Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A06
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: 115140250
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2234201 characters in sequence are not A, C, G, or T
File 5 of 345
Found at i:1600569 original size:43 final size:43
Alignment explanation
Indices: 1600522--1600616 Score: 156
Period size: 43 Copynumber: 2.2 Consensus size: 43
1600512 GTTAAAGGTT
*
1600522 ATGACTTTTAGCGGCGTTTTTCCC-ACAAACGCCGCTAAAAGCC
1 ATGACTTTTAGCGGCG-CTTTCCCAACAAACGCCGCTAAAAGCC
*
1600565 ATGACTTTTAGCGGCGCTTTCCCAACAGACGCCGCTAAAAGCC
1 ATGACTTTTAGCGGCGCTTTCCCAACAAACGCCGCTAAAAGCC
1600608 ATGACTTTT
1 ATGACTTTT
1600617 CGTGGCTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
42 6 0.12
43 43 0.88
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.26
Consensus pattern (43 bp):
ATGACTTTTAGCGGCGCTTTCCCAACAAACGCCGCTAAAAGCC
Found at i:1601180 original size:23 final size:24
Alignment explanation
Indices: 1601154--1601200 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1601144 GAATGGAAAA
*
1601154 TAAAGAA-AAAAAAGAAGAAAATT
1 TAAAGAACAAAAAAGAAAAAAATT
*
1601177 TAAAGAACATAAAAGAAAAAAATT
1 TAAAGAACAAAAAAGAAAAAAATT
1601201 GTTCAAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (24 bp):
TAAAGAACAAAAAAGAAAAAAATT
Found at i:1601709 original size:18 final size:15
Alignment explanation
Indices: 1601665--1601718 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 15
1601655 AAACCCTAGC
1601665 CCCAAAACCCAACAA
1 CCCAAAACCCAACAA
1601680 CCCACTAAACCCAACAGAA
1 CCCA--AAACCCAAC--AA
1601699 GCCCAAAACCCAACTAA
1 -CCCAAAACCCAAC-AA
1601716 CCC
1 CCC
1601719 TTAACCCTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
15 4 0.12
16 3 0.09
17 11 0.33
18 9 0.27
19 2 0.06
20 4 0.12
ACGTcount: A:0.46, C:0.46, G:0.04, T:0.04
Consensus pattern (15 bp):
CCCAAAACCCAACAA
Found at i:1603352 original size:25 final size:25
Alignment explanation
Indices: 1603335--1603386 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1603325 TTTTATATAT
1603335 TACGTGTATATATCTTTTAATATTG
1 TACGTGTATATATCTTTTAATATTG
1603360 TACGTGTATATATCTTTTAATATTG
1 TACGTGTATATATCTTTTAATATTG
1603385 TA
1 TA
1603387 TTTTTATTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.29, C:0.08, G:0.12, T:0.52
Consensus pattern (25 bp):
TACGTGTATATATCTTTTAATATTG
Found at i:1603630 original size:3 final size:3
Alignment explanation
Indices: 1603585--1603643 Score: 50
Period size: 3 Copynumber: 20.0 Consensus size: 3
1603575 TAATACTATA
* * * * *
1603585 TAT TA- TAT TCT TAC TAT TAT CAT TAC TA- TATT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
1603629 TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT
1603644 CTTTACTTAT
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
2 4 0.09
3 38 0.86
4 2 0.05
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:1605969 original size:27 final size:26
Alignment explanation
Indices: 1605909--1605970 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
1605899 ATTTTATTTT
1605909 ATTTTATTAGGATAATTAATATTAAG
1 ATTTTATTAGGATAATTAATATTAAG
* * *
1605935 ATAATTATTAGGATTATTCAA-ATTTAGG
1 AT-TTTATTAGGATAATT-AATA-TTAAG
1605963 ATTTTATT
1 ATTTTATT
1605971 TTAATTATCT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.07
27 19 0.66
28 8 0.28
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Found at i:1608235 original size:26 final size:26
Alignment explanation
Indices: 1608179--1608228 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
1608169 AACAAAATAA
* *
1608179 ACAAAACACAAACCATGATAGTGTAG
1 ACAAAACAAAAACCATGATAATGTAG
*
1608205 ACAAAACAAAAACTATGATAATGT
1 ACAAAACAAAAACCATGATAATGT
1608229 GGTCAAAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.54, C:0.16, G:0.12, T:0.18
Consensus pattern (26 bp):
ACAAAACAAAAACCATGATAATGTAG
Found at i:1612297 original size:38 final size:38
Alignment explanation
Indices: 1612241--1612319 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
1612231 CTCATGGGAT
*
1612241 TCTGTTAGGTTACTTTTTAATCAAATTAAGAGAGACAA
1 TCTGATAGGTTACTTTTTAATCAAATTAAGAGAGACAA
*
1612279 TCTGATAGGTTCCTTTTTAATCAAATTAAGAGAGACAA
1 TCTGATAGGTTACTTTTTAATCAAATTAAGAGAGACAA
1612317 TCT
1 TCT
1612320 CTTTGTAGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (38 bp):
TCTGATAGGTTACTTTTTAATCAAATTAAGAGAGACAA
Found at i:1613414 original size:34 final size:34
Alignment explanation
Indices: 1613343--1613415 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 34
1613333 GACTTTACCT
*
1613343 TCATATTGTAATTCACAAAAAAAAAATAAAAAAA
1 TCATATTGTAATTCACAAAAAAAAAAGAAAAAAA
* *
1613377 TCATATTGTAAAATT-A-AAAAAAAAAAGATAAAGA
1 TCATATTGT--AATTCACAAAAAAAAAAGAAAAAAA
1613411 TCATA
1 TCATA
1613416 CCTAAAAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
34 29 0.85
35 1 0.03
36 4 0.12
ACGTcount: A:0.63, C:0.07, G:0.05, T:0.25
Consensus pattern (34 bp):
TCATATTGTAATTCACAAAAAAAAAAGAAAAAAA
Found at i:1615615 original size:267 final size:268
Alignment explanation
Indices: 1615139--1615623 Score: 708
Period size: 268 Copynumber: 1.8 Consensus size: 268
1615129 TCTTCTCCCC
* * * * *
1615139 AAATAATATAATTTATTTTATAAAGTAATGATATATTCGTCATTATCCAACTGAGTTGATATCCG
1 AAATAATACAATTTATTATATAAAATAATGATATATTCGTCATTATACAACTGAGTTGATAGCCG
* ** *
1615204 GTCGACCGTGACATCAAATTCGGTACAAAATTTAATATTAATAGAGATATATGAATGATAAAAAA
66 GTCGACCATGACATCAAATTCAATACAAAATTTAATATTAATAAAGATATATGAATGATAAAAAA
* * *
1615269 ACACTTTCGAAATAATATAATTTACTTTATTAGTAGAGATATATGAGCAGAAGTTGAAGCCCTAA
131 ACACTATCGAAATAATATAATTTACTTTATTAGTAGAAATATATGAGCAGAAGCTGAAGCCCTAA
* *
1615334 AACTTGCAAATACATCCCTCTACATATTAAAGGAATATACGGAGAAATGAGTATTGTACATTAAA
196 AAATTACAAATACATCCCTCTACATATTAAAGGAATATACGGAGAAATGAGTATTGTACATTAAA
1615399 CATCCTTG
261 CATCCTTG
* * *
1615407 AAATAATACAATTTATTATATAAAATAATGGTATATTCGTCATTATACAACTTAGTTGGT-GCCT
1 AAATAATACAATTTATTATATAAAATAATGATATATTCGTCATTATACAACTGAGTTGATAGCC-
* * *
1615471 GGTCGATTCATGACATCAAATTCAATACAAGATTTAATATTAGTAAAGATATATGAATGAT-AAA
65 GGTCGA-CCATGACATCAAATTCAATACAAAATTTAATATTAATAAAGATATATGAATGATAAAA
* *
1615535 AAACACTATC-AAATAATATAATTTACTTTATTAGTAGAAATATATGAAG-AGAAGCTGGAGTCC
129 AAACACTATCGAAATAATATAATTTACTTTATTAGTAGAAATATATG-AGCAGAAGCTGAAGCCC
*
1615598 TAAAAATTACAAATACATCGCTCTAC
193 TAAAAATTACAAATACATCCCTCTAC
1615624 TCAATAAAGG
Statistics
Matches: 191, Mismatches: 23, Indels: 7
0.86 0.10 0.03
Matches are distributed among these distances:
267 71 0.37
268 73 0.38
269 47 0.25
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (268 bp):
AAATAATACAATTTATTATATAAAATAATGATATATTCGTCATTATACAACTGAGTTGATAGCCG
GTCGACCATGACATCAAATTCAATACAAAATTTAATATTAATAAAGATATATGAATGATAAAAAA
ACACTATCGAAATAATATAATTTACTTTATTAGTAGAAATATATGAGCAGAAGCTGAAGCCCTAA
AAATTACAAATACATCCCTCTACATATTAAAGGAATATACGGAGAAATGAGTATTGTACATTAAA
CATCCTTG
Found at i:1615634 original size:267 final size:268
Alignment explanation
Indices: 1615139--1615634 Score: 705
Period size: 267 Copynumber: 1.9 Consensus size: 268
1615129 TCTTCTCCCC
* * * * *
1615139 AAATAATATAATTTATTTTATAAAGTAATGATATATTCGTCATTATCCAACTGAGTTGATATCCG
1 AAATAATACAATTTATTATATAAAATAATGATATATTCGTCATTATACAACTGAGTTGATAGCCG
* ** *
1615204 GTCGACCGTGACATCAAATTCGGTACAAAATTTAATATTAATAGAGATATATGAATGATAAAAAA
66 GTCGACCATGACATCAAATTCAATACAAAATTTAATATTAATAAAGATATATGAATGATAAAAAA
* * *
1615269 ACACTTTCGAAATAATATAATTTACTTTATTAGTAGAGATATATGAGCAGAAGTTGAAGCCCTAA
131 ACACTATCGAAATAATATAATTTACTTTATTAGTAGAAATATATGAGCAGAAGCTGAAGCCCTAA
* * *
1615334 AACTTGCAAATACATCCCTCTACATATTAAAGGAATATACGGAGAAATGAGTATTGTACATTAAA
196 AAATTACAAATACATCCCTCTACATAATAAAGGAATATACGGAGAAATGAGTATTGTACATTAAA
1615399 CATCCTTG
261 CATCCTTG
* * *
1615407 AAATAATACAATTTATTATATAAAATAATGGTATATTCGTCATTATACAACTTAGTTGGT-GCCT
1 AAATAATACAATTTATTATATAAAATAATGATATATTCGTCATTATACAACTGAGTTGATAGCC-
* * *
1615471 GGTCGATTCATGACATCAAATTCAATACAAGATTTAATATTAGTAAAGATATATGAATGAT-AAA
65 GGTCGA-CCATGACATCAAATTCAATACAAAATTTAATATTAATAAAGATATATGAATGATAAAA
* *
1615535 AAACACTATC-AAATAATATAATTTACTTTATTAGTAGAAATATATGAAG-AGAAGCTGGAGTCC
129 AAACACTATCGAAATAATATAATTTACTTTATTAGTAGAAATATATG-AGCAGAAGCTGAAGCCC
*
1615598 TAAAAATTACAAATACATCGCTCTAC-TCAATAAAGGA
193 TAAAAATTACAAATACATCCCTCTACAT-AATAAAGGA
1615635 TTTAATACGA
Statistics
Matches: 200, Mismatches: 24, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
266 1 0.00
267 79 0.40
268 73 0.37
269 47 0.23
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.32
Consensus pattern (268 bp):
AAATAATACAATTTATTATATAAAATAATGATATATTCGTCATTATACAACTGAGTTGATAGCCG
GTCGACCATGACATCAAATTCAATACAAAATTTAATATTAATAAAGATATATGAATGATAAAAAA
ACACTATCGAAATAATATAATTTACTTTATTAGTAGAAATATATGAGCAGAAGCTGAAGCCCTAA
AAATTACAAATACATCCCTCTACATAATAAAGGAATATACGGAGAAATGAGTATTGTACATTAAA
CATCCTTG
Found at i:1618706 original size:5 final size:5
Alignment explanation
Indices: 1618696--1618728 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
1618686 TTTGTGTGTT
1618696 TTTTA TTTTA -TTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1618729 TCACAACGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:1618711 original size:9 final size:9
Alignment explanation
Indices: 1618697--1618727 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
1618687 TTGTGTGTTT
1618697 TTTATTTTA
1 TTTATTTTA
1618706 TTTATTTTA
1 TTTATTTTA
1618715 TTTTATTTTA
1 -TTTATTTTA
1618725 TTT
1 TTT
1618728 TTCACAACGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:1618715 original size:14 final size:15
Alignment explanation
Indices: 1618696--1618728 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
1618686 TTTGTGTGTT
1618696 TTTTATTTTA-TTTA
1 TTTTATTTTATTTTA
1618710 TTTTATTTTATTTTA
1 TTTTATTTTATTTTA
1618725 TTTT
1 TTTT
1618729 TCACAACGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTATTTTATTTTA
Found at i:1618768 original size:13 final size:13
Alignment explanation
Indices: 1618750--1618775 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1618740 ATATGTAGTA
1618750 ATATTAATTTAAT
1 ATATTAATTTAAT
1618763 ATATTAATTTAAT
1 ATATTAATTTAAT
1618776 CTTGTATGAG
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATATTAATTTAAT
Found at i:1619813 original size:18 final size:19
Alignment explanation
Indices: 1619778--1619814 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1619768 CTCCTTTCCC
1619778 CTCTCCCTCCTCTCTCTTT
1 CTCTCCCTCCTCTCTCTTT
*
1619797 CTCTCCCTTCT-TCTCTTT
1 CTCTCCCTCCTCTCTCTTT
1619815 TTTTTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (19 bp):
CTCTCCCTCCTCTCTCTTT
Found at i:1621121 original size:35 final size:35
Alignment explanation
Indices: 1621082--1621207 Score: 99
Period size: 35 Copynumber: 3.4 Consensus size: 35
1621072 TATACACATG
1621082 TTTTTTTTATTATATATATGTTATGTATATGTATC
1 TTTTTTTTATTATATATATGTTATGTATATGTATC
* * * * *** *
1621117 TTTTTAATTATACTATGTAAATATTTTAATATATACACATG
1 TTTTT--TT-TA-T-TATATATATGTT-ATGTATATGTATC
*
1621158 GTTTTTTTATTATATATATGTTATGTATATGTATC
1 TTTTTTTTATTATATATATGTTATGTATATGTATC
**
1621193 TTTTTAATATTATAT
1 TTTTTTTTATTATAT
1621208 CTTTATATAT
Statistics
Matches: 65, Mismatches: 20, Indels: 12
0.67 0.21 0.12
Matches are distributed among these distances:
35 25 0.38
36 9 0.14
37 3 0.05
38 4 0.06
39 3 0.05
40 9 0.14
41 12 0.18
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.58
Consensus pattern (35 bp):
TTTTTTTTATTATATATATGTTATGTATATGTATC
Found at i:1621129 original size:76 final size:76
Alignment explanation
Indices: 1621049--1621200 Score: 295
Period size: 76 Copynumber: 2.0 Consensus size: 76
1621039 CCAATAGGAG
*
1621049 TATACTATGTAAATATTTTAATATATACACATGTTTTTTTTATTATATATATGTTATGTATATGT
1 TATACTATGTAAATATTTTAATATATACACATGGTTTTTTTATTATATATATGTTATGTATATGT
1621114 ATCTTTTTAAT
66 ATCTTTTTAAT
1621125 TATACTATGTAAATATTTTAATATATACACATGGTTTTTTTATTATATATATGTTATGTATATGT
1 TATACTATGTAAATATTTTAATATATACACATGGTTTTTTTATTATATATATGTTATGTATATGT
1621190 ATCTTTTTAAT
66 ATCTTTTTAAT
1621201 ATTATATCTT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (76 bp):
TATACTATGTAAATATTTTAATATATACACATGGTTTTTTTATTATATATATGTTATGTATATGT
ATCTTTTTAAT
Found at i:1623389 original size:131 final size:130
Alignment explanation
Indices: 1623152--1623411 Score: 369
Period size: 131 Copynumber: 2.0 Consensus size: 130
1623142 TAATTATTCT
* *
1623152 TTTAAAAATTCTCTAAAACGAAGGCAATACTCGAAGTTTAGCAATTCGGGAATCGTGCTCTATCG
1 TTTAAAAACTCTCTAAAACGAAGGCAATACTCGAAGTTTAGCAATTCGGGAATCGTGCCCTATCG
* ** *
1623217 TGATGGGTTGCGATTTCCCGTTTGTTCAAAACAATTGAATATTCCTTTGGAATTTCACTCATGTC
66 TGATAGGTTGCGATTTCCCGTTTGTTCAAAACAATCAAATATTCCTTTAGAATTTCACTCATGTC
* * * *
1623282 TTTAAAAACTCT-TCAAAACGAAGGTAATACTCGATGTTTGGCAATTTGGGGAATCGTGCCCTAT
1 TTTAAAAACTCTCT-AAAACGAAGGCAATACTCGAAGTTTAGCAA-TTCGGGAATCGTGCCCTAT
* ** *
1623346 CGTGCTAGGTTGCGATTTCTTGTTTGTTCAAAATAATCAAATATTCCTTTAGAATTTCACTCATG
64 CGTGATAGGTTGCGATTTCCCGTTTGTTCAAAACAATCAAATATTCCTTTAGAATTTCACTCATG
1623411 T
129 T
1623412 TCTCTAAATT
Statistics
Matches: 114, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
129 1 0.01
130 38 0.33
131 75 0.66
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (130 bp):
TTTAAAAACTCTCTAAAACGAAGGCAATACTCGAAGTTTAGCAATTCGGGAATCGTGCCCTATCG
TGATAGGTTGCGATTTCCCGTTTGTTCAAAACAATCAAATATTCCTTTAGAATTTCACTCATGTC
Found at i:1624733 original size:20 final size:21
Alignment explanation
Indices: 1624707--1624753 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
1624697 TGAAATCATC
*
1624707 AGGGTTCGAGGTTTAAGATTT
1 AGGGTTCGAGGTTCAAGATTT
*
1624728 -GGGTTCTAGGTTCAAGATTT
1 AGGGTTCGAGGTTCAAGATTT
1624748 AGGGTT
1 AGGGTT
1624754 TATGGTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.21, C:0.06, G:0.34, T:0.38
Consensus pattern (21 bp):
AGGGTTCGAGGTTCAAGATTT
Found at i:1627130 original size:42 final size:46
Alignment explanation
Indices: 1627067--1627277 Score: 161
Period size: 49 Copynumber: 4.6 Consensus size: 46
1627057 CTTCGTTTTC
** *
1627067 TCGATGCCATAGTTCAACTATGGTCTTACAC-AT-C-T-TCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACAATACATATCACAT-A
1627110 T-GATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC--AAT-ACATATCACATA
* *
1627158 TCGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCA-C
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-AAT-ACATATCACATA
* ** * * *
1627205 T-GATGCCATATCCCAAATATGGTCTTATACAGTAGCATA-CATCACA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACAATA-CATATCA-CATA
* *
1627251 -CTGATGCCATATCCCAGATATGGTCTT
1 TC-GATGCCATAGCCCAGCTATGGTCTT
1627278 GTACGGAAAT
Statistics
Matches: 141, Mismatches: 14, Indels: 22
0.80 0.08 0.12
Matches are distributed among these distances:
42 26 0.18
43 1 0.01
44 2 0.01
45 10 0.07
46 25 0.18
47 26 0.18
48 16 0.11
49 35 0.25
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (46 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACAATACATATCACATA
Found at i:1627168 original size:49 final size:47
Alignment explanation
Indices: 1627102--1627277 Score: 185
Period size: 47 Copynumber: 3.7 Consensus size: 47
1627092 TTACACATCT
1627102 TCACATAATGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATA
1 TCACAT-ATGATGCCATAGCCCAGCTATGGTCTTACACG-AATCACATA
1627151 TCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATA
1 TCACATAT-GATGCCATAGCCCAGCTATGGTCTTACACGAATCACATA
* * * ** * * * * *
1627199 TCTCA-CTGATGCCATATCCCAAATATGGTCTTATACAGTAGCATACA
1 TCACATATGATGCCATAGCCCAGCTATGGTCTTACAC-GAATCACATA
* * *
1627246 TCACA-CTGATGCCATATCCCAGATATGGTCTT
1 TCACATATGATGCCATAGCCCAGCTATGGTCTT
1627278 GTACGGAAAT
Statistics
Matches: 113, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
46 25 0.22
47 37 0.33
48 15 0.13
49 36 0.32
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (47 bp):
TCACATATGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATA
Found at i:1627335 original size:31 final size:31
Alignment explanation
Indices: 1627300--1627448 Score: 237
Period size: 31 Copynumber: 4.8 Consensus size: 31
1627290 CTTGTCACTT
*
1627300 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
1627331 GTAGCCGGTA-CTACCACTTTTCACTGATCAG
1 GTAGCC-GAAGCTACCACTTTTCACTGATCAG
*
1627362 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
1627393 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
1627424 GTAGCTGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
1627449 TGTCATTTGT
Statistics
Matches: 111, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
30 2 0.02
31 107 0.96
32 2 0.02
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:1627530 original size:50 final size:51
Alignment explanation
Indices: 1627424--1627552 Score: 190
Period size: 50 Copynumber: 2.5 Consensus size: 51
1627414 CACTGATCAG
* * * *
1627424 GTAGCTGAAGCTACCACTTTTCACTTGTCATTTGTCATTGATCGGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
*
1627475 GTAGCCGAAGCTATCACTTATCACTT-TCACTTT-TCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCA-TTTGTCATTGATCAGATAAGT
1627525 GTAGCCGAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
1627553 TGTCATGGTC
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
50 44 0.62
51 27 0.38
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
Found at i:1632646 original size:17 final size:17
Alignment explanation
Indices: 1632624--1632657 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1632614 TGATGTGTGG
1632624 TGGGTGAAAAAGTTCAA
1 TGGGTGAAAAAGTTCAA
1632641 TGGGTGAAAAAGTTCAA
1 TGGGTGAAAAAGTTCAA
1632658 GGATTGCAAC
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:0.41, C:0.06, G:0.29, T:0.24
Consensus pattern (17 bp):
TGGGTGAAAAAGTTCAA
Found at i:1633674 original size:27 final size:28
Alignment explanation
Indices: 1633605--1633674 Score: 74
Period size: 27 Copynumber: 2.5 Consensus size: 28
1633595 TTTGGGCATA
1633605 ATGTAAAAAAAAAT-GATAAACATTGTG
1 ATGTAAAAAAAAATGGATAAACATTGTG
* * *
1633632 ATAGCAAAATAAAATGGAATAATCA-TGT-
1 AT-GTAAAAAAAAATGG-ATAAACATTGTG
1633660 ATGTAAAAAAAAATG
1 ATGTAAAAAAAAATG
1633675 AAATGGTGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
27 13 0.37
28 12 0.34
29 4 0.11
30 6 0.17
ACGTcount: A:0.57, C:0.04, G:0.14, T:0.24
Consensus pattern (28 bp):
ATGTAAAAAAAAATGGATAAACATTGTG
Found at i:1634746 original size:18 final size:17
Alignment explanation
Indices: 1634725--1634763 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
1634715 TTCGTTTCGA
1634725 TTTTCGTCCTTATTTTACT
1 TTTTC-TCCTTATTTTA-T
1634744 TTTTCTCCTTATTTTAT
1 TTTTCTCCTTATTTTAT
1634761 TTT
1 TTT
1634764 AATTTTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 4 0.20
18 11 0.55
19 5 0.25
ACGTcount: A:0.10, C:0.18, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTTCTCCTTATTTTAT
Found at i:1634807 original size:31 final size:30
Alignment explanation
Indices: 1634756--1634822 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
1634746 TTCTCCTTAT
*
1634756 TTTATTTTAATTTTAATATTATATATACTA
1 TTTATTTTAATTTTAATATTAGATATACTA
* *
1634786 TTATATTTT-ATTATTATTATTAGATTTACTA
1 TT-TATTTTAATT-TTAATATTAGATATACTA
1634817 TTTATT
1 TTTATT
1634823 AGCCTTAGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 9 0.28
31 23 0.72
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (30 bp):
TTTATTTTAATTTTAATATTAGATATACTA
Found at i:1635085 original size:28 final size:28
Alignment explanation
Indices: 1635054--1635107 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
1635044 GTTTTTCTTA
*
1635054 AATATTATAT-TATATGTATTTAAATACT
1 AATACTATATATATATGT-TTTAAATACT
* *
1635082 AATACTATGTATATATGTTTTCAATA
1 AATACTATATATATATGTTTTAAATA
1635108 TATATATGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 15 0.68
29 7 0.32
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.48
Consensus pattern (28 bp):
AATACTATATATATATGTTTTAAATACT
Found at i:1635688 original size:20 final size:20
Alignment explanation
Indices: 1635663--1635718 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
1635653 TTTAATATCA
*
1635663 CTATTATGATTTTTTTATTG
1 CTATTATGATTATTTTATTG
*
1635683 CTATTATTATTATTTTATT-
1 CTATTATGATTATTTTATTG
*
1635702 -TATTAT-AATATTTTATT
1 CTATTATGATTATTTTATT
1635719 TTTACTATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 10 0.30
18 6 0.18
20 17 0.52
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.66
Consensus pattern (20 bp):
CTATTATGATTATTTTATTG
Found at i:1635713 original size:23 final size:23
Alignment explanation
Indices: 1635643--1635720 Score: 70
Period size: 23 Copynumber: 3.4 Consensus size: 23
1635633 TTTCTGTTAC
* * *
1635643 TATTACTTTATTTAATATCACTAT
1 TATTATTTTATTTATTAT-AATAT
* * *
1635667 TATGATTTT-TTTATTGCTATTAT
1 TATTATTTTATTTATT-ATAATAT
1635690 TATTATTTTATTTATTATAATAT
1 TATTATTTTATTTATTATAATAT
1635713 T-TTATTTT
1 TATTATTTT
1635721 TACTATTATT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
22 7 0.16
23 23 0.52
24 14 0.32
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (23 bp):
TATTATTTTATTTATTATAATAT
Found at i:1635730 original size:17 final size:18
Alignment explanation
Indices: 1635684--1635756 Score: 78
Period size: 17 Copynumber: 4.0 Consensus size: 18
1635674 TTTTTATTGC
*
1635684 TATTATTATTATTTTATT
1 TATTACTATTATTTTATT
*
1635702 TATTA-TAATATTTTATT
1 TATTACTATTATTTTATT
1635719 T-TTACTATTATTGTTATT
1 TATTACTATTATT-TTATT
*
1635737 ATCATTACTATTATATTATT
1 -T-ATTACTATTATTTTATT
1635757 AGCACATTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
16 3 0.06
17 18 0.38
18 10 0.21
19 1 0.02
20 5 0.11
21 10 0.21
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (18 bp):
TATTACTATTATTTTATT
Found at i:1635775 original size:3 final size:3
Alignment explanation
Indices: 1635684--1635757 Score: 57
Period size: 3 Copynumber: 25.7 Consensus size: 3
1635674 TTTTTATTGC
* * *
1635684 TAT TAT TAT TAT T-T TATT TAT TA- TAA TAT T-T TAT TTT TAC TAT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
1635727 TAT TGT TAT TAT CAT TAC TAT TA- TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1635758 GCACATTATT
Statistics
Matches: 55, Mismatches: 11, Indels: 10
0.72 0.14 0.13
Matches are distributed among these distances:
2 8 0.15
3 44 0.80
4 3 0.05
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1636882 original size:6 final size:6
Alignment explanation
Indices: 1636866--1636934 Score: 56
Period size: 6 Copynumber: 11.7 Consensus size: 6
1636856 TGTAATAAGC
* *
1636866 AAAAAT AAAAA- ATAAA- AAAAAT -AAAAT AAATGAA- GAAAAT AAAAATT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAA--AAT AAAAAT AAAAA-T
*
1636913 AGAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAA
1636935 GAAACATGTT
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
5 15 0.29
6 27 0.53
7 7 0.14
8 2 0.04
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:1637656 original size:11 final size:11
Alignment explanation
Indices: 1637640--1637664 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1637630 CCCAAAATTT
1637640 AAAAATAATAA
1 AAAAATAATAA
1637651 AAAAATAATAA
1 AAAAATAATAA
1637662 AAA
1 AAA
1637665 TTCATTTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAATAATAA
Found at i:1641077 original size:38 final size:38
Alignment explanation
Indices: 1641006--1641232 Score: 233
Period size: 38 Copynumber: 5.9 Consensus size: 38
1640996 GCTAAGATTG
* * *
1641006 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATTA
1 TATCCGGG-TTAAA-TCCCGCAGGCTTTGTGCTGGAATTA
*
1641046 TATCCGGGTTAAATCCCGCGGGCTTTGTGCTGGTAA-TA
1 TATCCGGGTTAAATCCCGCAGGCTTTGTGCTGG-AATTA
*
1641084 TATCCGGGTTAAATCCCACAGGCTTTGTGCTGGTAA-TA
1 TATCCGGGTTAAATCCCGCAGGCTTTGTGCTGG-AATTA
* * * *
1641122 TATACAGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTTGTGCTGGAATTA
* * * *
1641160 TATCTGGGTTAAATCCCGCAGGCCTAGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTTGTGCTGGAATTA
* * * *
1641198 TATCTGAGTTTAAAGTCCCGTAGGCTTCGTGCTGG
1 TATCCG-GGTTAAA-TCCCGCAGGCTTTGTGCTGG
1641233 TGTTATGTTT
Statistics
Matches: 163, Mismatches: 20, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
37 1 0.01
38 124 0.76
39 13 0.08
40 25 0.15
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCTTTGTGCTGGAATTA
Found at i:1641124 original size:76 final size:76
Alignment explanation
Indices: 1641006--1641233 Score: 260
Period size: 76 Copynumber: 2.9 Consensus size: 76
1640996 GCTAAGATTG
* * * *
1641006 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGG-AATTATATCCGGGTTAAATCCCGCGGGCT
1 TATCCGGG-TTAAA-TCCCGCAGGCTTTGTGCTGGTAA-TATATCCGGGTTAAATCCCGCAGGCT
*
1641070 TTGTGCTGGTAATA
63 TCGTGCTGGTAATA
* * *
1641084 TATCCGGGTTAAATCCCACAGGCTTTGTGCTGGTAATATATACAGGTTAAATCCCGCAGGCTTCG
1 TATCCGGGTTAAATCCCGCAGGCTTTGTGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCG
*
1641149 TGCTGGTATTA
66 TGCTGGTAATA
* * * * * * *
1641160 TATCTGGGTTAAATCCCGCAGGCCTAGTGCTGGTATTATATCTGAGTTTAAAGTCCCGTAGGCTT
1 TATCCGGGTTAAATCCCGCAGGCTTTGTGCTGGTAATATATCCG-GGTTAAA-TCCCGCAGGCTT
1641225 CGTGCTGGT
64 CGTGCTGGT
1641234 GTTATGTTTG
Statistics
Matches: 128, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
76 87 0.68
77 13 0.10
78 28 0.22
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (76 bp):
TATCCGGGTTAAATCCCGCAGGCTTTGTGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCG
TGCTGGTAATA
Found at i:1643925 original size:19 final size:17
Alignment explanation
Indices: 1643878--1643911 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1643868 TAAGTCCCCA
1643878 AAAAAAAAAACCTAACC
1 AAAAAAAAAACCTAACC
1643895 AAAAAAAAAACCTAACC
1 AAAAAAAAAACCTAACC
1643912 CTCCAAAAAA
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:0.71, C:0.24, G:0.00, T:0.06
Consensus pattern (17 bp):
AAAAAAAAAACCTAACC
Found at i:1656449 original size:16 final size:15
Alignment explanation
Indices: 1656419--1656451 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1656409 TTAGGAAACG
1656419 TACATAAAAAATATA
1 TACATAAAAAATATA
1656434 TACATAAAAAAT-TA
1 TACATAAAAAATATA
1656448 TACA
1 TACA
1656452 ACAATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (15 bp):
TACATAAAAAATATA
Found at i:1656509 original size:26 final size:28
Alignment explanation
Indices: 1656454--1656523 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 28
1656444 ATTATACAAC
* *
1656454 AATATATA-TAAATAATGATATGTGCAAA
1 AATATATACTATATAA-CATATGTGCAAA
1656482 AATA-ATA-TATATAACATATGT-CATAA
1 AATATATACTATATAACATATGTGCA-AA
1656508 AATATATACTATATAA
1 AATATATACTATATAA
1656524 TAATAGTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
25 2 0.05
26 12 0.32
27 12 0.32
28 11 0.30
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.34
Consensus pattern (28 bp):
AATATATACTATATAACATATGTGCAAA
Found at i:1657140 original size:16 final size:17
Alignment explanation
Indices: 1657097--1657141 Score: 65
Period size: 16 Copynumber: 2.6 Consensus size: 17
1657087 AGGGTTTCTT
1657097 GGTTTTTTTTTGGGGGTTA
1 GGTTTTTTTTT--GGGTTA
1657116 GGTTTTTTTTT-GGTTA
1 GGTTTTTTTTTGGGTTA
1657132 GGTTTTTTTT
1 GGTTTTTTTT
1657142 GGGGGGCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.58
19 11 0.42
ACGTcount: A:0.04, C:0.00, G:0.29, T:0.67
Consensus pattern (17 bp):
GGTTTTTTTTTGGGTTA
Found at i:1657799 original size:14 final size:13
Alignment explanation
Indices: 1657768--1657801 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1657758 ATTGACTCTC
*
1657768 TAAAAACAGACAT
1 TAAAAACAGAAAT
1657781 TAAAAACAGAAAT
1 TAAAAACAGAAAT
*
1657794 TGAAAACA
1 TAAAAACA
1657802 AGCTCAGCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.65, C:0.12, G:0.09, T:0.15
Consensus pattern (13 bp):
TAAAAACAGAAAT
Found at i:1658019 original size:49 final size:47
Alignment explanation
Indices: 1657940--1658033 Score: 143
Period size: 49 Copynumber: 2.0 Consensus size: 47
1657930 GATTTTGAAA
*
1657940 AACAGAAATTAAAAGACTCAGCGTGTCTTGAGGCTCAACTCATTTTG
1 AACAGAAATTAAAAGACTCAACGTGTCTTGAGGCTCAACTCATTTTG
**
1657987 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
1 AACAGAAATT-AAAAGA-CTCAACGTGTCTTGAGGCTCAACTCATTT
1658034 CTCGGCAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
47 10 0.24
48 4 0.10
49 28 0.67
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (47 bp):
AACAGAAATTAAAAGACTCAACGTGTCTTGAGGCTCAACTCATTTTG
Found at i:1658276 original size:54 final size:55
Alignment explanation
Indices: 1658176--1658281 Score: 135
Period size: 54 Copynumber: 1.9 Consensus size: 55
1658166 TAACCGAGGC
* * *
1658176 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCACAATATGAGCTGATTTTGAAAAAGCAGAAATTGAAAAGGT
* * *
1658230 TCAACCCACCTCTCACAATATGAGTTGATTCTTGAACAA-CATAAATTGAAAA
1 TCAACCCACCTCTCACAATATGAGCTGATT-TTGAAAAAGCAGAAATTGAAAA
1658282 CAGAAATTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
54 33 0.75
55 11 0.25
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (55 bp):
TCAACCCACCTCTCACAATATGAGCTGATTTTGAAAAAGCAGAAATTGAAAAGGT
Found at i:1658288 original size:13 final size:13
Alignment explanation
Indices: 1658261--1658294 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1658251 GAGTTGATTC
*
1658261 TTGAACAACATAAA
1 TTGAA-AACAGAAA
1658275 TTGAAAACAGAAA
1 TTGAAAACAGAAA
1658288 TTGAAAA
1 TTGAAAA
1658295 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.21
Consensus pattern (13 bp):
TTGAAAACAGAAA
Found at i:1658323 original size:140 final size:140
Alignment explanation
Indices: 1658133--1658419 Score: 481
Period size: 140 Copynumber: 2.0 Consensus size: 140
1658123 GAATTTTTTT
1658133 TTGAAAGACAGAAATTGAAATACCTCAGCAGTGTAACCGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAGACAGAAATTGAAATACCTCAGCAGTG-AACCGAGGCTCAACTCACCTCTCGCAATATG
*
1658198 AGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCACAATATGAGTTGATTCTT
65 AGCTGATTTTAAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCACAATATGAGTTGATTCTT
1658263 GAACAACATAAA
130 -AACAACATAAA
1658275 TTGAAA-ACAGAAATTGAAAATACCTCAGC-GTG-ACCTGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAGACAGAAATTG-AAATACCTCAGCAGTGAACC-GAGGCTCAACTCACCTCTCGCAATAT
* *
1658337 GAGCTGATTTTAAAAAAGTAGAAATTAAAAGGTTCAACCCACTTCTCGCAATATGAGTTGATTCT
64 GAGCTGATTTTAAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCACAATATGAGTTGATTCT
*
1658402 TAACAACGTAAA
129 TAACAACATAAA
1658414 TTGAAA
1 TTGAAA
1658420 TAGAAATATT
Statistics
Matches: 139, Mismatches: 4, Indels: 7
0.93 0.03 0.05
Matches are distributed among these distances:
139 19 0.14
140 89 0.64
141 13 0.09
142 18 0.13
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (140 bp):
TTGAAAGACAGAAATTGAAATACCTCAGCAGTGAACCGAGGCTCAACTCACCTCTCGCAATATGA
GCTGATTTTAAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCACAATATGAGTTGATTCTTA
ACAACATAAA
Found at i:1658924 original size:70 final size:71
Alignment explanation
Indices: 1658824--1658960 Score: 251
Period size: 70 Copynumber: 1.9 Consensus size: 71
1658814 TTTCAAAAAA
1658824 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTG-GTAATTTC-ATTTCT
1 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGT-ATTTCAATTTCT
1658887 GTTTTTC
65 GTTTTTC
1658894 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGTATTTCAATTTCTG
1 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGTATTTCAATTTCTG
1658959 TT
66 TT
1658961 CAAAATGAGT
Statistics
Matches: 65, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
70 54 0.83
71 11 0.17
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (71 bp):
AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGTATTTCAATTTCTG
TTTTTC
Found at i:1658970 original size:47 final size:47
Alignment explanation
Indices: 1658916--1659007 Score: 157
Period size: 47 Copynumber: 2.0 Consensus size: 47
1658906 ATATTGCGAG
*
1658916 AAATGAGTTGAGCCTCAAGACACGTTGAGTATTTCAATTTCTGTTCA
1 AAATGAGTTGAGCCTCAAGACACGCTGAGTATTTCAATTTCTGTTCA
* *
1658963 AAATGAGTTGAGCCTCAAGACACGCTGAGTCTTTTAATTTCTGTT
1 AAATGAGTTGAGCCTCAAGACACGCTGAGTATTTCAATTTCTGTT
1659008 TTTCAAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (47 bp):
AAATGAGTTGAGCCTCAAGACACGCTGAGTATTTCAATTTCTGTTCA
Found at i:1659832 original size:17 final size:18
Alignment explanation
Indices: 1659810--1659852 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
1659800 TTAGCCCCCC
1659810 AAAAAACCTAA-CCAAAA
1 AAAAAACCTAACCCAAAA
*
1659827 AAAAAACCTAACCCCAAA
1 AAAAAACCTAACCCAAAA
1659845 AAAAAACC
1 AAAAAACC
1659853 AAGAAACCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.67, C:0.28, G:0.00, T:0.05
Consensus pattern (18 bp):
AAAAAACCTAACCCAAAA
Found at i:1660647 original size:18 final size:18
Alignment explanation
Indices: 1660580--1660649 Score: 54
Period size: 20 Copynumber: 3.7 Consensus size: 18
1660570 TTTATTGTAG
1660580 ATATTATTATTAT-TACAT
1 ATATTATT-TTATGTACAT
* *
1660598 ACT-TTATTATATGCATATAT
1 A-TATTATTTTATG--TACAT
1660618 ATATGTATTTTTATGTACAT
1 ATAT-TA-TTTTATGTACAT
1660638 ATATTATTTTAT
1 ATATTATTTTAT
1660650 ATTATTATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
17 3 0.07
18 12 0.29
19 4 0.10
20 14 0.34
21 2 0.05
22 6 0.15
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (18 bp):
ATATTATTTTATGTACAT
Found at i:1673876 original size:21 final size:21
Alignment explanation
Indices: 1673850--1673890 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1673840 TATTAAAAAT
* *
1673850 AAAAATATAAAAATTTATAAA
1 AAAAATACAAAAACTTATAAA
1673871 AAAAATACAAAAACTTATAA
1 AAAAATACAAAAACTTATAA
1673891 TAATTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAATACAAAAACTTATAAA
Found at i:1681178 original size:18 final size:18
Alignment explanation
Indices: 1681125--1681178 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
1681115 GGTCTGACTT
1681125 ATTTTTA-AT-TT-TATA
1 ATTTTTATATATTATATA
* * *
1681140 ATTCTT-TATATTATGTT
1 ATTTTTATATATTATATA
1681157 ATTTTTATATATTATATA
1 ATTTTTATATATTATATA
1681175 ATTT
1 ATTT
1681179 AGAACATATT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
15 7 0.24
16 2 0.07
17 7 0.24
18 13 0.45
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
ATTTTTATATATTATATA
Found at i:1692327 original size:5 final size:5
Alignment explanation
Indices: 1692313--1692345 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
1692303 TGGTTAGAAT
1692313 TTTTA TTTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA TT
1692346 ATTAATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:1694670 original size:3 final size:3
Alignment explanation
Indices: 1694662--1694693 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1694652 TAATCAGACA
*
1694662 AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1694694 ATCATCCAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1695461 original size:17 final size:18
Alignment explanation
Indices: 1695439--1695475 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1695429 CTTCTCTTTT
1695439 TTTAAAAAATA-ATAAAA
1 TTTAAAAAATATATAAAA
*
1695456 TTTAAAAACTATATAAAA
1 TTTAAAAAATATATAAAA
1695474 TT
1 TT
1695476 ATTATTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
TTTAAAAAATATATAAAA
Found at i:1702818 original size:16 final size:16
Alignment explanation
Indices: 1702797--1702827 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1702787 TAACATTATA
*
1702797 TTAATGGCAGACAATT
1 TTAATGGCAAACAATT
1702813 TTAATGGCAAACAAT
1 TTAATGGCAAACAAT
1702828 CCAAGTGGTG
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:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (16 bp):
TTAATGGCAAACAATT
Found at i:1707958 original size:18 final size:18
Alignment explanation
Indices: 1707935--1707970 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1707925 AATGAGAACA
1707935 GTCTCTTTTATTCAGTTG
1 GTCTCTTTTATTCAGTTG
1707953 GTCTCTTTTATTCAGTTG
1 GTCTCTTTTATTCAGTTG
1707971 AACTCCAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.17, G:0.17, T:0.56
Consensus pattern (18 bp):
GTCTCTTTTATTCAGTTG
Found at i:1711198 original size:18 final size:18
Alignment explanation
Indices: 1711175--1711241 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
1711165 CAATAAATAT
1711175 CTATTTGAATAATTATAA
1 CTATTTGAATAATTATAA
1711193 CTATTT-ATTATTAATTAATAAATA
1 CTATTTGA--A-TAATT-AT--A-A
1711217 TCTATTTGAATAATTATAA
1 -CTATTTGAATAATTATAA
1711236 CTATTT
1 CTATTT
1711242 ATTATTAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 18
0.69 0.00 0.31
Matches are distributed among these distances:
17 1 0.03
18 12 0.30
19 2 0.05
20 6 0.15
21 2 0.05
22 2 0.05
23 6 0.15
24 2 0.05
25 6 0.15
26 1 0.03
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (18 bp):
CTATTTGAATAATTATAA
Found at i:1711213 original size:43 final size:43
Alignment explanation
Indices: 1711166--1711255 Score: 180
Period size: 43 Copynumber: 2.1 Consensus size: 43
1711156 ATAATTATTC
1711166 AATAAATATCTATTTGAATAATTATAACTATTTATTATTAATT
1 AATAAATATCTATTTGAATAATTATAACTATTTATTATTAATT
1711209 AATAAATATCTATTTGAATAATTATAACTATTTATTATTAATT
1 AATAAATATCTATTTGAATAATTATAACTATTTATTATTAATT
1711252 AATA
1 AATA
1711256 TAATTTTTGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (43 bp):
AATAAATATCTATTTGAATAATTATAACTATTTATTATTAATT
Found at i:1728242 original size:196 final size:198
Alignment explanation
Indices: 1727709--1728250 Score: 783
Period size: 197 Copynumber: 2.7 Consensus size: 198
1727699 AAACCCAAAA
* * * * *
1727709 GATACTACACACTTAAGTGTGCTCAAATCCACAAGCTCCAAGTTGCTGCAATAGCTATGCTTGAA
1 GATATTACGCACTTAAGTGTGCTCGAATCCACAACCTCCAAGTTGCTGCAATAGCAATGCTTGAA
* *
1727774 TAATTTGAAATTGGGTTTTTGGTTTTGCTGTGTAACATTAGAGGAACCTCATTTTGAAGTAGAAC
66 TAATTTGAAATTGGGTTATTGGTTTTGCTGTGTAACATTAGAGGAACCTTATTTTGAAGTAGAAC
* * *
1727839 GATGGTCGGAACTTC-TTTTTTGGCAAATTTCTAAACTACTCGTAGACCCCGACTAATTAAATTT
131 GATGGTCGGTACTTCTTTTTTTGACAAATTTCTAAACTACTCGTAGACACCGACTAATTAAATTT
1727903 GAT
196 GAT
* * * *
1727906 GATATTACGCACTTAAGTGTGTTCGAATCCATAACCTCCAAGTTGTTGCAATAGCAATACTTGAA
1 GATATTACGCACTTAAGTGTGCTCGAATCCACAACCTCCAAGTTGCTGCAATAGCAATGCTTGAA
* * *
1727971 TAAATTTAAAATTGGGTTATTGGTTTTGCCGTGTGACATTAGAGGAACCTTATTTTGAAGTAGAA
66 T-AATTTGAAATTGGGTTATTGGTTTTGCTGTGTAACATTAGAGGAACCTTATTTTGAAGTAGAA
1728036 CGATGGTCGGTACTTCTTTTTTTGAC-AA-TTCTAAACTAC-CTGTA-A-ACCGAAGCTAATTAA
130 CGATGGTCGGTACTTCTTTTTTTGACAAATTTCTAAACTACTC-GTAGACACCG-A-CTAATTAA
1728096 ATTTGAT
192 ATTTGAT
* * * ** *
1728103 GATATTACGCAGTTAAGCGTGCTCGAATCCACAATCTCTGAGTTGCTGCAATAGCAATGCTTAAA
1 GATATTACGCACTTAAGTGTGCTCGAATCCACAACCTCCAAGTTGCTGCAATAGCAATGCTTGAA
1728168 TAATTTGAAATTGGGTTATTGGTTTTGCTGTGTAACATTAGAGGAACCTTATTTTGAAGTAGAAC
66 TAATTTGAAATTGGGTTATTGGTTTTGCTGTGTAACATTAGAGGAACCTTATTTTGAAGTAGAAC
1728233 G-TCGGTCGGTACTTCTTT
131 GAT-GGTCGGTACTTCTTT
1728251 ATAGAGGCTT
Statistics
Matches: 309, Mismatches: 30, Indels: 13
0.88 0.09 0.04
Matches are distributed among these distances:
195 4 0.01
196 80 0.26
197 142 0.46
198 75 0.24
199 8 0.03
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (198 bp):
GATATTACGCACTTAAGTGTGCTCGAATCCACAACCTCCAAGTTGCTGCAATAGCAATGCTTGAA
TAATTTGAAATTGGGTTATTGGTTTTGCTGTGTAACATTAGAGGAACCTTATTTTGAAGTAGAAC
GATGGTCGGTACTTCTTTTTTTGACAAATTTCTAAACTACTCGTAGACACCGACTAATTAAATTT
GAT
Found at i:1733200 original size:14 final size:14
Alignment explanation
Indices: 1733177--1733219 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
1733167 TTTTGTTTAG
1733177 TTTT-TAAATATTT
1 TTTTATAAATATTT
*
1733190 TTTTATAAATATAT
1 TTTTATAAATATTT
*
1733204 TTTTACAAAT-TTT
1 TTTTATAAATATTT
1733217 TTT
1 TTT
1733220 CATTCATATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 9 0.35
14 17 0.65
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTATAAATATTT
Found at i:1737589 original size:40 final size:39
Alignment explanation
Indices: 1737533--1737609 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 39
1737523 TTAATTCACC
* * * *
1737533 AGCATTAAGCCTGCGGGACTTTAAACCCGGATACAATCCT
1 AGCATGAAGCCAGCGGGACTCT-AACCCAGATACAATCCT
*
1737573 AGCATGAAGCCAGCGGGTCTCTAACCCAGATACAATC
1 AGCATGAAGCCAGCGGGACTCTAACCCAGATACAATC
1737610 TCAGCACAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
39 14 0.44
40 18 0.56
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (39 bp):
AGCATGAAGCCAGCGGGACTCTAACCCAGATACAATCCT
Found at i:1737794 original size:47 final size:47
Alignment explanation
Indices: 1737686--1737888 Score: 252
Period size: 47 Copynumber: 4.3 Consensus size: 47
1737676 TGCACACTTT
* * *
1737686 TCACAATTGGTCATTCGGCCTTATCACATAT--TCACTTACACATAT-A
1 TCAC-ATTGGCCATTCGGCCTTATCACATATACACACTTTCACAT-TCA
* * * ** *
1737732 TCACATT-TCATATTCGGCCTTATCACATGTATGCACTATCACATTCA
1 TCACATTGGC-CATTCGGCCTTATCACATATACACACTTTCACATTCA
*
1737779 TCACATTGGCCATTCGGCCTTATCACATATACACATTTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATACACACTTTCACATTCA
*
1737826 TCACATTGGCCATTCGGCCTTATCACAAATACACACTTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATACACACTTTCACATTCA
1737873 TCACATTGGCCATTCG
1 TCACATTGGCCATTCG
1737889 ATCTTAAGCT
Statistics
Matches: 136, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
45 21 0.15
46 5 0.04
47 109 0.80
48 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATACACACTTTCACATTCA
Found at i:1737806 original size:22 final size:22
Alignment explanation
Indices: 1737778--1737852 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
1737768 TATCACATTC
1737778 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
1737800 ATCACATAT-ACACATTTTC-ACATT
1 ATCACAT-TGGC-CA--TTCGGCCTT
1737824 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
1737847 ATCACA
1 ATCACA
1737853 AATACACACT
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 17 0.43
23 6 0.15
24 6 0.15
25 11 0.28
ACGTcount: A:0.27, C:0.31, G:0.11, T:0.32
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:1745193 original size:186 final size:183
Alignment explanation
Indices: 1744838--1745170 Score: 467
Period size: 186 Copynumber: 1.8 Consensus size: 183
1744828 AGAAAAGGGA
* * *
1744838 GAAAAAAGAGGAATAGTGTTTTTTTTTTTTGCTTCTTTATTTCAATTTCTCAGTGCAATGCATGA
1 GAAAAAAGAGGAATAGTGTTATTTTTTTTTGCTTC--TATTTCAATTTCTAAGTGCAATGCATAA
* * * * **
1744903 GTAGAGGAAGCTGTAACAGTGTACATCGTGATCGATCATTGTTTATCAATTTGCATGCTATTTTT
64 GCAGAGGAACCTCTAACAATGTACATCGTGATCGATCATTGTCGATCAATTTGCATGCTATTTTT
* *
1744968 AATTTTTTTTTCTCTTTTTAAATCTGATTTAAGTTTTTTTTTGTTACTTTTTAAT
129 AATTTTATTCTCTCTTTTTAAATCTGATTTAAGTTTTTTTTTGTTACTTTTTAAT
1745023 GAAAAAAGAGGAATAGTGTTGATTTTTTTTT-CTTC-ATTTCAATTTCTAAGTGCAATGCATAAG
1 GAAAAAAGAGGAATAGTGTT-ATTTTTTTTTGCTTCTATTTCAATTTCTAAGTGCAATGCATAAG
*
1745086 CAGAGGAAACCGTAACTAACAATGTACATCGTGATCTATCATTGTCGATCAATTTGCATGCTA-T
65 CAGAGG-AACC-T--CTAACAATGTACATCGTGATCGATCATTGTCGATCAATTTGCATGCTATT
1745150 TTT-ATTTTATTCTCTCTTTTT
126 TTTAATTTTATTCTCTCTTTTT
1745171 TATCTGTTTT
Statistics
Matches: 131, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
182 31 0.24
183 3 0.02
184 17 0.13
185 28 0.21
186 52 0.40
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (183 bp):
GAAAAAAGAGGAATAGTGTTATTTTTTTTTGCTTCTATTTCAATTTCTAAGTGCAATGCATAAGC
AGAGGAACCTCTAACAATGTACATCGTGATCGATCATTGTCGATCAATTTGCATGCTATTTTTAA
TTTTATTCTCTCTTTTTAAATCTGATTTAAGTTTTTTTTTGTTACTTTTTAAT
Found at i:1748198 original size:36 final size:36
Alignment explanation
Indices: 1748158--1748226 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
1748148 CACGTAAGCG
1748158 AGTGCTTCAAGTCTCAGTTATCTGGCATTTTAAACT
1 AGTGCTTCAAGTCTCAGTTATCTGGCATTTTAAACT
1748194 AGTGCTTCAAGTCTCAGTTATCTGGCATTTTAA
1 AGTGCTTCAAGTCTCAGTTATCTGGCATTTTAA
1748227 CTTTCGAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (36 bp):
AGTGCTTCAAGTCTCAGTTATCTGGCATTTTAAACT
Found at i:1748501 original size:13 final size:14
Alignment explanation
Indices: 1748478--1748514 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
1748468 TGCATGTATG
1748478 TATGCATGTATATA
1 TATGCATGTATATA
*
1748492 TATG-ATGTATATG
1 TATGCATGTATATA
1748505 TATGCATGTA
1 TATGCATGTA
1748515 ATCAACCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.43
Consensus pattern (14 bp):
TATGCATGTATATA
Found at i:1748879 original size:79 final size:80
Alignment explanation
Indices: 1748785--1748945 Score: 315
Period size: 79 Copynumber: 2.0 Consensus size: 80
1748775 TTTATAAAAG
1748785 TTTGTTTTTTTTCCCTTCTCGTTATTTGTTCATTTGCTATTTCGCTGGTGGGTTAATCTATAAAA
1 TTTGTTTTTTTTCCCTTCTCGTTATTTGTTCATTTGCTATTTCGCTGGTGGGTTAATCTATAAAA
1748850 AATAGTCACTTTTGT
66 AATAGTCACTTTTGT
1748865 TTTG-TTTTTTTCCCTTCTCGTTATTTGTTCATTTGCTATTTCGCTGGTGGGTTAATCTATAAAA
1 TTTGTTTTTTTTCCCTTCTCGTTATTTGTTCATTTGCTATTTCGCTGGTGGGTTAATCTATAAAA
1748929 AATAGTCACTTTTGT
66 AATAGTCACTTTTGT
1748944 TT
1 TT
1748946 GTCTCAGATT
Statistics
Matches: 81, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
79 77 0.95
80 4 0.05
ACGTcount: A:0.17, C:0.15, G:0.15, T:0.53
Consensus pattern (80 bp):
TTTGTTTTTTTTCCCTTCTCGTTATTTGTTCATTTGCTATTTCGCTGGTGGGTTAATCTATAAAA
AATAGTCACTTTTGT
Found at i:1750599 original size:97 final size:97
Alignment explanation
Indices: 1750433--1750626 Score: 388
Period size: 97 Copynumber: 2.0 Consensus size: 97
1750423 TGAAGAGTTC
1750433 TCCCACGGCTTTTAAATCAAGAAGAAAACCTACTTATAAAATAAACAAAAAAGAAATCTCAATCA
1 TCCCACGGCTTTTAAATCAAGAAGAAAACCTACTTATAAAATAAACAAAAAAGAAATCTCAATCA
1750498 AGATATCTTTATAATCTATAATGAATAATGAA
66 AGATATCTTTATAATCTATAATGAATAATGAA
1750530 TCCCACGGCTTTTAAATCAAGAAGAAAACCTACTTATAAAATAAACAAAAAAGAAATCTCAATCA
1 TCCCACGGCTTTTAAATCAAGAAGAAAACCTACTTATAAAATAAACAAAAAAGAAATCTCAATCA
1750595 AGATATCTTTATAATCTATAATGAATAATGAA
66 AGATATCTTTATAATCTATAATGAATAATGAA
1750627 GAGAACTTCA
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 97 1.00
ACGTcount: A:0.49, C:0.15, G:0.08, T:0.27
Consensus pattern (97 bp):
TCCCACGGCTTTTAAATCAAGAAGAAAACCTACTTATAAAATAAACAAAAAAGAAATCTCAATCA
AGATATCTTTATAATCTATAATGAATAATGAA
Found at i:1751528 original size:3 final size:3
Alignment explanation
Indices: 1751520--1751559 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
1751510 TTTCTGCATT
1751520 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
1751560 GTGTATATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1751663 original size:3 final size:3
Alignment explanation
Indices: 1751655--1751681 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1751645 TGTATTTCTA
1751655 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1751682 AATAATATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1751813 original size:16 final size:15
Alignment explanation
Indices: 1751782--1751824 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
1751772 CCTTCATTCC
*
1751782 ATTATTATTATTACT
1 ATTATTATTTTTACT
1751797 ATTATTATATTTTACT
1 ATTATTAT-TTTTACT
*
1751813 ATCATTATTTTT
1 ATTATTATTTTT
1751825 CATACGTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTATTATTTTTACT
Found at i:1752145 original size:20 final size:20
Alignment explanation
Indices: 1752100--1752146 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1752090 TTATTTAATA
1752100 TATTAT-TTTTACTATTATC
1 TATTATATTTTACTATTATC
*
1752119 T-TCATATTGTTACTATTA-C
1 TATTATATT-TTACTATTATC
1752138 TATTATATT
1 TATTATATT
1752147 ATTAGGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
18 3 0.13
19 5 0.22
20 15 0.65
ACGTcount: A:0.28, C:0.11, G:0.02, T:0.60
Consensus pattern (20 bp):
TATTATATTTTACTATTATC
Found at i:1752193 original size:22 final size:22
Alignment explanation
Indices: 1752163--1752223 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
1752153 TTATTATATC
*
1752163 TTTTACTATTATTATTGTTGTA
1 TTTTACTATTATTATTGTTATA
* * *
1752185 TTTTTCTATTATTGTTATTATA
1 TTTTACTATTATTATTGTTATA
* *
1752207 TTTTCCT-TTATTTTTGT
1 TTTTACTATTATTATTGT
1752224 ATTTACTTAT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 8 0.25
22 24 0.75
ACGTcount: A:0.18, C:0.07, G:0.07, T:0.69
Consensus pattern (22 bp):
TTTTACTATTATTATTGTTATA
Found at i:1752197 original size:3 final size:3
Alignment explanation
Indices: 1751958--1752178 Score: 55
Period size: 3 Copynumber: 72.3 Consensus size: 3
1751948 TTCTCATCAC
* * * *
1751958 TAT TAT TAT AATT TAT CAT TGT TACT TAT TAT T-T TAC TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
* * * * * *
1752004 CTAA TAT GTCAT CAT TAT CAT TAT T-T TCAT TAT AACT TAA TA- GAT
1 -TAT TAT -T-AT TAT TAT TAT TAT TAT T-AT TAT TA-T TAT TAT TAT
* * * *
1752049 TAT TAT TAT TAT TAT TAT TAT TAG CAC TACT T-T TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
* * * * * * *
1752094 T-T AAT ATAT TAT TTT TAC TAT TAT CT-T CA- TAT TGT TAC TAT TAC
1 TAT TAT -TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT
* *
1752138 TAT TA- TAT TAT TAGGT TAT TA- TAT CTTT TAC TAT TAT TAT T
1 TAT TAT TAT TAT TA--T TAT TAT TAT -TAT TAT TAT TAT TAT T
1752179 GTTGTATTTT
Statistics
Matches: 152, Mismatches: 44, Indels: 44
0.63 0.18 0.18
Matches are distributed among these distances:
2 13 0.09
3 116 0.76
4 18 0.12
5 5 0.03
ACGTcount: A:0.31, C:0.09, G:0.03, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:1756753 original size:31 final size:30
Alignment explanation
Indices: 1756718--1756790 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 30
1756708 ATAAAAATTT
*
1756718 AAGTTTCATATATACATTTAAACCACAATCA
1 AAGTTTCATATATACAATTAAACCA-AATCA
* * * * *
1756749 AAGTTTAATGTATATAATTACACCAAATTA
1 AAGTTTCATATATACAATTAAACCAAATCA
1756779 AAG-TTCATATAT
1 AAGTTTCATATAT
1756791 TAAACTACAT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
29 7 0.21
30 7 0.21
31 20 0.59
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (30 bp):
AAGTTTCATATATACAATTAAACCAAATCA
Found at i:1762430 original size:26 final size:27
Alignment explanation
Indices: 1762394--1762447 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
1762384 AAGTAAATAT
*
1762394 TAATAATTTTATT-TAAATATAATTAAA
1 TAATAATTTTATTATAAATA-AATGAAA
1762421 TAATAA-TTTATTATAAATAAATGAAA
1 TAATAATTTTATTATAAATAAATGAAA
1762447 T
1 T
1762448 TTTGTTTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 13 0.52
27 12 0.48
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
TAATAATTTTATTATAAATAAATGAAA
Found at i:1769480 original size:25 final size:26
Alignment explanation
Indices: 1769452--1769500 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
1769442 TTCAATTATT
*
1769452 TTTATATTGGAATTT-AATTTTTTGG
1 TTTAAATTGGAATTTGAATTTTTTGG
**
1769477 TTTAAATTGGTGTTTGAATTTTTT
1 TTTAAATTGGAATTTGAATTTTTT
1769501 TAATTTAAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 12 0.60
26 8 0.40
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.61
Consensus pattern (26 bp):
TTTAAATTGGAATTTGAATTTTTTGG
Found at i:1770106 original size:12 final size:12
Alignment explanation
Indices: 1770089--1770116 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1770079 TTTTTGTGCC
1770089 TTGAGTAGTAAG
1 TTGAGTAGTAAG
1770101 TTGAGTAGTAAG
1 TTGAGTAGTAAG
1770113 TTGA
1 TTGA
1770117 TTTTGAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (12 bp):
TTGAGTAGTAAG
Found at i:1772249 original size:27 final size:27
Alignment explanation
Indices: 1772213--1772267 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
1772203 TTATTAAAAT
*
1772213 AAATATTAAATATTA-AATATTTTATTA
1 AAATAATAAATATTATAA-ATTTTATTA
* *
1772240 AAATAATAAATTTTATGAATTTTATTA
1 AAATAATAAATATTATAAATTTTATTA
1772267 A
1 A
1772268 TAATTTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
AAATAATAAATATTATAAATTTTATTA
Found at i:1772530 original size:15 final size:15
Alignment explanation
Indices: 1772495--1772530 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1772485 TGAATGGAAG
*
1772495 TAAAAATTTTGAAAT
1 TAAAAATTTTGAAAA
*
1772510 TTAAAATTTTGAAAA
1 TAAAAATTTTGAAAA
1772525 TAAAAA
1 TAAAAA
1772531 ATTGATTTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (15 bp):
TAAAAATTTTGAAAA
Found at i:1772934 original size:37 final size:37
Alignment explanation
Indices: 1772893--1772979 Score: 111
Period size: 37 Copynumber: 2.4 Consensus size: 37
1772883 GTTATTGTTG
* *
1772893 ATCTCCGTCTTTTCTTTATAGAGAATTATCACTATTC
1 ATCTCCGTCTTTTCTTTACAGAGAATTATCACTATCC
* * * * *
1772930 ATCTCCATCTTTTCTTTGCATAGAATTATTACTGTCC
1 ATCTCCGTCTTTTCTTTACAGAGAATTATCACTATCC
1772967 ATCTCCGTCTTTT
1 ATCTCCGTCTTTT
1772980 GTCTTCCAGA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.21, C:0.24, G:0.08, T:0.47
Consensus pattern (37 bp):
ATCTCCGTCTTTTCTTTACAGAGAATTATCACTATCC
Found at i:1773102 original size:21 final size:22
Alignment explanation
Indices: 1773077--1773126 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
1773067 ATAAATCTAA
1773077 GTTTTAAAAATTTTTAAATT-T
1 GTTTTAAAAATTTTTAAATTCT
* * *
1773098 GTTTTCAATATTTTTGAATTCT
1 GTTTTAAAAATTTTTAAATTCT
*
1773120 GATTTAA
1 GTTTTAA
1773127 CTATCTTTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (22 bp):
GTTTTAAAAATTTTTAAATTCT
Found at i:1773879 original size:37 final size:36
Alignment explanation
Indices: 1773792--1773891 Score: 128
Period size: 36 Copynumber: 2.8 Consensus size: 36
1773782 TAAAAGACGG
* *
1773792 AGATAAACAATAATGATTCTCTGCAAAGAAAACAGA
1 AGATAAACAATAACGATTCTCTGTAAAGAAAACAGA
* * *
1773828 AGATAAATAGTAACGATTCTCTGTAAAGAAAATATGA
1 AGATAAACAATAACGATTCTCTGTAAAGAAAACA-GA
* *
1773865 AGATGAACAATAACGATTCTTTGTAAA
1 AGATAAACAATAACGATTCTCTGTAAA
1773892 AATTCTCTCA
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 29 0.54
37 25 0.46
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.25
Consensus pattern (36 bp):
AGATAAACAATAACGATTCTCTGTAAAGAAAACAGA
Found at i:1773943 original size:50 final size:50
Alignment explanation
Indices: 1773843--1773945 Score: 120
Period size: 50 Copynumber: 2.1 Consensus size: 50
1773833 AATAGTAACG
** * * *
1773843 ATTCTCTGTAAAGAAAATATGAAGATGAACAATAACGATTCTTTGTAAAA
1 ATTCTCTCAAAAGAAAAGATGAAGATGAACAATAAAGATTCTTTGCAAAA
*
1773893 ATTCTCTCAAAAGAAAAGATGAAGAT-ACACAGTAAAGATT-TCTTGCAAAA
1 ATTCTCTCAAAAGAAAAGATGAAGATGA-ACAATAAAGATTCT-TTGCAAAA
1773943 ATT
1 ATT
1773946 TTGTAATTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
49 2 0.04
50 43 0.96
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.28
Consensus pattern (50 bp):
ATTCTCTCAAAAGAAAAGATGAAGATGAACAATAAAGATTCTTTGCAAAA
Found at i:1775529 original size:20 final size:20
Alignment explanation
Indices: 1775504--1775550 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1775494 TATTTAATAA
1775504 TATAATAACA-TTATTATTTT
1 TATAATAACATTTATTA-TTT
1775524 TATAATAACATTTATTATTT
1 TATAATAACATTTATTATTT
1775544 TATAATA
1 TATAATA
1775551 TTTCTTACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 20 0.77
21 6 0.23
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (20 bp):
TATAATAACATTTATTATTT
Found at i:1775987 original size:54 final size:54
Alignment explanation
Indices: 1775905--1776011 Score: 214
Period size: 54 Copynumber: 2.0 Consensus size: 54
1775895 GTGGGACAAG
1775905 TCTTATATTAGTTACTTACAATCCATTACATAGTTTATAGCATATTCAACAACA
1 TCTTATATTAGTTACTTACAATCCATTACATAGTTTATAGCATATTCAACAACA
1775959 TCTTATATTAGTTACTTACAATCCATTACATAGTTTATAGCATATTCAACAAC
1 TCTTATATTAGTTACTTACAATCCATTACATAGTTTATAGCATATTCAACAAC
1776012 TTCTATTGTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.39
Consensus pattern (54 bp):
TCTTATATTAGTTACTTACAATCCATTACATAGTTTATAGCATATTCAACAACA
Found at i:1786789 original size:50 final size:49
Alignment explanation
Indices: 1786674--1786790 Score: 130
Period size: 49 Copynumber: 2.4 Consensus size: 49
1786664 TGGGTTAAGT
** *
1786674 ATGCCATGTCCCAGACATGGTCTTACACTGGCTATCCTTATCGAGGCCG
1 ATGCCATGTCCCAGACATAATCTTACACTAGCTATCCTTATCGAGGCCG
* * * *
1786723 ATGCCATATCCCAGACATAATCTTACACTAGCTCTCGTACTTA-C-ATGCTG
1 ATGCCATGTCCCAGACATAATCTTACACTAGCTATC---CTTATCGAGGCCG
1786773 ATGCCATGTCCCAGACAT
1 ATGCCATGTCCCAGACAT
1786791 GGTATTACAC
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
49 31 0.54
50 21 0.37
51 1 0.02
52 4 0.07
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (49 bp):
ATGCCATGTCCCAGACATAATCTTACACTAGCTATCCTTATCGAGGCCG
Found at i:1786799 original size:50 final size:49
Alignment explanation
Indices: 1786674--1786988 Score: 194
Period size: 50 Copynumber: 6.6 Consensus size: 49
1786664 TGGGTTAAGT
* * * *
1786674 ATGCCATGTCCCAGACATGGTCTTACACTGGCTATC--CTTATCGAGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTCTTA-C-ATGCTG
* **
1786723 ATGCCATATCCCAGACATAATCTTACACTAGCTCTCGTACTTACATGCTG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGT-CTTACATGCTG
* * * * *
1786773 ATGCCATGTCCCAGACATGGTATTACACTAACTCTTGTGTATCCATG-TCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTCT-TACATGCT-G
* * * * * *
1786823 ATGCCATGTCCCAGGCATGGTTTTACACTTA-C-AT-GTC--CCGTTGCCG
1 ATGCCATGTCCCAGACATGGTCTTACAC-TAGCTCTCGTCTTAC-ATGCTG
* * * **
1786869 ATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TAGTC-T-CGAGGCCA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTCTTAC-ATGCTG
** * * *
1786914 ATG-CATGTCCTGGACAT-GTCTTACACTAGCACTCGTCTCA-ATGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTCTTACATGCTG
1786960 ATGCCATGTCCCAGACATGGTCTTACACT
1 ATGCCATGTCCCAGACATGGTCTTACACT
1786989 GGCACACAAA
Statistics
Matches: 212, Mismatches: 37, Indels: 35
0.75 0.13 0.12
Matches are distributed among these distances:
43 1 0.00
44 10 0.05
45 50 0.24
46 17 0.08
47 12 0.06
48 12 0.06
49 34 0.16
50 69 0.33
51 3 0.01
52 4 0.02
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.29
Consensus pattern (49 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTCTTACATGCTG
Found at i:1786918 original size:45 final size:46
Alignment explanation
Indices: 1786869--1786993 Score: 153
Period size: 45 Copynumber: 2.7 Consensus size: 46
1786859 CCCGTTGCCG
* *
1786869 ATGCATGTCCCAGACATGTCTTACACTGGC-TTAGTCTCGAGGCCA
1 ATGCATGTCCCAGACATGTCTTACACTGGCACTAGTCTCAAGGCCA
** * * * *
1786914 ATGCATGTCCTGGACATGTCTTACACTAGCACTCGTCTCAATGCCG
1 ATGCATGTCCCAGACATGTCTTACACTGGCACTAGTCTCAAGGCCA
1786960 ATGCCATGTCCCAGACATGGTCTTACACTGGCAC
1 ATG-CATGTCCCAGACAT-GTCTTACACTGGCAC
1786994 ACAAATTACC
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
45 27 0.41
46 13 0.20
47 12 0.18
48 14 0.21
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.26
Consensus pattern (46 bp):
ATGCATGTCCCAGACATGTCTTACACTGGCACTAGTCTCAAGGCCA
Found at i:1787725 original size:12 final size:12
Alignment explanation
Indices: 1787708--1787732 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1787698 CAAAAATGTA
1787708 AAAATCATCAAG
1 AAAATCATCAAG
1787720 AAAATCATCAAG
1 AAAATCATCAAG
1787732 A
1 A
1787733 TCACTTACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAATCATCAAG
Found at i:1789024 original size:13 final size:13
Alignment explanation
Indices: 1789006--1789042 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
1788996 GGAAGGTAGA
*
1789006 GAGAAAAAAAATT
1 GAGAAAAAAAACT
1789019 GAGAAAAAAAACT
1 GAGAAAAAAAACT
1789032 GAGAAAAAAAA
1 GAGAAAAAAAA
1789043 GAAAATATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.73, C:0.03, G:0.16, T:0.08
Consensus pattern (13 bp):
GAGAAAAAAAACT
Found at i:1789362 original size:19 final size:19
Alignment explanation
Indices: 1789325--1789369 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 19
1789315 TTAAAATTTT
1789325 TTTAATAGGTGAAAAAATAA
1 TTTAATAGGTG-AAAAATAA
1789345 TTTAATAGGTTG-AAAATAA
1 TTTAATAGG-TGAAAAATAA
1789364 TTTAAT
1 TTTAAT
1789370 TGGTATTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.54
20 9 0.38
21 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (19 bp):
TTTAATAGGTGAAAAATAA
Found at i:1792600 original size:46 final size:46
Alignment explanation
Indices: 1792550--1792722 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
1792540 TGGTTGAGCA
*
1792550 TCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
1792596 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAAATGTAACTAG-GCAT-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT--TATG-GA-T-GCGAATG
*
1792644 T-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
1792689 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
1792723 GGGGCGGGTT
Statistics
Matches: 106, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 2 0.02
46 62 0.58
47 30 0.28
48 3 0.03
49 4 0.04
50 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:1792711 original size:93 final size:93
Alignment explanation
Indices: 1792547--1792717 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
1792537 GGATGGTTGA
* * *
1792547 GCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
1792612 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
1792640 GCATTCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
1792705 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
1792718 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:1795846 original size:24 final size:24
Alignment explanation
Indices: 1795800--1795848 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
1795790 AATAAATTGA
*
1795800 TATTTTTGTTAAAAATTTTATTTT
1 TATTTTTGTTAAAAATTTGATTTT
1795824 TATTTATTGTTAAAAA-TTGATTTT
1 TATTT-TTGTTAAAAATTTGATTTT
1795848 T
1 T
1795849 GTACACTATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (24 bp):
TATTTTTGTTAAAAATTTGATTTT
Found at i:1812589 original size:30 final size:30
Alignment explanation
Indices: 1812555--1812615 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1812545 AGTGGTGGTA
1812555 GAGCAAGTGTGGCTAGTGGAGTAGGTAGTG
1 GAGCAAGTGTGGCTAGTGGAGTAGGTAGTG
* *
1812585 GAGCAAGTGTGGCTAGTGGAGTTGGTGGTG
1 GAGCAAGTGTGGCTAGTGGAGTAGGTAGTG
1812615 G
1 G
1812616 CAAAGGCTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.20, C:0.07, G:0.49, T:0.25
Consensus pattern (30 bp):
GAGCAAGTGTGGCTAGTGGAGTAGGTAGTG
Found at i:1813534 original size:90 final size:89
Alignment explanation
Indices: 1813399--1813648 Score: 310
Period size: 89 Copynumber: 2.8 Consensus size: 89
1813389 ACTTAATTTG
* * ** * *
1813399 AAAACAG--ATTGAAAATACTTC-GACATGTGCCCCGAGGCTCAACTCATTTATCGCAATATGAA
1 AAAACAGAAATTGAAAATACCTCAG-CATGT--CCTGAGGCTCAACTCACCTCTCGCAATATGAG
* *
1813461 TTAATTTTT-AAAAATATCAATTGAAAAA
63 TTGATTTTTGAAAAATATAAATTG--AAA
* ** *
1813489 AAAATAGAAATTGAAAATACCTCAGTGTGTCCTGAGGCTAAACTCACCTCTCGCAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
*
1813554 ATTTTTGAAAAATATAAATTGTAA
66 ATTTTTGAAAAATATAAATTGAAA
1813578 AAAACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
1813643 ATTTTT
66 ATTTTT
1813649 TTGAAAAGCA
Statistics
Matches: 139, Mismatches: 17, Indels: 9
0.84 0.10 0.05
Matches are distributed among these distances:
89 69 0.50
90 40 0.29
91 13 0.09
92 16 0.12
93 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (89 bp):
AAAACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
ATTTTTGAAAAATATAAATTGAAA
Found at i:1813778 original size:73 final size:73
Alignment explanation
Indices: 1813579--1814101 Score: 757
Period size: 73 Copynumber: 7.1 Consensus size: 73
1813569 AAATTGTAAA
* * *
1813579 AAACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1813644 TTTTTTTGA-
66 --TTTTTGAC
* ** * *
1813653 AAAGCAGAACTTGAAAAGCACCTCAGCGTGCCCTGAGGCTCAACTCATCTCTCGTAATATGAGTT
1 AAA-CAGAAATTG-AAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
1813718 GATTTTTGAC
64 GATTTTTGAC
1813728 AAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-
1 AAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1813792 TGTTTTGAC
66 T-TTTTGAC
**
1813801 AAACAGAAATTGAAATTACCTCAGTATGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1813866 TTTTTGAC
66 TTTTTGAC
* * * *
1813874 AAATAGAAATTGAAATTACATCAGCGTGACCTGAGGCTTAACTCACCTCTCGCAATATGAGTTG-
1 AAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1813938 TGTTTTGAC
66 T-TTTTGAC
1813947 AAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1814012 TTTTTGAC
66 TTTTTGAC
* ** * * **
1814020 AAACAGAAATTGAAATTACCTTAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
1 AAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
*
1814085 ATTTTGA-
66 TTTTTGAC
*
1814092 AAATAGAAAT
1 AAACAGAAAT
1814102 AAAAACATCA
Statistics
Matches: 409, Mismatches: 33, Indels: 16
0.89 0.07 0.03
Matches are distributed among these distances:
72 11 0.03
73 320 0.78
74 20 0.05
75 11 0.03
76 47 0.11
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (73 bp):
AAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
TTTTTGAC
Found at i:1823919 original size:19 final size:20
Alignment explanation
Indices: 1823878--1823919 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
1823868 GACACCTAAT
*
1823878 AAATCTTATTTTTCAAAAGA
1 AAATCTTATTTTTCAAAACA
* *
1823898 AAAT-TTATTTTTTAAACCA
1 AAATCTTATTTTTCAAAACA
1823917 AAA
1 AAA
1823920 AGAAGGCCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (20 bp):
AAATCTTATTTTTCAAAACA
Found at i:1824994 original size:13 final size:13
Alignment explanation
Indices: 1824976--1825005 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1824966 TCATTGATTA
1824976 CTTTCCAAAAAAC
1 CTTTCCAAAAAAC
*
1824989 CTTTCCAAAAATC
1 CTTTCCAAAAAAC
1825002 CTTT
1 CTTT
1825006 ACAATAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.30, G:0.00, T:0.33
Consensus pattern (13 bp):
CTTTCCAAAAAAC
Found at i:1825154 original size:18 final size:18
Alignment explanation
Indices: 1825131--1825184 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
1825121 ACAAGTGGTG
1825131 GTGGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
*
1825149 GT-G-G--AGT-AGG-TA
1 GTGGAGCAAGTGTGGCTA
1825161 GTGGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
1825179 GTGGAG
1 GTGGAG
1825185 TTGGTGGTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 4 0.14
13 3 0.11
14 4 0.14
16 4 0.14
17 3 0.11
18 10 0.36
ACGTcount: A:0.22, C:0.07, G:0.48, T:0.22
Consensus pattern (18 bp):
GTGGAGCAAGTGTGGCTA
Found at i:1825167 original size:30 final size:30
Alignment explanation
Indices: 1825126--1825224 Score: 171
Period size: 30 Copynumber: 3.3 Consensus size: 30
1825116 TAGGTACAAG
1825126 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
* *
1825156 AGGTAGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
*
1825186 TGGTGGTGGAGCAAGTGTGGTTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
1825216 TGGTGGTGG
1 TGGTGGTGG
1825225 CAAAGGCTAG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.17, C:0.05, G:0.51, T:0.27
Consensus pattern (30 bp):
TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
Found at i:1825214 original size:18 final size:17
Alignment explanation
Indices: 1825125--1825214 Score: 56
Period size: 18 Copynumber: 5.7 Consensus size: 17
1825115 GTAGGTACAA
*
1825125 GTGGTGGTGGAGCAAGT
1 GTGGTAGTGGAGCAAGT
1825142 GTGGCTAGT-G-G--AGT
1 GTGG-TAGTGGAGCAAGT
*
1825156 -AGGTAGTGGAGCAAGT
1 GTGGTAGTGGAGCAAGT
1825172 GTGGCTAGT-G-G--AGT
1 GTGG-TAGTGGAGCAAGT
*
1825186 -TGGTGGTGGAGCAAGT
1 GTGGTAGTGGAGCAAGT
1825202 GTGGTTAGTGGAG
1 GTGG-TAGTGGAG
1825215 TTGGTGGTGG
Statistics
Matches: 55, Mismatches: 5, Indels: 25
0.65 0.06 0.29
Matches are distributed among these distances:
12 7 0.13
13 7 0.13
14 8 0.15
16 8 0.15
17 11 0.20
18 14 0.25
ACGTcount: A:0.19, C:0.06, G:0.50, T:0.26
Consensus pattern (17 bp):
GTGGTAGTGGAGCAAGT
Found at i:1834510 original size:31 final size:31
Alignment explanation
Indices: 1834436--1834533 Score: 87
Period size: 31 Copynumber: 3.2 Consensus size: 31
1834426 AGGGTTTAAT
*
1834436 TTAGTACCTAAAATTTA---TTTTGG-TCCAA
1 TTAGTACCT-AAATTTAGTTTTTTGGTTCAAA
*
1834464 TTAGATACCTGAATTTAGTTTTTTGGTTCAAA
1 TTAG-TACCTAAATTTAGTTTTTTGGTTCAAA
* * * * *
1834496 TTAGTTCCTAAATTTGGTTTTGTAGTCCAAA
1 TTAGTACCTAAATTTAGTTTTTTGGTTCAAA
1834527 TTAGTAC
1 TTAGTAC
1834534 TTATGAAAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
28 10 0.18
29 5 0.09
31 33 0.59
32 8 0.14
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (31 bp):
TTAGTACCTAAATTTAGTTTTTTGGTTCAAA
Found at i:1844477 original size:31 final size:31
Alignment explanation
Indices: 1844415--1844480 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
1844405 AATAGCTCAA
* *
1844415 TGACTTAAATAAAAACTTTTGAATAAGTTAG
1 TGACTTAAATAAAAACTTTTCAAAAAGTTAG
*
1844446 TGACTTAAATGAAAAC-TTTCAAAAAGTTTAG
1 TGACTTAAATAAAAACTTTTCAAAAAG-TTAG
1844477 TGAC
1 TGAC
1844481 CAAATTGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 8 0.26
31 23 0.74
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTTCAAAAAGTTAG
Found at i:1846673 original size:14 final size:14
Alignment explanation
Indices: 1846654--1846681 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1846644 GAAAACTATC
1846654 GCACCTTACAGATT
1 GCACCTTACAGATT
1846668 GCACCTTACAGATT
1 GCACCTTACAGATT
1846682 TCTTCCACGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (14 bp):
GCACCTTACAGATT
Found at i:1848994 original size:2 final size:2
Alignment explanation
Indices: 1848987--1849019 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1848977 ATATCAACCA
*
1848987 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1849020 AAAACAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1850929 original size:23 final size:23
Alignment explanation
Indices: 1850899--1850945 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1850889 TTATTGTATG
1850899 TGTGAAGCATATTATGAGAGAAA
1 TGTGAAGCATATTATGAGAGAAA
1850922 TGTGAAGCATATTATGAGAGAAA
1 TGTGAAGCATATTATGAGAGAAA
1850945 T
1 T
1850946 CTTGTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.26, T:0.28
Consensus pattern (23 bp):
TGTGAAGCATATTATGAGAGAAA
Found at i:1863922 original size:145 final size:146
Alignment explanation
Indices: 1863642--1863927 Score: 369
Period size: 145 Copynumber: 2.0 Consensus size: 146
1863632 CACAATCCCG
* * * *
1863642 GGGTTGAATTGATCTTCACTCGAATTCAATCCAATCTTTAAAGGGCAGTGATTGGTTTCTATAGA
1 GGGTTGAATTGA-CTTCACTCGAATCCAATCCAATCTTCAAAAGGCAATGATTGGTTTCTATAGA
** * * * *
1863707 TGAACCATAATATCTTCAATATAGTAGCACATTAATAGGTCCAAAAATTTTCTTTATTAAATTGT
65 TGAACCATAATATCTTCAATATAACAACACACTAATAGATCCAAAAATTTTCTTTATTAAATTAT
*
1863772 TAATCCAAATATTCCAA
130 CAATCCAAATATTCCAA
* * * *
1863789 GGGTTGAATTG-GTTCACTTGAATCCAATCTAATCTTCAAAAGTCAATGATTGGTTTCTATAGAT
1 GGGTTGAATTGACTTCACTCGAATCCAATCCAATCTTCAAAAGGCAATGATTGGTTTCTATAGAT
* * * *
1863853 GAACCATAGTGTCTTCAATATAACAACACACTAATAGATTCAAAGATTTT-TTTAATTAAATTAT
66 GAACCATAATATCTTCAATATAACAACACACTAATAGATCCAAAAATTTTCTTT-ATTAAATTAT
1863917 CAATCCAAATA
130 CAATCCAAATA
1863928 AGACAAGTAA
Statistics
Matches: 119, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
144 3 0.03
145 105 0.88
147 11 0.09
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (146 bp):
GGGTTGAATTGACTTCACTCGAATCCAATCCAATCTTCAAAAGGCAATGATTGGTTTCTATAGAT
GAACCATAATATCTTCAATATAACAACACACTAATAGATCCAAAAATTTTCTTTATTAAATTATC
AATCCAAATATTCCAA
Found at i:1874115 original size:53 final size:53
Alignment explanation
Indices: 1874034--1874184 Score: 205
Period size: 53 Copynumber: 2.8 Consensus size: 53
1874024 CTTACACGGT
* *
1874034 TCACATATCATACCGAAGCCATATCCCAGACATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAGACATGGTCTTATACGGAATCACATTA
*
1874089 TCACATTATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGAC-ATGGTCTTATACGGAATCACATTA
** * *
1874142 TCACATTGCACCGATGCCATAGCCCAGATATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGACATGGTCTTATACGG
1874185 GCGCACTTAT
Statistics
Matches: 87, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
52 1 0.01
53 79 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGACATGGTCTTATACGGAATCACATTA
Found at i:1878091 original size:8 final size:8
Alignment explanation
Indices: 1878080--1878121 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
1878070 GATAATAAAA
1878080 TTATAATT
1 TTATAATT
*
1878088 TTATTATT
1 TTATAATT
1878096 TTA-ATATT
1 TTATA-ATT
*
1878104 TTATATTT
1 TTATAATT
1878112 TTATAATT
1 TTATAATT
1878120 TT
1 TT
1878122 TAAATAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
8 27 0.96
9 1 0.04
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (8 bp):
TTATAATT
Found at i:1878120 original size:16 final size:17
Alignment explanation
Indices: 1878080--1878121 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
1878070 GATAATAAAA
1878080 TTATAATTTTATTATTT
1 TTATAATTTTATTATTT
*
1878097 TAAT-ATTTTA-TATTT
1 TTATAATTTTATTATTT
1878112 TTATAATTTT
1 TTATAATTTT
1878122 TAAATAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 8 0.36
16 11 0.50
17 3 0.14
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTATAATTTTATTATTT
Found at i:1891540 original size:36 final size:36
Alignment explanation
Indices: 1891429--1891542 Score: 95
Period size: 36 Copynumber: 3.1 Consensus size: 36
1891419 TAATATTGCA
* **
1891429 ACTGTCATTTTTACGATCCGCTTATCTAAGATCGCA
1 ACTGTCATTTTTACGGTCCGCTTATCTAAGATCGTG
* ** * **
1891465 ACCT-TCGATTTTCTAACAGTTTGCTTGATTTAATCTCGTG
1 A-CTGTC-ATTTT-T-ACGGTCCGCTT-ATCTAAGATCGTG
1891505 ACTGTCATTTTTACGGTCCGCTTATCTAAGATCGTG
1 ACTGTCATTTTTACGGTCCGCTTATCTAAGATCGTG
1891541 AC
1 AC
1891543 CTTCGATTTT
Statistics
Matches: 57, Mismatches: 15, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
36 15 0.26
37 15 0.26
38 2 0.04
39 14 0.25
40 11 0.19
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.39
Consensus pattern (36 bp):
ACTGTCATTTTTACGGTCCGCTTATCTAAGATCGTG
Found at i:1891609 original size:36 final size:35
Alignment explanation
Indices: 1891569--1891686 Score: 112
Period size: 36 Copynumber: 3.2 Consensus size: 35
1891559 GTTCACTTGC
*
1891569 TTTAATCTCGCAACTATCATTTTTACGGTCCGCTGA
1 TTTAATCTCGCAACT-TCATTTTTATGGTCCGCTGA
* * *
1891605 TTTAATATCGCAACCTTCAGTTTTCTAATAGTTCGCTTGA
1 TTTAATCTCGCAA-CTTCA-TTTT-T-ATGGTCCGC-TGA
*
1891645 TTTAATCTCGCAACTGTCATTTTTATGG-CTCGTTGA
1 TTTAATCTCGCAACT-TCATTTTTATGGTC-CGCTGA
1891681 TTTAAT
1 TTTAAT
1891687 ATCACGACTT
Statistics
Matches: 67, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
36 24 0.36
37 11 0.16
38 2 0.03
39 12 0.18
40 18 0.27
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.43
Consensus pattern (35 bp):
TTTAATCTCGCAACTTCATTTTTATGGTCCGCTGA
Found at i:1891648 original size:40 final size:39
Alignment explanation
Indices: 1891602--1891713 Score: 106
Period size: 40 Copynumber: 2.9 Consensus size: 39
1891592 TACGGTCCGC
1891602 TGATTTAATATCGCAACCTTCAGTTTTCTAATAGTTCGCT
1 TGATTTAATATCGCAACCTTCAGTTTTCTAATAGTTCG-T
* * *
1891642 TGATTTAATCTCGCAA-CTGTCA-TTTT-T-ATGGCTCGT
1 TGATTTAATATCGCAACCT-TCAGTTTTCTAATAGTTCGT
* * * * *
1891678 TGATTTAATATCACGACTTTCGGTTTTCTAACAGTT
1 TGATTTAATATCGCAACCTTCAGTTTTCTAATAGTT
1891714 TGCCAATTCA
Statistics
Matches: 56, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
36 16 0.29
37 11 0.20
38 2 0.04
39 9 0.16
40 18 0.32
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.44
Consensus pattern (39 bp):
TGATTTAATATCGCAACCTTCAGTTTTCTAATAGTTCGT
Found at i:1891682 original size:76 final size:76
Alignment explanation
Indices: 1891299--1891713 Score: 385
Period size: 76 Copynumber: 5.5 Consensus size: 76
1891289 ATCCACTGAT
* ** * * * **
1891299 TTGATTTAATATCGTGACTTTCGGTTTTTTAACAATT-GCTTGATTTAATCTCGTGA-TAGTCAT
1 TTGATTTAAGATCGCAACCTTCGGTTTTCTAACAGTTCGCTTGATTTAATCTCGCAACT-GTCAT
* *
1891362 TTTTATGGTCTG
65 TTTTACGGTCCG
* * * * * * *
1891374 TTGATTTAAGATTG-AGACCATCGGTTTTCTAATAATTTG-TTGATTTAATATTGCAACTGTCAT
1 TTGATTTAAGATCGCA-ACCTTCGGTTTTCTAACAGTTCGCTTGATTTAATCTCGCAACTGTCAT
*
1891437 TTTTACGATCCG
65 TTTTACGGTCCG
* * * **
1891449 CTT-ATCTAAGATCGCAACCTTCGATTTTCTAACAGTTTGCTTGATTTAATCTCGTGACTGTCAT
1 -TTGATTTAAGATCGCAACCTTCGGTTTTCTAACAGTTCGCTTGATTTAATCTCGCAACTGTCAT
1891513 TTTTACGGTCCG
65 TTTTACGGTCCG
* ** * * * *
1891525 CTT-ATCTAAGATCGTGACCTTCGATTTTCTAACAGTTCACTTGCTTTAATCTCGCAACTATCAT
1 -TTGATTTAAGATCGCAACCTTCGGTTTTCTAACAGTTCGCTTGATTTAATCTCGCAACTGTCAT
1891589 TTTTACGGTCCG
65 TTTTACGGTCCG
* * * *
1891601 CTGATTTAATATCGCAACCTTCAGTTTTCTAATAGTTCGCTTGATTTAATCTCGCAACTGTCATT
1 TTGATTTAAGATCGCAACCTTCGGTTTTCTAACAGTTCGCTTGATTTAATCTCGCAACTGTCATT
*
1891666 TTTATGG-CTCG
66 TTTACGGTC-CG
* * * *
1891677 TTGATTTAATATCACGACTTTCGGTTTTCTAACAGTT
1 TTGATTTAAGATCGCAACCTTCGGTTTTCTAACAGTT
1891714 TGCCAATTCA
Statistics
Matches: 281, Mismatches: 51, Indels: 15
0.81 0.15 0.04
Matches are distributed among these distances:
75 86 0.31
76 195 0.69
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (76 bp):
TTGATTTAAGATCGCAACCTTCGGTTTTCTAACAGTTCGCTTGATTTAATCTCGCAACTGTCATT
TTTACGGTCCG
Found at i:1891705 original size:152 final size:147
Alignment explanation
Indices: 1891247--1891713 Score: 443
Period size: 152 Copynumber: 3.1 Consensus size: 147
1891237 TCATTTAAGA
* ** * *
1891247 TAACAGTTTACTTTATTTAATATCGCAGTTATCATCTTTACGATCCACTGATTTGATTTAATATC
1 TAACAG-TTACTTGATTTAATATCGCAACTATCATTTTTACGAT-C-C-G--CTGATTTAATATC
** * * *
1891312 GTGACTTTCGGTTTTTTAACAATTGCTTGATTTAATCTCGTGA-TAGTCATTTTTATGGTCTGTT
60 GCAACCTTC-GTTTTCTAACAGTTGCTTGATTTAATCTCGTGACT-GTCATTTTTATGGTC-GTT
* *
1891376 GATTTAAGATTGAGACCATCGGTTTTC
122 GATTTAAGA-TCAGACCTTCGGTTTTC
* * ** * * * * *
1891403 TAATAATTTGTTGATTTAATATTGCAACTGTCATTTTTACGATCCGCTTATCTAAGATCGCAACC
1 TAACAGTTACTTGATTTAATATCGCAACTATCATTTTTACGATCCGCTGATTTAATATCGCAACC
* *
1891468 TTCGATTTTCTAACAGTTTGCTTGATTTAATCTCGTGACTGTCATTTTTACGGTCCGCTT-ATCT
66 TTCG-TTTTCTAACAG-TTGCTTGATTTAATCTCGTGACTGTCATTTTTATGGT-CG-TTGATTT
* *
1891532 AAGATCGTGACCTTCGATTTTC
127 AAGATC-AGACCTTCGGTTTTC
* * *
1891554 TAACAGTTCACTTGCTTTAATCTCGCAACTATCATTTTTACGGTCCGCTGATTTAATATCGCAAC
1 TAACAGTT-ACTTGATTTAATATCGCAACTATCATTTTTACGATCCGCTGATTTAATATCGCAAC
* **
1891619 CTTCAGTTTTCTAATAGTTCGCTTGATTTAATCTCGCAACTGTCATTTTTATGGCTCGTTGATTT
65 CTTC-GTTTTCTAACAGTT-GCTTGATTTAATCTCGTGACTGTCATTTTTATGG-TCGTTGATTT
* *
1891684 AATATCACGACTTTCGGTTTTC
127 AAGATCA-GACCTTCGGTTTTC
1891706 TAACAGTT
1 TAACAGTT
1891714 TGCCAATTCA
Statistics
Matches: 253, Mismatches: 46, Indels: 28
0.77 0.14 0.09
Matches are distributed among these distances:
149 1 0.00
150 25 0.10
151 64 0.25
152 126 0.50
153 3 0.01
154 1 0.00
155 29 0.11
156 4 0.02
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.43
Consensus pattern (147 bp):
TAACAGTTACTTGATTTAATATCGCAACTATCATTTTTACGATCCGCTGATTTAATATCGCAACC
TTCGTTTTCTAACAGTTGCTTGATTTAATCTCGTGACTGTCATTTTTATGGTCGTTGATTTAAGA
TCAGACCTTCGGTTTTC
Found at i:1892128 original size:18 final size:19
Alignment explanation
Indices: 1892102--1892144 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
1892092 CTCTCTTTGT
*
1892102 TTTTGAAATTTTAAA-ATA
1 TTTTAAAATTTTAAATATA
1892120 TTTTAAAATTTTAAATATA
1 TTTTAAAATTTTAAATATA
1892139 TATTTA
1 T-TTTA
1892145 TATACATCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.64
19 4 0.18
20 4 0.18
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TTTTAAAATTTTAAATATA
Found at i:1894938 original size:14 final size:14
Alignment explanation
Indices: 1894894--1894938 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
1894884 TTGTTTCAAC
1894894 TTATATTTTAATTA
1 TTATATTTTAATTA
*
1894908 TT-TATGTTTGAAATA
1 TTATAT-TTT-AATTA
1894923 TTATATTTTAATTA
1 TTATATTTTAATTA
1894937 TT
1 TT
1894939 TATGTTATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 3 0.12
14 11 0.42
15 9 0.35
16 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (14 bp):
TTATATTTTAATTA
Done.