Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397257.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_95.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 12062019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 103452 characters in sequence are not A, C, G, or T
File 4 of 26
Found at i:1232579 original size:144 final size:144
Alignment explanation
Indices: 1232316--1232584 Score: 364
Period size: 144 Copynumber: 1.9 Consensus size: 144
1232306 CAGCGGCTTA
* * * * * *
1232316 AACAAGGTGTTTTTGGGTGTGGCATGAAGCATGTGAAGATGAATAAATAGTTTAGAAAGGATTCA
1 AACAAGGTGCTTTTAGGTATGACATGAAGCATGCGAAGATGAATAAATAGTCTAGAAAGGATTCA
* * *
1232381 TCACCCCCAATGATTGAAGGGTACATATTTCATTTGCTCTTGGCTTATATTGACTAAAAGTCCTA
66 TCACCCCCAATGATTAAAGGGTACATATCTCATTTGCTCTTGGCTTATACTGACTAAAAGTCCTA
1232446 AGCCTAGATGCCTC
131 AGCCTAGATGCCTC
* * *
1232460 AACAAGGTGCTTTTAGGTATGACATGAAGCATGCGAAGATGAATGAGTAGTCTAGAGAGGATTCA
1 AACAAGGTGCTTTTAGGTATGACATGAAGCATGCGAAGATGAATAAATAGTCTAGAAAGGATTCA
**
1232525 TCA-CTTCAAGTGATTTAAAAGGG-A-ATATCTCATTTGCTCTTGGCTTATACTGACTAAAAG
66 TCACCCCCAA-TGA-TT-AAAGGGTACATATCTCATTTGCTCTTGGCTTATACTGACTAAAAG
1232585 CCCTTGGCCA
Statistics
Matches: 108, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
143 4 0.04
144 96 0.89
145 3 0.03
146 5 0.05
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (144 bp):
AACAAGGTGCTTTTAGGTATGACATGAAGCATGCGAAGATGAATAAATAGTCTAGAAAGGATTCA
TCACCCCCAATGATTAAAGGGTACATATCTCATTTGCTCTTGGCTTATACTGACTAAAAGTCCTA
AGCCTAGATGCCTC
Found at i:1235045 original size:21 final size:20
Alignment explanation
Indices: 1235015--1235054 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
1235005 TTAGATGAGC
1235015 AACTTAAATTGTA-TTTTGAA
1 AACTTAAATT-TAGTTTTGAA
1235035 AACTTGAAATTTAGTTTTGA
1 AACTT-AAATTTAGTTTTGA
1235055 GAATGGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
AACTTAAATTTAGTTTTGAA
Found at i:1236012 original size:23 final size:23
Alignment explanation
Indices: 1235981--1236026 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1235971 CTTTCGAAAC
1235981 TATTGTGATATGTAAAGTTGAAG
1 TATTGTGATATGTAAAGTTGAAG
*
1236004 TATTTTGATATGTAAAGTTGAAG
1 TATTGTGATATGTAAAGTTGAAG
1236027 CATGATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.24, T:0.41
Consensus pattern (23 bp):
TATTGTGATATGTAAAGTTGAAG
Found at i:1242980 original size:76 final size:76
Alignment explanation
Indices: 1242854--1243015 Score: 245
Period size: 76 Copynumber: 2.1 Consensus size: 76
1242844 AATACCATCT
*
1242854 ATTTTAATTTTGGGTGATCCATAAAAATAGAAAATTGTTTCCTACTTTAAAA-ACAATTCCTAAA
1 ATTTTAATTTTGGATGATCCATAAAAATAGAAAATTGTTTCCTACTTTAAAAGA-AATTCCTAAA
1242918 ATTAAGAATAGA
65 ATTAAGAATAGA
* * *
1242930 ATTTTAGTTTTGGATGATGCATAAAAATAGGAAATTGTTTCCTACTTTAAAAGAAATTCCTAAAA
1 ATTTTAATTTTGGATGATCCATAAAAATAGAAAATTGTTTCCTACTTTAAAAGAAATTCCTAAAA
* *
1242995 TTAAGGATAGT
66 TTAAGAATAGA
*
1243006 GTTTTAATTT
1 ATTTTAATTT
1243016 GGGGAAATTG
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
76 76 0.99
77 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (76 bp):
ATTTTAATTTTGGATGATCCATAAAAATAGAAAATTGTTTCCTACTTTAAAAGAAATTCCTAAAA
TTAAGAATAGA
Found at i:1243880 original size:171 final size:171
Alignment explanation
Indices: 1243307--1243894 Score: 631
Period size: 170 Copynumber: 3.4 Consensus size: 171
1243297 NNNNNNNNNN
* * * * * *
1243307 TTTTAGTTAAAATAGATTACAATTGAATGT-TAACCTCAAGAAACGTGAAGAAAAAAATGTTCAT
1 TTTTAGTTAAAACAGATTATAATT-AATGTCT-ACCTCGAGAAACATGAAGAAAAAGATATTCAT
* * * * * *
1243371 TGACAAGAAAAGTCCATTTATAGCCATTTATGACTTCAAAAGCCTTATTACTTGCTTTAAATGGT
64 TGGCAAGAAAAGTCTATTTATAGTCACTTATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGT
*
1243436 TTTATAATCTCATAATTGACTTTAAGTTGAA-CTGTTTTCTT-T
129 TTTATAATCTCATAATTGACTTTAAGTTGAATCT-TTTTTTTAT
* * * **
1243478 TTTT-GTTAAAACAGATTATAATTAAATGTCTACCTTGAGAAA-AGTAAAAAAAAAGCCATTCAT
1 TTTTAGTTAAAACAGATTATAATT-AATGTCTACCTCGAGAAACA-TGAAGAAAAAGATATTCAT
** * * *
1243541 TGGCAAGAAAAGTCTATTTATAGTCACCCATGCCTTCGAAATCCTTATT-CTCACTTTAAATGGT
64 TGGCAAGAAAAGTCTATTTATAGTCACTTATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGT
* * *
1243605 TTGATAATCTCATAATTGA-TTTGAAGTTGAAT-TTATTTGTAT
129 TTTATAATCTCATAATTGACTTT-AAGTTGAATCTTTTTTTTAT
* * * ** * * *
1243647 TTTTTGTTAAAACAAATTTTAAATGGAGGTCTATCTCGGGAAACATGAAGAAAAAGATATTCATT
1 TTTTAGTTAAAACAGATTAT-AATTAATGTCTACCTCGAGAAACATGAAGAAAAAGATATTCATT
* * * *
1243712 GGTAAGAAAAGTTTATCTATAGTCACTTATGCCTTTC-AAAGGCTTATTACTCGCTTTAAATGGT
65 GGCAAGAAAAGTCTATTTATAGTCACTTATGCC-TTCAAAAGCCTTATTACTCGCTTTAAATGGT
* *
1243776 TTTATAATCTCATACTTGACTTTAAGCTGAATCTTTTTTTTAT
129 TTTATAATCTCATAATTGACTTTAAGTTGAATCTTTTTTTTAT
* *
1243819 TTTTAGTTAAAATC-GATTATAATTATATGTCTACCTTGAGAAACATGAAG-ACAAGATATTCAT
1 TTTTAGTTAAAA-CAGATTATAATTA-ATGTCTACCTCGAGAAACATGAAGAAAAAGATATTCAT
1243882 TGGCAAGAAAAGT
64 TGGCAAGAAAAGT
1243895 GTAACATCCG
Statistics
Matches: 340, Mismatches: 63, Indels: 28
0.79 0.15 0.06
Matches are distributed among these distances:
168 7 0.02
169 45 0.13
170 163 0.48
171 78 0.23
172 46 0.14
173 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.38
Consensus pattern (171 bp):
TTTTAGTTAAAACAGATTATAATTAATGTCTACCTCGAGAAACATGAAGAAAAAGATATTCATTG
GCAAGAAAAGTCTATTTATAGTCACTTATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTT
TATAATCTCATAATTGACTTTAAGTTGAATCTTTTTTTTAT
Found at i:1257253 original size:4 final size:4
Alignment explanation
Indices: 1257244--1257270 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1257234 GACTATTGGT
1257244 TCAA TCAA TCAA TCAA TCAA TCAA TCA
1 TCAA TCAA TCAA TCAA TCAA TCAA TCA
1257271 GACCCGTCAC
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:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
TCAA
Found at i:1265924 original size:258 final size:258
Alignment explanation
Indices: 1265456--1265932 Score: 837
Period size: 258 Copynumber: 1.8 Consensus size: 258
1265446 AATTATTTTA
* *
1265456 AACCTCACATTTAAATGTATTTTGACCAACTTTGTGATGTGAAAAACAGTTTCAAGTTTGTTTTA
1 AACCTCACATTTAAATGTATTTTGACAAACTTTGTAATGTGAAAAACAGTTTCAAGTTTGTTTTA
* *
1265521 TGAAATCTATGTATACTATGTAAATATGTTATTATGTATTTACTTTTGAGCATAGGGAAAAAGCC
66 TGAAATCTATATATAATATGTAAATATGTTATTATGTATTTACTTTTGAGCATAGGGAAAAAGCC
*
1265586 TTTCAATTGTTTAATGCCTCAAAATTTTGATATCTATCTATTGATAATTGCTTGATTGATGATTT
131 TTTCAATTGTTTAATGCCTCAAAAATTTGATATCTATCTATTGATAATTGCTTGATTGATGATTT
*
1265651 GAAAATTTAGAATGAAAAGTAATTGCTTAATTATTTTAATATAATTAAGCATGCCTATTCTAT
196 GAAAATTTAGAATGAAAAATAATTGCTTAATTATTTTAATATAATTAAGCATGCCTATTCTAT
*
1265714 AACCTCGCATTTAAATGTATTTTGACAAACTTTGTAATGTGAAAAACAGTTTCAAGTTTGTTTTA
1 AACCTCACATTTAAATGTATTTTGACAAACTTTGTAATGTGAAAAACAGTTTCAAGTTTGTTTTA
* * *
1265779 TGAAATCTATATATAATATGTAAATATGTTATTATGTATTTACTTTTGAGCATGGGGAAAAGGCT
66 TGAAATCTATATATAATATGTAAATATGTTATTATGTATTTACTTTTGAGCATAGGGAAAAAGCC
* *
1265844 TTTCAATTGTTTAATGCCTCAAAAATTTGATATTTGTCTATTGATAATTGCTTGATTGATGATTT
131 TTTCAATTGTTTAATGCCTCAAAAATTTGATATCTATCTATTGATAATTGCTTGATTGATGATTT
*
1265909 GAAAATTTGGAATGAAAAATAATT
196 GAAAATTTAGAATGAAAAATAATT
1265933 TGTCTTTGAG
Statistics
Matches: 206, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
258 206 1.00
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.42
Consensus pattern (258 bp):
AACCTCACATTTAAATGTATTTTGACAAACTTTGTAATGTGAAAAACAGTTTCAAGTTTGTTTTA
TGAAATCTATATATAATATGTAAATATGTTATTATGTATTTACTTTTGAGCATAGGGAAAAAGCC
TTTCAATTGTTTAATGCCTCAAAAATTTGATATCTATCTATTGATAATTGCTTGATTGATGATTT
GAAAATTTAGAATGAAAAATAATTGCTTAATTATTTTAATATAATTAAGCATGCCTATTCTAT
Found at i:1269703 original size:14 final size:15
Alignment explanation
Indices: 1269686--1269714 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1269676 CAGGAATCAA
1269686 TTTAAG-ATATGTTC
1 TTTAAGCATATGTTC
1269700 TTTAAGCATATGTTC
1 TTTAAGCATATGTTC
1269715 GAATTCGACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.28, C:0.10, G:0.14, T:0.48
Consensus pattern (15 bp):
TTTAAGCATATGTTC
Found at i:1275005 original size:20 final size:21
Alignment explanation
Indices: 1274982--1275033 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1274972 TAGGCAAACG
* *
1274982 TATCGATACATT-GCCAACTA
1 TATCGATACATTGGCAAAATA
* *
1275002 TATCAATACATTGGCAAAATG
1 TATCGATACATTGGCAAAATA
1275023 TATCGATACAT
1 TATCGATACAT
1275034 CACAGAGAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (21 bp):
TATCGATACATTGGCAAAATA
Found at i:1280015 original size:215 final size:215
Alignment explanation
Indices: 1279639--1280055 Score: 647
Period size: 215 Copynumber: 1.9 Consensus size: 215
1279629 CATGTTGTGC
* * * * *
1279639 AGTATATGCATTTCCTATGAGGAAAAGAATATTAAATAATGTGGTTTTGAGGAATGATTTCTTGC
1 AGTATATGCATTTCCTATAAGGAAAAGAATATGAAAGAATGTGGTTTTAAGGAAGGATTTCTTGC
* * *
1279704 CATTATGTAGGCCGACAATGTTTCAGTCTTGATGTGATTATGGATGTAGGGCACATGAAGTTGAA
66 CATTATGTAGGCCGACAACGTTTCAGTCTTGATGTGATTATGGATGTAGGGCACATAAAGGTGAA
* * *
1279769 AGATTGCCTGATAATGATAAGGTACAAGTTGGATTGTGATCCACATAATTTGGAGTTTTGATTTG
131 AGATTACCTAATAATGATAAGGTACAAGTTGGATTGTGATCCACAGAATTTGGAGTTTTGATTTG
1279834 TGAGTTGGAAGGGACAACTA
196 TGAGTTGGAAGGGACAACTA
* * *
1279854 AGTATATGGATTTCCTATAAGGATAAGAATATGCAAGAATGTGGTTTTAAGGAAGGATTTCTTGC
1 AGTATATGCATTTCCTATAAGGAAAAGAATATGAAAGAATGTGGTTTTAAGGAAGGATTTCTTGC
*
1279919 CATTATGTAGGCCGACAACGTTTC-GATCTTGATGTGCTTATGGATGTAGGGCACATAAAGGTGA
66 CATTATGTAGGCCGACAACGTTTCAG-TCTTGATGTGATTATGGATGTAGGGCACATAAAGGTGA
* ** *
1279983 AAGATTACCTAATAATGATAAGGTATAAGTTGGATTGTGATTTATAGAATTTGGAGTTTTGATTT
130 AAGATTACCTAATAATGATAAGGTACAAGTTGGATTGTGATCCACAGAATTTGGAGTTTTGATTT
1280048 GTGAGTTG
195 GTGAGTTG
1280056 TAGGTGTAAG
Statistics
Matches: 182, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
214 1 0.01
215 181 0.99
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.35
Consensus pattern (215 bp):
AGTATATGCATTTCCTATAAGGAAAAGAATATGAAAGAATGTGGTTTTAAGGAAGGATTTCTTGC
CATTATGTAGGCCGACAACGTTTCAGTCTTGATGTGATTATGGATGTAGGGCACATAAAGGTGAA
AGATTACCTAATAATGATAAGGTACAAGTTGGATTGTGATCCACAGAATTTGGAGTTTTGATTTG
TGAGTTGGAAGGGACAACTA
Found at i:1282233 original size:18 final size:19
Alignment explanation
Indices: 1282203--1282238 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1282193 GAATTTGTGC
1282203 ATTTTCAAAAAGTTAGGAT
1 ATTTTCAAAAAGTTAGGAT
1282222 ATTTTC-AAAAGTTAGGA
1 ATTTTCAAAAAGTTAGGA
1282239 AATAATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.36
Consensus pattern (19 bp):
ATTTTCAAAAAGTTAGGAT
Found at i:1282626 original size:30 final size:29
Alignment explanation
Indices: 1282590--1282698 Score: 107
Period size: 31 Copynumber: 3.7 Consensus size: 29
1282580 TTTAGACAGG
*
1282590 AAAATATGTTTGTCTTAATTTAAGATAAAA
1 AAAATATTTTTGTCTTAATTTAAGA-AAAA
* * *
1282620 AAAATATTTTTTATCTTAATCTTAACAGAAA
1 AAAATA-TTTTTGTCTTAAT-TTAAGAAAAA
*
1282651 AACAT-TTTTT-TCTTAATTT-AGACAAAA
1 AAAATATTTTTGTCTTAATTTAAGA-AAAA
1282678 TAAAATATTTTTGTCTTAATT
1 -AAAATATTTTTGTCTTAATT
1282699 AAACACAAGA
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
26 2 0.03
27 5 0.08
28 11 0.17
29 10 0.15
30 14 0.22
31 18 0.28
32 5 0.08
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.45
Consensus pattern (29 bp):
AAAATATTTTTGTCTTAATTTAAGAAAAA
Found at i:1293705 original size:14 final size:14
Alignment explanation
Indices: 1293674--1293704 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1293664 TGGATTCTAA
1293674 TTTTCTTTCTTCTT
1 TTTTCTTTCTTCTT
1293688 TTTTCTTTCTT-TT
1 TTTTCTTTCTTCTT
1293701 TTTT
1 TTTT
1293705 TTGTTATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTCTTTCTTCTT
Found at i:1314209 original size:16 final size:16
Alignment explanation
Indices: 1314190--1314222 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1314180 TAAATTTTTT
1314190 AAAAAA-TAAAATTAAA
1 AAAAAACTAAAA-TAAA
1314206 AAAAAACTAAAATAAA
1 AAAAAACTAAAATAAA
1314222 A
1 A
1314223 GCTACAGGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (16 bp):
AAAAAACTAAAATAAA
Found at i:1315436 original size:20 final size:20
Alignment explanation
Indices: 1315413--1315453 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1315403 GATAAATGAG
*
1315413 CAGATCTATCCATAGATGGT
1 CAGATCTATCAATAGATGGT
1315433 CAGATCTATCAATAGATGGT
1 CAGATCTATCAATAGATGGT
1315453 C
1 C
1315454 GTCAAGAAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (20 bp):
CAGATCTATCAATAGATGGT
Found at i:1315595 original size:92 final size:92
Alignment explanation
Indices: 1315436--1315613 Score: 232
Period size: 92 Copynumber: 1.9 Consensus size: 92
1315426 AGATGGTCAG
** * ** * * * *
1315436 ATCTATCAATAGATGGTCGTCAAGAAGCTTCCAAAAATTGTTTTAAAGCTCATTTGTTGATAGAT
1 ATCTATCAATAGATGACCATCAAGAAGCTTCCAAAAAGGGTTTTAAAGCTCATCTATCGATAAAT
**
1315501 AGCTTGATCTAG-TGATAGATGGCTCCC
66 AGCCCGATCTAGCT-ATAGATGGCTCCC
*
1315528 ATCTATCAATAGATGACCATTAAGAAGCTTCCAAAAAGGGTTTTAAAGCTCATCTATCGATAAAT
1 ATCTATCAATAGATGACCATCAAGAAGCTTCCAAAAAGGGTTTTAAAGCTCATCTATCGATAAAT
1315593 AGCCCGATCTAGCTATAGATG
66 AGCCCGATCTAGCTATAGATG
1315614 ACATCATTTT
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
92 72 0.99
93 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (92 bp):
ATCTATCAATAGATGACCATCAAGAAGCTTCCAAAAAGGGTTTTAAAGCTCATCTATCGATAAAT
AGCCCGATCTAGCTATAGATGGCTCCC
Found at i:1337491 original size:35 final size:35
Alignment explanation
Indices: 1337452--1337527 Score: 134
Period size: 35 Copynumber: 2.2 Consensus size: 35
1337442 CGGGAAAAAC
* *
1337452 CATTGTTGAAGGTTGTGCCTGAGCCTTTGAAAAGT
1 CATTGTTGAAGGTTGTGACTGAGCCTGTGAAAAGT
1337487 CATTGTTGAAGGTTGTGACTGAGCCTGTGAAAAGT
1 CATTGTTGAAGGTTGTGACTGAGCCTGTGAAAAGT
1337522 CATTGT
1 CATTGT
1337528 AAAAGCTTGG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.24, C:0.13, G:0.29, T:0.34
Consensus pattern (35 bp):
CATTGTTGAAGGTTGTGACTGAGCCTGTGAAAAGT
Found at i:1338790 original size:16 final size:16
Alignment explanation
Indices: 1338767--1338806 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1338757 TTTAGAATTG
1338767 AAACAATTTGAACTTA
1 AAACAATTTGAACTTA
* * *
1338783 AAATAATTTAAACTCA
1 AAACAATTTGAACTTA
1338799 AAACAATT
1 AAACAATT
1338807 CAAATTTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.55, C:0.12, G:0.03, T:0.30
Consensus pattern (16 bp):
AAACAATTTGAACTTA
Found at i:1340458 original size:85 final size:86
Alignment explanation
Indices: 1340304--1340474 Score: 272
Period size: 85 Copynumber: 2.0 Consensus size: 86
1340294 AATAATGAAA
* * *
1340304 AACTTCAAACCAGCAGCTACAAAATAATGCCCCTCAAATAGAGAGTATTTGTGACACCCCATATT
1 AACTTCAAACCAGCAGCTACAAAATAATGCCCCTCAAATACAGAGTATTTATGACACCCAATATT
1340369 TGTAATAATTTCATTATGTAT
66 TGTAATAATTTCATTATGTAT
** * *
1340390 AACTTCAAACCAGTGGCTACAAAATACTGCCCC-CAAATACAGCGTATTTATGACACCCAATATT
1 AACTTCAAACCAGCAGCTACAAAATAATGCCCCTCAAATACAGAGTATTTATGACACCCAATATT
1340454 TGTAATAATTTCATTATGTAT
66 TGTAATAATTTCATTATGTAT
1340475 CTGGACACTT
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
85 48 0.62
86 30 0.38
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (86 bp):
AACTTCAAACCAGCAGCTACAAAATAATGCCCCTCAAATACAGAGTATTTATGACACCCAATATT
TGTAATAATTTCATTATGTAT
Found at i:1358525 original size:74 final size:75
Alignment explanation
Indices: 1358425--1358768 Score: 416
Period size: 74 Copynumber: 4.7 Consensus size: 75
1358415 GACAAAGTAT
* * * * *
1358425 TCTTAGTTGACTAACCATACTTCTTAGTC-ATTTAAGTCT-TCTTTGTCTTGTAATTAAATTCTC
1 TCTTAGTTCACTAACCATGCTTCTTAGTCGA-TTAAGTCTCTCTTTGTCTTGTAATTGAAGTCTT
* *
1358488 TAGCAGTAAGC
65 TAGCAATGAGC
* *
1358499 TCTTAGTTCACTAACCTTGCTTCTTAGTCGATTAAGT-TCTCTCTGTCTTGTAATTGAAGTCTTT
1 TCTTAGTTCACTAACCATGCTTCTTAGTCGATTAAGTCTCTCTTTGTCTTGTAATTGAAGTCTTT
1358563 AGCAATGAGC
66 AGCAATGAGC
* *
1358573 TCTTAGTTCACTAACCTTGCTTCTTAGTCGATTAAGT-TCTCTCTGTCTTGTAATTGAAGTCTTT
1 TCTTAGTTCACTAACCATGCTTCTTAGTCGATTAAGTCTCTCTTTGTCTTGTAATTGAAGTCTTT
* * *
1358637 GGTAGTGAGC
66 AGCAATGAGC
* * * *
1358647 TCTTAGTTGACTAACCATGCTACTTAATCAATTAAG-CTCTCTTTGTCTTGTAATTGAAGTCTTT
1 TCTTAGTTCACTAACCATGCTTCTTAGTCGATTAAGTCTCTCTTTGTCTTGTAATTGAAGTCTTT
1358711 -GACAATGAGC
66 AG-CAATGAGC
* * *
1358721 TCTTAG-TCGACTAACCATACTTCTTAGTCGACTAAGTCT-TTTTTGTCT
1 TCTTAGTTC-ACTAACCATGCTTCTTAGTCGATTAAGTCTCTCTTTGTCT
1358769 CACAATCTGC
Statistics
Matches: 237, Mismatches: 27, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
73 3 0.01
74 231 0.97
75 3 0.01
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (75 bp):
TCTTAGTTCACTAACCATGCTTCTTAGTCGATTAAGTCTCTCTTTGTCTTGTAATTGAAGTCTTT
AGCAATGAGC
Found at i:1361532 original size:49 final size:48
Alignment explanation
Indices: 1361475--1361572 Score: 151
Period size: 49 Copynumber: 2.0 Consensus size: 48
1361465 AAAACTTAGT
* *
1361475 TTGGCTATATAAATATGCTATGTTAGCAAACTAAAACTCTAAGCTTTCA
1 TTGGCTATAAAAATATGCTATGTTA-CAAACTAAAACTCTAAGCCTTCA
* *
1361524 TTGGCTATAAAAATATGTTATGTTACCAACTAAAACTCTAAGCCTTCA
1 TTGGCTATAAAAATATGCTATGTTACAAACTAAAACTCTAAGCCTTCA
1361572 T
1 T
1361573 CCACTTCTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
48 22 0.49
49 23 0.51
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (48 bp):
TTGGCTATAAAAATATGCTATGTTACAAACTAAAACTCTAAGCCTTCA
Found at i:1366810 original size:22 final size:21
Alignment explanation
Indices: 1366784--1366840 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
1366774 ATTTAATTTT
*
1366784 ATTAATATATTTCTTATAAATG
1 ATTAATATATTT-TTAAAAATG
* *
1366806 ATTAATAAAATTTTTAAAAATT
1 ATTAAT-ATATTTTTAAAAATG
*
1366828 CTTAATATATTTT
1 ATTAATATATTTT
1366841 AAATAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 6 0.21
22 18 0.62
23 5 0.17
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (21 bp):
ATTAATATATTTTTAAAAATG
Found at i:1371688 original size:2 final size:2
Alignment explanation
Indices: 1371634--1371669 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1371624 TTAAAAGAAG
1371634 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1371670 GAGAAGCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1377756 original size:21 final size:22
Alignment explanation
Indices: 1377727--1377770 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1377717 AAGTGATTAA
1377727 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
* *
1377748 TTTAGGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
1377770 T
1 T
1377771 ACTTTAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:1378442 original size:12 final size:12
Alignment explanation
Indices: 1378416--1378451 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
1378406 CAGAGATTTT
1378416 AGAGGCAGC-AG
1 AGAGGCAGCAAG
1378427 AGAGGCAGCAAG
1 AGAGGCAGCAAG
1378439 AGAGGCAGCAAG
1 AGAGGCAGCAAG
1378451 A
1 A
1378452 AAATTCTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.42, C:0.17, G:0.42, T:0.00
Consensus pattern (12 bp):
AGAGGCAGCAAG
Found at i:1388665 original size:20 final size:21
Alignment explanation
Indices: 1388640--1388679 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1388630 AACTGGTTAA
* *
1388640 AAATTACAAT-TTATTATTAT
1 AAATTAAAATATTATAATTAT
1388660 AAATTAAAATATTATAATTA
1 AAATTAAAATATTATAATTA
1388680 AATAAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (21 bp):
AAATTAAAATATTATAATTAT
Found at i:1389241 original size:13 final size:13
Alignment explanation
Indices: 1389223--1389256 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
1389213 TTGTACACAC
1389223 AAATTTCTCATCG
1 AAATTTCTCATCG
*
1389236 AAATTTCTCGTCG
1 AAATTTCTCATCG
1389249 AAATTTCT
1 AAATTTCT
1389257 TAACTTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (13 bp):
AAATTTCTCATCG
Found at i:1389443 original size:51 final size:51
Alignment explanation
Indices: 1389388--1389494 Score: 160
Period size: 51 Copynumber: 2.1 Consensus size: 51
1389378 ACTTTACTTA
* * *
1389388 ATCTTCACTTCAAGGGTCTTTACGACTTAATCTTGATCATGAACACTTGAT
1 ATCTTCACTTCAAGGGACTTCACGACTTAATCTTGATCACGAACACTTGAT
** *
1389439 ATCTTTGCTTCAAGGGACTTCACGACTTAATCTTGATCACGAATACTTGAT
1 ATCTTCACTTCAAGGGACTTCACGACTTAATCTTGATCACGAACACTTGAT
1389490 ATCTT
1 ATCTT
1389495 GATCACGAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.37
Consensus pattern (51 bp):
ATCTTCACTTCAAGGGACTTCACGACTTAATCTTGATCACGAACACTTGAT
Found at i:1389965 original size:81 final size:81
Alignment explanation
Indices: 1389876--1390069 Score: 264
Period size: 81 Copynumber: 2.4 Consensus size: 81
1389866 TAATTATTAG
* * *
1389876 AGATAAATTAGACGACCAATAATTAAATTTTGATTGGTTAAAAATATGAATATTACCTCTAAATT
1 AGATAAATTAGACGACCAATAACTAAATTTTGATTGGTCAAAAATATAAATATTACCTCTAAATT
1389941 ATTTTGATTTATTTAA
66 ATTTTGATTTATTTAA
* * * *
1389957 AGATAAATTGGATGACCAATAACTAATTTTTGATTGGTCAAAAATATAAATATTATCTCTAAATT
1 AGATAAATTAGACGACCAATAACTAAATTTTGATTGGTCAAAAATATAAATATTACCTCTAAATT
**
1390022 ATTTTGATTTATTTGG
66 ATTTTGATTTATTTAA
* *
1390038 AGATAAATTGGATG-CTCAATAACTAATATTTT
1 AGATAAATTAGACGAC-CAATAACTAA-ATTTT
1390070 TATTAGTCCA
Statistics
Matches: 101, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
80 1 0.01
81 96 0.95
82 4 0.04
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.41
Consensus pattern (81 bp):
AGATAAATTAGACGACCAATAACTAAATTTTGATTGGTCAAAAATATAAATATTACCTCTAAATT
ATTTTGATTTATTTAA
Found at i:1395078 original size:71 final size:68
Alignment explanation
Indices: 1395000--1395214 Score: 209
Period size: 71 Copynumber: 3.0 Consensus size: 68
1394990 CGCATAAAGG
* * *
1395000 GTCAATCTTGTGAAGTAAAAAATAGGGGAAGTAATGCATTATGGTCCAAGATCGACTATAAGCCC
1 GTCAATCTTATGAAG-AAAAAAT-GGGGAA-TAATGCATTCTAGTCCAAGATCGACTATAAGCCC
1395065 TCTATA
63 TCTATA
* * ** *
1395071 GTCAATCTTATGAAGGAAAAATGGAGAAAATACAAACATTCTAGTCCAAGATC-AGCTATAAACC
1 GTCAATCTTATGAAGAAAAAATGG-G-GAATA-ATGCATTCTAGTCCAAGATCGA-CTATAAGCC
1395135 CTCTATA
62 CTCTATA
* * * *
1395142 GTCGATCTTATGAAGAAAAAATGAGTGAAAAATGAACATTCTAGTCCAAGATCGACTGT-AGACC
1 GTCAATCTTATGAAGAAAAAATG-GGGAATAATG--CATTCTAGTCCAAGATCGACTATAAG-CC
1395206 CTCTATA
62 CTCTATA
1395213 GT
1 GT
1395215 TGAATTTGTG
Statistics
Matches: 118, Mismatches: 17, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
69 3 0.03
70 14 0.12
71 99 0.84
72 2 0.02
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.26
Consensus pattern (68 bp):
GTCAATCTTATGAAGAAAAAATGGGGAATAATGCATTCTAGTCCAAGATCGACTATAAGCCCTCT
ATA
Found at i:1395227 original size:71 final size:71
Alignment explanation
Indices: 1395043--1395286 Score: 239
Period size: 71 Copynumber: 3.4 Consensus size: 71
1395033 ATGCATTATG
* *
1395043 GTCCAAGATCGACTATAAGCCCTCTATAG-TCAATCTTATGAAGGAAAAATGGAGAAAATACAAA
1 GTCCAAGATCGACTATAA-CCCTCTATAGTTGAATCTTATGAAGAAAAAATGGAGAAAATACAAA
1395107 CATTCTA
65 CATTCTA
* * **
1395114 GTCCAAGATC-AGCTATAAACCCTCTATAGTCG-ATCTTATGAAGAAAAAATGAGTGAAAA-ATG
1 GTCCAAGATCGA-CTAT-AACCCTCTATAGTTGAATCTTATGAAGAAAAAATG-GAGAAAATACA
1395176 AACATTCTA
63 AACATTCTA
* * ** *
1395185 GTCCAAGATCGACTGTAGACCCTCTATAGTTGAAT-TTGTGAAGAGGAAATGGATG-AAATGCAA
1 GTCCAAGATCGACTATA-ACCCTCTATAGTTGAATCTTATGAAGAAAAAATGGA-GAAAATAC-A
*
1395248 AACCTTCTA
63 AACATTCTA
* * *
1395257 GTCTAGGATCGACTATAGACCCTCCATAGT
1 GTCCAAGATCGACTATA-ACCCTCTATAGT
1395287 CAATCCTAGA
Statistics
Matches: 143, Mismatches: 20, Indels: 19
0.79 0.11 0.10
Matches are distributed among these distances:
70 6 0.04
71 92 0.64
72 45 0.31
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (71 bp):
GTCCAAGATCGACTATAACCCTCTATAGTTGAATCTTATGAAGAAAAAATGGAGAAAATACAAAC
ATTCTA
Found at i:1398253 original size:36 final size:36
Alignment explanation
Indices: 1398213--1398310 Score: 124
Period size: 36 Copynumber: 2.7 Consensus size: 36
1398203 TTGATTTAAT
*
1398213 GGTTATCGTTTGATCCTGTTAAAAAGCAGCTATAAC
1 GGTTATCGCTTGATCCTGTTAAAAAGCAGCTATAAC
* * * * * *
1398249 GGTTATCACTTGATCCTGTGAAAAAACTGTTATAAG
1 GGTTATCGCTTGATCCTGTTAAAAAGCAGCTATAAC
*
1398285 GGTTATTGCTTGATCCTGTTAAAAAG
1 GGTTATCGCTTGATCCTGTTAAAAAG
1398311 TCAATGTAAG
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (36 bp):
GGTTATCGCTTGATCCTGTTAAAAAGCAGCTATAAC
Found at i:1398332 original size:36 final size:36
Alignment explanation
Indices: 1398287--1398363 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
1398277 GTTATAAGGG
* * *
1398287 TTATTGCTTGATCCTGTTAAAAAGTCAATGTAAGAT
1 TTATCGCTTGATCCCGTGAAAAAGTCAATGTAAGAT
*
1398323 TTATCGCTTGATCCCGTGAAAAAGTCAATGTAAGGT
1 TTATCGCTTGATCCCGTGAAAAAGTCAATGTAAGAT
1398359 TTATC
1 TTATC
1398364 TCTTTATCTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.36
Consensus pattern (36 bp):
TTATCGCTTGATCCCGTGAAAAAGTCAATGTAAGAT
Found at i:1398381 original size:36 final size:36
Alignment explanation
Indices: 1398305--1398411 Score: 115
Period size: 36 Copynumber: 3.0 Consensus size: 36
1398295 TGATCCTGTT
* * * * *
1398305 AAAAAGTCAATGTAAGATTTATCGCTTGATCCCGTG
1 AAAAAGTCAATGTAAGGTTTATCACTTGATCTCATC
* *
1398341 AAAAAGTCAATGTAAGGTTTATCTCTTTATCTCATC
1 AAAAAGTCAATGTAAGGTTTATCACTTGATCTCATC
* * * *
1398377 AAAAAATTAGTGTAAGGGTTATCACTTGATCTCAT
1 AAAAAGTCAATGTAAGGTTTATCACTTGATCTCAT
1398412 GACAAGTTTT
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (36 bp):
AAAAAGTCAATGTAAGGTTTATCACTTGATCTCATC
Found at i:1404029 original size:22 final size:22
Alignment explanation
Indices: 1404004--1404084 Score: 74
Period size: 22 Copynumber: 3.7 Consensus size: 22
1403994 CTTGAATCAT
1404004 TAGTTTTTAGGCATTACGAGAC
1 TAGTTTTTAGGCATTACGAGAC
* * *
1404026 TAGTTTTTAAGCATTATGATAC
1 TAGTTTTTAGGCATTACGAGAC
* * *
1404048 T-GATTTTTAGACATTACAAGAT
1 TAG-TTTTTAGGCATTACGAGAC
* *
1404070 TGGCTTTTAGGCATT
1 TAGTTTTTAGGCATT
1404085 GCGTGACATA
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
21 1 0.02
22 44 0.96
23 1 0.02
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (22 bp):
TAGTTTTTAGGCATTACGAGAC
Found at i:1404148 original size:21 final size:21
Alignment explanation
Indices: 1404124--1404259 Score: 74
Period size: 21 Copynumber: 6.3 Consensus size: 21
1404114 TTAGGCACGA
*
1404124 CGTGACTAGTTTTAGGTATTC
1 CGTGACTAGTTTTAGGTATTG
* *
1404145 CGTGACTAATTTTTAAGTATTG
1 CGTGACT-AGTTTTAGGTATTG
** * * *
1404167 TATGATTGGTTTTAGGCATTG
1 CGTGACTAGTTTTAGGTATTG
* *
1404188 TGTGATTAGTTTTAGGTATTG
1 CGTGACTAGTTTTAGGTATTG
* ** * * *
1404209 TGTGGTTACGTTGTAAGCATTG
1 CGTGACTA-GTTTTAGGTATTG
* *
1404231 CATGACTAGTCTTTAGGCATTG
1 CGTGACTAGT-TTTAGGTATTG
*
1404253 CTTGACT
1 CGTGACT
1404260 TAGGCATTAT
Statistics
Matches: 88, Mismatches: 24, Indels: 5
0.75 0.21 0.04
Matches are distributed among these distances:
21 44 0.50
22 44 0.50
ACGTcount: A:0.21, C:0.10, G:0.25, T:0.44
Consensus pattern (21 bp):
CGTGACTAGTTTTAGGTATTG
Found at i:1404164 original size:22 final size:21
Alignment explanation
Indices: 1404124--1404165 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1404114 TTAGGCACGA
*
1404124 CGTGACTAGTTTTAGGTATTC
1 CGTGACTAGTTTTAAGTATTC
*
1404145 CGTGACTAATTTTTAAGTATT
1 CGTGACT-AGTTTTAAGTATT
1404166 GTATGATTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.24, C:0.12, G:0.19, T:0.45
Consensus pattern (21 bp):
CGTGACTAGTTTTAAGTATTC
Found at i:1404365 original size:22 final size:21
Alignment explanation
Indices: 1404306--1404372 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 21
1404296 CTTAATCATA
*
1404306 GCATGTCTGGTTTTTAAGCATT
1 GCATG-CTGGTTTTTAGGCATT
* *
1404328 GCGTGATGGTTCTTTAGGCATT
1 GCATGCTGGTT-TTTAGGCATT
*
1404350 GCATAGCTGGTTTTTAGGTATT
1 GCAT-GCTGGTTTTTAGGCATT
1404372 G
1 G
1404373 TGTGAAACGT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
21 5 0.14
22 26 0.70
23 6 0.16
ACGTcount: A:0.16, C:0.12, G:0.28, T:0.43
Consensus pattern (21 bp):
GCATGCTGGTTTTTAGGCATT
Found at i:1410471 original size:22 final size:21
Alignment explanation
Indices: 1410441--1410494 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
1410431 GGGGTAATGT
1410441 AATGTCTAAAAGCCAATCACAC
1 AATG-CTAAAAGCCAATCACAC
* * *
1410463 AATGCCTAATATCCAGTCACAC
1 AATG-CTAAAAGCCAATCACAC
1410485 AATGCTAAAA
1 AATGCTAAAA
1410495 AGATTGTCAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.44, C:0.26, G:0.09, T:0.20
Consensus pattern (21 bp):
AATGCTAAAAGCCAATCACAC
Found at i:1414953 original size:30 final size:28
Alignment explanation
Indices: 1414905--1415030 Score: 117
Period size: 30 Copynumber: 4.3 Consensus size: 28
1414895 TTTTGTCTTT
* *
1414905 AATTAAGATAAAAATATTTTATCTTGTCTA
1 AATTAAGACAAAAATA-TTT-TCTTATCTA
* *
1414935 AATTGAGACAAATATATTTTCTTATCTA
1 AATTAAGACAAAAATATTTTCTTATCTA
* * *
1414963 GATTAAGATAAAAAATATTTTTCTTGTCTTA
1 AATTAAGA-CAAAAATA-TTTTCTTATC-TA
* * *
1414994 AATTAGGATAAACATATTTTCTTATCTA
1 AATTAAGACAAAAATATTTTCTTATCTA
1415022 AATTAAGAC
1 AATTAAGAC
1415031 CAAACATGTT
Statistics
Matches: 77, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
28 23 0.30
29 18 0.23
30 28 0.36
31 8 0.10
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (28 bp):
AATTAAGACAAAAATATTTTCTTATCTA
Found at i:1415011 original size:59 final size:58
Alignment explanation
Indices: 1414905--1415029 Score: 182
Period size: 59 Copynumber: 2.1 Consensus size: 58
1414895 TTTTGTCTTT
*
1414905 AATTAAGATAAAAATATTTTATCTTGTCTAAATTGAGACAAATATATTTTCTTATCTA
1 AATTAAGATAAAAATATTTTATCTTGTCTAAATTGAGACAAACATATTTTCTTATCTA
* *
1414963 GATTAAGATAAAAAATATTTT-TCTTGTCTTAAATT-AGGATAAACATATTTTCTTATCTA
1 AATTAAGAT-AAAAATATTTTATCTTGTC-TAAATTGA-GACAAACATATTTTCTTATCTA
1415022 AATTAAGA
1 AATTAAGA
1415030 CCAAACATGT
Statistics
Matches: 60, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
58 16 0.27
59 44 0.73
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (58 bp):
AATTAAGATAAAAATATTTTATCTTGTCTAAATTGAGACAAACATATTTTCTTATCTA
Found at i:1415035 original size:29 final size:28
Alignment explanation
Indices: 1414905--1415043 Score: 116
Period size: 29 Copynumber: 4.8 Consensus size: 28
1414895 TTTTGTCTTT
* * *
1414905 AATTAAGATAAAAATATTTTATCTTGTCTA
1 AATTAAGACAAACATA-TTT-TCTTATCTA
* *
1414935 AATTGAGACAAATATATTTTCTTATCTA
1 AATTAAGACAAACATATTTTCTTATCTA
* * * *
1414963 GATTAAGATAAAAAATATTTTTCTTGTCTTA
1 AATTAAGA-CAAACATA-TTTTCTTATC-TA
* *
1414994 AATTAGGATAAACATATTTTCTTATCTA
1 AATTAAGACAAACATATTTTCTTATCTA
*
1415022 AATTAAGACCAAACATGTTTTC
1 AATTAAGA-CAAACATATTTTC
1415044 AAATTTAGAC
Statistics
Matches: 88, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
28 23 0.26
29 29 0.33
30 28 0.32
31 8 0.09
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (28 bp):
AATTAAGACAAACATATTTTCTTATCTA
Found at i:1416301 original size:44 final size:45
Alignment explanation
Indices: 1416218--1416325 Score: 105
Period size: 44 Copynumber: 2.4 Consensus size: 45
1416208 TATCAATCAG
* * * *
1416218 TCACACAATACCTAAAAA-CTAGTCATGCAATGATGAACAGCCAA
1 TCACGCAATGCCTAAAAACCTAGTCATACAATAATGAACAGCCAA
* * *
1416262 TCATGCAATGCCTAAAAACCTA-TCATACAATAACT-AACAGCTAG
1 TCACGCAATGCCTAAAAACCTAGTCATACAATAA-TGAACAGCCAA
* *
1416306 TCACGTAATGCTTAAAAACC
1 TCACGCAATGCCTAAAAACC
1416326 ATTCATGCAA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
44 48 0.92
45 4 0.08
ACGTcount: A:0.44, C:0.25, G:0.10, T:0.21
Consensus pattern (45 bp):
TCACGCAATGCCTAAAAACCTAGTCATACAATAATGAACAGCCAA
Found at i:1416463 original size:45 final size:45
Alignment explanation
Indices: 1416407--1416509 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 45
1416397 ACGCAATTCT
* *
1416407 TATCAATTAGTCAAGCAATGACTAAAAATCAG-TCACGTAATATCC-
1 TATCAACTAGTCAAGCAATGACTAAAAA-CAGATCACGTAAT-CCCA
* * *
1416452 TATCAACTAGTCATGCAATGCCTAAAAACTGATCACGTAATCCCA
1 TATCAACTAGTCAAGCAATGACTAAAAACAGATCACGTAATCCCA
*
1416497 TATCAACCAGTCA
1 TATCAACTAGTCA
1416510 TGTAAACCCT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
44 4 0.08
45 46 0.92
ACGTcount: A:0.40, C:0.24, G:0.11, T:0.25
Consensus pattern (45 bp):
TATCAACTAGTCAAGCAATGACTAAAAACAGATCACGTAATCCCA
Found at i:1416889 original size:19 final size:19
Alignment explanation
Indices: 1416865--1416910 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1416855 TTTGATTGGC
*
1416865 GAGGAATGCTTGGTCTGTA
1 GAGGAAAGCTTGGTCTGTA
* *
1416884 GAGGAAAGCTTGGTTTGTC
1 GAGGAAAGCTTGGTCTGTA
1416903 GAGGAAAG
1 GAGGAAAG
1416911 TTGAAACATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.26, C:0.09, G:0.39, T:0.26
Consensus pattern (19 bp):
GAGGAAAGCTTGGTCTGTA
Found at i:1433483 original size:29 final size:29
Alignment explanation
Indices: 1433451--1433511 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
1433441 ATGCTTTTCC
* *
1433451 AATGAATTTCCAACGGAACTTCTGTTGGA
1 AATGAATTTCAAACGGAAATTCTGTTGGA
** *
1433480 AATGCTTTTCAAATGGAAATTCTGTTGGA
1 AATGAATTTCAAACGGAAATTCTGTTGGA
1433509 AAT
1 AAT
1433512 TTCCAACGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (29 bp):
AATGAATTTCAAACGGAAATTCTGTTGGA
Found at i:1435179 original size:29 final size:29
Alignment explanation
Indices: 1435146--1435205 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
1435136 CAGAATACAT
1435146 TCGATGTTGTAAATATCAGTGTTCCTTTC
1 TCGATGTTGTAAATATCAGTGTTCCTTTC
1435175 TCGATGTTGTAAATATCAGTGTTCCTTTC
1 TCGATGTTGTAAATATCAGTGTTCCTTTC
1435204 TC
1 TC
1435206 TGAGCTAGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.20, C:0.18, G:0.17, T:0.45
Consensus pattern (29 bp):
TCGATGTTGTAAATATCAGTGTTCCTTTC
Found at i:1440632 original size:12 final size:13
Alignment explanation
Indices: 1440615--1440646 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1440605 GTGGATTTAA
1440615 TATATATATAT-T
1 TATATATATATGT
1440627 TATATATATATGT
1 TATATATATATGT
1440640 TA-ATATA
1 TATATATA
1440647 AGTGTTTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 16 0.84
13 3 0.16
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (13 bp):
TATATATATATGT
Found at i:1440645 original size:14 final size:14
Alignment explanation
Indices: 1440611--1440646 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1440601 TAATGTGGAT
1440611 TTAATATATATATA
1 TTAATATATATATA
* *
1440625 TTTATATATATATG
1 TTAATATATATATA
1440639 TTAATATA
1 TTAATATA
1440647 AGTGTTTAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
TTAATATATATATA
Found at i:1442123 original size:21 final size:20
Alignment explanation
Indices: 1442075--1442127 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
1442065 GTACTAAAAT
1442075 TCTAATAAAAAAAATCTCAA
1 TCTAATAAAAAAAATCTCAA
*
1442095 ACTAAATAAAATAAAATC-CTAA
1 TCT-AATAAAA-AAAATCTC-AA
1442117 TCTAATAAAAA
1 TCTAATAAAAA
1442128 TATTGAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 3 0.11
21 15 0.54
22 10 0.36
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.25
Consensus pattern (20 bp):
TCTAATAAAAAAAATCTCAA
Found at i:1449567 original size:17 final size:18
Alignment explanation
Indices: 1449527--1449567 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
1449517 AATATAAGTA
*
1449527 ACTTAAATATAATAAATG
1 ACTTAAAAATAATAAATG
*
1449545 AC-TAAAAATAATTAAT-
1 ACTTAAAAATAATAAATG
1449561 ACTTAAA
1 ACTTAAA
1449568 CTAAATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 2 0.10
17 16 0.80
18 2 0.10
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.32
Consensus pattern (18 bp):
ACTTAAAAATAATAAATG
Found at i:1466210 original size:2 final size:2
Alignment explanation
Indices: 1466203--1466235 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1466193 ATCTAAATAT
1466203 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1466236 TAACTTAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1467572 original size:3 final size:3
Alignment explanation
Indices: 1467564--1467598 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1467554 TAAATATAGT
1467564 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
1467599 GAGATAAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:1470518 original size:12 final size:12
Alignment explanation
Indices: 1470501--1470526 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1470491 TAAAGCTTTA
1470501 TTACTTACCTCT
1 TTACTTACCTCT
1470513 TTACTTACCTCT
1 TTACTTACCTCT
1470525 TT
1 TT
1470527 TCCATTTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.31, G:0.00, T:0.54
Consensus pattern (12 bp):
TTACTTACCTCT
Found at i:1470756 original size:21 final size:21
Alignment explanation
Indices: 1470696--1470758 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
1470686 TTGAATGGAG
* *
1470696 GCATCAGTCCTTGTCATAAAT
1 GCATCAGTCTTTGTCATGAAT
*
1470717 GCATCAGTCTTTGTTATGAAT
1 GCATCAGTCTTTGTCATGAAT
1470738 GCATCAGTCTTTGTCATGAAT
1 GCATCAGTCTTTGTCATGAAT
1470759 TGTATGAACA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.38
Consensus pattern (21 bp):
GCATCAGTCTTTGTCATGAAT
Found at i:1473203 original size:20 final size:19
Alignment explanation
Indices: 1473180--1473233 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
1473170 TAAATATAAA
1473180 TAACATAAAAGT-AACATTAT
1 TAACATAAAA-TAAACATT-T
*
1473200 TAACTTAAAATAAACATTT
1 TAACATAAAATAAACATTT
* *
1473219 AAACATAAATTAAAC
1 TAACATAAAATAAAC
1473234 TAACTACTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (19 bp):
TAACATAAAATAAACATTT
Found at i:1473680 original size:13 final size:13
Alignment explanation
Indices: 1473644--1473683 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
1473634 ATTTTATCTA
*
1473644 AATAATTAAAATT
1 AATAATTAAAACT
1473657 AA-AATTAAAACT
1 AATAATTAAAACT
*
1473669 AATAACTAAAACT
1 AATAATTAAAACT
1473682 AA
1 AA
1473684 ACTAACATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (13 bp):
AATAATTAAAACT
Found at i:1482051 original size:28 final size:28
Alignment explanation
Indices: 1481974--1482173 Score: 229
Period size: 28 Copynumber: 7.0 Consensus size: 28
1481964 TGACAGTTTT
* *
1481974 AACATATTTGTCTTAATTTAGATAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAA
*
1482002 AGCATGTTATGTCTTAATTTAGACAAGAA
1 AACATGTT-TGTCTTAATTTAGACAAGAA
*
1482031 AACATGTTTGTCTTAATTTAGACAATAA
1 AACATGTTTGTCTTAATTTAGACAAGAA
*
1482059 ATCATGTTTGTCTTAATTTAGACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAA
* *
1482087 ATCATGTTTGGCCTTAATTTAAGACAAGAAA
1 AACATGTTT-GTCTTAATTT-AGACAAG-AA
* * * * *
1482118 AATATTTTTTGTCTTAATCTAAATAAGAA
1 AACA-TGTTTGTCTTAATTTAGACAAGAA
* *
1482147 AACATATTTATCTTAATTTAGACAAGA
1 AACATGTTTGTCTTAATTTAGACAAGA
1482174 TAAAATATTT
Statistics
Matches: 146, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
28 78 0.53
29 40 0.27
30 12 0.08
31 12 0.08
32 4 0.03
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGACAAGAA
Found at i:1482143 original size:85 final size:85
Alignment explanation
Indices: 1481974--1482173 Score: 228
Period size: 85 Copynumber: 2.3 Consensus size: 85
1481964 TGACAGTTTT
* *
1481974 AACATATTTGTCTTAATTTAGATAAGAAAGCATGTTATGTCTTAATTTAGACAAGAAAACATGTT
1 AACATATTTGTCTTAATTTAGACAAGAAAGCATGTTATGCCTTAATTTAGACAAGAAAACATGTT
*
1482039 TGTCTTAATTTAGACAAT-AA
66 TGTCTTAATCTA-ACAATAAA
* * * *
1482059 ATCATGTTTGTCTTAATTTAGACAAGAAATCATGTT-TGGCCTTAATTTAAGACAAGAAAAATAT
1 AACATATTTGTCTTAATTTAGACAAGAAAGCATGTTAT-GCCTTAATTT-AGACAAG-AAAACA-
*
1482123 TTTTTGTCTTAATCT-A-AATAAGAA
62 TGTTTGTCTTAATCTAACAAT-A-AA
*
1482147 AACATATTTATCTTAATTTAGACAAGA
1 AACATATTTGTCTTAATTTAGACAAGA
1482174 TAAAATATTT
Statistics
Matches: 97, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
84 1 0.01
85 44 0.45
86 8 0.08
87 5 0.05
88 39 0.40
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (85 bp):
AACATATTTGTCTTAATTTAGACAAGAAAGCATGTTATGCCTTAATTTAGACAAGAAAACATGTT
TGTCTTAATCTAACAATAAA
Found at i:1482204 original size:31 final size:29
Alignment explanation
Indices: 1482013--1482204 Score: 112
Period size: 28 Copynumber: 6.6 Consensus size: 29
1482003 GCATGTTATG
* * * *
1482013 TCTTAATTTAGACAAG-AAAACATGTTTG
1 TCTTAATTAAGACAAGAAAAATATTTTTA
* * * *
1482041 TCTTAATTTAGAC-A-ATAAATCATGTTTG
1 TCTTAATTAAGACAAGAAAAAT-ATTTTTA
* **
1482069 TCTTAATTTAGACAAG--AAATCATGTTTGG
1 TCTTAATTAAGACAAGAAAAAT-AT-TTTTA
* *
1482098 CCTTAATTTAAGACAAGAAAAATATTTTTTG
1 TCTTAA-TTAAGACAAGAAAAATA-TTTTTA
*
1482129 TCTTAATCTAA-ATAAGAAAACATA--TTTA
1 TCTTAAT-TAAGACAAGAAAA-ATATTTTTA
*
1482157 TCTTAATTTAGACAAGATAAAATATTTTTA
1 TCTTAATTAAGACAAGA-AAAATATTTTTA
1482187 TCTTAATTAAAGACAAGA
1 TCTTAATT-AAGACAAGA
1482205 GTTATCTTAA
Statistics
Matches: 135, Mismatches: 13, Indels: 29
0.76 0.07 0.16
Matches are distributed among these distances:
27 6 0.04
28 58 0.43
29 12 0.09
30 30 0.22
31 24 0.18
32 5 0.04
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (29 bp):
TCTTAATTAAGACAAGAAAAATATTTTTA
Found at i:1482368 original size:17 final size:17
Alignment explanation
Indices: 1482346--1482378 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1482336 ATAATAATAT
1482346 AATAAG-AGTTATTATTC
1 AATAAGAAGTT-TTATTC
1482363 AATAAGAAGTTTTATT
1 AATAAGAAGTTTTATT
1482379 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (17 bp):
AATAAGAAGTTTTATTC
Found at i:1489191 original size:12 final size:13
Alignment explanation
Indices: 1489167--1489195 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1489157 CGTTGTATGA
1489167 AATAAATGTTTTC
1 AATAAATGTTTTC
1489180 AATAAA-GTTTTC
1 AATAAATGTTTTC
1489192 AATA
1 AATA
1489196 TACTATGTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (13 bp):
AATAAATGTTTTC
Found at i:1491168 original size:21 final size:21
Alignment explanation
Indices: 1491144--1491183 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1491134 AAGTCATAAG
*
1491144 CAATTCATCAGTAATTAAAAT
1 CAATCCATCAGTAATTAAAAT
1491165 CAATCCATCAGTAATTAAA
1 CAATCCATCAGTAATTAAA
1491184 GTAACATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.17, G:0.05, T:0.30
Consensus pattern (21 bp):
CAATCCATCAGTAATTAAAAT
Found at i:1494361 original size:73 final size:73
Alignment explanation
Indices: 1494178--1494361 Score: 221
Period size: 73 Copynumber: 2.5 Consensus size: 73
1494168 AGACTGAATC
* * * *
1494178 CTCTTAGT-TAACTAACATTACTACTTAGTCGATTAAGTCGTTTATGTCTTTGAATCCAGTTTCT
1 CTCTTAGTCT-ACTAACAATACTTCTTAGTCGATTAAGTCGTTTATATCTCTGAATCCAGTTTCT
*
1494242 GACTATAGG
65 GACTATAAG
* * * *
1494251 CTCTTAGTCGACTAACAATACTTCTTAGTCAATTAAGTCGTTTCTATCTCTGAA-CTCAGTTTTT
1 CTCTTAGTCTACTAACAATACTTCTTAGTCGATTAAGTCGTTTATATCTCTGAATC-CAGTTTCT
1494315 GAC-AGTAAG
65 GACTA-TAAG
* *
1494324 CTCTTAGTCTACTAAAAATACTTCTTAGTCGACTAAGT
1 CTCTTAGTCTACTAACAATACTTCTTAGTCGATTAAGT
1494362 GTTGTTTGTT
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
72 2 0.02
73 93 0.98
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.39
Consensus pattern (73 bp):
CTCTTAGTCTACTAACAATACTTCTTAGTCGATTAAGTCGTTTATATCTCTGAATCCAGTTTCTG
ACTATAAG
Found at i:1494759 original size:35 final size:34
Alignment explanation
Indices: 1494680--1494766 Score: 95
Period size: 35 Copynumber: 2.5 Consensus size: 34
1494670 TTGCCCACCA
** *
1494680 TGGGGGTAAGAATACCATTTGACAAAGCTTATTG
1 TGGGGGTAAGAATACCACATGACAAAGCTTATCG
** *
1494714 TAAGGATAAGAATACCACATGA-ATAACGCTTATCG
1 TGGGGGTAAGAATACCACATGACA-AA-GCTTATCG
1494749 TGGGGGTAAGAATACCAC
1 TGGGGGTAAGAATACCAC
1494767 CTTGATATTG
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
33 1 0.02
34 19 0.45
35 22 0.52
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (34 bp):
TGGGGGTAAGAATACCACATGACAAAGCTTATCG
Found at i:1496446 original size:27 final size:27
Alignment explanation
Indices: 1496411--1496495 Score: 65
Period size: 27 Copynumber: 3.3 Consensus size: 27
1496401 TGGACAATTG
*
1496411 TTTGGTTTGATGTTTGAACTTGATACA
1 TTTGATTTGATGTTTGAACTTGATACA
*
1496438 TTTGATTTGGAAT-TTGGATA-TT--T-C-
1 TTTGATTT-G-ATGTTTGA-ACTTGATACA
* *
1496462 TTTGGTTTGATGTTTGAACGTGATACA
1 TTTGATTTGATGTTTGAACTTGATACA
1496489 TTTGATT
1 TTTGATT
1496496 CAAACTTTGG
Statistics
Matches: 43, Mismatches: 6, Indels: 18
0.64 0.09 0.27
Matches are distributed among these distances:
22 3 0.07
23 6 0.14
24 7 0.16
25 2 0.05
26 2 0.05
27 13 0.30
28 7 0.16
29 3 0.07
ACGTcount: A:0.21, C:0.06, G:0.22, T:0.51
Consensus pattern (27 bp):
TTTGATTTGATGTTTGAACTTGATACA
Found at i:1496454 original size:51 final size:51
Alignment explanation
Indices: 1496335--1496515 Score: 218
Period size: 51 Copynumber: 3.5 Consensus size: 51
1496325 TTTGACATAA
* * * * *
1496335 TTGATTTGGACTATGGATATTTGTTTGGCTTTGATGTTCTAAATTTGTTATAT
1 TTGATTTGGACTTTGGATATTTGTTTGG-TTTGATGTT-TGAACTTGATACAT
* * *
1496388 TTGATTTAGACTTTGGACAATTGTTTGGTTTGATGTTTGAACTTGATACAT
1 TTGATTTGGACTTTGGATATTTGTTTGGTTTGATGTTTGAACTTGATACAT
* * *
1496439 TTGATTTGGAATTTGGATATTTCTTTGGTTTGATGTTTGAACGTGATACAT
1 TTGATTTGGACTTTGGATATTTGTTTGGTTTGATGTTTGAACTTGATACAT
***
1496490 TTGATTCAAACTTTGGATATTTGTTT
1 TTGATTTGGACTTTGGATATTTGTTT
1496516 CATTTAAAGT
Statistics
Matches: 109, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
51 76 0.70
52 9 0.08
53 24 0.22
ACGTcount: A:0.22, C:0.07, G:0.21, T:0.50
Consensus pattern (51 bp):
TTGATTTGGACTTTGGATATTTGTTTGGTTTGATGTTTGAACTTGATACAT
Found at i:1496528 original size:102 final size:104
Alignment explanation
Indices: 1496335--1496541 Score: 231
Period size: 102 Copynumber: 2.0 Consensus size: 104
1496325 TTTGACATAA
* * ** * * * *
1496335 TTGATTTGGACTATGGATATTTGTTTGGCTTTGATGTTCTAAATTTGTTATATTTGATTTAGACT
1 TTGATTTGGAATATGGATATTTCTTTGGCTTTGATGTTCTAAACGTGATACATTTGATTCAAACT
** * *
1496400 TTGGACAATTGTTTGGTTTGATGTTTGAAC-TTGATACAT
66 TTGGACAATTGTTTCATTTAAAGTTTGAACTTTGAT-CAT
* *
1496439 TTGATTTGGAATTTGGATATTTCTTTGG-TTTGATGTT-TGAACGTGATACATTTGATTCAAACT
1 TTGATTTGGAATATGGATATTTCTTTGGCTTTGATGTTCTAAACGTGATACATTTGATTCAAACT
* * *
1496502 TTGGATATTTGTTTCATTTAAAGTTTGGACTTTGATCAT
66 TTGGACAATTGTTTCATTTAAAGTTTGAACTTTGATCAT
1496541 T
1 T
1496542 CCATTCTGAT
Statistics
Matches: 85, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
102 46 0.54
103 14 0.16
104 25 0.29
ACGTcount: A:0.23, C:0.07, G:0.20, T:0.50
Consensus pattern (104 bp):
TTGATTTGGAATATGGATATTTCTTTGGCTTTGATGTTCTAAACGTGATACATTTGATTCAAACT
TTGGACAATTGTTTCATTTAAAGTTTGAACTTTGATCAT
Found at i:1496923 original size:43 final size:44
Alignment explanation
Indices: 1496863--1496968 Score: 133
Period size: 44 Copynumber: 2.4 Consensus size: 44
1496853 TGTCACATGC
* *
1496863 AAATCTTTGAAATATTTGATACGCTTGCAA-AAGTGGACTTTGA
1 AAATCTTTGAAATATTTGATACGCTTGCAACAAATAGACTTTGA
* ** * * *
1496906 AAATTTTTGTGATATTTGATATGCTTTCAACAAATAGACTTTGG
1 AAATCTTTGAAATATTTGATACGCTTGCAACAAATAGACTTTGA
1496950 AAATCTTTGAAATATTTGA
1 AAATCTTTGAAATATTTGA
1496969 AACATTTGAA
Statistics
Matches: 51, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
43 25 0.49
44 26 0.51
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (44 bp):
AAATCTTTGAAATATTTGATACGCTTGCAACAAATAGACTTTGA
Found at i:1499543 original size:17 final size:17
Alignment explanation
Indices: 1499508--1499570 Score: 56
Period size: 19 Copynumber: 3.5 Consensus size: 17
1499498 TGTTATTTTC
1499508 CTTTTTTCCCTTTTATT
1 CTTTTTTCCCTTTTATT
1499525 CTTTTCTTCCCTTTCT-TCT
1 CTTTT-TTCCCTTT-TAT-T
*
1499544 CTTTTTCTCTCCTTTTTTT
1 CTTTTT-TC-CCTTTTATT
*
1499563 CATTTTTC
1 CTTTTTTC
1499571 TTCTTTCTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
17 5 0.13
18 12 0.31
19 16 0.41
20 6 0.15
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (17 bp):
CTTTTTTCCCTTTTATT
Found at i:1499551 original size:20 final size:21
Alignment explanation
Indices: 1499526--1499574 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
1499516 CCTTTTATTC
1499526 TTTTCTTC-CCTTTCTTCTC-T
1 TTTTCTTCTCCTTT-TTCTCAT
*
1499546 TTTTC-TCTCCTTTTTTTCAT
1 TTTTCTTCTCCTTTTTCTCAT
1499566 TTTTCTTCT
1 TTTTCTTCT
1499575 TTCTTCCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 6 0.24
20 16 0.64
21 3 0.12
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTCTTCTCCTTTTTCTCAT
Found at i:1499558 original size:38 final size:35
Alignment explanation
Indices: 1499508--1499580 Score: 85
Period size: 38 Copynumber: 2.0 Consensus size: 35
1499498 TGTTATTTTC
1499508 CTTTTTTCCCTTTTATTC-TTTTCTTCCCTTTCTTCT
1 CTTTTTTCCCTTTTATTCATTTTCTT--CTTTCTTCT
*
1499544 CTTTTTCTCTCCTTTTTTTCATTTTTCTTCTTTCTTC
1 CTTTTT-TC-CCTTTTATTCA-TTTTCTTCTTTCTTC
1499581 CCAACCTCTG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
36 6 0.19
37 2 0.06
38 17 0.53
40 7 0.22
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (35 bp):
CTTTTTTCCCTTTTATTCATTTTCTTCTTTCTTCT
Found at i:1501519 original size:294 final size:295
Alignment explanation
Indices: 1501132--1501694 Score: 824
Period size: 294 Copynumber: 1.9 Consensus size: 295
1501122 ACATGAGATG
* * *
1501132 CATTTTTCTCAATTTTCTACAAAATCAAACTAAAACCTACAAAGTTAACTTAGAGAACAAGCTTC
1 CATTTTTCTCAAGTTTCTACAAAATCAAACTAAAACCTACAAAGTAAACCTAGAGAACAAGCTTC
** * *
1501197 AAATCTAGACAAACCACTTGGTGCATCAAAATCAAGCAAATACAATCCAAGACACTTCCCAATTT
66 AAATCTAGACAAACCACTTGAAGCATCAAAACCAAGCAAATACAATCCAACACACTTCCCAATTT
* * *
1501262 CCATAAGACA-CA-CACAAATTAAATCAGTAAAGACCCATGTGACTAAAAACGGATGACTATCTT
131 CCAGAAGACACCAGCACAAATTAAATCAGTAAAGACCCATGTGACTAAAAACGAATGAATATCTT
* *
1501325 TAGGAGTACTTTAAATTTTAAATCCAAACAAAATATGCTTCAATTCCAAACTAAACAACTAGAAC
196 TAGGAGTAATTTAAATTTTAAATCCAAACAAAA-AAGCTTCAATTCCAAACTAAACAACTAGAAC
*
1501390 ATTTAAATAACCATAGAGTCCATAGTACACAAGAAA
260 ATTAAAATAACCATAGAGTCCATAGTACACAAGAAA
* *
1501426 CATTTTTCTGAAGTTTCTACAAAATCAAACTAAAACCTACAAAGTAAACCTGGAGAACAAGCTTC
1 CATTTTTCTCAAGTTTCTACAAAATCAAACTAAAACCTACAAAGTAAACCTAGAGAACAAGCTTC
* * * * *
1501491 AAGTCTAGACAAATCACTTGAAGCATCAAAACCAAGCAAATACCATCCAACTCACTTTCCAATTT
66 AAATCTAGACAAACCACTTGAAGCATCAAAACCAAGCAAATACAATCCAACACACTTCCCAATTT
* * * *
1501556 CCAGAAGACACGCATGCACAAATTAAATCAGTACAGACCCATTTGACTAAACATGAATGAATATC
131 CCAGAAGACAC-CA-GCACAAATTAAATCAGTAAAGACCCATGTGACTAAAAACGAATGAATATC
** * * *
1501621 TTTAGGAGTAATTTAAATTTTAAATCCAATTAAAAAAGCTTCAATTCCAATCTAGACACCTAGAA
194 TTTAGGAGTAATTTAAATTTTAAATCCAAACAAAAAAGCTTCAATTCCAAACTAAACAACTAGAA
1501686 CATTAAAAT
259 CATTAAAAT
1501695 CATTTTGGAG
Statistics
Matches: 236, Mismatches: 29, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
294 125 0.53
296 2 0.01
297 34 0.14
298 75 0.32
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.25
Consensus pattern (295 bp):
CATTTTTCTCAAGTTTCTACAAAATCAAACTAAAACCTACAAAGTAAACCTAGAGAACAAGCTTC
AAATCTAGACAAACCACTTGAAGCATCAAAACCAAGCAAATACAATCCAACACACTTCCCAATTT
CCAGAAGACACCAGCACAAATTAAATCAGTAAAGACCCATGTGACTAAAAACGAATGAATATCTT
TAGGAGTAATTTAAATTTTAAATCCAAACAAAAAAGCTTCAATTCCAAACTAAACAACTAGAACA
TTAAAATAACCATAGAGTCCATAGTACACAAGAAA
Found at i:1505318 original size:15 final size:16
Alignment explanation
Indices: 1505298--1505327 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1505288 TTTATTGCTT
1505298 TTTTCAA-ACATAAAA
1 TTTTCAATACATAAAA
1505313 TTTTCAATACATAAA
1 TTTTCAATACATAAA
1505328 GCAATCAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (16 bp):
TTTTCAATACATAAAA
Found at i:1515510 original size:31 final size:31
Alignment explanation
Indices: 1515412--1515634 Score: 138
Period size: 29 Copynumber: 7.6 Consensus size: 31
1515402 AAGACAACTT
* *
1515412 TTATCTTTAATTAAGA-TAAAAATATTTTATC
1 TTATCTTAAATTAAGACAAAAAATATTTT-TC
*
1515443 TTGTC-TAAATTAAGAC---AAATATGTTTTC
1 TTATCTTAAATTAAGACAAAAAATAT-TTTTC
* *
1515471 TTGT-TTAAATTAAAACAAAAAATATTTTTC
1 TTATCTTAAATTAAGACAAAAAATATTTTTC
*
1515501 TTATCTTAAATTAAGAC-AAACAT-TTTTTC
1 TTATCTTAAATTAAGACAAAAAATATTTTTC
* * * *
1515530 TTCTC-AAAATTAAGACCAAACATGA--TTTC
1 TTATCTTAAATTAAGACAAAAAAT-ATTTTTC
* * *
1515559 TTGTC-TAAATTAAGAC-AAACAT-GTTTTC
1 TTATCTTAAATTAAGACAAAAAATATTTTTC
* * * *
1515587 TTATC-TAAATTAAGACATAACAT-GTTTTG
1 TTATCTTAAATTAAGACAAAAAATATTTTTC
*
1515616 TTGT-TTAAATTAAGACAAA
1 TTATCTTAAATTAAGACAAA
1515635 CATGTTAAAG
Statistics
Matches: 163, Mismatches: 15, Indels: 30
0.78 0.07 0.14
Matches are distributed among these distances:
28 57 0.35
29 63 0.39
30 22 0.13
31 21 0.13
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.41
Consensus pattern (31 bp):
TTATCTTAAATTAAGACAAAAAATATTTTTC
Found at i:1515549 original size:29 final size:28
Alignment explanation
Indices: 1515441--1515640 Score: 238
Period size: 29 Copynumber: 7.0 Consensus size: 28
1515431 AAATATTTTA
*
1515441 TCTTGTCTAAATTAAGACAAATATGTTT
1 TCTTGTCTAAATTAAGACAAACATGTTT
* * * *
1515469 TCTTGTTTAAATTAAAACAAAAAATATTTT
1 TCTTGTCTAAATTAAGAC-AAACAT-GTTT
* *
1515499 TCTTATCTTAAATTAAGACAAACATTTTT
1 TCTTGTC-TAAATTAAGACAAACATGTTT
* * *
1515528 TCTTCTCAAAATTAAGACCAAACATGATT
1 TCTTGTCTAAATTAAGA-CAAACATGTTT
1515557 TCTTGTCTAAATTAAGACAAACATGTTT
1 TCTTGTCTAAATTAAGACAAACATGTTT
*
1515585 TCTTATCTAAATTAAGACATAACATGTTT
1 TCTTGTCTAAATTAAGACA-AACATGTTT
* *
1515614 TGTTGTTTAAATTAAGACAAACATGTT
1 TCTTGTCTAAATTAAGACAAACATGTT
1515641 AAAGCTACCA
Statistics
Matches: 148, Mismatches: 19, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
28 61 0.41
29 64 0.43
30 13 0.09
31 10 0.07
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAACATGTTT
Found at i:1515579 original size:57 final size:57
Alignment explanation
Indices: 1515441--1515640 Score: 233
Period size: 57 Copynumber: 3.5 Consensus size: 57
1515431 AAATATTTTA
* * * * * *
1515441 TCTTGTCTAAATTAAGACAAATATGTTTTCTTGTTTAAATTAAAACAAAAAAT-ATTTT
1 TCTTGTCTAAATTAAGACAAACATGTTTTCTTATCTAAATTAAGACCAAACATGA--TT
* * * *
1515499 TCTTATCTTAAATTAAGACAAACATTTTTTCTTCTCAAAATTAAGACCAAACATGATT
1 TCTTGTC-TAAATTAAGACAAACATGTTTTCTTATCTAAATTAAGACCAAACATGATT
*
1515557 TCTTGTCTAAATTAAGACAAACATGTTTTCTTATCTAAATTAAGA-CATAACATGTTT
1 TCTTGTCTAAATTAAGACAAACATGTTTTCTTATCTAAATTAAGACCA-AACATGATT
* *
1515614 TGTTGTTTAAATTAAGACAAACATGTT
1 TCTTGTCTAAATTAAGACAAACATGTT
1515641 AAAGCTACCA
Statistics
Matches: 123, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
56 2 0.02
57 68 0.55
58 14 0.11
59 38 0.31
60 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (57 bp):
TCTTGTCTAAATTAAGACAAACATGTTTTCTTATCTAAATTAAGACCAAACATGATT
Found at i:1522077 original size:20 final size:21
Alignment explanation
Indices: 1522054--1522101 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
1522044 TGCTTCCCAG
*
1522054 CAGCA-TGTGCTGTTGTCCGA
1 CAGCATTGTGCTGTTGTCCAA
1522074 CAGCAGTTTGTGCTGTTGTCCAA
1 CAGCA--TTGTGCTGTTGTCCAA
1522097 CAGCA
1 CAGCA
1522102 CACAACAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 5 0.21
23 19 0.79
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.29
Consensus pattern (21 bp):
CAGCATTGTGCTGTTGTCCAA
Found at i:1522880 original size:29 final size:29
Alignment explanation
Indices: 1522784--1522980 Score: 158
Period size: 29 Copynumber: 6.8 Consensus size: 29
1522774 AAATATTCTA
* *
1522784 TCTTTTCTAAATTGAGAC-AA-ATATGTTT
1 TCTTGTCTAAATTAAGACAAACATAT-TTT
* * *
1522812 TCTTGTTTAGATTAAGACAAAAAATATTGGTT
1 TCTTGTCTAAATTAAGAC-AAACATATT--TT
* *
1522844 TC-T-ACTAAATTAAGATAAACATATTTT
1 TCTTGTCTAAATTAAGACAAACATATTTT
* * **
1522871 TTTTGTCTAAATTAAGACTAA-ATACGATT
1 TCTTGTCTAAATTAAGACAAACATA-TTTT
* *
1522900 TCTTGTCGT-AATTAAGACGAATAT-TTTT
1 TCTTGTC-TAAATTAAGACAAACATATTTT
1522928 TCTTGTCTAAATTAAGACATAACATA-TTT
1 TCTTGTCTAAATTAAGACA-AACATATTTT
1522957 TCTTGTCTAAATTAAGACAAACAT
1 TCTTGTCTAAATTAAGACAAACAT
1522981 GTTAAAACTA
Statistics
Matches: 135, Mismatches: 21, Indels: 26
0.74 0.12 0.14
Matches are distributed among these distances:
27 4 0.03
28 41 0.30
29 66 0.49
30 15 0.11
31 5 0.04
32 4 0.03
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.42
Consensus pattern (29 bp):
TCTTGTCTAAATTAAGACAAACATATTTT
Found at i:1522934 original size:57 final size:56
Alignment explanation
Indices: 1522864--1522974 Score: 156
Period size: 57 Copynumber: 2.0 Consensus size: 56
1522854 TAAGATAAAC
1522864 ATATTTTTTTTGTCTAAATTAAGAC-TAA-ATACGATTTCTTGTCGT-AATTAAGACGA
1 ATATTTTTTTTGTCTAAATTAAGACATAACATA--ATTTCTTGTC-TAAATTAAGACGA
*
1522920 ATATTTTTTCTTGTCTAAATTAAGACATAACATATTTTCTTGTCTAAATTAAGAC
1 ATATTTTTT-TTGTCTAAATTAAGACATAACATAATTTCTTGTCTAAATTAAGAC
1522975 AAACATGTTA
Statistics
Matches: 50, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
56 10 0.20
57 34 0.68
58 3 0.06
59 3 0.06
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (56 bp):
ATATTTTTTTTGTCTAAATTAAGACATAACATAATTTCTTGTCTAAATTAAGACGA
Found at i:1529274 original size:27 final size:27
Alignment explanation
Indices: 1529233--1529323 Score: 76
Period size: 27 Copynumber: 3.4 Consensus size: 27
1529223 GGCCTAGAGG
*
1529233 TGTTCCAAGCGTGGAAGCGTCCAGGGA
1 TGTTCCAAGCATGGAAGCGTCCAGGGA
* * *
1529260 TGTTCTAAGCATGGAAG-TTACCAGGGG
1 TGTTCCAAGCATGGAAGCGT-CCAGGGA
* * ** * *
1529287 TGCTCTAAATATGGAAGCGCCCAAGGA
1 TGTTCCAAGCATGGAAGCGTCCAGGGA
1529314 TGTTCCAAGC
1 TGTTCCAAGC
1529324 GCAGAAATGC
Statistics
Matches: 47, Mismatches: 15, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
26 1 0.02
27 46 0.98
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (27 bp):
TGTTCCAAGCATGGAAGCGTCCAGGGA
Found at i:1533577 original size:15 final size:15
Alignment explanation
Indices: 1533559--1533587 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1533549 GTGATATGTT
1533559 AAAGTAAATTCATTC
1 AAAGTAAATTCATTC
1533574 AAAGTAAATTCATT
1 AAAGTAAATTCATT
1533588 TTCAGCCGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.34
Consensus pattern (15 bp):
AAAGTAAATTCATTC
Found at i:1535317 original size:22 final size:23
Alignment explanation
Indices: 1535289--1535335 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
1535279 ATTTCTATAC
1535289 ATTACTA-CAAGAACTAAGCT-AA
1 ATTACTATCAA-AACTAAGCTCAA
*
1535311 ATTACTATCAAAATTAAGCTCAA
1 ATTACTATCAAAACTAAGCTCAA
1535334 AT
1 AT
1535336 AGCTCTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.49, C:0.17, G:0.06, T:0.28
Consensus pattern (23 bp):
ATTACTATCAAAACTAAGCTCAA
Found at i:1536384 original size:33 final size:33
Alignment explanation
Indices: 1536331--1536441 Score: 132
Period size: 33 Copynumber: 3.4 Consensus size: 33
1536321 TTGGTTGATG
*
1536331 GCATTCACATCATCACCACCAACTCCAGTAGTA
1 GCATCCACATCATCACCACCAACTCCAGTAGTA
* * * *
1536364 GCACCCACATCGTCATCACCAACTCCAGTAGCA
1 GCATCCACATCATCACCACCAACTCCAGTAGTA
* * * **
1536397 ACATTCACATCATCACCACTAACTTTAGTAGTA
1 GCATCCACATCATCACCACCAACTCCAGTAGTA
1536430 GCATCCACATCA
1 GCATCCACATCA
1536442 CCATCGCTGA
Statistics
Matches: 62, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
33 62 1.00
ACGTcount: A:0.33, C:0.36, G:0.09, T:0.22
Consensus pattern (33 bp):
GCATCCACATCATCACCACCAACTCCAGTAGTA
Found at i:1540541 original size:2 final size:2
Alignment explanation
Indices: 1540534--1540560 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1540524 GTAAAAGTGA
1540534 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1540561 AACATTATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1540849 original size:58 final size:58
Alignment explanation
Indices: 1540754--1540871 Score: 164
Period size: 58 Copynumber: 2.0 Consensus size: 58
1540744 GAGCGCCCGG
* * * ** * *
1540754 GGTGTTTCAAGCGTAGAAATGCTTTAAGCATGAAAATGCTTAGAGGTGTTTCAAGTGT
1 GGTGTTTCAAGAGTAGAAACGCCTTAAGCATGAAAATGCCGAGAGGTGTTCCAAGCGT
*
1540812 GGTGTTTCAAGAGTAGAAACGCCTTAAGCATGGAAATGCCGAGAGGTGTTCCAAGCGT
1 GGTGTTTCAAGAGTAGAAACGCCTTAAGCATGAAAATGCCGAGAGGTGTTCCAAGCGT
1540870 GG
1 GG
1540872 AAGCGCTCAA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.29, C:0.14, G:0.31, T:0.27
Consensus pattern (58 bp):
GGTGTTTCAAGAGTAGAAACGCCTTAAGCATGAAAATGCCGAGAGGTGTTCCAAGCGT
Found at i:1540886 original size:27 final size:27
Alignment explanation
Indices: 1540856--1540920 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
1540846 AATGCCGAGA
* * *
1540856 GGTGTTCCAAGCGTGGAAGCG-CTCAAG
1 GGTGTTCCAAGCATGAAAGCGCCT-AAC
1540883 GGTGTTCCAAGCATGAAAGCGCCTAAC
1 GGTGTTCCAAGCATGAAAGCGCCTAAC
1540910 GGTGTTCCAAG
1 GGTGTTCCAAG
1540921 TACGCCCAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 32 0.94
28 2 0.06
ACGTcount: A:0.25, C:0.23, G:0.32, T:0.20
Consensus pattern (27 bp):
GGTGTTCCAAGCATGAAAGCGCCTAAC
Found at i:1541052 original size:161 final size:161
Alignment explanation
Indices: 1540862--1541192 Score: 495
Period size: 161 Copynumber: 2.1 Consensus size: 161
1540852 GAGAGGTGTT
* * *
1540862 CCAAGCGTGGAAGCGCTCAAGGGTGTTCCAAGCATGAAAGCGCCTAACGGTGTTCCAAGTACGCC
1 CCAAGGGTGGAAGCGCTCAAGGGTGTTCCAAGCATGAAAGCACCTAAAGGTGTTCCAAGTACGCC
*
1540927 CAGGGGTGTTCCAAGCCCAAAAATGCCTAGGGTGTTCCAAGCGTAG-AAGCACCCTAAGCATGGA
66 CAGGGGTGTTCCAAGCCCAAAAATCCCTAGGGTGTTCCAAGCG-AGAAAGCACCCTAAGCATGGA
1540991 AAAGCCCAGAGGTGTTCCAAGCATGGAAGTGC
130 AAAGCCCAGAGGTGTTCCAAGCATGGAAGTGC
* * * *
1541023 CCAAGGGTGGAAGCG-TCTAGAGGTGTTCCAAGTATGAAAGCACCTAAAGGTGTTCCAAGTGCGT
1 CCAAGGGTGGAAGCGCTCAAG-GGTGTTCCAAGCATGAAAGCACCTAAAGGTGTTCCAAGTACGC
* * * * **
1541087 CCAGGGGTGTTCCAAGCGCGAAAGTCCCTAGGGTGTTCCAAGCGCGAAAGTGCCCTAAGCATGGA
65 CCAGGGGTGTTCCAAGCCCAAAAATCCCTAGGGTGTTCCAAGCGAGAAAGCACCCTAAGCATGGA
*
1541152 AAAGCCTAGAGGTGTTCCAAGCATGGAAGTGC
130 AAAGCCCAGAGGTGTTCCAAGCATGGAAGTGC
1541184 CCAAGGGTG
1 CCAAGGGTG
1541193 TTCCAAGCAC
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
160 5 0.03
161 148 0.97
ACGTcount: A:0.28, C:0.24, G:0.31, T:0.18
Consensus pattern (161 bp):
CCAAGGGTGGAAGCGCTCAAGGGTGTTCCAAGCATGAAAGCACCTAAAGGTGTTCCAAGTACGCC
CAGGGGTGTTCCAAGCCCAAAAATCCCTAGGGTGTTCCAAGCGAGAAAGCACCCTAAGCATGGAA
AAGCCCAGAGGTGTTCCAAGCATGGAAGTGC
Found at i:1541110 original size:48 final size:47
Alignment explanation
Indices: 1541035--1541128 Score: 109
Period size: 48 Copynumber: 2.0 Consensus size: 47
1541025 AAGGGTGGAA
* * *
1541035 GCGTCTAGAGGTGTTCCAAGTATGAAAG-CACCTAAAGGTGTTCCAAGT
1 GCGTCCAGAGGTGTTCCAAGCACGAAAGTC-CCT-AAGGTGTTCCAAGT
* * *
1541083 GCGTCCAGGGGTGTTCCAAGCGCGAAAGTCCCTAGGGTGTTCCAAG
1 GCGTCCAGAGGTGTTCCAAGCACGAAAGTCCCTAAGGTGTTCCAAG
1541129 CGCGAAAGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
47 12 0.31
48 26 0.67
49 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.22
Consensus pattern (47 bp):
GCGTCCAGAGGTGTTCCAAGCACGAAAGTCCCTAAGGTGTTCCAAGT
Found at i:1541120 original size:26 final size:27
Alignment explanation
Indices: 1541091--1541143 Score: 99
Period size: 26 Copynumber: 2.0 Consensus size: 27
1541081 GTGCGTCCAG
1541091 GGGTGTTCCAAGCGCGAAAGT-CCCTA
1 GGGTGTTCCAAGCGCGAAAGTGCCCTA
1541117 GGGTGTTCCAAGCGCGAAAGTGCCCTA
1 GGGTGTTCCAAGCGCGAAAGTGCCCTA
1541144 AGCATGGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.23, C:0.26, G:0.32, T:0.19
Consensus pattern (27 bp):
GGGTGTTCCAAGCGCGAAAGTGCCCTA
Found at i:1541173 original size:27 final size:27
Alignment explanation
Indices: 1541143--1541206 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
1541133 AAAGTGCCCT
*
1541143 AAGCATGGAAAAG-CCTAGAGGTGTTCC
1 AAGCATGGAAAAGCCCAAG-GGTGTTCC
**
1541170 AAGCATGGAAGTGCCCAAGGGTGTTCC
1 AAGCATGGAAAAGCCCAAGGGTGTTCC
*
1541197 AAGCACGGAA
1 AAGCATGGAA
1541207 GCGCCCAGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 28 0.88
28 4 0.12
ACGTcount: A:0.33, C:0.20, G:0.31, T:0.16
Consensus pattern (27 bp):
AAGCATGGAAAAGCCCAAGGGTGTTCC
Found at i:1541207 original size:27 final size:27
Alignment explanation
Indices: 1541162--1541213 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1541152 AAAGCCTAGA
* *
1541162 GGTGTTCCAAGCATGGAAGTGCCCAAG
1 GGTGTTCCAAGCACGGAAGCGCCCAAG
1541189 GGTGTTCCAAGCACGGAAGCGCCCA
1 GGTGTTCCAAGCACGGAAGCGCCCA
1541214 GCAGTGTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.25, C:0.27, G:0.33, T:0.15
Consensus pattern (27 bp):
GGTGTTCCAAGCACGGAAGCGCCCAAG
Found at i:1541220 original size:27 final size:27
Alignment explanation
Indices: 1541163--1541226 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
1541153 AAGCCTAGAG
* * *
1541163 GTGTTCCAAGCATGGAAGTGCCCAAGG
1 GTGTTCCAAGCACGGAAGCGCCCAAGA
1541190 GTGTTCCAAGCACGGAAGCGCCC-AGCA
1 GTGTTCCAAGCACGGAAGCGCCCAAG-A
*
1541217 GTGTTTCAAG
1 GTGTTCCAAG
1541227 TGTAGAAAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 2 0.06
27 30 0.94
ACGTcount: A:0.25, C:0.25, G:0.31, T:0.19
Consensus pattern (27 bp):
GTGTTCCAAGCACGGAAGCGCCCAAGA
Found at i:1541331 original size:27 final size:27
Alignment explanation
Indices: 1541276--1541332 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
1541266 CCTAAGCGAA
** *
1541276 GAAATGCCTAGAGGTGTTCCAAGCGTG
1 GAAATGCCTAGAGGCATTCCAAGCATG
* *
1541303 GAAATGCCTAGGGGCATTCCAAGTATG
1 GAAATGCCTAGAGGCATTCCAAGCATG
1541330 GAA
1 GAA
1541333 GCGCTTAAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.18, G:0.32, T:0.21
Consensus pattern (27 bp):
GAAATGCCTAGAGGCATTCCAAGCATG
Found at i:1543546 original size:30 final size:30
Alignment explanation
Indices: 1543469--1543594 Score: 119
Period size: 30 Copynumber: 4.2 Consensus size: 30
1543459 GACCAAATCC
* * *
1543469 TCCACCACCACCTGAACCCAGACCACCAAA
1 TCCACCACCACCTGAAGCCATACCAGCAAA
* * *
1543499 TACAACACCACCAGAAGCCATACCAGCAAA
1 TCCACCACCACCTGAAGCCATACCAGCAAA
* * *
1543529 TCCCCCACCACCTGAAGCCAAAGCAGCAAA
1 TCCACCACCACCTGAAGCCATACCAGCAAA
* * * *
1543559 GCCACCACTA-CTAGAGGCAATACCAGCAAA
1 TCCACCACCACCT-GAAGCCATACCAGCAAA
1543589 TCCACC
1 TCCACC
1543595 TCCTGTTGCA
Statistics
Matches: 75, Mismatches: 20, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
29 2 0.03
30 73 0.97
ACGTcount: A:0.39, C:0.42, G:0.11, T:0.08
Consensus pattern (30 bp):
TCCACCACCACCTGAAGCCATACCAGCAAA
Found at i:1548068 original size:151 final size:151
Alignment explanation
Indices: 1547808--1548099 Score: 487
Period size: 151 Copynumber: 1.9 Consensus size: 151
1547798 CAAAGCCATC
* *
1547808 GTGGTAAAGCACAGCAAAATAGTTCGTCACCACACTACAAATGTTAGTAAACTCAATCCAATCAC
1 GTGGTAAAGCACAGCAAAATAGTTCATCACCACACTACAAATGTCAGTAAACTCAATCCAATCAC
* *
1547873 CTCTGCTGGCCATTAGGATAACTCTAATTAAACATTGTCTAATGCATATTGATTCCTTTTATTAT
66 CTATGCTGGCCATTAGGATAACTCTAATTAAACATTGTCTAATGCATATTGATTACTTTTATTAT
1547938 TTTGAGCCTTACTGAGCCACT
131 TTTGAGCCTTACTGAGCCACT
* * * *
1547959 GTGGTAAAGTACAGCAAAATAGTTCATCACCACAGTACAAATGTCAGTAACCTCAATCCAATCAG
1 GTGGTAAAGCACAGCAAAATAGTTCATCACCACACTACAAATGTCAGTAAACTCAATCCAATCAC
*
1548024 CTATGCTGGCCGTTAGGAT-ACATCTAATTAAACATTGTCTAATGCATATTGATTACTTTTATTA
66 CTATGCTGGCCATTAGGATAAC-TCTAATTAAACATTGTCTAATGCATATTGATTACTTTTATTA
1548088 TTTTGAGCCTTA
130 TTTTGAGCCTTA
1548100 TTGTGGGTGT
Statistics
Matches: 131, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
150 2 0.02
151 129 0.98
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (151 bp):
GTGGTAAAGCACAGCAAAATAGTTCATCACCACACTACAAATGTCAGTAAACTCAATCCAATCAC
CTATGCTGGCCATTAGGATAACTCTAATTAAACATTGTCTAATGCATATTGATTACTTTTATTAT
TTTGAGCCTTACTGAGCCACT
Found at i:1561567 original size:30 final size:29
Alignment explanation
Indices: 1561494--1561589 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 29
1561484 AAAAACTTTT
* **
1561494 AAATAAATTTTTATATTTTTA-TTACGTC
1 AAATAAAATTTTATATTTTTATTTAAATC
* *
1561522 TAATCAAATTTTTATATTTTCT-TTTAAAATC
1 AAAT-AAAATTTTATATTTT-TATTT-AAATC
1561553 AAATAAAATTTTATATTTTTAATTTAAATC
1 AAATAAAATTTTATATTTTT-ATTTAAATC
1561583 AAATAAA
1 AAATAAA
1561590 CTCTTATAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
28 3 0.05
29 16 0.28
30 29 0.51
31 9 0.16
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.50
Consensus pattern (29 bp):
AAATAAAATTTTATATTTTTATTTAAATC
Found at i:1562499 original size:55 final size:55
Alignment explanation
Indices: 1562449--1562551 Score: 142
Period size: 54 Copynumber: 1.9 Consensus size: 55
1562439 AATTAAAATA
1562449 AAATATATAATATA-G-AATAA-AAATTAAAATAAA-ATAAAATATAAAAATTAAT
1 AAATATATAATATAGGTAA-AATAAATTAAAATAAATATAAAATATAAAAATTAAT
** *
1562501 ATTTATATAATATAGGTAAAATAAATTAAAATAAATATATAATATAAAAAT
1 AAATATATAATATAGGTAAAATAAATTAAAATAAATATAAAATATAAAAAT
1562552 ATATTAAAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
52 12 0.27
53 3 0.07
54 15 0.34
55 14 0.32
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (55 bp):
AAATATATAATATAGGTAAAATAAATTAAAATAAATATAAAATATAAAAATTAAT
Found at i:1562570 original size:48 final size:53
Alignment explanation
Indices: 1562457--1562573 Score: 124
Period size: 54 Copynumber: 2.3 Consensus size: 53
1562447 TAAAATATAT
* *
1562457 AATATAG-AATAA-AAATTAAAATAAAATAAAATATAAAAATTAATATTTATAT
1 AATATAGTAA-AATAAATTAAAATAAAATAAAATATAAAAATTAATATTTAAAG
*
1562509 AATATAGGTAAAATAAATTAAAATAAATATATAATATAAAAA-T-ATA-TTAAAG
1 AATATA-GTAAAATAAATTAAAATAAA-ATAAAATATAAAAATTAATATTTAAAG
1562561 AA-AT-G-AAAATAAA
1 AATATAGTAAAATAAA
1562574 ATATATAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 12
0.79 0.04 0.16
Matches are distributed among these distances:
48 8 0.14
49 1 0.02
51 2 0.03
52 12 0.21
53 6 0.10
54 16 0.28
55 13 0.22
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (53 bp):
AATATAGTAAAATAAATTAAAATAAAATAAAATATAAAAATTAATATTTAAAG
Found at i:1562580 original size:34 final size:33
Alignment explanation
Indices: 1562542--1562610 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
1562532 TAAATATATA
* *
1562542 ATATAAAAATATATTAAAGAAATGAAAATAAAAT
1 ATATAAAAATATAAT-AAGAAATAAAAATAAAAT
* *
1562576 ATATAAAATTATAATAATAAATAAAAATAAAAT
1 ATATAAAAATATAATAAGAAATAAAAATAAAAT
1562609 AT
1 AT
1562611 TGACATTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 18 0.58
34 13 0.42
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (33 bp):
ATATAAAAATATAATAAGAAATAAAAATAAAAT
Found at i:1562603 original size:33 final size:33
Alignment explanation
Indices: 1562529--1562722 Score: 126
Period size: 32 Copynumber: 5.6 Consensus size: 33
1562519 AAATAAATTA
* * * *
1562529 AAATAAATATATAATATA-AAAA-TATATTAAAG
1 AAATAAAAATAAAATATATAAAATTATAAT-AAT
*
1562561 AAATGAAAATAAAATATATAAAATTATAATAAT
1 AAATAAAAATAAAATATATAAAATTATAATAAT
* * *
1562594 AAATAAAAATAAAATAT-TGACATTAAAATAAT
1 AAATAAAAATAAAATATATAAAATTATAATAAT
** * *
1562626 ATTTAAAATATGATATTATATAAAATTAATAAT-AT
1 AAATAAAA-AT-AAAATATATAAAATT-ATAATAAT
1562661 AAATATAAATATATTAAAATAAAATATAAAATATTATAATAAT
1 -AA-ATAAA-A-A-TAAAAT---ATAT-AAA-ATTATAATAAT
1562704 AAATAAAAATAAAATATAT
1 AAATAAAAATAAAATATAT
1562723 GACATTAAAA
Statistics
Matches: 126, Mismatches: 20, Indels: 29
0.72 0.11 0.17
Matches are distributed among these distances:
32 33 0.26
33 24 0.19
34 10 0.08
35 11 0.09
36 5 0.04
37 4 0.03
38 12 0.10
39 2 0.02
40 1 0.01
41 9 0.07
42 10 0.08
43 5 0.04
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (33 bp):
AAATAAAAATAAAATATATAAAATTATAATAAT
Found at i:1562620 original size:24 final size:24
Alignment explanation
Indices: 1562593--1562660 Score: 66
Period size: 25 Copynumber: 2.8 Consensus size: 24
1562583 ATTATAATAA
*
1562593 TAAATAAAAATAAAATATTGACAT
1 TAAATAAAATTAAAATATTGACAT
* *
1562617 TAAAATAATATTTAAAATA-TGATAT
1 T-AAATAA-AATTAAAATATTGACAT
*
1562642 TATATAAAATTAATAATAT
1 TAAATAAAATTAA-AATAT
1562661 AAATATAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
23 5 0.14
24 10 0.29
25 12 0.34
26 8 0.23
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (24 bp):
TAAATAAAATTAAAATATTGACAT
Found at i:1562633 original size:32 final size:33
Alignment explanation
Indices: 1562561--1562711 Score: 108
Period size: 33 Copynumber: 4.4 Consensus size: 33
1562551 TATATTAAAG
* *
1562561 AAATGAAAATAAAATATATAAAATTATAATAAT
1 AAATAAAAATAAAATATATAAAATTAAAATAAT
* *
1562594 AAATAAAAATAAAATAT-TGACATTAAAATAAT
1 AAATAAAAATAAAATATATAAAATTAAAATAAT
** * *
1562626 ATTTAAAATATGATATTATATAAAATTAATAAT-AT
1 AAATAAAA-AT-AAAATATATAAAATTAA-AATAAT
* * * * *
1562661 AAATATAAATATATTAAAATAAAATATAAAATATT
1 AAATAAAAATAAAAT-ATATAAAAT-TAAAATAAT
1562696 ATAATAATAAATAAAA
1 A-AATAA-AAATAAAA
1562712 ATAAAATATA
Statistics
Matches: 91, Mismatches: 18, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
32 18 0.20
33 23 0.25
34 18 0.20
35 19 0.21
36 7 0.08
37 6 0.07
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (33 bp):
AAATAAAAATAAAATATATAAAATTAAAATAAT
Found at i:1562667 original size:6 final size:6
Alignment explanation
Indices: 1562656--1562721 Score: 50
Period size: 6 Copynumber: 11.0 Consensus size: 6
1562646 TAAAATTAAT
*
1562656 AATATA AATATA AATAT- ATTA-A AATA-A AATATAA AATATTA TAATAATA
1 AATATA AATATA AATATA AATATA AATATA AATAT-A AATA-TA -AAT-ATA
*
1562705 AATAAA AATA-A AATATA
1 AATATA AATATA AATATA
1562722 TGACATTAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
5 16 0.32
6 18 0.36
7 9 0.18
8 6 0.12
9 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AATATA
Found at i:1562668 original size:20 final size:19
Alignment explanation
Indices: 1562643--1562721 Score: 65
Period size: 20 Copynumber: 3.9 Consensus size: 19
1562633 ATATGATATT
1562643 ATATAAAATTAATAATATAA
1 ATATAAAATTAA-AATATAA
1562663 ATATAAATATATTAAAATA-AA
1 ATAT-AA-A-ATTAAAATATAA
*
1562684 ATATAAAATATTATAATAATAA
1 ATAT-AAA-ATTAAAAT-ATAA
1562706 ATA-AAAA-TAAAATATA
1 ATATAAAATTAAAATATA
1562722 TGACATTAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
17 3 0.06
18 5 0.10
19 1 0.02
20 16 0.31
21 12 0.23
22 10 0.19
23 5 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
ATATAAAATTAAAATATAA
Found at i:1562701 original size:110 final size:112
Alignment explanation
Indices: 1562566--1562901 Score: 544
Period size: 112 Copynumber: 3.0 Consensus size: 112
1562556 TAAAGAAATG
1562566 AAAATAAAATATATAAA-ATTATAATAATAAATAAAAATAAAATAT-TGACATT-AAAATAATAT
1 AAAATAAAATATA-AAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAAT-ATAT
1562628 TTAA-AATATGATATTATAT-AAAATTAATAATATAAATATAAATATATT
64 TTAAGAA-ATGATATTATATAAAAATTAATAATATAAATATAAATATATT
1562676 AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
1 AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
1562741 AAGAAATGATATTATATAAAAATTAATAATA-AAATAATAAATATATT
66 AAGAAATGATATTATATAAAAATTAATAATATAAAT-ATAAATATATT
* *
1562788 AAAAAAATAAATATAAAATATTATAATAAT-AATAAAAAT-AAATATATGATATTAAAAATATAT
1 -AAAATA-AAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATAT
1562851 TTAAGAAATGATATTATATAAAAATTAATAATATAAATATAAATATATT
64 TTAAGAAATGATATTATATAAAAATTAATAATATAAATATAAATATATT
1562900 AA
1 AA
1562902 CTTATATTTT
Statistics
Matches: 215, Mismatches: 2, Indels: 17
0.92 0.01 0.07
Matches are distributed among these distances:
109 3 0.01
110 41 0.19
111 33 0.15
112 98 0.46
113 18 0.08
114 22 0.10
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (112 bp):
AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
AAGAAATGATATTATATAAAAATTAATAATATAAATATAAATATATT
Found at i:1562786 original size:48 final size:49
Alignment explanation
Indices: 1562731--1562834 Score: 119
Period size: 48 Copynumber: 2.2 Consensus size: 49
1562721 ATGACATTAA
* * *
1562731 AAATATATTTAAGAAATGATATTATATAAAA-A-T-TAATAATAA-AATAAT
1 AAATATATTTAA-AAA-AATA-AATATAAAATATTATAATAATAATAAAAAT
1562779 AAATATA-TTAAAAAAATAAATATAAAATATTATAATAATAATAAAAAT
1 AAATATATTTAAAAAAATAAATATAAAATATTATAATAATAATAAAAAT
1562827 AAATATAT
1 AAATATAT
1562835 GATATTAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
44 8 0.17
45 4 0.08
46 4 0.08
47 13 0.27
48 19 0.40
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (49 bp):
AAATATATTTAAAAAAATAAATATAAAATATTATAATAATAATAAAAAT
Found at i:1562796 original size:17 final size:17
Alignment explanation
Indices: 1562744--1562802 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
1562734 TATATTTAAG
1562744 AAATGATATTATATAAAAAT
1 AAAT-ATATTA-A-AAAAAT
* *
1562764 TAATA-A-TAAAATAAT
1 AAATATATTAAAAAAAT
1562779 AAATATATTAAAAAAAT
1 AAATATATTAAAAAAAT
1562796 AAATATA
1 AAATATA
1562803 AAATATTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
15 9 0.27
16 2 0.06
17 17 0.52
18 1 0.03
19 1 0.03
20 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (17 bp):
AAATATATTAAAAAAAT
Found at i:1562796 original size:25 final size:25
Alignment explanation
Indices: 1562768--1562834 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 25
1562758 AAAAATTAAT
1562768 AATAAAATAATAAATATATTAAAAA
1 AATAAAATAATAAATATATTAAAAA
* *
1562793 AAT-AAAT-ATAAA-ATATTATAAT
1 AATAAAATAATAAATATATTAAAAA
*
1562815 AATAATAAAAATAAATATAT
1 AATAA-AATAATAAATATAT
1562835 GATATTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
22 11 0.31
23 6 0.17
24 6 0.17
25 8 0.23
26 4 0.11
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (25 bp):
AATAAAATAATAAATATATTAAAAA
Found at i:1562827 original size:20 final size:20
Alignment explanation
Indices: 1562665--1562827 Score: 67
Period size: 21 Copynumber: 7.5 Consensus size: 20
1562655 TAATATAAAT
* *
1562665 ATAAATATATTAAAATAA-A
1 ATAAAAATATTATAATAATA
1562684 ATATAAAATATTATAATAATAA
1 ATA-AAAATATTATAATAAT-A
** * *
1562706 ATAAAAATAAAATATATGACA
1 ATAAAAATATTATA-ATAATA
* * *
1562727 TTAAAAATATATTTAAGAAATGA
1 ATAAAAATAT-TATAA-TAAT-A
*
1562750 TATTATATAAAAATTAATAATAAAATA
1 -A-TA-A-AAATATT-ATAAT--AATA
* * *
1562777 ATAAATATATTAAAAAAATAA
1 ATAAAAATATTATAATAAT-A
1562798 ATATAAAATATTATAATAATA
1 ATA-AAAATATTATAATAATA
1562819 ATAAAAATA
1 ATAAAAATA
1562828 AATATATGAT
Statistics
Matches: 104, Mismatches: 24, Indels: 31
0.65 0.15 0.19
Matches are distributed among these distances:
19 3 0.03
20 22 0.21
21 27 0.26
22 26 0.25
23 6 0.06
24 1 0.01
25 4 0.04
26 3 0.03
27 9 0.09
28 3 0.03
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.33
Consensus pattern (20 bp):
ATAAAAATATTATAATAATA
Found at i:1562875 original size:16 final size:15
Alignment explanation
Indices: 1562714--1562875 Score: 54
Period size: 16 Copynumber: 10.3 Consensus size: 15
1562704 AAATAAAAAT
* *
1562714 AAAATATATGACATTA
1 AAAATATATTATA-TA
1562730 AAAATATATT-TA-A
1 AAAATATATTATATA
*
1562743 GAAATGATATTATATA
1 AAAAT-ATATTATATA
* *
1562759 AAAATTAATAATAAAATA
1 AAAA-T-AT-ATTATATA
1562777 ATAAATATATTA-A-A
1 A-AAATATATTATATA
1562791 AAAATA-A--ATATA
1 AAAATATATTATATA
*
1562803 AAATATTATAATAATAATA
1 AAA-A-TAT-ATTAT-ATA
1562822 AAAATAAATATATGATATTA
1 AAAAT--ATAT-T-ATA-TA
1562842 AAAATATATT-TA-A
1 AAAATATATTATATA
*
1562855 GAAATGATATTATATA
1 AAAAT-ATATTATATA
1562871 AAAAT
1 AAAAT
1562876 TAATAATATA
Statistics
Matches: 112, Mismatches: 11, Indels: 46
0.66 0.07 0.27
Matches are distributed among these distances:
10 1 0.01
11 1 0.01
12 5 0.04
13 16 0.14
14 14 0.12
15 8 0.07
16 22 0.20
17 7 0.06
18 17 0.15
19 12 0.11
20 9 0.08
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.34
Consensus pattern (15 bp):
AAAATATATTATATA
Found at i:1562895 original size:15 final size:15
Alignment explanation
Indices: 1562619--1562895 Score: 86
Period size: 15 Copynumber: 17.3 Consensus size: 15
1562609 ATTGACATTA
*
1562619 AAATAATATTTAAAAT
1 AAATAATA-TAAAAAT
* *
1562635 ATGATATTATATAAAAT
1 A-AATAATATA-AAAAT
* *
1562652 TAATAATATAAATAT
1 AAATAATATAAAAAT
*
1562667 AAAT-ATATTAAAAT
1 AAATAATATAAAAAT
1562681 -AA-AATATAAAATATT
1 AAATAATATAAAA-A-T
1562696 ATAATAATAAATAAAAAT
1 A-AATAAT--ATAAAAAT
*
1562714 AAA-ATATATGACATTAA-
1 AAATA-ATAT-A-A-AAAT
*
1562731 AAATATATTTAAGAAAT
1 AAATA-ATATAA-AAAT
* *
1562748 GATATTATATAAAAAT
1 -AAATAATATAAAAAT
*
1562764 TAATAATA-AAATAAT
1 AAATAATATAAA-AAT
*
1562779 AAAT-ATATTAAAA-
1 AAATAATATAAAAAT
1562792 AAATAAATATAAAATATT
1 AAAT-AATATAAAA-A-T
1562810 ATAATAATAATAAAAAT
1 A-AATAAT-ATAAAAAT
**
1562827 AAATATATGATATTAA-
1 AAATA-AT-ATAAAAAT
*
1562843 AAATATATTTAAGAAAT
1 AAATA-ATATAA-AAAT
* *
1562860 GATATTATATAAAAAT
1 -AAATAATATAAAAAT
* *
1562876 TAATAATATAAATAT
1 AAATAATATAAAAAT
1562891 AAATA
1 AAATA
1562896 TATTAACTTA
Statistics
Matches: 193, Mismatches: 38, Indels: 61
0.66 0.13 0.21
Matches are distributed among these distances:
13 13 0.07
14 17 0.09
15 47 0.24
16 37 0.19
17 40 0.21
18 23 0.12
19 10 0.05
20 6 0.03
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (15 bp):
AAATAATATAAAAAT
Found at i:1563071 original size:15 final size:15
Alignment explanation
Indices: 1563051--1563089 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
1563041 TTTTCCCTAT
*
1563051 AATCACATTACTTGC
1 AATCACATTACCTGC
*
1563066 AATCACATTACCTGT
1 AATCACATTACCTGC
1563081 AATCACATT
1 AATCACATT
1563090 GCATTGTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (15 bp):
AATCACATTACCTGC
Found at i:1568090 original size:36 final size:36
Alignment explanation
Indices: 1567982--1568193 Score: 283
Period size: 35 Copynumber: 6.1 Consensus size: 36
1567972 ATTTAATTTA
* *
1567982 AATTAGGCCCAATAACTTAATTAAA-TAATTTAATT
1 AATTAGGCCCAATAACTTAATTAAACAAATTTAATC
* *
1568017 AATTAGGTCCAATAACTTAATTAAAC-AATTTGATC
1 AATTAGGCCCAATAACTTAATTAAACAAATTTAATC
*
1568052 AATTAGGCCCAATAACTTGATTAAACAAATTTAATC
1 AATTAGGCCCAATAACTTAATTAAACAAATTTAATC
*
1568088 AATTAGGCCTAATAACTTAATTAAACAAATTTAATC
1 AATTAGGCCCAATAACTTAATTAAACAAATTTAATC
* * *
1568124 AATTAGGCCTAATAACATAATTAAAC-AATTTAATG
1 AATTAGGCCCAATAACTTAATTAAACAAATTTAATC
* *
1568159 AATTAGG--C-ACAACTTAATTAAACAATTTTAATC
1 AATTAGGCCCAATAACTTAATTAAACAAATTTAATC
1568192 AA
1 AA
1568194 GTGCTTGAGA
Statistics
Matches: 159, Mismatches: 15, Indels: 8
0.87 0.08 0.04
Matches are distributed among these distances:
32 13 0.08
33 9 0.06
35 70 0.44
36 67 0.42
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.33
Consensus pattern (36 bp):
AATTAGGCCCAATAACTTAATTAAACAAATTTAATC
Found at i:1568106 original size:71 final size:69
Alignment explanation
Indices: 1567982--1568193 Score: 293
Period size: 71 Copynumber: 3.0 Consensus size: 69
1567972 ATTTAATTTA
* *
1567982 AATTAGGCCCAATAACTTAATTAAATAATTTAATTAATTAGGTCCAATAACTTAATTAAACAATT
1 AATTAGGCCCAATAACTTAATTAAACAATTTAATCAATTAGG-CCAATAACTTAATTAAACAATT
*
1568047 TGATC
65 TAATC
*
1568052 AATTAGGCCCAATAACTTGATTAAACAAATTTAATCAATTAGGCCTAATAACTTAATTAAACAAA
1 AATTAGGCCCAATAACTTAATTAAAC-AATTTAATCAATTAGGCC-AATAACTTAATTAAAC-AA
1568117 TTTAATC
63 TTTAATC
* * * *
1568124 AATTAGGCCTAATAACATAATTAAACAATTTAATGAATTAGG-C-ACAACTTAATTAAACAATTT
1 AATTAGGCCCAATAACTTAATTAAACAATTTAATCAATTAGGCCAATAACTTAATTAAACAA-TT
1568187 TAATC
65 TAATC
1568192 AA
1 AA
1568194 GTGCTTGAGA
Statistics
Matches: 129, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
67 2 0.02
68 23 0.18
70 27 0.21
71 46 0.36
72 31 0.24
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.33
Consensus pattern (69 bp):
AATTAGGCCCAATAACTTAATTAAACAATTTAATCAATTAGGCCAATAACTTAATTAAACAATTT
AATC
Found at i:1574414 original size:21 final size:21
Alignment explanation
Indices: 1574390--1574467 Score: 122
Period size: 21 Copynumber: 3.8 Consensus size: 21
1574380 TGCTAAATCC
*
1574390 TCAAAAACATTATGAAATTTA
1 TCAAAAGCATTATGAAATTTA
*
1574411 TCAAAAGCATTATGCAATTTA
1 TCAAAAGCATTATGAAATTTA
*
1574432 TCAAAAGCATTATGCAATTTA
1 TCAAAAGCATTATGAAATTTA
1574453 TCAAAAGCA-TATGAA
1 TCAAAAGCATTATGAA
1574468 TTAAGTTTAC
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 5 0.09
21 49 0.91
ACGTcount: A:0.47, C:0.13, G:0.09, T:0.31
Consensus pattern (21 bp):
TCAAAAGCATTATGAAATTTA
Found at i:1579039 original size:2 final size:2
Alignment explanation
Indices: 1579027--1579067 Score: 55
Period size: 2 Copynumber: 19.5 Consensus size: 2
1579017 GTATTTTGTG
*
1579027 TA TA CTA TA TA TA TA TA TA TA TA TG TA TA TA TA TGA TA TA T
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA T
1579068 GTAAAGTGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 31 0.89
3 4 0.11
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1579533 original size:25 final size:25
Alignment explanation
Indices: 1579502--1579560 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
1579492 CATAGGTTAT
*
1579502 TATACGTGGCTAAGCTACAAGTTTA
1 TATACGTGGCTAAGCCACAAGTTTA
*
1579527 TATACGTGGCTAGGCCACAAGTTTA
1 TATACGTGGCTAAGCCACAAGTTTA
1579552 TATACGTGG
1 TATACGTGG
1579561 TTGCAACCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.31
Consensus pattern (25 bp):
TATACGTGGCTAAGCCACAAGTTTA
Found at i:1582919 original size:21 final size:23
Alignment explanation
Indices: 1582895--1582938 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
1582885 CTTTTGTTAT
1582895 AATATTTA-ATTTT-TAATTTAA
1 AATATTTATATTTTATAATTTAA
1582916 AATATTTATATTTTAATAATTTA
1 AATATTTATATTTT-ATAATTTA
1582939 TTAAAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 8 0.40
22 5 0.25
24 7 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
AATATTTATATTTTATAATTTAA
Found at i:1582986 original size:21 final size:21
Alignment explanation
Indices: 1582947--1582986 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1582937 TATTAAAAAT
*
1582947 ATTTTAAAATTATTATTTAAA
1 ATTTTAAAATGATTATTTAAA
* *
1582968 ATTTTAATATGATTGTTTA
1 ATTTTAAAATGATTATTTA
1582987 TTTTTATTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (21 bp):
ATTTTAAAATGATTATTTAAA
Done.