAAAATAACGAAATGAT
1 AACAAAAATAACGAAATGAT
1716366 AACAAAAATAACGAAATGA
1 AACAAAAATAACGAAATGA
1716385 GGCTTTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.67, C:0.10, G:0.10, T:0.13
Consensus pattern (20 bp):
AACAAAAATAACGAAATGAT
Found at i:1717237 original size:79 final size:83
Alignment explanation
Indices: 1717134--1717294 Score: 217
Period size: 80 Copynumber: 2.0 Consensus size: 83
1717124 TTAACTCATA
*
1717134 AATAAATAAATAAAACCACAAATAATAT-AAAAATTTATATGTATA-TTTGCATTTTATA-TTCT
1 AATAAATAAATAAAACCACAAATAATATGAAAAATTTAAATGTATATTTTGCATTTTATACTT-T
1717196 -TTTTACAAAATAAGTGTG
65 GTTTTACAAAATAAGTGTG
* * **
1717214 AATAAA-AAATAAAATCATC-AATAATTTGAAATTTTTAAATGTATATTTTGCATTTTATACTTT
1 AATAAATAAATAAAACCA-CAAATAATATGAAAAATTTAAATGTATATTTTGCATTTTATACTTT
1717277 GTTTTACAAAATAAGTGT
65 GTTTTACAAAATAAGTGT
1717295 TAAGTATATA
Statistics
Matches: 71, Mismatches: 5, Indels: 8
0.85 0.06 0.10
Matches are distributed among these distances:
79 17 0.24
80 21 0.30
81 14 0.20
82 19 0.27
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (83 bp):
AATAAATAAATAAAACCACAAATAATATGAAAAATTTAAATGTATATTTTGCATTTTATACTTTG
TTTTACAAAATAAGTGTG
Found at i:1722151 original size:117 final size:116
Alignment explanation
Indices: 1721967--1722179 Score: 302
Period size: 117 Copynumber: 1.8 Consensus size: 116
1721957 TCCTTAGCTA
* * **
1721967 CATACAACTTTTGAGTTTGAGAAACATAACTGTATGAAGATATGTGGAGCAAATGGATCTCAATT
1 CATACAACATTTGAGTTTGAGAAACATAACTGTATGAAGAAACATGGAGCAAATGGATCTCAATT
1722032 TCAGGAGTCATTTCAGTTAGTGATTCAATTTGAATTAGAGAAATGTGGCTG
66 TCAGGAGTCATTTCAGTTAGTGATTCAATTTGAATTAGAGAAATGTGGCTG
* * * **
1722083 CATACAGCATTTGAGTTTGAGAAACATGAACTGTATGGAA-AAACATGGAGCAAATTGTTCTCGG
1 CATACAACATTTGAGTTTGAGAAACAT-AACTGTAT-GAAGAAACATGGAGCAAATGGATCTCAA
* *
1722147 TTTCAGGAGTCATTTCAGTTAGTGGTTTAATTT
64 TTTCAGGAGTCATTTCAGTTAGTGATTCAATTT
1722180 TGTCCTGAAA
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
116 25 0.30
117 56 0.67
118 3 0.04
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (116 bp):
CATACAACATTTGAGTTTGAGAAACATAACTGTATGAAGAAACATGGAGCAAATGGATCTCAATT
TCAGGAGTCATTTCAGTTAGTGATTCAATTTGAATTAGAGAAATGTGGCTG
Found at i:1727536 original size:48 final size:48
Alignment explanation
Indices: 1727465--1727562 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 48
1727455 AATGTTGAAG
*
1727465 ACATCATCTTTCTGTACCGGTACAATTCTGTTGCATTTATATCACGTT
1 ACATCATCTTTCTGTACCGGTACAATTCCGTTGCATTTATATCACGTT
* *
1727513 ACATCATCTTTCTGTATCGGTACAGTTCCGTTGCATTTATATCACGTT
1 ACATCATCTTTCTGTACCGGTACAATTCCGTTGCATTTATATCACGTT
1727561 AC
1 AC
1727563 CGGAATCACA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.41
Consensus pattern (48 bp):
ACATCATCTTTCTGTACCGGTACAATTCCGTTGCATTTATATCACGTT
Found at i:1735686 original size:64 final size:62
Alignment explanation
Indices: 1735573--1735693 Score: 172
Period size: 64 Copynumber: 1.9 Consensus size: 62
1735563 AGGTTTGATG
*
1735573 GGTGAGGAGTGAAATGAATGGTTGTGTTTTAATAGAAGGTTTCAAGGGTGAGAGATTTCTTA
1 GGTGAGGACTGAAATGAATGGTTGTGTTTTAATAGAAGGTTTCAAGGGTGAGAGATTTCTTA
* * *
1735635 GGTGAGGACTGAAATGAATGATTTTGTGCTTTT-ATAGAAGGTTTCATGGGTGATAGATT
1 GGTGAGGACTGAAATGAATG--GTTGTG-TTTTAATAGAAGGTTTCAAGGGTGAGAGATT
1735694 ACTTTTTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
62 19 0.37
64 29 0.56
65 4 0.08
ACGTcount: A:0.28, C:0.04, G:0.32, T:0.36
Consensus pattern (62 bp):
GGTGAGGACTGAAATGAATGGTTGTGTTTTAATAGAAGGTTTCAAGGGTGAGAGATTTCTTA
Found at i:1743183 original size:13 final size:14
Alignment explanation
Indices: 1743167--1743198 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1743157 TTATTATTAT
1743167 TATTATTA-GTTTG
1 TATTATTAGGTTTG
1743180 TATTATTAGGTTTG
1 TATTATTAGGTTTG
1743194 T-TTAT
1 TATTAT
1743199 GGGTCGAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (14 bp):
TATTATTAGGTTTG
Found at i:1746784 original size:16 final size:17
Alignment explanation
Indices: 1746765--1746802 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1746755 ATTGCATTTC
1746765 AATTTCA-AACCAAAAA
1 AATTTCAGAACCAAAAA
* *
1746781 AATTTCAGAACTATAAA
1 AATTTCAGAACCAAAAA
1746798 AATTT
1 AATTT
1746803 GAACGTAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.55, C:0.13, G:0.03, T:0.29
Consensus pattern (17 bp):
AATTTCAGAACCAAAAA
Found at i:1748869 original size:5 final size:5
Alignment explanation
Indices: 1748859--1748884 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1748849 ACTTTTATTA
1748859 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
1748885 TTTGGATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:1749502 original size:16 final size:15
Alignment explanation
Indices: 1749481--1749516 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
1749471 TAAATAATTT
1749481 AAAATTAAAAAATATA
1 AAAATTAAAAAA-ATA
*
1749497 AAAATTATAAAAATA
1 AAAATTAAAAAAATA
1749512 AAAAT
1 AAAAT
1749517 ATCATAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAATTAAAAAAATA
Found at i:1749514 original size:23 final size:24
Alignment explanation
Indices: 1749471--1749524 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
1749461 GTCAAGTCAG
*
1749471 TAAATAATTTAAAATTAAAAAATA
1 TAAATAATTTAAAAATAAAAAATA
1749495 TAAA-AATTATAAAAATAAAAATATCA
1 TAAATAATT-TAAAAATAAAAA-AT-A
1749521 TAAA
1 TAAA
1749525 GTGCACGTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 4 0.15
24 15 0.58
25 2 0.08
26 5 0.19
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (24 bp):
TAAATAATTTAAAAATAAAAAATA
Found at i:1749713 original size:20 final size:18
Alignment explanation
Indices: 1749688--1749725 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
1749678 TTATCATTAT
1749688 ACATATTATTTATTACAATA
1 ACATATT-TTTATT-CAATA
1749708 ACATATTTTTATTCAATA
1 ACATATTTTTATTCAATA
1749726 TTTTTTGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 6 0.33
20 7 0.39
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (18 bp):
ACATATTTTTATTCAATA
Found at i:1750396 original size:18 final size:17
Alignment explanation
Indices: 1750355--1750397 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
1750345 CCCTAAAATT
*
1750355 TAAAATTTTATATTATTT
1 TAAAA-TTTATATTATTA
*
1750373 TTAAATTTATATTATTAA
1 TAAAATTTATATTATT-A
1750391 TAAAATT
1 TAAAATT
1750398 CTTAATTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAAAATTTATATTATTA
Found at i:1751852 original size:16 final size:16
Alignment explanation
Indices: 1751833--1751864 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1751823 TCAATGCTTA
1751833 TTTCTAACGACTATTT
1 TTTCTAACGACTATTT
*
1751849 TTTCTAACGATTATTT
1 TTTCTAACGACTATTT
1751865 AATTAGTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.06, T:0.53
Consensus pattern (16 bp):
TTTCTAACGACTATTT
Found at i:1752300 original size:4 final size:4
Alignment explanation
Indices: 1752291--1752324 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
1752281 AAGTTTTATT
1752291 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA GTTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA
1752325 AATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:1752332 original size:22 final size:22
Alignment explanation
Indices: 1752274--1752333 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
1752264 AAGTGGCCCA
*
1752274 AGTTGTAAAGTTTTATTTTTATTT
1 AGTT-TAAATTTTTA-TTTTATTT
*
1752298 A-TTT-ATTTATTTATTTTATTT
1 AGTTTAAATT-TTTATTTTATTT
1752319 AGTTTAAATTTTTAT
1 AGTTTAAATTTTTAT
1752334 ATTCAGTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 11 0.37
22 13 0.43
23 5 0.17
24 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (22 bp):
AGTTTAAATTTTTATTTTATTT
Found at i:1753649 original size:20 final size:20
Alignment explanation
Indices: 1753621--1753664 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1753611 AAATTTATTA
1753621 AAAACTAAAGA-ATATATAAT
1 AAAACTAAA-ATATATATAAT
* *
1753641 AAAATTAAAATATTTATAAT
1 AAAACTAAAATATATATAAT
1753661 AAAA
1 AAAA
1753665 AACTCAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (20 bp):
AAAACTAAAATATATATAAT
Found at i:1755366 original size:12 final size:12
Alignment explanation
Indices: 1755351--1755379 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1755341 ACGAAGACTT
1755351 CGAGGAAGAAGA
1 CGAGGAAGAAGA
1755363 CGAGGAAGAAGA
1 CGAGGAAGAAGA
1755375 -GAGGA
1 CGAGGA
1755380 GGAGAGAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.48, C:0.07, G:0.45, T:0.00
Consensus pattern (12 bp):
CGAGGAAGAAGA
Found at i:1755562 original size:15 final size:15
Alignment explanation
Indices: 1755532--1755576 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
1755522 GGAGGAAGTG
* *
1755532 GAGGAGGAAGAAGAA
1 GAGGAAGAAGAGGAA
* *
1755547 GATGAAGATGAGGAA
1 GAGGAAGAAGAGGAA
1755562 GAGGAAGAAGAGGAA
1 GAGGAAGAAGAGGAA
1755577 AGTGAGAGAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.44, T:0.04
Consensus pattern (15 bp):
GAGGAAGAAGAGGAA
Found at i:1755582 original size:24 final size:23
Alignment explanation
Indices: 1755523--1755592 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 23
1755513 AACGGCGAAG
*
1755523 GAGGAAGTGGAGGAGGAAGAAGAA
1 GAGGAAGT-GAGGAAGAAGAAGAA
* *
1755547 GATGAAGATGAGGAAGAGGAAGAA
1 GAGGAAG-TGAGGAAGAAGAAGAA
1755571 GAGGAAAGTGAGAGAAGGAAGA
1 GAGG-AAGTGAG-GAA-GAAGA
1755593 GAAAGATTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
24 26 0.70
25 7 0.19
26 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.46, T:0.06
Consensus pattern (23 bp):
GAGGAAGTGAGGAAGAAGAAGAA
Found at i:1756054 original size:19 final size:18
Alignment explanation
Indices: 1756032--1756067 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
1756022 TCCCCTTTAG
1756032 CTGTCACTGTCTCCTGTCA
1 CTGTCACTGTCT-CTGTCA
1756051 CTGTCACTGTCTCTGTC
1 CTGTCACTGTCTCTGTC
1756068 TCATTCTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.08, C:0.36, G:0.17, T:0.39
Consensus pattern (18 bp):
CTGTCACTGTCTCTGTCA
Found at i:1766009 original size:29 final size:29
Alignment explanation
Indices: 1765967--1766024 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
1765957 GAAGTTAGAT
*
1765967 TGCATTTTGCCCTATCTACTCGAAACATA
1 TGCATTTTGCCCTATCTACTCAAAACATA
*
1765996 TGCATTTTGCCCTATTTACTCAAAACATA
1 TGCATTTTGCCCTATCTACTCAAAACATA
1766025 AGCAAAAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.36
Consensus pattern (29 bp):
TGCATTTTGCCCTATCTACTCAAAACATA
Found at i:1770715 original size:30 final size:30
Alignment explanation
Indices: 1770679--1770740 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1770669 AACACTGTTA
1770679 AAATCAGTTTGTTAAATTCAAATTCATTAC
1 AAATCAGTTTGTTAAATTCAAATTCATTAC
1770709 AAATCAGTTTGTTAAATTCAAATTCATTAC
1 AAATCAGTTTGTTAAATTCAAATTCATTAC
1770739 AA
1 AA
1770741 CGTGTCATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (30 bp):
AAATCAGTTTGTTAAATTCAAATTCATTAC
Found at i:1771241 original size:6 final size:6
Alignment explanation
Indices: 1771230--1771287 Score: 116
Period size: 6 Copynumber: 9.7 Consensus size: 6
1771220 GTGTTGGTGC
1771230 TGCTGG TGCTGG TGCTGG TGCTGG TGCTGG TGCTGG TGCTGG TGCTGG
1 TGCTGG TGCTGG TGCTGG TGCTGG TGCTGG TGCTGG TGCTGG TGCTGG
1771278 TGCTGG TGCT
1 TGCTGG TGCT
1771288 AGTTGATTCT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.00, C:0.17, G:0.48, T:0.34
Consensus pattern (6 bp):
TGCTGG
Found at i:1777612 original size:3 final size:3
Alignment explanation
Indices: 1777598--1777626 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1777588 TTATATGCAG
1777598 CAT CAT -AT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1777627 AATTATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
CAT
Found at i:1779560 original size:9 final size:9
Alignment explanation
Indices: 1779546--1779570 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1779536 CAATATAAAA
1779546 ATATATTAT
1 ATATATTAT
1779555 ATATATTAT
1 ATATATTAT
1779564 ATATATT
1 ATATATT
1779571 TATTTCGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
ATATATTAT
Found at i:1780674 original size:983 final size:957
Alignment explanation
Indices: 1778779--1780736 Score: 2373
Period size: 983 Copynumber: 2.0 Consensus size: 957
1778769 CTTCATGCAT
* * * *
1778779 ATTGTATAACATGTTTTTAAAATCGGATTGATGGTTAAATTGATCAGTTTATTGATTTTCAGTTT
1 ATTGTATAACATGTTTTTAAAATCGGATTAATGGCTAAATTGATCAATTTATTAATTTTCA---T
* *
1778844 GAAACTTTGAATAATTTAATTGGTTTATTCGGTTTAAATAAATAAATTATTTAAAATAAAAAAAT
63 G--A-TTTGAATAATTTAATTGGTCTATTCGGTTCAAATAAATAAATTATTTAAAAT-AAAAAA-
*
1778909 TATAAAAATTATAAAATCTAATTCTACCAATTTTTAACTCAAGTCAACTGATCTATTCCTGTTTG
123 TATAAAAATTATAAAATCTAATTCTACCAATTTTTAACTCAAGTCAACTGATCTATACCTGTTTG
* * * * *
1778974 TGAATCAATCAATTTTTTATCACTTTCTAAACTAATACCTCGATATGTTCTTAATCCAACCGACT
188 TGAATCAAACAATTTTTTATCACTCTCCAAACTAATACCTCGACATGTTCCTAATCCAACCGACT
* * * *
1779039 GATCTAGACTAATTCAAACATCACTTATTTCAAGCTGACAAAAAAAAATTGATCTAAAATAGACT
253 AATCCAGACTAATCCAAACATCACTTATTTCAAGCTCACAAAAAAAAATTGATCTAAAATAGACT
1779104 ATACCTGGTTTAGCTGGCCATCAAGTTTGCAACAAAATTTTGCTTCACAAAAATCCACATGTAAC
318 ATACCTGGTTTAGCTGGCCATCAAGTTTGCAACAAAATTTTGCTTCACAAAAATCCACATGTAAC
* *
1779169 ACGATAATTGCCTTGTCAGTTTCAAGAATTATTAGGGTTGGAAAAAAAAATCAAGAAATCTAAAA
383 ACAATAATTGCCTTGTCAGTTTCAAGAATTATTAGGGTTGGAAAAAAAAATCAACAAATCTAAAA
* * * * * *
1779234 CTGATCTGAATAATTAAGGGTGTTTAAATGGTTAGTTTAGTTATTACTCGAATTGAATTATTATT
448 CTGATCTGAATAAATAAGGGTGCTCAAATGATCAGTTTAGTTATTA-TC-AATCGAA-TATTATT
* * ** * *
1779299 AATTGAATTATTTGATATGTAAAAATTTTTAACTGTTAACTGAATCGATTTTTTTTAAATATATT
510 -ACTGAA-TA--T-ATA-GTAAAAATCTTTAACCATTAACTGAATCAATTTTTTTTAAATACATT
* *
1779364 AACCGAACTGAAATATTTCGGTTAACCAAATTAACTAAAATTTTAATAAGTATAAAATATATAAA
569 AACCGAACCGAAATATTTCGGTTAACCAAATTAACTAAAATTTTAATAAGTATAAAACATATAAA
*
1779429 AATACATTGTTAATGTTCATTTTTTAATCGTTAAAAAAATATATTATATATAATATATATTTTTA
634 AATACATTGTTAATGTTCATTTTTTAATAGTTAAAAAAATATATTATATATAATATATATTTTTA
*
1779494 TTTCGATTAATATAAAAAATAATAGTCCAGAAAATACATTGTCAATATAAAAATATATTATATAT
699 TTTCGATTAATATAAAAAATAATAGTCCAAAAAATACATTGTCAATATAAAAATATATTATATAT
*
1779559 ATTATATATATTTATTTCGTTTAATTACCTGATTTCAAATCGAATTAACCGATAATCAAAATTTC
764 ATTATATATATTTATTTCGGTTAATTACCTGATTTCAAATCGAATTAACCGATAATCAAAATTTC
* * ** * * * **
1779624 AATAAATTATTAATTGGCCTTCGACCGAACTAAATTTGGCCATCGACCGATTAACCGAATTAGAT
829 AAAAAATCATTAACCGACCTCCAACCGAACTAAATTCAGCCATCGACCGATTAACCGAATTAGAT
* ** *
1779689 CGATTCAATTGATCAATTCGGCTTTAACCAAACTATGAACACCCCTATGAATAAGTAGTGTTTA
894 CGATTCAATCGATCAATTCAACTTTAACCAAACTATGAACACCCCTATGAATAAGTAGTATTTA
* *
1779753 ATTGTATAACATGTTTTTGAAATCGGATTAATGGCTAAATTGGTCAATTTATTAATTTTCA-G-T
1 ATTGTATAACATGTTTTTAAAATCGGATTAATGGCTAAATTGATCAATTTATTAATTTTCATGAT
*
1779816 TTGAATAATTTAATTGGTCTATTCGGTTCAAAGTAAATAAATTCTTTAAAAT-AAAAA-A-AAAA
66 TTGAATAATTTAATTGGTCTATTCGGTTCAAA-TAAATAAATTATTTAAAATAAAAAATATAAAA
** * * * * *
1779878 A-T-TAAAATCTGGTTCTACCAATTTTTTTAACTCGATTCAATTGATCTGTACCTGTTTGTGAGT
130 ATTATAAAATCTAATTCTACCAA--TTTTTAACTCAAGTCAACTGATCTATACCTGTTTGTGAAT
* *
1779941 CAAACATTTTTTTATCACTCTCCAAATTAATACCTCGACATGTTCCTAATCCAACCGACTAATCC
193 CAAACAATTTTTTATCACTCTCCAAACTAATACCTCGACATGTTCCTAATCCAACCGACTAATCC
* * *
1780006 AGTCTAATCCAAACATCACTTATTTCAAGTTCACAAAGAAAAATTGATCTAAAATAGACTATACC
258 AGACTAATCCAAACATCACTTATTTCAAGCTCACAAAAAAAAATTGATCTAAAATAGACTATACC
1780071 TGGATTATAGACAAGCTGGCCATCAAGTTTGCAACAAAATTTTGCTTCACAAAATTGTGATTGAT
323 TGG-TT-T-----AGCTGGCCATCAAGTTTGCAACAAAATTTTGCTTCAC--AA-----A---A-
* *
1780136 TTTCACCTCCACATGT-ACACAATAATTTCCTTGTTAGTTTCAAGAATTATTAGGGTTGG-AAAA
370 ----A--TCCACATGTAACACAATAATTGCCTTGTCAGTTTCAAGAATTATTAGGGTTGGAAAAA
* * *
1780199 AAAATCAACAAATCTAAAA-TCGATTTGAATAAATAGGGGTGCTCAAATGATCGGTTTAGTTA-T
429 AAAATCAACAAATCTAAAACT-GATCTGAATAAATAAGGGTGCTCAAATGATCAGTTTAGTTATT
* * *
1780262 -T-AATCG-A-ATTA-T-CTG-A-A-ATA-TAAAAGTCTTTAACCATT-AGTCGAATTAATTTTT
493 ATCAATCGAATATTATTACTGAATATATAGTAAAAATCTTTAACCATTAACT-GAATCAATTTTT
*
1780316 TTTCAAATACATTAACCGAACCGAAATATTTCGGTTAACCGAATTAACTAAATTTTTTTTTGTCT
557 TTT-AAATACATTAACCGAACCGAAATATTTCGGTTAACCAAATTAACTAAA-------------
* * *
1780381 TTTAGTTAAAATAAGTATAAAACATATAAAACATATATTGTTAATGTTCATTTTTTAATAGTTTA
608 ATT--TT--AATAAGTATAAAACATATAAAA-ATACATTGTTAATGTTCATTTTTTAATAGTTAA
*
1780446 AAAAATATATTATATATAATATATATTATTTATTTCGATTAATAT-AAAAA-AATAGTTCAAAAA
668 AAAAATATATTATATATAATATATATT-TTTATTTCGATTAATATAAAAAATAATAGTCCAAAAA
*
1780509 ATACATTG-CTAATATAAAAAATATATTATATATGTTATATATATTTATTTCGGTTAATTACCTG
732 ATACATTGTC-AATAT-AAAAATATATTATATATATTATATATATTTATTTCGGTTAATTACCTG
*
1780573 ATTTCAAATCGAATTAACCGATAATCAAAATTTTAAAAAATCATTAACCGACCTCCAACCGAACT
795 ATTTCAAATCGAATTAACCGATAATCAAAATTTCAAAAAATCATTAACCGACCTCCAACCGAACT
* ** * * *
1780638 AAATTCAGCTATCGACTTATTAACCGAATTAGATCGATTTAGTCGATCAATTCAATTTTAACCAA
860 AAATTCAGCCATCGACCGATTAACCGAATTAGATCGATTCAATCGATCAATTCAACTTTAACCAA
1780703 ACTATGAACACCCCTATGAATAAGTAGTATTTA
925 ACTATGAACACCCCTATGAATAAGTAGTATTTA
1780736 A
1 A
1780737 ATGGTTTAAA
Statistics
Matches: 849, Mismatches: 84, Indels: 93
0.83 0.08 0.09
Matches are distributed among these distances:
960 17 0.02
961 1 0.00
962 158 0.19
963 5 0.01
964 28 0.03
965 50 0.06
966 34 0.04
967 18 0.02
969 37 0.04
970 2 0.00
971 2 0.00
972 1 0.00
973 2 0.00
974 55 0.06
975 1 0.00
976 5 0.01
978 3 0.00
979 5 0.01
980 2 0.00
981 2 0.00
982 45 0.05
983 254 0.30
984 73 0.09
985 40 0.05
986 9 0.01
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (957 bp):
ATTGTATAACATGTTTTTAAAATCGGATTAATGGCTAAATTGATCAATTTATTAATTTTCATGAT
TTGAATAATTTAATTGGTCTATTCGGTTCAAATAAATAAATTATTTAAAATAAAAAATATAAAAA
TTATAAAATCTAATTCTACCAATTTTTAACTCAAGTCAACTGATCTATACCTGTTTGTGAATCAA
ACAATTTTTTATCACTCTCCAAACTAATACCTCGACATGTTCCTAATCCAACCGACTAATCCAGA
CTAATCCAAACATCACTTATTTCAAGCTCACAAAAAAAAATTGATCTAAAATAGACTATACCTGG
TTTAGCTGGCCATCAAGTTTGCAACAAAATTTTGCTTCACAAAAATCCACATGTAACACAATAAT
TGCCTTGTCAGTTTCAAGAATTATTAGGGTTGGAAAAAAAAATCAACAAATCTAAAACTGATCTG
AATAAATAAGGGTGCTCAAATGATCAGTTTAGTTATTATCAATCGAATATTATTACTGAATATAT
AGTAAAAATCTTTAACCATTAACTGAATCAATTTTTTTTAAATACATTAACCGAACCGAAATATT
TCGGTTAACCAAATTAACTAAAATTTTAATAAGTATAAAACATATAAAAATACATTGTTAATGTT
CATTTTTTAATAGTTAAAAAAATATATTATATATAATATATATTTTTATTTCGATTAATATAAAA
AATAATAGTCCAAAAAATACATTGTCAATATAAAAATATATTATATATATTATATATATTTATTT
CGGTTAATTACCTGATTTCAAATCGAATTAACCGATAATCAAAATTTCAAAAAATCATTAACCGA
CCTCCAACCGAACTAAATTCAGCCATCGACCGATTAACCGAATTAGATCGATTCAATCGATCAAT
TCAACTTTAACCAAACTATGAACACCCCTATGAATAAGTAGTATTTA
Found at i:1782246 original size:7 final size:7
Alignment explanation
Indices: 1782234--1782277 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
1782224 CTAAAACTAC
1782234 CACTTAT
1 CACTTAT
1782241 CACTTAT
1 CACTTAT
*
1782248 CACTTGT
1 CACTTAT
* *
1782255 CGCTTGT
1 CACTTAT
1782262 CACTTAT
1 CACTTAT
*
1782269 CACTGAT
1 CACTTAT
1782276 CA
1 CA
1782278 GATAAGTGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.23, C:0.30, G:0.09, T:0.39
Consensus pattern (7 bp):
CACTTAT
Found at i:1782993 original size:180 final size:180
Alignment explanation
Indices: 1782752--1783125 Score: 739
Period size: 180 Copynumber: 2.1 Consensus size: 180
1782742 AATTTTACCT
1782752 GAAACTAGACTCATATATCTTCTTATCATAAAATTTTTAGAATTTTTGGTTTAGCCAATAAGTAC
1 GAAA-TAGACTCATATATCTTCTTATCATAAAATTTTTAGAATTTTTGGTTTAGCCAATAAGTAC
1782817 AGTTTATTCTTTAAAGTCACCCTTGTTCTGCTGTCTAACAATTCCGACCCTTCTTCACTAAAAAT
65 AGTTTATTCTTTAAAGTCACCCTTGTTCTGCTGTCTAACAATTCCGACCCTTCTTCACTAAAAAT
1782882 TAATTATCTCTTCGTACAGAATTCGGATGATGTCCATGTTTGTTTCTATTG
130 TAATTATCTCTTCGTACAGAATTCGGATGATGTCCATGTTTGTTTCTATTG
1782933 GAAATAGACTCATATATCTTCTTATCATAAAATTTTTAGAATTTTTGGTTTAGCCAATAAGTACA
1 GAAATAGACTCATATATCTTCTTATCATAAAATTTTTAGAATTTTTGGTTTAGCCAATAAGTACA
1782998 GTTTATTCTTTAAAGTCACCCTTGTTCTGCTGTCTAACAATTCCGACCCTTCTTCACTAAAAATT
66 GTTTATTCTTTAAAGTCACCCTTGTTCTGCTGTCTAACAATTCCGACCCTTCTTCACTAAAAATT
1783063 AATTATCTCTTCGTACAGAATTCGGATGATGTCCATGTTTGTTTCTATTG
131 AATTATCTCTTCGTACAGAATTCGGATGATGTCCATGTTTGTTTCTATTG
1783113 GAAATAGACTCAT
1 GAAATAGACTCAT
1783126 TAAGGATTTT
Statistics
Matches: 193, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
180 189 0.98
181 4 0.02
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.40
Consensus pattern (180 bp):
GAAATAGACTCATATATCTTCTTATCATAAAATTTTTAGAATTTTTGGTTTAGCCAATAAGTACA
GTTTATTCTTTAAAGTCACCCTTGTTCTGCTGTCTAACAATTCCGACCCTTCTTCACTAAAAATT
AATTATCTCTTCGTACAGAATTCGGATGATGTCCATGTTTGTTTCTATTG
Found at i:1785982 original size:272 final size:271
Alignment explanation
Indices: 1785485--1786027 Score: 736
Period size: 272 Copynumber: 2.0 Consensus size: 271
1785475 TTAATAATTT
* * * * *
1785485 AATTGGCACGGGTTCAAGTCCCATCGTATGTATATTTTTTAATTGGTTTTGCTAAAATGAAAAGA
1 AATTGGCACGGGGTCAAATCCCACCATATGCATATTTTTTAATTGGTTTTGCTAAAATGAAAAGA
* * * **
1785550 TTAAAATACCCTTGACTAATATAACTTTTTTTAATTACGAAAAGACATTTCCGTAATTTTTTGCC
66 TTAAAATACCCTTAAATAATATAACTCTTTTTAATTACGAAAAGACATTTCCGTAATTTTTAACC
* * * * * *
1785615 TGAGTTGGTGACTATGTTGAGGGTGACACCAATTTAGCCAGGGGCTTAATAAATAGTAAGTATGG
131 TGAGTTGGTGACTAGGTTGAGGGTGACACCAACTCAGCCAAGGGCTCAATAAATAGTAAGTATAG
* *
1785680 ATATACAACTGATGAAAATAATATATTGTGCATATTAAAACCAAAATGTATAAAAATACATTAAA
196 ATATAAAACTGATGAAAATAATAAATTGTGCATATTAAAACCAAAATGTAT-AAAATACATTAAA
1785745 ATA-ATGCTTTGG
260 ATAGA-GCTTTGG
*
1785757 AATTGGCA-GAGGGTCAAATCCCACCATATGCATATTTTTTAATTGGTTTTTGTTAAAATGAAAA
1 AATTGGCACG-GGGTCAAATCCCACCATATGCATATTTTTTAATTGG-TTTTGCTAAAATGAAAA
* * * *
1785821 TATTAAAATACCCTTAAATGATATAAC-CTTTTTAATTACG-AAAGAATATTTTCGTAATTTCTT
64 GATTAAAATACCCTTAAATAATATAACTCTTTTTAATTACGAAAAG-ACATTTCCGTAATTT-TT
* * *
1785884 AACC-GAGTTGGTGACTCGGTTGAGGGTGACACCAACTCAGTCAAGGGCTCAATACATAGTAAGT
127 AACCTGAGTTGGTGACTAGGTTGAGGGTGACACCAACTCAGCCAAGGGCTCAATAAATAGTAAGT
* * *
1785948 ATAGATATAAAAGTGATGAAGATAATAAATTGTGCATATTAAAACCAAAATGTATAAAATATATT
192 ATAGATATAAAACTGATGAAAATAATAAATTGTGCATATTAAAACCAAAATGTATAAAATACATT
1786013 AAAATAGAGCTTTGG
257 AAAATAGAGCTTTGG
1786028 TTGAGTGATG
Statistics
Matches: 237, Mismatches: 29, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
271 27 0.11
272 167 0.70
273 43 0.18
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.34
Consensus pattern (271 bp):
AATTGGCACGGGGTCAAATCCCACCATATGCATATTTTTTAATTGGTTTTGCTAAAATGAAAAGA
TTAAAATACCCTTAAATAATATAACTCTTTTTAATTACGAAAAGACATTTCCGTAATTTTTAACC
TGAGTTGGTGACTAGGTTGAGGGTGACACCAACTCAGCCAAGGGCTCAATAAATAGTAAGTATAG
ATATAAAACTGATGAAAATAATAAATTGTGCATATTAAAACCAAAATGTATAAAATACATTAAAA
TAGAGCTTTGG
Found at i:1786513 original size:29 final size:29
Alignment explanation
Indices: 1786464--1786521 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
1786454 TTTTGTCATT
1786464 CAACTATAAAAAATTACAAAATAATCACC
1 CAACTATAAAAAATTACAAAATAATCACC
* * *
1786493 CAACTATGAAAAGTTGA-AAAATGATCACC
1 CAACTATAAAAAATT-ACAAAATAATCACC
1786522 TAGCTATTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 24 0.96
30 1 0.04
ACGTcount: A:0.53, C:0.19, G:0.07, T:0.21
Consensus pattern (29 bp):
CAACTATAAAAAATTACAAAATAATCACC
Found at i:1791135 original size:30 final size:30
Alignment explanation
Indices: 1791061--1791136 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
1791051 GCCCAGAATA
* *
1791061 CCACACGCCCGTATGGTCTACCCGTGTGAC
1 CCACACGCCCGTGTGGTCCACCCGTGTGAC
*
1791091 CCACACGCCCGTGTGGTCCACCTGTGTGAC
1 CCACACGCCCGTGTGGTCCACCCGTGTGAC
* *
1791121 CCATACGCCTGTGTGG
1 CCACACGCCCGTGTGG
1791137 CCTACACGGC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.14, C:0.38, G:0.26, T:0.21
Consensus pattern (30 bp):
CCACACGCCCGTGTGGTCCACCCGTGTGAC
Found at i:1793955 original size:42 final size:42
Alignment explanation
Indices: 1793908--1793991 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
1793898 TCACCACCCA
1793908 TTCAAACCCACCCTAAGTATATCTAATAGATATCTAATAAGT
1 TTCAAACCCACCCTAAGTATATCTAATAGATATCTAATAAGT
1793950 TTCAAACCCACCCTAAGTATATCTAATAGATATCTAATAAGT
1 TTCAAACCCACCCTAAGTATATCTAATAGATATCTAATAAGT
1793992 GCAAGGAATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.31
Consensus pattern (42 bp):
TTCAAACCCACCCTAAGTATATCTAATAGATATCTAATAAGT
Found at i:1794869 original size:13 final size:13
Alignment explanation
Indices: 1794851--1794876 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1794841 AAATAATTTA
1794851 AAATTTAAAAAAT
1 AAATTTAAAAAAT
1794864 AAATTTAAAAAAT
1 AAATTTAAAAAAT
1794877 TAATACAAAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATTTAAAAAAT
Found at i:1795208 original size:30 final size:30
Alignment explanation
Indices: 1795174--1795233 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1795164 AGACAGTGAG
1795174 AGCCTTATATAATTGACCTCAGCTTTCCTC
1 AGCCTTATATAATTGACCTCAGCTTTCCTC
*
1795204 AGCCTTGTATAATTGACCTCAGCTTTCCTC
1 AGCCTTATATAATTGACCTCAGCTTTCCTC
1795234 TTCTTCAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.22, C:0.30, G:0.12, T:0.37
Consensus pattern (30 bp):
AGCCTTATATAATTGACCTCAGCTTTCCTC
Found at i:1797103 original size:31 final size:32
Alignment explanation
Indices: 1797034--1797106 Score: 89
Period size: 31 Copynumber: 2.3 Consensus size: 32
1797024 AAAAAATTAC
*
1797034 CAACTTTTAAGGGGCTCCAAAATTATTTTTTT
1 CAACTTTTAAGGGACTCCAAAATTATTTTTTT
* *
1797066 -AGCTTTTAAGGGAC-CTAAAATT-TTTTTCTT
1 CAACTTTTAAGGGACTCCAAAATTATTTTT-TT
1797096 CAACTTTTAAG
1 CAACTTTTAAG
1797107 AAATCTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 5 0.14
30 9 0.26
31 21 0.60
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (32 bp):
CAACTTTTAAGGGACTCCAAAATTATTTTTTT
Found at i:1798393 original size:15 final size:15
Alignment explanation
Indices: 1798373--1798427 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
1798363 TTCAATATTT
1798373 ATATTTTAATAATAA
1 ATATTTTAATAATAA
*
1798388 ATATTTATTCAATTATAA
1 ATA-TT-TT-AATAATAA
*
1798406 ATATATTAATAATAA
1 ATATTTTAATAATAA
*
1798421 ATGTTTT
1 ATATTTT
1798428 GTAGTATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 15 0.47
16 4 0.12
17 3 0.09
18 10 0.31
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (15 bp):
ATATTTTAATAATAA
Found at i:1820113 original size:23 final size:23
Alignment explanation
Indices: 1820087--1820142 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
1820077 TTCTAAATTT
*
1820087 AAGGAAATATGTCAGTGATTTTG
1 AAGGAAATACGTCAGTGATTTTG
**
1820110 AAGGAAATACGTTGGTGATTTTG
1 AAGGAAATACGTCAGTGATTTTG
1820133 AAGAGAAATA
1 AAG-GAAATA
1820143 GAAAATGCGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 23 0.79
24 6 0.21
ACGTcount: A:0.39, C:0.04, G:0.27, T:0.30
Consensus pattern (23 bp):
AAGGAAATACGTCAGTGATTTTG
Found at i:1820522 original size:25 final size:26
Alignment explanation
Indices: 1820458--1820522 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
1820448 TTCTAATTTT
* *
1820458 CTATTTCACTTTCTTGTTTTTTTTTTC
1 CTATTTCACTTT-TTGTTTATTCTTTC
* *
1820485 CTTTTTCCCTTTTT-TTTATTCTTTC
1 CTATTTCACTTTTTGTTTATTCTTTC
*
1820510 CTATTTCAATTTT
1 CTATTTCACTTTT
1820523 ATTTCTTTCT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
25 19 0.61
26 2 0.06
27 10 0.32
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.69
Consensus pattern (26 bp):
CTATTTCACTTTTTGTTTATTCTTTC
Found at i:1823758 original size:22 final size:22
Alignment explanation
Indices: 1823715--1823759 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1823705 TGTAACAAAA
***
1823715 TTTTAATTTAACATGTTTAATT
1 TTTTAATTTAACATGAACAATT
*
1823737 TTTTAATTTAACTTGAACAATT
1 TTTTAATTTAACATGAACAATT
1823759 T
1 T
1823760 CACTCGATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (22 bp):
TTTTAATTTAACATGAACAATT
Found at i:1824612 original size:18 final size:18
Alignment explanation
Indices: 1824580--1824629 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
1824570 TTTTTATTTA
**
1824580 CTTTTTTTAACTTTTATC
1 CTTTTTTTATTTTTTATC
1824598 CTTTTTTTATTTTTTTATC
1 CTTTTTTTA-TTTTTTATC
*
1824617 C-TTATTTATTTTT
1 CTTTTTTTATTTTT
1824630 ATTTATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 5 0.18
18 15 0.54
19 8 0.29
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.74
Consensus pattern (18 bp):
CTTTTTTTATTTTTTATC
Found at i:1824613 original size:19 final size:18
Alignment explanation
Indices: 1824591--1824629 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
1824581 TTTTTTTAAC
*
1824591 TTTTATCCTTTTTTTATTT
1 TTTTATCC-TTATTTATTT
1824610 TTTTATCCTTATTTATTT
1 TTTTATCCTTATTTATTT
1824628 TT
1 TT
1824630 ATTTATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTATCCTTATTTATTT
Found at i:1824690 original size:23 final size:21
Alignment explanation
Indices: 1824658--1824714 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 21
1824648 AAAAAACTTG
*
1824658 AAATGTATATTTGAAATATTTT
1 AAATATATATTTGAAA-ATTTT
**
1824680 ATAATATATATTTTTTAAATTTT
1 A-AATATATA-TTTGAAAATTTT
1824703 AAATATATATTT
1 AAATATATATTT
1824715 TTGAAATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 3 0.10
22 9 0.30
23 13 0.43
24 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (21 bp):
AAATATATATTTGAAAATTTT
Found at i:1824710 original size:22 final size:23
Alignment explanation
Indices: 1824675--1824722 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
1824665 TATTTGAAAT
*
1824675 ATTTTATAATATATATTTTTTAA
1 ATTTTATAATATATATTTTTGAA
1824698 ATTTTA-AATATATATTTTTGAA
1 ATTTTATAATATATATTTTTGAA
1824720 ATT
1 ATT
1824723 ATTTTTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
ATTTTATAATATATATTTTTGAA
Found at i:1824714 original size:36 final size:34
Alignment explanation
Indices: 1824673--1824758 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 34
1824663 TATATTTGAA
1824673 ATATTTTATAATATATATTTTTTAAATTTTAAATAT
1 ATATTTT-TAA-ATATATTTTTTAAATTTTAAATAT
*
1824709 ATATTTTTGAAATTATTTTTTTTAAATTTTAAATAT
1 ATATTTTT-AAA-TATATTTTTTAAATTTTAAATAT
1824745 -TATTTTTTAAATAT
1 ATA-TTTTTAAATAT
1824759 TAAATATATT
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
34 3 0.07
35 7 0.15
36 36 0.78
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (34 bp):
ATATTTTTAAATATATTTTTTAAATTTTAAATAT
Found at i:1824750 original size:21 final size:21
Alignment explanation
Indices: 1824713--1825068 Score: 133
Period size: 21 Copynumber: 16.0 Consensus size: 21
1824703 AAATATATAT
1824713 TTTTGAAATTATT-TTTTTTAAA
1 TTTT-AAA-TATTATTTTTTAAA
1824735 TTTTAAATATTATTTTTTAAA
1 TTTTAAATATTATTTTTTAAA
*
1824756 TATTAAATA-TATTTTTTAATA
1 TTTTAAATATTATTTTTTAA-A
* * *
1824777 ATATAAA-A-TA--TTTAAATA
1 TTTTAAATATTATTTTTTAA-A
** *
1824795 TTTTAAATATATGAACTTTCAAA
1 TTTTAAATAT-T-ATTTTTTAAA
* *
1824818 -TTT-ATTATTAGTTTTATAATA
1 TTTTAAATATTA-TTTTTTAA-A
* *
1824839 TTTTAAAT-GTATATTTTAAA
1 TTTTAAATATTATTTTTTAAA
* **
1824859 TTTTAAATATTTTTTAATTTATTT
1 TTTTAAATATTATTT--TTTA-AA
*
1824883 TTTTAAATATTAAATATATTTT-AT
1 TTTTAAATATT--AT-T-TTTTAAA
* *
1824907 TTATTTATTATTATTAATTTTAAAAAA
1 TT-TTAAATATTATT--TTTT---AAA
* * **
1824934 TTTGAAATGTGTA-TTTGAAATA
1 TTTTAAATAT-TATTTTTTAA-A
1824956 TTTTATAATATATATTTTTTAAAA
1 TTTTA-AATAT-TATTTTTT-AAA
1824980 TTTTAAATACATATTATTATTTTTAAA
1 TTTT--A-A-ATATTA-T-TTTTTAAA
1825007 TTTTAAATATATATTTTTTAAA
1 TTTTAAATAT-TATTTTTTAAA
1825029 TTTTAAATATTATTTTTTAAA
1 TTTTAAATATTATTTTTTAAA
*
1825050 TGTTAAATA-TATTTTTTAA
1 TTTTAAATATTATTTTTTAA
1825069 TAATATAAAA
Statistics
Matches: 258, Mismatches: 39, Indels: 76
0.69 0.10 0.20
Matches are distributed among these distances:
18 12 0.05
19 2 0.01
20 41 0.16
21 61 0.24
22 37 0.14
23 25 0.10
24 32 0.12
25 10 0.04
26 14 0.05
27 18 0.07
28 6 0.02
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.57
Consensus pattern (21 bp):
TTTTAAATATTATTTTTTAAA
Found at i:1824780 original size:22 final size:20
Alignment explanation
Indices: 1824685--1824774 Score: 100
Period size: 21 Copynumber: 4.7 Consensus size: 20
1824675 ATTTTATAAT
*
1824685 ATATATTTTTTAAATTTTAA
1 ATATATTTTTTAAATATTAA
*
1824705 ATATATATTTTTGAA-ATT--
1 ATATAT-TTTTTAAATATTAA
*
1824723 AT-T-TTTTTTAAATTTTAA
1 ATATATTTTTTAAATATTAA
1824741 ATATTATTTTTTAAATATTAA
1 ATA-TATTTTTTAAATATTAA
1824762 ATATATTTTTTAA
1 ATATATTTTTTAA
1824775 TAATATAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 14
0.75 0.06 0.18
Matches are distributed among these distances:
15 7 0.12
16 3 0.05
17 1 0.02
18 4 0.07
20 19 0.33
21 24 0.41
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (20 bp):
ATATATTTTTTAAATATTAA
Found at i:1824785 original size:22 final size:20
Alignment explanation
Indices: 1824679--1824787 Score: 77
Period size: 22 Copynumber: 5.5 Consensus size: 20
1824669 TGAAATATTT
*
1824679 TATAATATATATTTTTTAAA
1 TATAAAATATATTTTTTAAA
* *
1824699 TTTTAAATATATATTTTTGAAA
1 -TATAAA-ATATATTTTTTAAA
1824721 T-T---AT-T-TTTTTTAAA
1 TATAAAATATATTTTTTAAA
* *
1824735 TTTTAAATATTATTTTTTAAA
1 TATAAAATA-TATTTTTTAAA
*
1824756 TATTAAATATATTTTTTAATAA
1 TATAAAATATATTTTTT-A-AA
1824778 TATAAAATAT
1 TATAAAATAT
1824788 TTAAATATTT
Statistics
Matches: 72, Mismatches: 6, Indels: 19
0.74 0.06 0.20
Matches are distributed among these distances:
14 9 0.12
15 2 0.03
16 2 0.03
18 2 0.03
20 10 0.14
21 23 0.32
22 24 0.33
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (20 bp):
TATAAAATATATTTTTTAAA
Found at i:1824887 original size:31 final size:31
Alignment explanation
Indices: 1824850--1824930 Score: 101
Period size: 31 Copynumber: 2.5 Consensus size: 31
1824840 TTTAAATGTA
*
1824850 TATTTTAAATTTTAAATATTTTTTAATTTATT
1 TATTTTAAATTTTAAATATATTTT-ATTTATT
*
1824882 T-TTTTAAATATTAAATATATTTTATTTATT
1 TATTTTAAATTTTAAATATATTTTATTTATT
1824912 TATTATTATTAATTTTAAA
1 TATT-TTA--AATTTTAAA
1824931 AAATTTGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 8 0.19
31 22 0.52
32 4 0.10
34 8 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (31 bp):
TATTTTAAATTTTAAATATATTTTATTTATT
Found at i:1825002 original size:27 final size:24
Alignment explanation
Indices: 1824960--1825066 Score: 111
Period size: 22 Copynumber: 4.5 Consensus size: 24
1824950 GAAATATTTT
1824960 ATAATATATATTTTTTAAAATTTTAA
1 ATAATAT-TATTTTTT-AAATTTTAA
1824986 ATACATATTATTATTTTTAAATTTTAA
1 ATA-ATATTA-T-TTTTTAAATTTTAA
1825013 AT-ATA-TATTTTTTAAATTTT--
1 ATAATATTATTTTTTAAATTTTAA
*
1825033 A-AATATTATTTTTTAAATGTTAA
1 ATAATATTATTTTTTAAATTTTAA
1825056 AT-ATATT-TTTT
1 ATAATATTATTTT
1825067 AATAATATAA
Statistics
Matches: 72, Mismatches: 1, Indels: 20
0.77 0.01 0.22
Matches are distributed among these distances:
20 4 0.06
21 14 0.19
22 16 0.22
23 7 0.10
24 2 0.03
25 3 0.04
26 5 0.07
27 16 0.22
28 5 0.07
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (24 bp):
ATAATATTATTTTTTAAATTTTAA
Found at i:1825024 original size:22 final size:22
Alignment explanation
Indices: 1824955--1825066 Score: 138
Period size: 21 Copynumber: 4.9 Consensus size: 22
1824945 TATTTGAAAT
1824955 ATTTTATAATATATATTTTTTAAA
1 ATTTTA-AATATATATTTTTT-AA
1824979 ATTTTAAATACATATTATTATTTTTAA
1 ATTTTAAAT--ATA-TA-T-TTTTTAA
1825006 ATTTTAAATATATATTTTTTAA
1 ATTTTAAATATATATTTTTTAA
1825028 ATTTTAAATAT-TATTTTTTAA
1 ATTTTAAATATATATTTTTTAA
*
1825049 ATGTTAAATATAT-TTTTT
1 ATTTTAAATATATATTTTT
1825067 AATAATATAA
Statistics
Matches: 81, Mismatches: 1, Indels: 15
0.84 0.01 0.15
Matches are distributed among these distances:
21 25 0.31
22 19 0.23
23 4 0.05
24 8 0.10
25 6 0.07
26 2 0.02
27 12 0.15
28 5 0.06
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (22 bp):
ATTTTAAATATATATTTTTTAA
Found at i:1825265 original size:23 final size:24
Alignment explanation
Indices: 1825234--1825304 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 24
1825224 TATATTTTAA
*
1825234 ATATTTTTAAAAATTTTAAAA-AT
1 ATATATTTAAAAATTTTAAAATAT
1825257 ATATATTT-AAAA-TTTAAAATAT
1 ATATATTTAAAAATTTTAAAATAT
*
1825279 ATATATTATAAAACA-TTTCAAATAT
1 ATATATT-TAAAA-ATTTTAAAATAT
1825304 A
1 A
1825305 CATTTCAAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.17
22 13 0.31
23 8 0.19
24 3 0.07
25 11 0.26
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (24 bp):
ATATATTTAAAAATTTTAAAATAT
Found at i:1825322 original size:294 final size:291
Alignment explanation
Indices: 1824718--1825309 Score: 755
Period size: 294 Copynumber: 2.0 Consensus size: 291
1824708 TATATTTTTG
*
1824718 AAAT-TATTTTTTTTAAATTTTAAATATTATTTTTTAAATATTAAATATATTTTTTAATAATATA
1 AAATATATATTTTTTAAATTTTAAATATTATTTTTTAAATATTAAATATATTTTTTAATAATATA
*
1824782 AAATATTTAAATATTTTAAATATATGAACTTTCAAATTTATTATTAGTTTTATAATATTTTAAAT
66 AAACATTTAAATATTTTAAATATATGAACTTTCAAATTTATTATTAGTTTTATAATATTTTAAAT
* * * *
1824847 GTATATTTTAAATTTTAAATATTTTTTAATTTATTTTTTTAAATATTAAATATATTTTATTTATT
131 GTATATTTTAAATTTTAAATATTTTTTAATTTAGTTCTATAAATATTAAATATATTTTATTAATT
* * * * * *
1824912 TATTATTATTAATTTTAAAAAATTTGAAATGTGTATTTGAAATATTTTATAATATATATTTTTTA
196 TA-TA-TATAAATTTAAAAAAATTTGAAATATGTATTTGAAAAATTTTATAAAATATATTATTTA
* ** *
1824977 AAATTTTAAATACATATTATTATTTTTAAATTTT
259 AAATTTAAAATACATATTATTA-TTAAAAATTTC
*
1825011 AAATATATATTTTTTAAATTTTAAATATTATTTTTTAAATGTTAAATATATTTTTTAATAATATA
1 AAATATATATTTTTTAAATTTTAAATATTATTTTTTAAATATTAAATATATTTTTTAATAATATA
* *
1825076 AAACATTTAAATATTTTAAAGT-TATGACCTTTCAAATTTATTTTTAGTTTTATAATATTTTAAA
66 AAACATTTAAATATTTTAAA-TATATGAACTTTCAAATTTATTATTAGTTTTATAATATTTTAAA
*
1825140 TGTATATTTTAAATTTTAAATATTTTTTAATTT-GTTCTATAATATTTTAAATAT-TTTT-TTAA
130 TGTATATTTTAAATTTTAAATATTTTTTAATTTAGTTCTATAA-ATATTAAATATATTTTATT-A
*
1825202 ATTTA-A-A-AAAGTTTCAAAAATATATATTTTAAATAT-T-TTT-AAAAATTTTA-AAAATATA
193 ATTTATATATAAA-TTT--AAAA-A-A-ATTTGAAATATGTATTTGAAAAATTTTATAAAATATA
*
1825260 -TATTTAAAATTTAAAATATATA-TATTA-TAAAACATTTC
252 TTATTTAAAATTTAAAATACATATTATTATTAAAA-ATTTC
*
1825298 AAATATACATTT
1 AAATATATATTT
1825310 CAAGTTTTTT
Statistics
Matches: 265, Mismatches: 23, Indels: 28
0.84 0.07 0.09
Matches are distributed among these distances:
286 3 0.01
287 15 0.06
288 7 0.03
289 23 0.09
290 7 0.03
291 13 0.05
292 6 0.02
293 21 0.08
294 169 0.64
295 1 0.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (291 bp):
AAATATATATTTTTTAAATTTTAAATATTATTTTTTAAATATTAAATATATTTTTTAATAATATA
AAACATTTAAATATTTTAAATATATGAACTTTCAAATTTATTATTAGTTTTATAATATTTTAAAT
GTATATTTTAAATTTTAAATATTTTTTAATTTAGTTCTATAAATATTAAATATATTTTATTAATT
TATATATAAATTTAAAAAAATTTGAAATATGTATTTGAAAAATTTTATAAAATATATTATTTAAA
ATTTAAAATACATATTATTATTAAAAATTTC
Found at i:1830302 original size:12 final size:13
Alignment explanation
Indices: 1830285--1830321 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
1830275 GAACCGGACA
1830285 CGAACCGAA-CTC
1 CGAACCGAAGCTC
1830297 CGAACC-AAGCTC
1 CGAACCGAAGCTC
*
1830309 CGAACCGTAGCTC
1 CGAACCGAAGCTC
1830322 TGATACCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 2 0.09
12 15 0.68
13 5 0.23
ACGTcount: A:0.30, C:0.41, G:0.19, T:0.11
Consensus pattern (13 bp):
CGAACCGAAGCTC
Found at i:1839457 original size:12 final size:13
Alignment explanation
Indices: 1839432--1839460 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1839422 CTTTGTGTGT
1839432 TTTTATTATTTTA
1 TTTTATTATTTTA
1839445 TTTTATT-TTTTA
1 TTTTATTATTTTA
1839457 TTTT
1 TTTT
1839461 CACATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTATTATTTTA
Found at i:1839739 original size:10 final size:10
Alignment explanation
Indices: 1839705--1839769 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 10
1839695 TCATATCTTT
1839705 TAAAAAA-T-
1 TAAAAAATTA
*
1839713 TAAAAAATTT
1 TAAAAAATTA
1839723 TCAAAAAAATTA
1 T--AAAAAATTA
1839735 T-AAAAATATA
1 TAAAAAAT-TA
1839745 TAAAGAAATT-
1 TAAA-AAATTA
1839755 TAAAAAATTA
1 TAAAAAATTA
1839765 -AAAAA
1 TAAAAA
1839770 TTTCTAAAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 15
0.75 0.02 0.23
Matches are distributed among these distances:
8 7 0.15
9 17 0.35
10 8 0.17
11 3 0.06
12 13 0.27
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:1847109 original size:8 final size:8
Alignment explanation
Indices: 1847096--1847129 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
1847086 ACAATTAATT
1847096 AATTTAAA
1 AATTTAAA
*
1847104 ATTTTAAA
1 AATTTAAA
1847112 AATTTAAA
1 AATTTAAA
*
1847120 AATTCAAA
1 AATTTAAA
1847128 AA
1 AA
1847130 AATATAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (8 bp):
AATTTAAA
Found at i:1848623 original size:16 final size:15
Alignment explanation
Indices: 1848602--1848647 Score: 67
Period size: 14 Copynumber: 3.1 Consensus size: 15
1848592 AAAATTTTTA
*
1848602 ATAAATAAAAAATAT
1 ATAAATTAAAAATAT
1848617 ATAAAATTAAAAATAT
1 AT-AAATTAAAAATAT
1848633 -TAAATTAAAAATAT
1 ATAAATTAAAAATAT
1848647 A
1 A
1848648 AATATTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 13 0.46
15 3 0.11
16 12 0.43
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
ATAAATTAAAAATAT
Found at i:1848643 original size:21 final size:21
Alignment explanation
Indices: 1848618--1848659 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1848608 AAAAAATATA
*
1848618 TAAAATTAAAAATA-TTAAAT
1 TAAAAATAAAAATATTTAAAT
*
1848638 TAAAAATATAAATATTTAAAT
1 TAAAAATAAAAATATTTAAAT
1848659 T
1 T
1848660 TTTTTTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAAAATAAAAATATTTAAAT
Found at i:1853568 original size:21 final size:22
Alignment explanation
Indices: 1853515--1853569 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
1853505 CAATTTAAAT
*
1853515 AATAATAACAATAACAATAATA
1 AATAATAATAATAACAATAATA
* *
1853537 ATTAA-ATATAA-AACTATAATA
1 AATAATA-ATAATAACAATAATA
1853558 AATAATAATAAT
1 AATAATAATAAT
1853570 TTAATATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
21 18 0.69
22 8 0.31
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.29
Consensus pattern (22 bp):
AATAATAATAATAACAATAATA
Found at i:1853806 original size:14 final size:14
Alignment explanation
Indices: 1853787--1853816 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1853777 GATTAACTTC
*
1853787 ATAAATATTTTTTA
1 ATAAATATTTTCTA
1853801 ATAAATATTTTCTA
1 ATAAATATTTTCTA
1853815 AT
1 AT
1853817 CCATTTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
ATAAATATTTTCTA
Found at i:1856633 original size:46 final size:45
Alignment explanation
Indices: 1856573--1856846 Score: 379
Period size: 46 Copynumber: 6.0 Consensus size: 45
1856563 TTTGACATGA
* * * * * * *
1856573 TGCCATAGTGTCTTTCAACTACGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCA-GC
** *
1856619 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA-GC
1856665 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA-GC
1856711 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG-C
* *
1856757 TGCCATGGTATTTTTCAACCATGGTCTTACACATTTCATATCAGAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG-C
1856803 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1856847 AGAGTACACT
Statistics
Matches: 212, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
45 5 0.02
46 207 0.98
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.38
Consensus pattern (45 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGC
Found at i:1856847 original size:46 final size:46
Alignment explanation
Indices: 1856619--1856847 Score: 388
Period size: 46 Copynumber: 5.0 Consensus size: 46
1856609 TCTGTCATGT
** *
1856619 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACG-C
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA-GAC
*
1856665 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGAC
1856711 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGAC
* *
1856757 TGCCATGGTATTTTTCAACCATGGTCTTACACATTTCATATCAGAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGAC
1856803 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGA
1856848 GAGTACACTC
Statistics
Matches: 175, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
45 1 0.01
46 174 0.99
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.37
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGAC
Found at i:1864990 original size:17 final size:17
Alignment explanation
Indices: 1864956--1865006 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
1864946 ATTACATTTA
*
1864956 TAATATAAAA-AAATAAT
1 TAATATAAAATTAA-AAT
1864973 TAATATAAAATTAAAAT
1 TAATATAAAATTAAAAT
*
1864990 TAAAATTAAAATTAAAA
1 TAATA-TAAAATTAAAA
1865007 ATATTAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 17 0.57
18 13 0.43
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TAATATAAAATTAAAAT
Found at i:1865015 original size:6 final size:6
Alignment explanation
Indices: 1864978--1865006 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1864968 ATAATTAATA
1864978 TAAAAT TAAAAT TAAAAT TAAAAT TAAAA
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAA
1865007 ATATTAATAA
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):
TAAAAT
Found at i:1870339 original size:27 final size:27
Alignment explanation
Indices: 1870309--1870361 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
1870299 TTAGAAGTGC
* *
1870309 GACTAGTTGAGCCTTTCTCAGAGGCGT
1 GACTAATTGAGCCTATCTCAGAGGCGT
*
1870336 GACTAATTGTGCCTATCTCAGAGGCG
1 GACTAATTGAGCCTATCTCAGAGGCG
1870362 CAAATGGTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (27 bp):
GACTAATTGAGCCTATCTCAGAGGCGT
Found at i:1871173 original size:20 final size:20
Alignment explanation
Indices: 1871148--1871208 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
1871138 TATATATTTA
1871148 AATATTTTTAATAAAAAAAT
1 AATATTTTTAATAAAAAAAT
* * *
1871168 AATA-TTTTATTTAAAAAAC
1 AATATTTTTAATAAAAAAAT
*
1871187 AATTTTTTTTAATATAAAAAAT
1 AA-TATTTTTAATA-AAAAAAT
1871209 TGAATCGCGC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
19 14 0.45
20 5 0.16
21 6 0.19
22 6 0.19
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
AATATTTTTAATAAAAAAAT
Found at i:1872978 original size:17 final size:16
Alignment explanation
Indices: 1872940--1872984 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
1872930 TTTATTTCAC
*
1872940 TTTCTTT-CTCTTTTT
1 TTTCTTTCCTATTTTT
1872955 TTT-TTTCCTATTTTT
1 TTTCTTTCCTATTTTT
1872970 TATTCTTTCCTATTT
1 T-TTCTTTCCTATTT
1872985 CAATTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 3 0.12
15 11 0.42
16 2 0.08
17 10 0.38
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTCTTTCCTATTTTT
Found at i:1882683 original size:16 final size:16
Alignment explanation
Indices: 1882662--1882692 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1882652 GCTCATGCAG
*
1882662 ATTCATGCACGTAAGA
1 ATTCATGCACATAAGA
1882678 ATTCATGCACATAAG
1 ATTCATGCACATAAG
1882693 TTGTCCGGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (16 bp):
ATTCATGCACATAAGA
Found at i:1888773 original size:98 final size:98
Alignment explanation
Indices: 1888604--1888799 Score: 297
Period size: 98 Copynumber: 2.0 Consensus size: 98
1888594 AGCCACTGTG
* * * *
1888604 AACGGTGGCTGGCGACGGTCGCCAGGGGCAATCAGTGGAGGAGACTGGCTGGAGCCTTCGCCGGA
1 AACGGTGGCCGACGACGGTCGCCAGCGGCAATCAGTGGAGGAGACTGGCCGGAGCCTTCGCCGGA
* *
1888669 GCACGCACCTGCAGGGAGAAAACAAAAGAACAA
66 GCACGCACCTACAGAGAGAAAACAAAAGAACAA
1888702 AACGGTGGCCGACGACGGTCGCC-GACGGCAATCAGTGGCA-GAGACTGGCCGGAGCCTTCGCCG
1 AACGGTGGCCGACGACGGTCGCCAG-CGGCAATCAGTGG-AGGAGACTGGCCGGAGCCTTCGCCG
*
1888765 GAGCACGCACCTACAGAGAGAAAACAGAAGAACAA
64 GAGCACGCACCTACAGAGAGAAAACAAAAGAACAA
1888800 TTTTTTTTTT
Statistics
Matches: 89, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
97 1 0.01
98 87 0.98
99 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.35, T:0.09
Consensus pattern (98 bp):
AACGGTGGCCGACGACGGTCGCCAGCGGCAATCAGTGGAGGAGACTGGCCGGAGCCTTCGCCGGA
GCACGCACCTACAGAGAGAAAACAAAAGAACAA
Found at i:1889268 original size:3 final size:3
Alignment explanation
Indices: 1889255--1889288 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1889245 TATTATCCAA
*
1889255 ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1889289 CCATTGTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1889421 original size:22 final size:22
Alignment explanation
Indices: 1889374--1889424 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
1889364 ATTCCTTTTC
*
1889374 TATTATTATTTATTATATTGTA
1 TATTATTATTGATTATATTGTA
1889396 TATTATTATTAGATTATCA-TGT-
1 TATTATTATT-GATTAT-ATTGTA
1889418 TATTATT
1 TATTATT
1889425 TCTTTCTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 17 0.65
23 8 0.31
24 1 0.04
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (22 bp):
TATTATTATTGATTATATTGTA
Found at i:1889493 original size:13 final size:14
Alignment explanation
Indices: 1889470--1889498 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1889460 GCTGTTACTA
1889470 TTTTTATTTTTATT
1 TTTTTATTTTTATT
1889484 TTTTTA-TTTTATT
1 TTTTTATTTTTATT
1889497 TT
1 TT
1889499 ACTACCAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTATTTTTATT
Found at i:1889569 original size:3 final size:3
Alignment explanation
Indices: 1889563--1889955 Score: 190
Period size: 3 Copynumber: 131.7 Consensus size: 3
1889553 TTTTTACTAC
* **
1889563 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT TTT ACC ATCT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
* * * *
1889612 AAT A-T ATT ACT A-T ACCTT ATT ATT ATT ATT ATT ACT ATT -GT ATT
1 ATT ATT ATT ATT ATT A--TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * *
1889656 AGT ACT ATT ATT ATT A-C ATT -TT CTT -TT -TT ATT ACT ATT ACT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
1889699 ATT ATT TTT ATCT -TT ATT -TCCT ATT ATT GTT ATC ATT ATT ATT AAT
1 ATT ATT ATT AT-T ATT ATT AT--T ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * *
1889745 ACT AAT ATA AAT ATT CTT ATT ATT ACTT -TT ATT ATT ATC ATT AGT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT
* * * * *
1889790 ATT ATT ATT -TGT ACT ACT ATT ATT ATT ACT ATC ATT -TAT ATT -TC
1 ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT
* * * *
1889834 ATT ATT ATT ATT AGT GTT ACT ATT -TCT ATT ATT GTT -TT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT
* * * *
1889878 ATT ATT ATT ATT ATT ATT ATTT ATTT GTT ATT ATG GTT GTT ATT ATT
1 ATT ATT ATT ATT ATT ATT A-TT A-TT ATT ATT ATT ATT ATT ATT ATT
*
1889925 ATT ATT ACCTC ATT ATTT ATT ATT -TT ATT AT
1 ATT ATT A--TT ATT A-TT ATT ATT ATT ATT AT
1889956 CGTCTATTAG
Statistics
Matches: 297, Mismatches: 63, Indels: 60
0.71 0.15 0.14
Matches are distributed among these distances:
2 26 0.09
3 250 0.84
4 16 0.05
5 5 0.02
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:1890041 original size:3 final size:3
Alignment explanation
Indices: 1890026--1890098 Score: 53
Period size: 3 Copynumber: 25.0 Consensus size: 3
1890016 TTAAAGAAAA
* * * * * *
1890026 TAT TAT TAC TAT TAT TAT TAT CAT TAC TAC TAT ATAT TAT TAG CA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
*
1890071 TAT TAT TAT T-T TCT T-T TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1890099 CCTTATTAAC
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
2 5 0.09
3 49 0.86
4 3 0.05
ACGTcount: A:0.32, C:0.08, G:0.01, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:1890041 original size:24 final size:25
Alignment explanation
Indices: 1889986--1890042 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
1889976 ACCTTTTTTG
* *
1889986 TATATTAAGGAAAATATATTAGATTA
1 TATATTAAAGAAAATATATTA-ACTA
1890012 TATATTAAAGAAAATATTATT-ACTA
1 TATATTAAAGAAAATA-TATTAACTA
1890037 T-TATTA
1 TATATTA
1890043 TTATCATTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 5 0.18
25 4 0.14
26 15 0.54
27 4 0.14
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (25 bp):
TATATTAAAGAAAATATATTAACTA
Found at i:1890051 original size:21 final size:21
Alignment explanation
Indices: 1890027--1890080 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1890017 TAAAGAAAAT
*
1890027 ATTATTACTATTATTATTATC
1 ATTATTACTATTATTATTAGC
*
1890048 ATTACTACTATATATTATTAGC
1 ATTATTACTAT-TATTATTAGC
*
1890070 A-TATTATTATT
1 ATTATTACTATT
1890081 TTCTTTTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 1 0.04
21 17 0.61
22 10 0.36
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.54
Consensus pattern (21 bp):
ATTATTACTATTATTATTAGC
Found at i:1903097 original size:26 final size:26
Alignment explanation
Indices: 1903067--1903174 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
1903057 TGAAATTCCC
1903067 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
1903093 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
1903119 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
1903145 ATCATGGAACACTTACCTAACTCATT
1 ATCATGGAACATTTACCTAACCCATT
1903171 ATCA
1 ATCA
1903175 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.36, C:0.27, G:0.06, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:1915141 original size:12 final size:12
Alignment explanation
Indices: 1915124--1915220 Score: 64
Period size: 12 Copynumber: 8.2 Consensus size: 12
1915114 TTTTTCTTTG
1915124 TATATTATTTAT
1 TATATTATTTAT
1915136 TATATTATTTA-
1 TATATTATTTAT
1915147 TATATTA-TTA-
1 TATATTATTTAT
1915157 TATATTA--TAT
1 TATATTATTTAT
*
1915167 TACCTA-CATTTAAT
1 TA--TATTATTT-AT
1915181 ATATATTATTT-T
1 -TATATTATTTAT
*
1915193 ATATATTACTTAT
1 -TATATTATTTAT
* *
1915206 CATATTGTTTAT
1 TATATTATTTAT
1915218 TAT
1 TAT
1915221 TATATATTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 18
0.73 0.07 0.19
Matches are distributed among these distances:
9 2 0.03
10 12 0.17
11 8 0.12
12 35 0.51
13 4 0.06
14 6 0.09
15 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.01, T:0.59
Consensus pattern (12 bp):
TATATTATTTAT
Found at i:1915457 original size:18 final size:15
Alignment explanation
Indices: 1915446--1915535 Score: 67
Period size: 15 Copynumber: 6.0 Consensus size: 15
1915436 TTATTTCATC
1915446 ATTTTTTTTTATTTA
1 ATTTTTTTTTATTTA
1915461 ATTTTTTTTT-TTT-
1 ATTTTTTTTTATTTA
* * *
1915474 TTTTTTTTTTTTTTT
1 ATTTTTTTTTATTTA
* *
1915489 TTTTTTTTTTATTTT
1 ATTTTTTTTTATTTA
* * *
1915504 ATATTTTTATAATTTT
1 AT-TTTTTTTTATTTA
*
1915520 GTTTATTTTTTATTTA
1 ATTT-TTTTTTATTTA
1915536 TGTTATTATT
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
13 9 0.15
14 6 0.10
15 27 0.44
16 20 0.32
ACGTcount: A:0.14, C:0.00, G:0.01, T:0.84
Consensus pattern (15 bp):
ATTTTTTTTTATTTA
Found at i:1915510 original size:25 final size:25
Alignment explanation
Indices: 1915447--1915534 Score: 82
Period size: 25 Copynumber: 3.8 Consensus size: 25
1915437 TATTTCATCA
1915447 TTTTTTTTTA-TTTA-A--TTTTTT
1 TTTTTTTTTATTTTATATTTTTTTT
1915468 TTTTTTTTT-TTTT-T-TTTTTTTT
1 TTTTTTTTTATTTTATATTTTTTTT
* *
1915490 TTTTTTTTTATTTTATATTTTTATA
1 TTTTTTTTTATTTTATATTTTTTTT
* * *
1915515 ATTTTGTTTATTTTTTATTT
1 TTTTTTTTTATTTTATATTT
1915535 ATGTTATTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
21 12 0.22
22 15 0.27
23 4 0.07
24 1 0.02
25 23 0.42
ACGTcount: A:0.12, C:0.00, G:0.01, T:0.86
Consensus pattern (25 bp):
TTTTTTTTTATTTTATATTTTTTTT
Found at i:1915511 original size:1 final size:1
Alignment explanation
Indices: 1915447--1915503 Score: 78
Period size: 1 Copynumber: 57.0 Consensus size: 1
1915437 TATTTCATCA
* ** *
1915447 TTTTTTTTTATTTAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1915504 ATATTTTTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:1915542 original size:16 final size:14
Alignment explanation
Indices: 1915446--1915536 Score: 74
Period size: 14 Copynumber: 6.1 Consensus size: 14
1915436 TTATTTCATC
1915446 ATTTTTTTTTATTT
1 ATTTTTTTTTATTT
*
1915460 AATTTTTTTTTTTTT
1 -ATTTTTTTTTATTT
* *
1915475 TTTTTTTTTTTTTT
1 ATTTTTTTTTATTT
*
1915489 TTTTTTTTTTATTTT
1 ATTTTTTTTTA-TTT
* *
1915504 ATATTTTTATAATTTT
1 AT-TTTTTTTTA-TTT
*
1915520 GTTTATTTTTTATTT
1 ATTT-TTTTTTATTT
1915535 AT
1 AT
1915537 GTTATTATTT
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
14 23 0.37
15 23 0.37
16 17 0.27
ACGTcount: A:0.14, C:0.00, G:0.01, T:0.85
Consensus pattern (14 bp):
ATTTTTTTTTATTT
Found at i:1917792 original size:27 final size:27
Alignment explanation
Indices: 1917686--1917797 Score: 93
Period size: 27 Copynumber: 4.1 Consensus size: 27
1917676 AGCATGGCTG
* ** *
1917686 CCAGAACAGATAA-TGTGATAGAGTCA
1 CCAGATCAGATAATTGTGGCAGAGCCA
* * *
1917712 CCAGATACAGATAATCGTGGTAGAACCA
1 CCAGAT-CAGATAATTGTGGCAGAGCCA
* * *
1917740 CCAGAACAAAT-ATATGTAGCAGAGCCA
1 CCAGATCAGATAAT-TGTGGCAGAGCCA
*
1917767 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGATCAGATAATTGTGGCAGAGCCA
1917794 CCAG
1 CCAG
1917798 GACACTTCCT
Statistics
Matches: 67, Mismatches: 15, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
26 7 0.10
27 44 0.66
28 16 0.24
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.18
Consensus pattern (27 bp):
CCAGATCAGATAATTGTGGCAGAGCCA
Found at i:1919246 original size:24 final size:24
Alignment explanation
Indices: 1919214--1919263 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
1919204 ACATAGTTCA
1919214 CCCTAATCAGCTCCTAAATCCTCT
1 CCCTAATCAGCTCCTAAATCCTCT
* *
1919238 CCCTGATCAGGTCCTAAATCCTCT
1 CCCTAATCAGCTCCTAAATCCTCT
1919262 CC
1 CC
1919264 AGATAGACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.42, G:0.08, T:0.28
Consensus pattern (24 bp):
CCCTAATCAGCTCCTAAATCCTCT
Found at i:1929101 original size:32 final size:32
Alignment explanation
Indices: 1929065--1929308 Score: 317
Period size: 32 Copynumber: 7.6 Consensus size: 32
1929055 TAAAAGGGTG
*
1929065 ACACTTGAAAAGGAAACGTACACTTTGTGTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
** *
1929097 ACACTTGAAAAGGATTTGTAGACTTTGTGTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
**
1929129 ACACTTGAAAAGGATTTGTACACTTTGTGTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
** *
1929161 ACACTTGAAAAGGAAACCTACACTTTGTATGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
* **
1929193 ACACTTGAAAAGTATTTGTACACTTTGTGTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
* * * *
1929225 GCACTTGAAAAGAAAATGTACCCTTTGTGTGC
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
1929257 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
* *
1929289 ACCATTTGAAAAGGGAATGT
1 A-CACTTGAAAAGGAAATGT
1929309 GCACCTCGGG
Statistics
Matches: 183, Mismatches: 28, Indels: 1
0.86 0.13 0.00
Matches are distributed among these distances:
32 167 0.91
33 16 0.09
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.32
Consensus pattern (32 bp):
ACACTTGAAAAGGAAATGTACACTTTGTGTGT
Found at i:1929202 original size:96 final size:96
Alignment explanation
Indices: 1929065--1929302 Score: 359
Period size: 96 Copynumber: 2.5 Consensus size: 96
1929055 TAAAAGGGTG
*
1929065 ACACTTGAAAAGGAAACGTACACTTTGTGTGTACACTTGAAAAGGATTTGTAGACTTTGTGTGTA
1 ACACTTGAAAAGGAAACGTACACTTTGTGTGTACACTTGAAAAGGATTTGTACACTTTGTGTGTA
* ** *
1929130 CACTTGAAAAGGATTTGTACACTTTGTGTGT
66 CACTTGAAAAGAAAATGTACACTTTGTGTGC
* * * *
1929161 ACACTTGAAAAGGAAACCTACACTTTGTATGTACACTTGAAAAGTATTTGTACACTTTGTGTGTG
1 ACACTTGAAAAGGAAACGTACACTTTGTGTGTACACTTGAAAAGGATTTGTACACTTTGTGTGTA
*
1929226 CACTTGAAAAGAAAATGTACCCTTTGTGTGC
66 CACTTGAAAAGAAAATGTACACTTTGTGTGC
* *
1929257 ACACTTGAAAAGGAAATGTACACTTTGTGTGTACCATTTGAAAAGG
1 ACACTTGAAAAGGAAACGTACACTTTGTGTGTA-CACTTGAAAAGG
1929303 GAATGTGCAC
Statistics
Matches: 126, Mismatches: 15, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
96 116 0.92
97 10 0.08
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.32
Consensus pattern (96 bp):
ACACTTGAAAAGGAAACGTACACTTTGTGTGTACACTTGAAAAGGATTTGTACACTTTGTGTGTA
CACTTGAAAAGAAAATGTACACTTTGTGTGC
Found at i:1936029 original size:27 final size:26
Alignment explanation
Indices: 1935980--1936030 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
1935970 CTAGGTTTGG
*
1935980 AAAATTAATTTAATTGGTGAATTAGT
1 AAAATTAATTTAATTGATGAATTAGT
* *
1936006 AAAATTTATTTCAATTGATTAATTA
1 AAAATTAATTT-AATTGATGAATTA
1936031 AATTATTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 10 0.48
27 11 0.52
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (26 bp):
AAAATTAATTTAATTGATGAATTAGT
Found at i:1937802 original size:32 final size:32
Alignment explanation
Indices: 1937745--1937987 Score: 335
Period size: 32 Copynumber: 7.6 Consensus size: 32
1937735 CAAAAGGGTG
* *
1937745 ACACCTGAAAAGGAAACGTACACTTTGTGTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
** * *
1937777 ACACTTGAAAAGGATTTGTAGACTTTGTCTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
**
1937809 ACACTTGAAAAGGATTTGTACACTTTGTGTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
* *
1937841 ACACTTGAAAAGGAAACGTACACTTTGTATGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
**
1937873 ACACTTGAAAAGGATTTGTACACTTTGTGTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
*
1937905 ACACTTGAAAAGGAAATGTAC-CCTTGTGTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
1937936 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
* *
1937968 ACCATTTGAAAAGGGAATGT
1 A-CACTTGAAAAGGAAATGT
1937988 GCACCTCGGG
Statistics
Matches: 187, Mismatches: 22, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
31 30 0.16
32 141 0.75
33 16 0.09
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.32
Consensus pattern (32 bp):
ACACTTGAAAAGGAAATGTACACTTTGTGTGT
Found at i:1937914 original size:96 final size:95
Alignment explanation
Indices: 1937745--1937981 Score: 375
Period size: 96 Copynumber: 2.5 Consensus size: 95
1937735 CAAAAGGGTG
* *
1937745 ACACCTGAAAAGGAAACGTACACTTTGTGTGTACACTTGAAAAGGATTTGTAGACTTTGTCTGTA
1 ACACTTGAAAAGGAAACGTACACTTTGTGTGTACACTTGAAAAGGATTTGTACACTTTGTCTGTA
** *
1937810 CACTTGAAAAGGATTTGTACACTTTGTGTGT
66 CACTTGAAAAGGAAATGTAC-CCTTGTGTGT
* *
1937841 ACACTTGAAAAGGAAACGTACACTTTGTATGTACACTTGAAAAGGATTTGTACACTTTGTGTGTA
1 ACACTTGAAAAGGAAACGTACACTTTGTGTGTACACTTGAAAAGGATTTGTACACTTTGTCTGTA
1937906 CACTTGAAAAGGAAATGTACCCTTGTGTGT
66 CACTTGAAAAGGAAATGTACCCTTGTGTGT
* *
1937936 ACACTTGAAAAGGAAATGTACACTTTGTGTGTACCATTTGAAAAGG
1 ACACTTGAAAAGGAAACGTACACTTTGTGTGTA-CACTTGAAAAGG
1937982 GAATGTGCAC
Statistics
Matches: 130, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
95 40 0.31
96 90 0.69
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (95 bp):
ACACTTGAAAAGGAAACGTACACTTTGTGTGTACACTTGAAAAGGATTTGTACACTTTGTCTGTA
CACTTGAAAAGGAAATGTACCCTTGTGTGT
Found at i:1944960 original size:19 final size:19
Alignment explanation
Indices: 1944920--1944961 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1944910 TGTAATTAGT
* *
1944920 AAATATATAATATATGTGA
1 AAATATATAATATATATAA
1944939 AAATATAATAATA-ATATAA
1 AAATAT-ATAATATATATAA
1944958 AAAT
1 AAAT
1944962 TGATGTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (19 bp):
AAATATATAATATATATAA
Found at i:1949417 original size:32 final size:32
Alignment explanation
Indices: 1949381--1949528 Score: 188
Period size: 32 Copynumber: 4.6 Consensus size: 32
1949371 CGAAAGGGTG
* *
1949381 ACACTTGAAAAGGAAACGTACACTTTGTATGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
** *
1949413 ACACTTGAAAAGGATTTGTAGACTTTGTGTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
* *
1949445 ACACTTGAAAAGGAAATGTACCCCTTGTGTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
* *
1949477 ACACTTGAAAATGAAATGTACACTTTCTGTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
* *
1949509 ACCATTTGAAAAGGGAATGT
1 A-CACTTGAAAAGGAAATGT
1949529 GCACCTCAGG
Statistics
Matches: 98, Mismatches: 17, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
32 83 0.85
33 15 0.15
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (32 bp):
ACACTTGAAAAGGAAATGTACACTTTGTGTGT
Found at i:1955188 original size:25 final size:26
Alignment explanation
Indices: 1955160--1955211 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
1955150 ATTTACATTT
1955160 TACCCCTAGAGG-TAAATT-ACCGAAA
1 TACCCCTAG-GGTTAAATTGACCGAAA
*
1955185 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGTTAAATTGACCGAAA
1955211 T
1 T
1955212 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 2 0.08
25 15 0.62
26 7 0.29
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGTTAAATTGACCGAAA
Found at i:1956826 original size:12 final size:12
Alignment explanation
Indices: 1956809--1956837 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1956799 ACTCGGGGAA
1956809 GAGGCCGTGGTC
1 GAGGCCGTGGTC
1956821 GAGGCCGTGGTC
1 GAGGCCGTGGTC
1956833 GAGGC
1 GAGGC
1956838 TGAAGTAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.24, G:0.52, T:0.14
Consensus pattern (12 bp):
GAGGCCGTGGTC
Found at i:1961719 original size:32 final size:32
Alignment explanation
Indices: 1961683--1961747 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
1961673 TGTATGCATT
1961683 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1961715 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1961747 T
1 T
1961748 GGTAAGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (32 bp):
TTAGCATTTTAATAGTTAATGGATGATGGGCA
Found at i:1966858 original size:31 final size:31
Alignment explanation
Indices: 1966820--1966896 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
1966810 TGTCCCAAGT
1966820 CACACGGGCGTGTGTAATCACAC-GACTTGAC
1 CACACGGGCGTGTGTAATCACACAG-CTTGAC
*
1966851 CACACGGGCATGTGTAATCACACAGCTTGAC
1 CACACGGGCGTGTGTAATCACACAGCTTGAC
*
1966882 CACACGGGTGTGTGT
1 CACACGGGCGTGTGT
1966897 GGTACTGTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
31 41 0.98
32 1 0.02
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.21
Consensus pattern (31 bp):
CACACGGGCGTGTGTAATCACACAGCTTGAC
Found at i:1968370 original size:17 final size:17
Alignment explanation
Indices: 1968348--1968381 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1968338 TTTCATACAC
1968348 ACATGATTTGTTTTATT
1 ACATGATTTGTTTTATT
1968365 ACATGATTTGTTTTATT
1 ACATGATTTGTTTTATT
1968382 GGCCAATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.06, G:0.12, T:0.59
Consensus pattern (17 bp):
ACATGATTTGTTTTATT
Found at i:1976490 original size:32 final size:32
Alignment explanation
Indices: 1976454--1976664 Score: 273
Period size: 32 Copynumber: 6.6 Consensus size: 32
1976444 CGAAAGGGTG
*
1976454 ACACTTGAAAAGGAAACGTACACTTTGTGTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
** *
1976486 ACACTTGAAAAGGATTTGTAGACTTTGTGTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
* *
1976518 ACACTTGAAAAGGAAACGTACACTTTGTATGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
* * *
1976550 ACACTT-AAAAAGAATTTGTACACTTTATGTGT
1 ACACTTGAAAAGGAA-ATGTACACTTTGTGTGT
* *
1976582 ACACTTGAAAAGGAAATGTACCCCTTGTGTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
1976614 ACACTTG-AAAGGAAATGTACACTTTGTGTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
* *
1976645 ACCATTTGAAAAGGGAATGT
1 A-CACTTGAAAAGGAAATGT
1976665 GCACCTCGGG
Statistics
Matches: 152, Mismatches: 23, Indels: 7
0.84 0.13 0.04
Matches are distributed among these distances:
31 30 0.20
32 105 0.69
33 17 0.11
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (32 bp):
ACACTTGAAAAGGAAATGTACACTTTGTGTGT
Found at i:1978230 original size:12 final size:12
Alignment explanation
Indices: 1978213--1978307 Score: 65
Period size: 12 Copynumber: 8.0 Consensus size: 12
1978203 TTTTTCTTTG
1978213 TATATTATTTAT
1 TATATTATTTAT
1978225 TATATTATTTA-
1 TATATTATTTAT
*
1978236 TATTTTA-TTA-
1 TATATTATTTAT
1978246 TATATTATATTACT
1 TATATTAT-TTA-T
* *
1978260 TACATT-TTAAT
1 TATATTATTTAT
1978271 ATATATTATTT-T
1 -TATATTATTTAT
*
1978283 ATATATTACTTAT
1 -TATATTATTTAT
* *
1978296 CATATTGTTTAT
1 TATATTATTTAT
1978308 ATTATGATAT
Statistics
Matches: 66, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
10 9 0.14
11 7 0.11
12 41 0.62
13 4 0.06
14 5 0.08
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.61
Consensus pattern (12 bp):
TATATTATTTAT
Found at i:1978244 original size:14 final size:14
Alignment explanation
Indices: 1978222--1978289 Score: 50
Period size: 14 Copynumber: 4.9 Consensus size: 14
1978212 GTATATTATT
*
1978222 TATTATATTATTTA
1 TATTTTATTATTTA
1978236 TATTTTATTA--TA
1 TATTTTATTATTTA
* *
1978248 TATTATATTACTTA
1 TATTTTATTATTTA
* * *
1978262 CATTTTAATATATA
1 TATTTTATTATTTA
1978276 TTATTTTATATATT
1 -TATTTTAT-TATT
1978290 ACTTATCATA
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
12 11 0.28
14 20 0.50
15 6 0.15
16 3 0.08
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTTTATTATTTA
Found at i:1978244 original size:19 final size:17
Alignment explanation
Indices: 1978220--1978256 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 17
1978210 TTGTATATTA
1978220 TTTATTATATTATTTATAT
1 TTTATTATA-TA-TTATAT
1978239 TTTATTATATATTATAT
1 TTTATTATATATTATAT
1978256 T
1 T
1978257 ACTTACATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 2 0.11
19 9 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTATTATATATTATAT
Found at i:1978244 original size:26 final size:26
Alignment explanation
Indices: 1978215--1978284 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 26
1978205 TTTCTTTGTA
* *
1978215 TATTATTTATTATATTATTTATATTT
1 TATTATATATTATATTATTTACATTT
*
1978241 TATTATATATTATATTACTTACATTT
1 TATTATATATTATATTATTTACATTT
* *
1978267 TAATATATATTATTTTAT
1 TATTATATATTATATTAT
1978285 ATATTACTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (26 bp):
TATTATATATTATATTATTTACATTT
Found at i:1978309 original size:33 final size:36
Alignment explanation
Indices: 1978213--1978320 Score: 107
Period size: 33 Copynumber: 3.0 Consensus size: 36
1978203 TTTTTCTTTG
* *
1978213 TATATTATTTATTATATTATTTATATTTTATTATATAT
1 TATATTACTTATCATATTATTTATA--TTATTATATAT
* *
1978251 TATATTACTTA-CATTTTAATATATATTATT-T-TA-
1 TATATTACTTATCATATT-ATTTATATTATTATATAT
* *
1978284 TATATTACTTATCATATTGTTTATATTATGATATAT
1 TATATTACTTATCATATTATTTATATTATTATATAT
1978320 T
1 T
1978321 TTTTTATAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
33 20 0.35
34 8 0.14
35 3 0.05
36 6 0.11
37 4 0.07
38 16 0.28
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (36 bp):
TATATTACTTATCATATTATTTATATTATTATATAT
Found at i:1978634 original size:16 final size:16
Alignment explanation
Indices: 1978598--1978630 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1978588 ATATCTTTTT
*
1978598 TATTTTATTTGATTTA
1 TATTTTATATGATTTA
1978614 TATTTTATATG-TTTA
1 TATTTTATATGATTTA
1978629 TA
1 TA
1978631 ATTTGCTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (16 bp):
TATTTTATATGATTTA
Found at i:1979893 original size:26 final size:26
Alignment explanation
Indices: 1979864--1979919 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
1979854 TGATACAAAT
*
1979864 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTCAGGTAAATGTTCCA
*
1979890 TGATAATGGGTCAGGTAAATGTTTCA
1 TGATAATGGGTCAGGTAAATGTTCCA
1979916 TGAT
1 TGAT
1979920 GGGAATTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTCAGGTAAATGTTCCA
Found at i:1993394 original size:44 final size:43
Alignment explanation
Indices: 1993328--1993635 Score: 324
Period size: 43 Copynumber: 7.5 Consensus size: 43
1993318 ATGTATATCG
* * * *
1993328 AAGATAACAGATTTGGCGTCTCTGTATTGTTAGAGAACAGATC
1 AAGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATC
* *
1993371 AAAGATAGCAGATTTGGCATCTCTCTATTGTTAGAGAGCAGATC
1 -AAGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATC
* *
1993415 GAGATAGCAGATTTGGCATCTCTGTATTGACAGAGAGCAGATC
1 AAGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATC
* *
1993458 AAGATAGCAGATTTGACATCTC--TA---TCAGAGAACA-ATC
1 AAGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATC
* *
1993495 -GGATAGCAGA-TTGGCATCTCTAT-TTGTCAGAG-GC--ATC
1 AAGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATC
* * *
1993532 --G-TAGCAGATTTAGCATCTCTATATTGTCAGAGAGCAGATTG
1 AAGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAGA-TC
1993573 AAGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATC
1 AAGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATC
* *
1993616 -GGAGTAACAGATTTGGCATC
1 AAGA-TAGCAGATTTGGCATC
1993636 GTGAGTTGCA
Statistics
Matches: 227, Mismatches: 22, Indels: 31
0.81 0.08 0.11
Matches are distributed among these distances:
35 16 0.07
36 22 0.10
37 16 0.07
38 11 0.05
39 6 0.03
40 1 0.00
41 3 0.01
42 2 0.01
43 76 0.33
44 74 0.33
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.28
Consensus pattern (43 bp):
AAGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATC
Found at i:1993434 original size:43 final size:43
Alignment explanation
Indices: 1993324--1993635 Score: 332
Period size: 44 Copynumber: 7.5 Consensus size: 43
1993314 GACAATGTAT
* * * *
1993324 ATCGAAGATAACAGATTTGGCGTCTCTGTATTGTTAGAGAACAG
1 ATCG-AGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAG
* * *
1993368 ATCAAAGATAGCAGATTTGGCATCTCTCTATTGTTAGAGAGCAG
1 ATC-GAGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAG
*
1993412 ATCGAGATAGCAGATTTGGCATCTCTGTATTGACAGAGAGCAG
1 ATCGAGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAG
* * *
1993455 ATCAAGATAGCAGATTTGACATCTC--TA---TCAGAGAACA-
1 ATCGAGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAG
*
1993492 ATCG-GATAGCAGA-TTGGCATCTCTAT-TTGTCAGAG-GC--
1 ATCGAGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAG
* *
1993529 ATC--G-TAGCAGATTTAGCATCTCTATATTGTCAGAGAGCAG
1 ATCGAGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAG
*
1993569 ATTGAAGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAG
1 ATCG-AGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAG
*
1993613 ATCG-GAGTAACAGATTTGGCATC
1 ATCGAGA-TAGCAGATTTGGCATC
1993636 GTGAGTTGCA
Statistics
Matches: 230, Mismatches: 22, Indels: 33
0.81 0.08 0.12
Matches are distributed among these distances:
35 16 0.07
36 22 0.10
37 16 0.07
38 11 0.05
39 6 0.03
40 2 0.01
41 2 0.01
42 2 0.01
43 75 0.33
44 78 0.34
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.28
Consensus pattern (43 bp):
ATCGAGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAG
Found at i:1993550 original size:114 final size:121
Alignment explanation
Indices: 1993374--1993595 Score: 314
Period size: 114 Copynumber: 1.9 Consensus size: 121
1993364 ACAGATCAAA
* * * *
1993374 GATAGCAGATTTGGCATCTCTCTATTGTTAGAGAGCAGATCGAGATAGCAGATTTGGCATCTCTG
1 GATAGCAGATTTGGCATCTCTATATTGTCAGAGAGCA-ATC-AGATAGCAGATTTAGCATCTCTA
1993439 TATTGACAGAGAGCAGA-TCAAGATAGCAGATTTGACATCTCTATCAGAGAACAATCG
64 TATTGACAGAGAGCAGATTCAAGATAGCAGATTTGACATCTCTATCAGAGAACAATCG
1993496 GATAGCAGA-TTGGCATCTCTAT-TTGTCAGAG-GC-ATC-G-TAGCAGATTTAGCATCTCTATA
1 GATAGCAGATTTGGCATCTCTATATTGTCAGAGAGCAATCAGATAGCAGATTTAGCATCTCTATA
* * *
1993555 TTGTCAGAGAGCAGATTGAAGATAGCAGATTTGGCATCTCT
66 TTGACAGAGAGCAGATTCAAGATAGCAGATTTGACATCTCT
1993596 GTATTGTCAG
Statistics
Matches: 92, Mismatches: 7, Indels: 9
0.85 0.06 0.08
Matches are distributed among these distances:
114 34 0.37
115 24 0.26
117 3 0.03
119 2 0.02
120 8 0.09
121 12 0.13
122 9 0.10
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (121 bp):
GATAGCAGATTTGGCATCTCTATATTGTCAGAGAGCAATCAGATAGCAGATTTAGCATCTCTATA
TTGACAGAGAGCAGATTCAAGATAGCAGATTTGACATCTCTATCAGAGAACAATCG
Found at i:2013935 original size:32 final size:31
Alignment explanation
Indices: 2013890--2013955 Score: 73
Period size: 30 Copynumber: 2.1 Consensus size: 31
2013880 AATTTTAAAA
*
2013890 AAATAGTTCTTAAAAGAAATGCAT-TATACACAT
1 AAATAATTCTT-AAAGAAA--CATATATACACAT
*
2013923 AAATAATT-TTAAAGAAACATATATATACAT
1 AAATAATTCTTAAAGAAACATATATACACAT
2013953 AAA
1 AAA
2013956 AGAAGTATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
29 3 0.10
30 11 0.37
31 7 0.23
32 2 0.07
33 7 0.23
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (31 bp):
AAATAATTCTTAAAGAAACATATATACACAT
Found at i:2017820 original size:15 final size:16
Alignment explanation
Indices: 2017800--2017832 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2017790 GGTGTTTTAA
2017800 TTTTATTT-TTTATTT
1 TTTTATTTGTTTATTT
2017815 TTTTATTTGGTTTATTT
1 TTTTATTT-GTTTATTT
2017832 T
1 T
2017833 AGGTTGGGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (16 bp):
TTTTATTTGTTTATTT
Found at i:2024853 original size:7 final size:7
Alignment explanation
Indices: 2024841--2024877 Score: 65
Period size: 7 Copynumber: 5.1 Consensus size: 7
2024831 AGCTAAATTA
2024841 AAATAAT
1 AAATAAT
2024848 AAATAAT
1 AAATAAT
2024855 AAATAAT
1 AAATAAT
2024862 AAATAAT
1 AAATAAT
2024869 AAAATAAT
1 -AAATAAT
2024877 A
1 A
2024878 TCTTATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 22 0.76
8 7 0.24
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAATAAT
Found at i:2025946 original size:32 final size:32
Alignment explanation
Indices: 2025879--2026122 Score: 263
Period size: 32 Copynumber: 7.6 Consensus size: 32
2025869 CCCGAGATGC
* * *
2025879 ACATTCCCTTTTCAAATGGTACACATAAAGTGT
1 ACATTTCCTTTTCAAGT-GTACACACAAAGTGT
* * * *
2025912 ACATTTCCTTTTCAAGTGTACATATAAGGGGT
1 ACATTTCCTTTTCAAGTGTACACACAAAGTGT
*
2025944 ACATTTCCTTTTCAAGTATACACACAAAGTGT
1 ACATTTCCTTTTCAAGTGTACACACAAAGTGT
** * *
2025976 ACAAATCCTTTTCAAGTGTACATAAAAAGTGT
1 ACATTTCCTTTTCAAGTGTACACACAAAGTGT
* * *
2026008 ACGTTTCCTCTCCAAGTGTACACACAAAGTGT
1 ACATTTCCTTTTCAAGTGTACACACAAAGTGT
** * *
2026040 ACAAATCCTTTTCAATTGTACACACAAAGTCT
1 ACATTTCCTTTTCAAGTGTACACACAAAGTGT
** *
2026072 ACAAATCCTTTTCAAGTGTACACACAAAGTCT
1 ACATTTCCTTTTCAAGTGTACACACAAAGTGT
**
2026104 ACAAATCCTTTTCAAGTGT
1 ACATTTCCTTTTCAAGTGT
2026123 CACCCTTTCA
Statistics
Matches: 181, Mismatches: 30, Indels: 1
0.85 0.14 0.00
Matches are distributed among these distances:
32 166 0.92
33 15 0.08
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.32
Consensus pattern (32 bp):
ACATTTCCTTTTCAAGTGTACACACAAAGTGT
Found at i:2025976 original size:64 final size:64
Alignment explanation
Indices: 2025879--2026122 Score: 308
Period size: 64 Copynumber: 3.8 Consensus size: 64
2025869 CCCGAGATGC
* * * ** * * *
2025879 ACATTCCCTTTTCAAATGGTACACATAAAGTGTACATTTCCTTTTCAAGTGTACATATAAGGGGT
1 ACATTTCCTTTTCAAGT-GTACACACAAAGTGTACAAATCCTTTTCAAGTGTACATAAAAAGTGT
*
2025944 ACATTTCCTTTTCAAGTATACACACAAAGTGTACAAATCCTTTTCAAGTGTACATAAAAAGTGT
1 ACATTTCCTTTTCAAGTGTACACACAAAGTGTACAAATCCTTTTCAAGTGTACATAAAAAGTGT
* * * * * * *
2026008 ACGTTTCCTCTCCAAGTGTACACACAAAGTGTACAAATCCTTTTCAATTGTACACACAAAGTCT
1 ACATTTCCTTTTCAAGTGTACACACAAAGTGTACAAATCCTTTTCAAGTGTACATAAAAAGTGT
** *
2026072 ACAAATCCTTTTCAAGTGTACACACAAAGTCTACAAATCCTTTTCAAGTGT
1 ACATTTCCTTTTCAAGTGTACACACAAAGTGTACAAATCCTTTTCAAGTGT
2026123 CACCCTTTCA
Statistics
Matches: 155, Mismatches: 24, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
64 140 0.90
65 15 0.10
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.32
Consensus pattern (64 bp):
ACATTTCCTTTTCAAGTGTACACACAAAGTGTACAAATCCTTTTCAAGTGTACATAAAAAGTGT
Found at i:2026007 original size:96 final size:96
Alignment explanation
Indices: 2025885--2026122 Score: 296
Period size: 96 Copynumber: 2.5 Consensus size: 96
2025875 ATGCACATTC
* * * * * **
2025885 CCTTTTCAAATGGTACACATAAAGTGTACATTTCCTTTTCAAGTGTACATATAAGGGGTACATTT
1 CCTTTTCAAGT-GTACACAAAAAGTGTACATTTCCTTTTCAAGTGTACACACAAAGGGTACAAAT
*
2025950 CCTTTTCAAGTATACACACAAAGTGTACAAAT
65 CCTTTTCAAGTATACACACAAAGTCTACAAAT
* * * * *
2025982 CCTTTTCAAGTGTACATAAAAAGTGTACGTTTCCTCTCCAAGTGTACACACAAAGTGTACAAATC
1 CCTTTTCAAGTGTACACAAAAAGTGTACATTTCCTTTTCAAGTGTACACACAAAGGGTACAAATC
* *
2026047 CTTTTCAATTGTACACACAAAGTCTACAAAT
66 CTTTTCAAGTATACACACAAAGTCTACAAAT
* * **
2026078 CCTTTTCAAGTGTACACACAAAGTCTACAAATCCTTTTCAAGTGT
1 CCTTTTCAAGTGTACACAAAAAGTGTACATTTCCTTTTCAAGTGT
2026123 CACCCTTTCA
Statistics
Matches: 118, Mismatches: 23, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
96 108 0.92
97 10 0.08
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.32
Consensus pattern (96 bp):
CCTTTTCAAGTGTACACAAAAAGTGTACATTTCCTTTTCAAGTGTACACACAAAGGGTACAAATC
CTTTTCAAGTATACACACAAAGTCTACAAAT
Found at i:2032653 original size:30 final size:30
Alignment explanation
Indices: 2032609--2032665 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
2032599 ACGGCCATGA
* *
2032609 CACACGGGCATGTGGTCTGCCCGTGTGCCT
1 CACACAGGCATGTGGTCTACCCGTGTGCCT
* *
2032639 CACACAGGCGTGTGGTTTACCCGTGTG
1 CACACAGGCATGTGGTCTACCCGTGTG
2032666 GACGTGCCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.12, C:0.30, G:0.33, T:0.25
Consensus pattern (30 bp):
CACACAGGCATGTGGTCTACCCGTGTGCCT
Found at i:2033474 original size:4 final size:4
Alignment explanation
Indices: 2033465--2033491 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2033455 TTACTACCAA
2033465 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
2033492 ATATATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Done.