Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 5 of 316
Found at i:1338043 original size:19 final size:19
Alignment explanation
Indices: 1338019--1338057 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1338009 AATACTTATT
*
1338019 TATTATTTA-TACATGTGTA
1 TATTA-TTAGTACATATGTA
1338038 TATTATTAGTACATATGTA
1 TATTATTAGTACATATGTA
1338057 T
1 T
1338058 CCATATATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.51
Consensus pattern (19 bp):
TATTATTAGTACATATGTA
Found at i:1338112 original size:17 final size:16
Alignment explanation
Indices: 1338086--1338118 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
1338076 TTTTCTTTCT
1338086 TTTATTTATTTAATTA
1 TTTATTTATTTAATTA
1338102 TTTACTTTATTTAATTA
1 TTTA-TTTATTTAATTA
1338119 ATATAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTATTTATTTAATTA
Found at i:1342432 original size:78 final size:78
Alignment explanation
Indices: 1342303--1342453 Score: 266
Period size: 78 Copynumber: 1.9 Consensus size: 78
1342293 CCGCCAGTAG
*
1342303 ATTCAGTAGCAACTTCTACTTCAGATTCTGGAGAAACTGCAATCTCATCAGCTAAGCCAGAAGTT
1 ATTCAGTAGCAACTTCTACATCAGATTCTGGAGAAACTGCAATCTCATCAGCTAAGCCAGAAGTT
1342368 GGCCCATCGGCAT
66 GGCCCATCGGCAT
* * *
1342381 ATTCAGTAGCAACTTCTACATCCGATTCTGGAGTAGCTGCAATCTCATCAGCTAAGCCAGAAGTT
1 ATTCAGTAGCAACTTCTACATCAGATTCTGGAGAAACTGCAATCTCATCAGCTAAGCCAGAAGTT
1342446 GGCCCATC
66 GGCCCATC
1342454 CACACTTTGG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 69 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.26
Consensus pattern (78 bp):
ATTCAGTAGCAACTTCTACATCAGATTCTGGAGAAACTGCAATCTCATCAGCTAAGCCAGAAGTT
GGCCCATCGGCAT
Found at i:1344652 original size:12 final size:12
Alignment explanation
Indices: 1344627--1344660 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1344617 GGAATACACC
* *
1344627 GTAACGGTAACA
1 GTAACAGTAGCA
1344639 GTAACAGTAGCA
1 GTAACAGTAGCA
1344651 GTAACAGTAG
1 GTAACAGTAG
1344661 TGGTACACAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.15, G:0.26, T:0.18
Consensus pattern (12 bp):
GTAACAGTAGCA
Found at i:1344749 original size:57 final size:59
Alignment explanation
Indices: 1344635--1344765 Score: 151
Period size: 57 Copynumber: 2.2 Consensus size: 59
1344625 CCGTAACGGT
* * * *
1344635 AACAGTAACAGTAGCAGTAACAGTAGTGGTACACAGAGTACCTCATCGGAATAAATCCGG
1 AACAGTAACAGTAACAGTAACAGTAGAGGTA-ACAGAGTACCTCATCGGAACAAATCCAG
* * *
1344695 AACAGTAACAGTAACAGTAATAGTA-AGGT-ACGGAGTACCT-ATTCGGAACGAATCCAG
1 AACAGTAACAGTAACAGTAACAGTAGAGGTAACAGAGTACCTCA-TCGGAACAAATCCAG
*
1344752 AACAGTAATAGTAA
1 AACAGTAACAGTAA
1344766 GGCGGCACTT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
56 1 0.02
57 35 0.56
59 3 0.05
60 23 0.37
ACGTcount: A:0.41, C:0.18, G:0.22, T:0.19
Consensus pattern (59 bp):
AACAGTAACAGTAACAGTAACAGTAGAGGTAACAGAGTACCTCATCGGAACAAATCCAG
Found at i:1345909 original size:19 final size:19
Alignment explanation
Indices: 1345885--1345923 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1345875 AATACTTATT
*
1345885 TATTATTTA-TACATGTGTA
1 TATTA-TTAGTACATATGTA
1345904 TATTATTAGTACATATGTA
1 TATTATTAGTACATATGTA
1345923 T
1 T
1345924 CCATATATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.51
Consensus pattern (19 bp):
TATTATTAGTACATATGTA
Found at i:1345977 original size:17 final size:16
Alignment explanation
Indices: 1345951--1345983 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
1345941 TTTTCTTTCT
1345951 TTTATTTATTTAATTA
1 TTTATTTATTTAATTA
1345967 TTTACTTTATTTAATTA
1 TTTA-TTTATTTAATTA
1345984 ATATAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTATTTATTTAATTA
Found at i:1350262 original size:78 final size:78
Alignment explanation
Indices: 1350133--1350283 Score: 266
Period size: 78 Copynumber: 1.9 Consensus size: 78
1350123 CCGCCAGTAG
*
1350133 ATTCAGTAGCAACTTCTACTTCAGATTCTGGAGAAACTGCAATCTCATCAGCTAAGCCAGAAGTT
1 ATTCAGTAGCAACTTCTACATCAGATTCTGGAGAAACTGCAATCTCATCAGCTAAGCCAGAAGTT
1350198 GGCCCATCGGCAT
66 GGCCCATCGGCAT
* * *
1350211 ATTCAGTAGCAACTTCTACATCCGATTCTGGAGTAGCTGCAATCTCATCAGCTAAGCCAGAAGTT
1 ATTCAGTAGCAACTTCTACATCAGATTCTGGAGAAACTGCAATCTCATCAGCTAAGCCAGAAGTT
1350276 GGCCCATC
66 GGCCCATC
1350284 CACACTTTGG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 69 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.26
Consensus pattern (78 bp):
ATTCAGTAGCAACTTCTACATCAGATTCTGGAGAAACTGCAATCTCATCAGCTAAGCCAGAAGTT
GGCCCATCGGCAT
Found at i:1352487 original size:12 final size:12
Alignment explanation
Indices: 1352462--1352495 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1352452 GGAATACACC
* *
1352462 GTAACGGTAACA
1 GTAACAGTAGCA
1352474 GTAACAGTAGCA
1 GTAACAGTAGCA
1352486 GTAACAGTAG
1 GTAACAGTAG
1352496 TGGTACACAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.15, G:0.26, T:0.18
Consensus pattern (12 bp):
GTAACAGTAGCA
Found at i:1352584 original size:57 final size:59
Alignment explanation
Indices: 1352470--1352600 Score: 151
Period size: 57 Copynumber: 2.2 Consensus size: 59
1352460 CCGTAACGGT
* * * *
1352470 AACAGTAACAGTAGCAGTAACAGTAGTGGTACACAGAGTACCTCATCGGAATAAATCCGG
1 AACAGTAACAGTAACAGTAACAGTAGAGGTA-ACAGAGTACCTCATCGGAACAAATCCAG
* * *
1352530 AACAGTAACAGTAACAGTAATAGTA-AGGT-ACGGAGTACCT-ATTCGGAACGAATCCAG
1 AACAGTAACAGTAACAGTAACAGTAGAGGTAACAGAGTACCTCA-TCGGAACAAATCCAG
*
1352587 AACAGTAATAGTAA
1 AACAGTAACAGTAA
1352601 GGCGGCACTT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
56 1 0.02
57 35 0.56
59 3 0.05
60 23 0.37
ACGTcount: A:0.41, C:0.18, G:0.22, T:0.19
Consensus pattern (59 bp):
AACAGTAACAGTAACAGTAACAGTAGAGGTAACAGAGTACCTCATCGGAACAAATCCAG
Found at i:1353748 original size:19 final size:19
Alignment explanation
Indices: 1353724--1353762 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1353714 AATACTTATT
*
1353724 TATTATTTA-TACATGTGTA
1 TATTA-TTAGTACATATGTA
1353743 TATTATTAGTACATATGTA
1 TATTATTAGTACATATGTA
1353762 T
1 T
1353763 CCATATATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.51
Consensus pattern (19 bp):
TATTATTAGTACATATGTA
Found at i:1353816 original size:17 final size:16
Alignment explanation
Indices: 1353790--1353822 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
1353780 TTTTCTTTCT
1353790 TTTATTTATTTAATTA
1 TTTATTTATTTAATTA
1353806 TTTACTTTATTTAATTA
1 TTTA-TTTATTTAATTA
1353823 ATATAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTATTTATTTAATTA
Found at i:1358149 original size:78 final size:78
Alignment explanation
Indices: 1358020--1358170 Score: 266
Period size: 78 Copynumber: 1.9 Consensus size: 78
1358010 CCGCCAGTAG
*
1358020 ATTCAGTAGCAACTTCTACTTCAGATTCTGGAGAAGCTGCAATCTCATCAGCTAAGCCAGAAGTT
1 ATTCAGTAGCAACTTCTACATCAGATTCTGGAGAAGCTGCAATCTCATCAGCTAAGCCAGAAGTT
1358085 GGCCCATCGGCAT
66 GGCCCATCGGCAT
* * *
1358098 ATTCAGTAGCAACTTCTACATCCGATTCTGGAGTAGCTGTAATCTCATCAGCTAAGCCAGAAGTT
1 ATTCAGTAGCAACTTCTACATCAGATTCTGGAGAAGCTGCAATCTCATCAGCTAAGCCAGAAGTT
1358163 GGCCCATC
66 GGCCCATC
1358171 CACACTTTGG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 69 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (78 bp):
ATTCAGTAGCAACTTCTACATCAGATTCTGGAGAAGCTGCAATCTCATCAGCTAAGCCAGAAGTT
GGCCCATCGGCAT
Found at i:1359077 original size:22 final size:22
Alignment explanation
Indices: 1359049--1359105 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
1359039 GAACAGTACC
* *
1359049 ACACGCCCATGTGGCTTATGTG
1 ACACGCCCGTGTGGCTTATGCG
*
1359071 ACACGCCTGTGTGGCTTATGCG
1 ACACGCCCGTGTGGCTTATGCG
*
1359093 ACACACCCGTGTG
1 ACACGCCCGTGTG
1359106 TCTCCATGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.25
Consensus pattern (22 bp):
ACACGCCCGTGTGGCTTATGCG
Found at i:1360245 original size:18 final size:18
Alignment explanation
Indices: 1360224--1360267 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1360214 ATAATCAGTA
1360224 ATTCAGTAACAGTCAAAT
1 ATTCAGTAACAGTCAAAT
* * *
1360242 ATTCAGTAGCAGTTAATT
1 ATTCAGTAACAGTCAAAT
1360260 ATTCAGTA
1 ATTCAGTA
1360268 CCTTTATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (18 bp):
ATTCAGTAACAGTCAAAT
Found at i:1362962 original size:78 final size:78
Alignment explanation
Indices: 1362833--1362983 Score: 266
Period size: 78 Copynumber: 1.9 Consensus size: 78
1362823 CCGCCGGTAG
* *
1362833 ATTCAGTAGCAACTTCTACTTCAGATTTTGGAGAAGCTGCAATCTCATCAGCTAAGCCAGAAGTT
1 ATTCAGTAGCAACTTCTACATCAGATTCTGGAGAAGCTGCAATCTCATCAGCTAAGCCAGAAGTT
1362898 GGCCCATCGGCAT
66 GGCCCATCGGCAT
* *
1362911 ATTCAGTAGCAACTTCTACATCCGATTCTGGAGTAGCTGCAATCTCATCAGCTAAGCCAGAAGTT
1 ATTCAGTAGCAACTTCTACATCAGATTCTGGAGAAGCTGCAATCTCATCAGCTAAGCCAGAAGTT
1362976 GGCCCATC
66 GGCCCATC
1362984 CACACTTTGG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 69 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (78 bp):
ATTCAGTAGCAACTTCTACATCAGATTCTGGAGAAGCTGCAATCTCATCAGCTAAGCCAGAAGTT
GGCCCATCGGCAT
Found at i:1365350 original size:78 final size:78
Alignment explanation
Indices: 1365221--1365370 Score: 273
Period size: 78 Copynumber: 1.9 Consensus size: 78
1365211 CGCCAATAGG
*
1365221 TTCAGTAGCAACTTCTACTTCAGATTCTGGAGAAGCTGCAATCTCATCAGCTAAGCCAGAAGTTG
1 TTCAGTAGCAACTTCTACATCAGATTCTGGAGAAGCTGCAATCTCATCAGCTAAGCCAGAAGTTG
1365286 GCCCATCGGCATA
66 GCCCATCGGCATA
* *
1365299 TTCAGTAGCAACTTCTACATCCGATTCTGGAGTAGCTGCAATCTCATCAGCTAAGCCAGAAGTTG
1 TTCAGTAGCAACTTCTACATCAGATTCTGGAGAAGCTGCAATCTCATCAGCTAAGCCAGAAGTTG
1365364 GCCCATC
66 GCCCATC
1365371 CACACTTTGG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 69 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (78 bp):
TTCAGTAGCAACTTCTACATCAGATTCTGGAGAAGCTGCAATCTCATCAGCTAAGCCAGAAGTTG
GCCCATCGGCATA
Found at i:1367718 original size:24 final size:24
Alignment explanation
Indices: 1367691--1367742 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1367681 TTAGTAAGTC
*
1367691 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
1367715 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
1367739 AAAT
1 AAAT
1367743 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:1369688 original size:24 final size:24
Alignment explanation
Indices: 1369661--1369712 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1369651 TTAGTAAGTC
*
1369661 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
1369685 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
1369709 AAAT
1 AAAT
1369713 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:1370157 original size:78 final size:78
Alignment explanation
Indices: 1370021--1370166 Score: 238
Period size: 78 Copynumber: 1.9 Consensus size: 78
1370011 TGGTAGATTC
* * * * *
1370021 AGTAGCAATTTCTACTTCCGATTCTGGAGAAGCTGCAATCTCATCAGCTAAGCTAGAAGTTGGCC
1 AGTAGAAACTTCTACTTCCGATTCTAGAGAAGCTGCAATCTCATCAGCGAAGCCAGAAGTTGGCC
1370086 CATTGATAAATTT
66 CATTGATAAATTT
*
1370099 AGTAGAAACTTCTACTTCTGATTCTAGAGAAGCTGCAATCTCATCAGCGAAGCCAGAAGTTGGCC
1 AGTAGAAACTTCTACTTCCGATTCTAGAGAAGCTGCAATCTCATCAGCGAAGCCAGAAGTTGGCC
1370164 CAT
66 CAT
1370167 CCACACTCTG
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
78 62 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (78 bp):
AGTAGAAACTTCTACTTCCGATTCTAGAGAAGCTGCAATCTCATCAGCGAAGCCAGAAGTTGGCC
CATTGATAAATTT
Found at i:1377722 original size:26 final size:26
Alignment explanation
Indices: 1377693--1377774 Score: 62
Period size: 27 Copynumber: 3.1 Consensus size: 26
1377683 CAAACCCTAA
1377693 TTTCTCTTTTCTCTTTTTTTTTCTTC
1 TTTCTCTTTTCTCTTTTTTTTTCTTC
* * * *
1377719 TTTCTTTCTTTCTATTTTGTTTCTCCTC
1 TTTCTCT-TTTCTCTTTT-TTTTTCTTC
*
1377747 TATT-TCTTTT-TC-TTGTTTTTCTTTC
1 T-TTCTCTTTTCTCTTTTTTTTTC-TTC
1377772 TTT
1 TTT
1377775 TATTTATTCT
Statistics
Matches: 43, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
24 7 0.16
25 5 0.12
26 7 0.16
27 12 0.28
28 10 0.23
29 2 0.05
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.74
Consensus pattern (26 bp):
TTTCTCTTTTCTCTTTTTTTTTCTTC
Found at i:1377951 original size:3 final size:3
Alignment explanation
Indices: 1377943--1377985 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
1377933 TTGATAAAAT
*
1377943 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1377986 GTAAATATCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1379469 original size:29 final size:30
Alignment explanation
Indices: 1379422--1379489 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
1379412 TGGCCCAAGA
* *
1379422 GTAAATACTCAAAATTTGAAGGATTAA-AGT
1 GTAAATA-TCAAAAGTTGAAGGACTAATAGT
*
1379452 GTAAATATGAAAAGTTGAAGGACTAATAGT
1 GTAAATATCAAAAGTTGAAGGACTAATAGT
*
1379482 GCAAATAT
1 GTAAATAT
1379490 TTTAAGGGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (30 bp):
GTAAATATCAAAAGTTGAAGGACTAATAGT
Found at i:1380211 original size:11 final size:10
Alignment explanation
Indices: 1380169--1380211 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
1380159 TTGATATGTT
1380169 AGTGAAGAGAA
1 AGTG-AGAGAA
* *
1380180 AATAAGAGAA
1 AGTGAGAGAA
1380190 AGTGAGAGAA
1 AGTGAGAGAA
1380200 AGTGATGAGAA
1 AGTGA-GAGAA
1380211 A
1 A
1380212 TTGTGTAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
10 19 0.70
11 8 0.30
ACGTcount: A:0.56, C:0.00, G:0.33, T:0.12
Consensus pattern (10 bp):
AGTGAGAGAA
Found at i:1381979 original size:46 final size:46
Alignment explanation
Indices: 1381927--1382150 Score: 360
Period size: 46 Copynumber: 4.9 Consensus size: 46
1381917 TGCTCTCTGG
*
1381927 TATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGA
1 TATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA
*
1381973 TATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGA
1 TATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA
1382019 TATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA
1 TATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA
*
1382065 TATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGA
1 TATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA
* * * * *
1382111 CA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 TATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
1382151 TCATGTCAAA
Statistics
Matches: 170, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
45 1 0.01
46 169 0.99
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.23
Consensus pattern (46 bp):
TATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA
Found at i:1385648 original size:65 final size:65
Alignment explanation
Indices: 1385570--1385700 Score: 244
Period size: 65 Copynumber: 2.0 Consensus size: 65
1385560 AGTCCCATGC
1385570 ATCAGATAATAATAACATGGCATGCAGTAAAAAGTAACAGTCAAACATGCATTCAGGTCAACCTT
1 ATCAGATAATAATAACATGGCATGCAGTAAAAAGTAACAGTCAAACATGCATTCAGGTCAACCTT
* *
1385635 ATCAGATAATAATAACATGGCATGTAGTAAATAGTAACAGTCAAACATGCATTCAGGTCAACCTT
1 ATCAGATAATAATAACATGGCATGCAGTAAAAAGTAACAGTCAAACATGCATTCAGGTCAACCTT
1385700 A
1 A
1385701 ACCCTAGGGG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.24
Consensus pattern (65 bp):
ATCAGATAATAATAACATGGCATGCAGTAAAAAGTAACAGTCAAACATGCATTCAGGTCAACCTT
Found at i:1387686 original size:19 final size:18
Alignment explanation
Indices: 1387649--1387692 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
1387639 ATACATACAG
1387649 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
1387666 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
1387685 TACTAATT
1 TAATAATT
1387693 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:1391445 original size:32 final size:32
Alignment explanation
Indices: 1391408--1391472 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
1391398 AATGCTTACC
*
1391408 ATGCCCATCATCTATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
1391440 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
1391472 A
1 A
1391473 AATGCATACA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.32
Consensus pattern (32 bp):
ATGCCCATCATCCATTAACTATTAAAATGCTA
Found at i:1396581 original size:31 final size:31
Alignment explanation
Indices: 1396489--1396584 Score: 120
Period size: 31 Copynumber: 3.1 Consensus size: 31
1396479 TATGTTTTAT
* * *
1396489 GTTAATCCATATCTAACGTCGACTCTGATTT
1 GTTAATCCGTATCTAACGTCGACTCGGATTC
* *
1396520 GTTAATCCGTATCTAACGCCGGCTCGGATTC
1 GTTAATCCGTATCTAACGTCGACTCGGATTC
* * *
1396551 GTTAATTCGTATCTAACATCGAATCGGATTC
1 GTTAATCCGTATCTAACGTCGACTCGGATTC
1396582 GTT
1 GTT
1396585 GAGAAGGAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (31 bp):
GTTAATCCGTATCTAACGTCGACTCGGATTC
Found at i:1400992 original size:11 final size:11
Alignment explanation
Indices: 1400976--1401001 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1400966 ATTGAGTTAA
1400976 TAAATTTTGAT
1 TAAATTTTGAT
1400987 TAAATTTTGAT
1 TAAATTTTGAT
1400998 TAAA
1 TAAA
1401002 GATTAGATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (11 bp):
TAAATTTTGAT
Found at i:1417047 original size:17 final size:18
Alignment explanation
Indices: 1417020--1417064 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1417010 AATAAAACCC
1417020 AAAAT-AAAAAAT-AAAA
1 AAAATAAAAAAATGAAAA
*
1417036 AAAATAAAAAAATGAAGA
1 AAAATAAAAAAATGAAAA
*
1417054 AAAAGAAAAAA
1 AAAATAAAAAA
1417065 CCTAACATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 5 0.20
17 7 0.28
18 13 0.52
ACGTcount: A:0.84, C:0.00, G:0.07, T:0.09
Consensus pattern (18 bp):
AAAATAAAAAAATGAAAA
Found at i:1417345 original size:19 final size:19
Alignment explanation
Indices: 1417313--1417351 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1417303 CTTTGTTCAT
1417313 TTTTCATTTTTTTATTTTA
1 TTTTCATTTTTTTATTTTA
1417332 TTTT-ATTTTGTTTATTTTA
1 TTTTCATTTT-TTTATTTTA
1417351 T
1 T
1417352 ATACATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (19 bp):
TTTTCATTTTTTTATTTTA
Found at i:1432799 original size:51 final size:51
Alignment explanation
Indices: 1432726--1432828 Score: 163
Period size: 51 Copynumber: 2.0 Consensus size: 51
1432716 TATTTTACCT
* * *
1432726 AAAAAAGGAAAGGTCTAGGTGAAAACCCGC-AAAGGGCGCTTTGAGACCAA
1 AAAAAAGGAAAGGCCAAGGTGAAAACCCGCAAAAGGGCACTTTGAGACCAA
1432776 AAAAAATGGAAAGGCCAAGGTGAAAACCCGCAAAAGGGCACTTTGAGACCAA
1 AAAAAA-GGAAAGGCCAAGGTGAAAACCCGCAAAAGGGCACTTTGAGACCAA
1432828 A
1 A
1432829 GGGGTTTTTG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
50 6 0.12
51 22 0.46
52 20 0.42
ACGTcount: A:0.45, C:0.18, G:0.26, T:0.11
Consensus pattern (51 bp):
AAAAAAGGAAAGGCCAAGGTGAAAACCCGCAAAAGGGCACTTTGAGACCAA
Found at i:1433829 original size:88 final size:88
Alignment explanation
Indices: 1433680--1433899 Score: 343
Period size: 88 Copynumber: 2.5 Consensus size: 88
1433670 GAAGATATCG
* * *
1433680 AAGATGATTTGGCATTTCTGTATCAGGCGGGGAGCAGATCGAATACATAGCTGATTTGGCTTTTA
1 AAGATGATTTGGCATCTCTGTATCAGGCGGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTCA
* *
1433745 CGTGTTTATGTTGAAGCAGATCC
66 CGTGTTTACGTTGAAGCAAATCC
1433768 AAGATGATTTGGCATCTCTGTATCAGGCGGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTCA
1 AAGATGATTTGGCATCTCTGTATCAGGCGGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTCA
1433833 CGTGTTTACGTTGAAGCAAATCC
66 CGTGTTTACGTTGAAGCAAATCC
* * * * *
1433856 AAGATGATTTGGCGTCTCTGTAGC-GGCAGAGAGCAAATCGAAGA
1 AAGATGATTTGGCATCTCTGTATCAGGCGGGGAGCAGATCGAAGA
1433900 TGATTTGGCA
Statistics
Matches: 122, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
87 17 0.14
88 105 0.86
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (88 bp):
AAGATGATTTGGCATCTCTGTATCAGGCGGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTCA
CGTGTTTACGTTGAAGCAAATCC
Found at i:1433962 original size:44 final size:44
Alignment explanation
Indices: 1433861--1434529 Score: 891
Period size: 44 Copynumber: 15.4 Consensus size: 44
1433851 AATCCAAGAT
*
1433861 GATTTGGCGTCTCTGTAGCGGC-AGAGAGCAAATCGAAGAT----
1 GATTTGGCGTCTCTGTAGCGGCGA-AGAGCAGATCGAAGATAACA
* *
1433901 GATTTGGCATCTCTGTAGCGGCGAACAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGAAGAGCAGATCGAAGATAACA
* *
1433945 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAGCA
1 GATTTGGCGTCTCTGTAGCGGCGAAGAGCAGATCGAAGATAACA
* * *
1433989 GATTTTGCGTCTCTGTAGTGGCGGAGAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGAAGAGCAGATCGAAGATAACA
* * *
1434033 GATTT-GCGTCTCTATAGCGGCGGAGAGCAGATCGATGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGAAGAGCAGATCGAAGATAACA
* *
1434076 GATTTGGCGTCTCTGTAGCAGCGGAGAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGAAGAGCAGATCGAAGATAACA
* *
1434120 GATTTGGCATCTCTATAGCGGC-AGAGAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGA-AGAGCAGATCGAAGATAACA
* *
1434164 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATTGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGAAGAGCAGATCGAAGATAACA
* * *
1434208 GATTTAGCGTCTCTGTAGCGGCGGAGAGCAGAT-GAAGATAACG
1 GATTTGGCGTCTCTGTAGCGGCGAAGAGCAGATCGAAGATAACA
* *
1434251 GATTTGGCGTCTGTATTAGACGG-G--GAGCAGAT-GAAGATAACA
1 GATTTGGCGTCTCT-GTAG-CGGCGAAGAGCAGATCGAAGATAACA
*
1434293 GATTTGGCGTCTCTGTAGCGGC-AGAGAGCAGATCGAAGATAATA
1 GATTTGGCGTCTCTGTAGCGGCGA-AGAGCAGATCGAAGATAACA
* *
1434337 GATTTGGCGTCTCAGTAACGGC-AGAGAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGA-AGAGCAGATCGAAGATAACA
* *
1434381 GATTTGGCGTCTCTGTAGCGG-AAGAGAGCAGATCAAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGA-AGAGCAGATCGAAGATAACA
*
1434425 GATTTGGCGTCTCTGTAGCGACGAAGAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGAAGAGCAGATCGAAGATAACA
* * *
1434469 GATTTGGCGTCTCTGTAACGGCGGAGAGCAGATCGAAGATAACG
1 GATTTGGCGTCTCTGTAGCGGCGAAGAGCAGATCGAAGATAACA
1434513 GATTTGGCGTCTCTGTA
1 GATTTGGCGTCTCTGTA
1434530 TTAGACGGGG
Statistics
Matches: 566, Mismatches: 46, Indels: 30
0.88 0.07 0.05
Matches are distributed among these distances:
40 38 0.07
41 4 0.01
42 30 0.05
43 69 0.12
44 421 0.74
45 4 0.01
ACGTcount: A:0.29, C:0.17, G:0.32, T:0.22
Consensus pattern (44 bp):
GATTTGGCGTCTCTGTAGCGGCGAAGAGCAGATCGAAGATAACA
Found at i:1434380 original size:261 final size:263
Alignment explanation
Indices: 1433861--1434560 Score: 1056
Period size: 261 Copynumber: 2.7 Consensus size: 263
1433851 AATCCAAGAT
* *
1433861 GATTTGGCGTCTCTGTAGCGGCAGAGAGCAAATCGAAGAT----GATTTGGCATCTCTGTAGCGG
1 GATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGG
* *
1433922 CGAACAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAG
66 CGAAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAA
* * * * *
1433987 CAGATTTTGCGTCTCTGTAGT-GGCGGAGAGCAGATCGAAGATAACAGATTTGCGTCTCTATAGC
131 CGGATTTGGCG-CTCTGTATTAGACGGGGAGCAGATCGAAGATAACAGATTTGCGTCTCTATAGC
* * * * *
1434051 GGCGGAGAGCAGATCGATGATAACAGATTTGGCGTCTCTGTAGCAGCGGAGAGCAGATCGAAGAT
195 GGCAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCAGTAACAGCAGAGAGCAGATCGAAGAT
1434116 AACA
260 AACA
* *
1434120 GATTTGGCATCTCTATAGCGGCAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGG
1 GATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGG
* * *
1434185 CGGAGAGCAGATTGAAGATAACAGATTTAGCGTCTCTGTAGCGGCGGAGAGCAGAT-GAAGATAA
66 CGAAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAA
*
1434249 CGGATTTGGCG-TCTGTATTAGACGGGGAGCAGAT-GAAGATAACAGATTTGGCGTCTCTGTAGC
131 CGGATTTGGCGCTCTGTATTAGACGGGGAGCAGATCGAAGATAACAGATTT-GCGTCTCTATAGC
* *
1434312 GGCAGAGAGCAGATCGAAGATAATAGATTTGGCGTCTCAGTAACGGCAGAGAGCAGATCGAAGAT
195 GGCAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCAGTAACAGCAGAGAGCAGATCGAAGAT
1434377 AACA
260 AACA
* * *
1434381 GATTTGGCGTCTCTGTAGCGGAAGAGAGCAGATCAAAGATAACAGATTTGGCGTCTCTGTAGCGA
1 GATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGG
*
1434446 CGAAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAACGGCGGAGAGCAGATCGAAGATAA
66 CGAAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAA
* * *
1434511 CGGATTTGGCGTCTCTGTATTAGACGGGGAACAGATCAAAGATAGCAGAT
131 CGGATTTGGCG-CTCTGTATTAGACGGGGAGCAGATCGAAGATAACAGAT
1434561 ATCGCCTTCC
Statistics
Matches: 397, Mismatches: 34, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
259 37 0.09
260 22 0.06
261 198 0.50
262 35 0.09
263 72 0.18
264 22 0.06
265 11 0.03
ACGTcount: A:0.30, C:0.17, G:0.31, T:0.22
Consensus pattern (263 bp):
GATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGG
CGAAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAA
CGGATTTGGCGCTCTGTATTAGACGGGGAGCAGATCGAAGATAACAGATTTGCGTCTCTATAGCG
GCAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCAGTAACAGCAGAGAGCAGATCGAAGATA
ACA
Found at i:1434838 original size:9 final size:8
Alignment explanation
Indices: 1434814--1434855 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
1434804 AATACAACCC
1434814 AAAAT-AA
1 AAAATAAA
1434821 AAAATAAA
1 AAAATAAA
1434829 AAAATAAA
1 AAAATAAA
1434837 AAAATGAAGA
1 AAAAT-AA-A
1434847 AAAA-AAA
1 AAAATAAA
1434854 AA
1 AA
1434856 CCTAACCTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
7 8 0.25
8 17 0.53
9 2 0.06
10 5 0.16
ACGTcount: A:0.86, C:0.00, G:0.05, T:0.10
Consensus pattern (8 bp):
AAAATAAA
Found at i:1435686 original size:13 final size:13
Alignment explanation
Indices: 1435668--1435692 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1435658 ATACTTTATG
1435668 TATTTTTTATTTT
1 TATTTTTTATTTT
1435681 TATTTTTTATTT
1 TATTTTTTATTT
1435693 ATTTTACGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TATTTTTTATTTT
Found at i:1441030 original size:27 final size:27
Alignment explanation
Indices: 1440988--1441099 Score: 118
Period size: 27 Copynumber: 4.1 Consensus size: 27
1440978 AGGAAGCGTC
*
1440988 CTGGTGGCTATGCCACAAATATCTGAT
1 CTGGTGGCTCTGCCACAAATATCTGAT
* * *
1441015 CTGGTGGCTCTACCACATATATCTGTT
1 CTGGTGGCTCTGCCACAAATATCTGAT
* *
1441042 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAAATATCTG-AT
* * * *
1441070 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAAATATCTGAT
1441096 CTGG
1 CTGG
1441100 CAGCCATGCT
Statistics
Matches: 72, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
26 5 0.07
27 52 0.72
28 15 0.21
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAAATATCTGAT
Found at i:1441092 original size:54 final size:54
Alignment explanation
Indices: 1440988--1441099 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
1440978 AGGAAGCGTC
*
1440988 CTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTACCACATATATCTGTT
1 CTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTACCACATATATCTGTT
* * * **
1441042 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTACCACATATATCTGTT
1441096 CTGG
1 CTGG
1441100 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 34 0.67
55 17 0.33
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTACCACATATATCTGTT
Found at i:1444523 original size:6 final size:6
Alignment explanation
Indices: 1444505--1444546 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
1444495 ATACTTTACT
* *
1444505 AGAAAA ATGAAAA AAAAAA AGAAAA AGAAAA AGAAAA GGAAA
1 AGAAAA A-GAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAA
1444547 TGTGAATAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
6 26 0.81
7 6 0.19
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (6 bp):
AGAAAA
Found at i:1449672 original size:19 final size:19
Alignment explanation
Indices: 1449644--1449689 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
1449634 TTTTAAATAC
*
1449644 TTTCGCAATTCAATTAAAT
1 TTTCGAAATTCAATTAAAT
1449663 TTTCGAAATTCAATTAAAT
1 TTTCGAAATTCAATTAAAT
1449682 TTTCGAAA
1 TTTCGAAA
1449690 GAAAACTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (19 bp):
TTTCGAAATTCAATTAAAT
Found at i:1453039 original size:29 final size:29
Alignment explanation
Indices: 1452993--1453049 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
1452983 CACCTAATTA
*
1452993 TGAAAAGTTACAAAATGATCATCCAACTG
1 TGAAAAGTTACAAAATGATCACCCAACTG
*
1453022 TGAAAAGTTACAAGATGATCACCCAACT
1 TGAAAAGTTACAAAATGATCACCCAACT
1453050 ATTCAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.23
Consensus pattern (29 bp):
TGAAAAGTTACAAAATGATCACCCAACTG
Found at i:1459064 original size:16 final size:17
Alignment explanation
Indices: 1459043--1459085 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
1459033 TTGAGATGAG
1459043 AATAAATTT-TTAATTA
1 AATAAATTTATTAATTA
1459059 AATAAATTTAATTAATTA
1 AATAAATTT-ATTAATTA
1459077 AA-AAATTTA
1 AATAAATTTA
1459086 AATTAAGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 10 0.40
17 6 0.24
18 9 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATAAATTTATTAATTA
Found at i:1459075 original size:18 final size:18
Alignment explanation
Indices: 1459043--1459091 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
1459033 TTGAGATGAG
1459043 AATAAATTT--TTAATTA
1 AATAAATTTAATTAATTA
1459059 AATAAATTTAATTAATTA
1 AATAAATTTAATTAATTA
1459077 AA-AAATTTAAATTAA
1 AATAAATTT-AATTAA
1459092 GTACACATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.30
17 6 0.20
18 15 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATAAATTTAATTAATTA
Found at i:1462252 original size:15 final size:15
Alignment explanation
Indices: 1462232--1462276 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 15
1462222 GCGTATAGTA
1462232 AAATATTAAAAATAT
1 AAATATTAAAAATAT
*
1462247 AAATATTAAAAAAACAT
1 AAATATT--AAAAATAT
1462264 AAAT-TTAAAAATA
1 AAATATTAAAAATA
1462277 ACTTAAACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 6 0.23
15 7 0.27
16 2 0.08
17 11 0.42
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATATTAAAAATAT
Found at i:1462258 original size:16 final size:16
Alignment explanation
Indices: 1462232--1462274 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
1462222 GCGTATAGTA
*
1462232 AAATATT-AAAAATAT
1 AAATATTAAAAAACAT
1462247 AAATATTAAAAAAACAT
1 AAATATT-AAAAAACAT
1462264 AAAT-TTAAAAA
1 AAATATTAAAAA
1462275 TAACTTAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 12 0.48
16 2 0.08
17 11 0.44
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (16 bp):
AAATATTAAAAAACAT
Found at i:1467816 original size:126 final size:125
Alignment explanation
Indices: 1467652--1467900 Score: 322
Period size: 126 Copynumber: 2.0 Consensus size: 125
1467642 TTCACTTTGG
* * * * *
1467652 AAATAATGAAAGGGGTTGAAGATTTCGAGATTCAAATATCGGATTTGCAGTTGTTTTTT-TAAGA
1 AAATAATGAAAGGGGTCGAAGATTTCGAGATTCAAATATCGAAATTGCAATTGTTTTTTAAAAG-
* *
1467716 ATATTAGTTGGTATGAACCAAATTTTGATTACA-ACTCGTATTCGACATTCATTCTATTCCGT
65 AGATTAGTT-GTATGAACCAAACTTTGATTACATACTCGTATTCGACATTCATTCT-TTCCGT
* * * **
1467778 AAATAGTGGAAGGGGTCGAAGATTTTGAGATTTGAATATCGAAATTGCAATTGTTTTTTAAAAGA
1 AAATAATGAAAGGGGTCGAAGATTTCGAGATTCAAATATCGAAATTGCAATTGTTTTTTAAAAGA
* * *
1467843 GATTAGTTGTGTGAACTAAACTTTGATTACATACTCGTATTTGACATTCATTCTTTCC
66 GATTAGTTGTATGAACCAAACTTTGATTACATACTCGTATTCGACATTCATTCTTTCC
1467901 CATGAAGGGG
Statistics
Matches: 106, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
125 24 0.23
126 79 0.75
127 3 0.03
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (125 bp):
AAATAATGAAAGGGGTCGAAGATTTCGAGATTCAAATATCGAAATTGCAATTGTTTTTTAAAAGA
GATTAGTTGTATGAACCAAACTTTGATTACATACTCGTATTCGACATTCATTCTTTCCGT
Found at i:1472748 original size:22 final size:23
Alignment explanation
Indices: 1472723--1472766 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
1472713 GGTAGAGTGA
*
1472723 TTTTATTTTTTTTCT-TTAAAAG
1 TTTTATTTTTTTTATGTTAAAAG
1472745 TTTTATTTTTTTTATGTTAAAA
1 TTTTATTTTTTTTATGTTAAAA
1472767 ACGGTTGTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (23 bp):
TTTTATTTTTTTTATGTTAAAAG
Found at i:1474547 original size:50 final size:50
Alignment explanation
Indices: 1474428--1474676 Score: 275
Period size: 50 Copynumber: 4.8 Consensus size: 50
1474418 GATAATAACA
* * ** * *
1474428 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* * *
1474479 TGCCCATGCCATATCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
1474529 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
1474579 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
1474634 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
1474677 TTACCCAAAT
Statistics
Matches: 168, Mismatches: 23, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.54
51 32 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:1474607 original size:100 final size:104
Alignment explanation
Indices: 1474427--1474676 Score: 348
Period size: 100 Copynumber: 2.4 Consensus size: 104
1474417 TGATAATAAC
**
1474427 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATA
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATA
* *
1474492 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* * *
1474529 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATA
1474592 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
1474634 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1474677 TTACCCAAAT
Statistics
Matches: 132, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
99 1 0.01
100 49 0.37
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATAT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:1474792 original size:13 final size:13
Alignment explanation
Indices: 1474771--1474802 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1474761 GCTTGGATCA
*
1474771 TCATCAAATAAAT
1 TCATAAAATAAAT
1474784 TCATAAAATAAAT
1 TCATAAAATAAAT
1474797 TCATAA
1 TCATAA
1474803 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:1475049 original size:30 final size:30
Alignment explanation
Indices: 1475014--1475071 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1475004 CCTCGACTCT
* *
1475014 AACTTTTTCAAAATTATAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
1475044 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
1475072 AAGGCTCGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.43
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:1491003 original size:36 final size:36
Alignment explanation
Indices: 1490956--1491027 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
1490946 GAGTGAGACA
1490956 TTGAATGTGATGGAAAAGGTGTAGTGGAGGTAGGTG
1 TTGAATGTGATGGAAAAGGTGTAGTGGAGGTAGGTG
* *
1490992 TTGAATGTGATGGGATAGGTGTAGTGGAGGTAGGTG
1 TTGAATGTGATGGAAAAGGTGTAGTGGAGGTAGGTG
1491028 GCGTATTTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.25, C:0.00, G:0.46, T:0.29
Consensus pattern (36 bp):
TTGAATGTGATGGAAAAGGTGTAGTGGAGGTAGGTG
Found at i:1500140 original size:28 final size:27
Alignment explanation
Indices: 1500100--1500156 Score: 96
Period size: 28 Copynumber: 2.1 Consensus size: 27
1500090 CCTAAAAAAT
*
1500100 TAAGTAAGTAACTAGGTAGTTTATATA
1 TAAGCAAGTAACTAGGTAGTTTATATA
1500127 TAAGCAAGCTAACTAGGTAGTTTATATA
1 TAAGCAAG-TAACTAGGTAGTTTATATA
1500155 TA
1 TA
1500157 TTTTATAGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (27 bp):
TAAGCAAGTAACTAGGTAGTTTATATA
Found at i:1503384 original size:29 final size:29
Alignment explanation
Indices: 1503351--1503418 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
1503341 AAAGATAGAG
*
1503351 AGATTAAATTCCTGAAAATAAGAATAAAA
1 AGATTAAATTCCTGAAAATAAAAATAAAA
*
1503380 AGATTAAATTCTTGAAAATAAAAATAAAA
1 AGATTAAATTCCTGAAAATAAAAATAAAA
* *
1503409 AAACTAAATT
1 AGATTAAATT
1503419 TCAACTATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.60, C:0.06, G:0.07, T:0.26
Consensus pattern (29 bp):
AGATTAAATTCCTGAAAATAAAAATAAAA
Found at i:1504197 original size:20 final size:20
Alignment explanation
Indices: 1504168--1504217 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1504158 GTAAAATTTC
*
1504168 TCTTCATCTTATATTTCTTT
1 TCTTCTTCTTATATTTCTTT
* *
1504188 TCTTCTTCTTTTTTTTCTTT
1 TCTTCTTCTTATATTTCTTT
1504208 TCTTCTTCTT
1 TCTTCTTCTT
1504218 TACACCATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (20 bp):
TCTTCTTCTTATATTTCTTT
Found at i:1504198 original size:11 final size:11
Alignment explanation
Indices: 1504182--1504218 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
1504172 CATCTTATAT
1504182 TTCTTTTCTTC
1 TTCTTTTCTTC
1504193 TTCTTTT-TT-
1 TTCTTTTCTTC
1504202 TTCTTTTCTTC
1 TTCTTTTCTTC
1504213 TTCTTT
1 TTCTTT
1504219 ACACCATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 7 0.29
10 4 0.17
11 13 0.54
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTCTTTTCTTC
Found at i:1504218 original size:20 final size:20
Alignment explanation
Indices: 1504181--1504218 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1504171 TCATCTTATA
1504181 TTTCTTTTCTTCTTCTTTTT
1 TTTCTTTTCTTCTTCTTTTT
1504201 TTTCTTTTCTTCTTCTTT
1 TTTCTTTTCTTCTTCTTT
1504219 ACACCATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTCTTTTCTTCTTCTTTTT
Found at i:1504797 original size:22 final size:22
Alignment explanation
Indices: 1504772--1504815 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1504762 AATTATTAAC
* *
1504772 ATAATGAATTTTAATTAATTTT
1 ATAATAAATTCTAATTAATTTT
*
1504794 ATAATAAATTCTGATTAATTTT
1 ATAATAAATTCTAATTAATTTT
1504816 GGTCATTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (22 bp):
ATAATAAATTCTAATTAATTTT
Found at i:1504989 original size:21 final size:21
Alignment explanation
Indices: 1504960--1505001 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1504950 CATTAATTCA
1504960 TAATATAA-TTAATTTTAATTT
1 TAATATAATTTAA-TTTAATTT
*
1504981 TAATCTAATTTAATTTAATTT
1 TAATATAATTTAATTTAATTT
1505002 GGGTTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TAATATAATTTAATTTAATTT
Found at i:1512571 original size:22 final size:19
Alignment explanation
Indices: 1512541--1512587 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 19
1512531 AAATATGATA
1512541 ATTATTAATATATAATTATATCT
1 ATTA-TAATATAT-ATTA-AT-T
1512564 ATTATAATATATATTAATT
1 ATTATAATATATATTAATT
1512583 ATTAT
1 ATTAT
1512588 CAACTTTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 2 0.08
21 4 0.17
22 8 0.33
23 4 0.17
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTATAATATATATTAATT
Found at i:1512583 original size:16 final size:15
Alignment explanation
Indices: 1512543--1512584 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
1512533 ATATGATAAT
1512543 TATTAATATATAATTA
1 TATTAAT-TATAATTA
1512559 TATCT-ATTATAATATA
1 TAT-TAATTATAAT-TA
1512575 TATTAATTAT
1 TATTAATTAT
1512585 TATCAACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 7 0.30
16 15 0.65
17 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTAATTATAATTA
Found at i:1513250 original size:25 final size:24
Alignment explanation
Indices: 1513219--1513279 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 24
1513209 AATTTTTCTC
*
1513219 TTAAATTTTAAATTTTATTTAATTA
1 TTAAATTTTAAA-TTTATTGAATTA
* *
1513244 TTTAATTTTTCAATTTATTGAATTA
1 -TTAAATTTTAAATTTATTGAATTA
1513269 TTAATATTTTA
1 TTAA-ATTTTA
1513280 TATTAATTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 4 0.14
25 15 0.52
26 10 0.34
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (24 bp):
TTAAATTTTAAATTTATTGAATTA
Found at i:1513292 original size:25 final size:25
Alignment explanation
Indices: 1513239--1513292 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
1513229 AATTTTATTT
* *
1513239 AATTATTTAATTTTTCAATTTATTG
1 AATTATTTAATTTTTCAATTAATTA
1513264 AATTA-TTAATATTTT-ATATTAATTA
1 AATTATTTAAT-TTTTCA-ATTAATTA
1513289 AATT
1 AATT
1513293 TTTGAGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
AATTATTTAATTTTTCAATTAATTA
Found at i:1516122 original size:22 final size:22
Alignment explanation
Indices: 1516097--1516140 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1516087 AATTATTAAA
* *
1516097 ATAATGAATTTTAATTAGTTTT
1 ATAATAAATTTTAATTAATTTT
*
1516119 ATAATAAATTTTGATTAATTTT
1 ATAATAAATTTTAATTAATTTT
1516141 GGTCATTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.55
Consensus pattern (22 bp):
ATAATAAATTTTAATTAATTTT
Found at i:1516305 original size:22 final size:22
Alignment explanation
Indices: 1516277--1516321 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1516267 TTTATGTGTA
*
1516277 TTAATTTATAATATAA-TTAATT
1 TTAATTT-TAATACAATTTAATT
1516299 TTAATTTTAATACAATTTAATT
1 TTAATTTTAATACAATTTAATT
1516321 T
1 T
1516322 GGGTTAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAATTTTAATACAATTTAATT
Found at i:1525204 original size:35 final size:35
Alignment explanation
Indices: 1525160--1525229 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
1525150 TTCGTATGTA
1525160 AATAATACCATACTGTACATGTATTTAAATGTTAT
1 AATAATACCATACTGTACATGTATTTAAATGTTAT
1525195 AATAATACCATACTGTACATGTATTTAAATGTTAT
1 AATAATACCATACTGTACATGTATTTAAATGTTAT
1525230 CATCACATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (35 bp):
AATAATACCATACTGTACATGTATTTAAATGTTAT
Found at i:1526873 original size:25 final size:25
Alignment explanation
Indices: 1526845--1526896 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1526835 TATGTGAGTA
1526845 AATTCTATGATATTTATTGCATAAG
1 AATTCTATGATATTTATTGCATAAG
1526870 AATTCTATGATATTTATTGCATAAG
1 AATTCTATGATATTTATTGCATAAG
1526895 AA
1 AA
1526897 ATTGACATGA
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:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (25 bp):
AATTCTATGATATTTATTGCATAAG
Found at i:1528070 original size:30 final size:31
Alignment explanation
Indices: 1528036--1528137 Score: 122
Period size: 30 Copynumber: 3.4 Consensus size: 31
1528026 AAAAAAATAA
*
1528036 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
1528066 AAATTTCATTTTGACCCTTAAAC-TTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
1528096 AAATTTCACTTAGACCCCTAAAC-TTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTTC-TCT
1528126 AAATTTCATTTT
1 AAATTTCATTTT
1528138 AATCCTAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 4 0.06
30 57 0.92
31 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.44
Consensus pattern (31 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTCT
Found at i:1528536 original size:9 final size:9
Alignment explanation
Indices: 1528522--1528573 Score: 61
Period size: 9 Copynumber: 5.8 Consensus size: 9
1528512 AAGGAAGAAG
1528522 AAGAAAAGA
1 AAGAAAAGA
*
1528531 AAGAAAAAA
1 AAGAAAAGA
1528540 AAGAAAA-A
1 AAGAAAAGA
*
1528548 AAGGGAAAGA
1 AA-GAAAAGA
*
1528558 AAAAAAAGA
1 AAGAAAAGA
1528567 AAGAAAA
1 AAGAAAA
1528574 AAATAAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
8 3 0.08
9 30 0.83
10 3 0.08
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAGAAAAGA
Found at i:1528558 original size:14 final size:13
Alignment explanation
Indices: 1528526--1528576 Score: 68
Period size: 13 Copynumber: 3.8 Consensus size: 13
1528516 AAGAAGAAGA
1528526 AAAGAAAGAAAAA-
1 AAAGAAA-AAAAAG
*
1528539 AAAGAAAAAAAGGG
1 AAAGAAAAAAA-AG
1528553 AAAGAAAAAAAAG
1 AAAGAAAAAAAAG
1528566 AAAGAAAAAAA
1 AAAGAAAAAAA
1528577 TAAAAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 4 0.12
13 19 0.56
14 11 0.32
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAAAAG
Found at i:1528559 original size:23 final size:24
Alignment explanation
Indices: 1528522--1528573 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
1528512 AAGGAAGAAG
1528522 AAGAAAA--GAAAGAAAAAAAAGA
1 AAGAAAAGGGAAAGAAAAAAAAGA
1528544 AA-AAAAGGGAAAGAAAAAAAAGA
1 AAGAAAAGGGAAAGAAAAAAAAGA
1528567 AAGAAAA
1 AAGAAAA
1528574 AAATAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.15
22 2 0.07
23 17 0.63
24 4 0.15
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (24 bp):
AAGAAAAGGGAAAGAAAAAAAAGA
Found at i:1528715 original size:23 final size:24
Alignment explanation
Indices: 1528682--1528735 Score: 101
Period size: 23 Copynumber: 2.3 Consensus size: 24
1528672 GCAACAAAAA
1528682 AAGCAGCAAAAAAGAAGAAGAAAG
1 AAGCAGCAAAAAAGAAGAAGAAAG
1528706 AAGCAG-AAAAAAGAAGAAGAAAG
1 AAGCAGCAAAAAAGAAGAAGAAAG
1528729 AAGCAGC
1 AAGCAGC
1528736 CCAAATGCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 23 0.79
24 6 0.21
ACGTcount: A:0.65, C:0.09, G:0.26, T:0.00
Consensus pattern (24 bp):
AAGCAGCAAAAAAGAAGAAGAAAG
Found at i:1528872 original size:10 final size:9
Alignment explanation
Indices: 1528857--1528917 Score: 79
Period size: 9 Copynumber: 6.7 Consensus size: 9
1528847 CCAGCAGAAA
1528857 AAAAAAAGAG
1 AAAAAAA-AG
1528867 AAAAAAAAG
1 AAAAAAAAG
*
1528876 AAAAAAGAG
1 AAAAAAAAG
*
1528885 -AGAAAAAG
1 AAAAAAAAG
1528893 AAAAAAAAG
1 AAAAAAAAG
1528902 AAAAAACAAG
1 AAAAAA-AAG
1528912 AAAAAA
1 AAAAAA
1528918 GGGGTTCAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
8 6 0.13
9 23 0.51
10 16 0.36
ACGTcount: A:0.84, C:0.02, G:0.15, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:1528917 original size:26 final size:25
Alignment explanation
Indices: 1528854--1528918 Score: 87
Period size: 26 Copynumber: 2.6 Consensus size: 25
1528844 AGCCCAGCAG
*
1528854 AAAAAA-AAAAGAGAAAAAAAAGAA
1 AAAAAAGAAAAAAGAAAAAAAAGAA
*
1528878 AAAAGAGAGAAAAAGAAAAAAAAGAA
1 AAAAAAGA-AAAAAGAAAAAAAAGAA
1528904 AAAACAAGAAAAAAG
1 AAAA-AAGAAAAAAG
1528919 GGGTTCAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.14
25 1 0.03
26 26 0.74
27 3 0.09
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (25 bp):
AAAAAAGAAAAAAGAAAAAAAAGAA
Found at i:1529309 original size:21 final size:20
Alignment explanation
Indices: 1529277--1529318 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
1529267 TCGCGTTTCG
1529277 AAATTTTCGTGTCTTCAAAA
1 AAATTTTCGTGTCTTCAAAA
*
1529297 AAATTTCTCGTGTTTTCAAAA
1 AAATTT-TCGTGTCTTCAAAA
1529318 A
1 A
1529319 TAAGGTAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
AAATTTTCGTGTCTTCAAAA
Found at i:1529319 original size:19 final size:19
Alignment explanation
Indices: 1529277--1529318 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
1529267 TCGCGTTTCG
1529277 AAATTTTCGTGTCTTCAAAA
1 AAATTTTCGTGTCTTC-AAA
*
1529297 AAATTTCTCGTGTTTTCAAA
1 AAATTT-TCGTGTCTTCAAA
1529317 AA
1 AA
1529319 TAAGGTAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (19 bp):
AAATTTTCGTGTCTTCAAA
Found at i:1529462 original size:17 final size:18
Alignment explanation
Indices: 1529423--1529913 Score: 249
Period size: 17 Copynumber: 27.3 Consensus size: 18
1529413 GAAAAATCAT
1529423 AAAAATTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
1529441 AAAAATTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
* * *
1529459 AAAAAATTCCAT-TTTTC
1 AAAAATTTTCGTGTTTTC
* *
1529476 AAAATTTTTCGTGTTTTTTTA
1 AAAAATTTTCGTG---TTTTC
* * *
1529497 AAAAATTTCCAT-ATTTC
1 AAAAATTTTCGTGTTTTC
*
1529514 TAAAATTTTCGTG-TTT-
1 AAAAATTTTCGTGTTTTC
* *
1529530 AAAAAATTTCGTATTTTC
1 AAAAATTTTCGTGTTTTC
* ** *
1529548 AAAATTTTTTATTTTTTTC
1 AAAA-ATTTTCGTGTTTTC
* *
1529567 AACAATTCTCGTG-TTTC
1 AAAAATTTTCGTGTTTTC
* * *
1529584 ACAAATTCTCGTATTTT-
1 AAAAATTTTCGTGTTTTC
* ** *
1529601 AAAATTTTTTATGTTTTA
1 AAAAATTTTCGTGTTTTC
1529619 AAAAATAAATTTC-TCGTGTTTC
1 AAAAAT---TTTCGT-GT-TTTC
* *
1529641 AAAAATTGTCATGTTTT-
1 AAAAATTTTCGTGTTTTC
*
1529658 AAAAATTTTCATG-TTTC
1 AAAAATTTTCGTGTTTTC
* * *
1529675 TAAAATGTTCGT-ATTTC
1 AAAAATTTTCGTGTTTTC
**
1529692 AAAAAATCCTCGTGTTTTC
1 -AAAAATTTTCGTGTTTTC
* *
1529711 AAAAATTCTCATG-TTTC
1 AAAAATTTTCGTGTTTTC
*
1529728 AAAAATCTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
* *
1529746 -AAAATTCTAGTG-TTTC
1 AAAAATTTTCGTGTTTTC
*
1529762 AAAAATTTTCATGTTTTC
1 AAAAATTTTCGTGTTTTC
* *
1529780 AAAAATTTCCCCTGTTTTC
1 AAAAATTT-TCGTGTTTTC
* *
1529799 AAAAATTCTCGT-ATTTC
1 AAAAATTTTCGTGTTTTC
* *
1529816 AAAAATTTTCTTTTTTTC
1 AAAAATTTTCGTGTTTTC
* *
1529834 AAAAAAAAACTTCCGTGTTTT-
1 ----AAAAATTTTCGTGTTTTC
* * *
1529855 ATAAATCTCCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
* **
1529873 AAAAAATTCTCG-ACTTTC
1 -AAAAATTTTCGTGTTTTC
*
1529891 AAAAAATTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
1529909 AAAAA
1 AAAAA
1529914 ATTGACATTG
Statistics
Matches: 353, Mismatches: 88, Indels: 64
0.70 0.17 0.13
Matches are distributed among these distances:
16 17 0.05
17 150 0.42
18 101 0.29
19 43 0.12
20 2 0.01
21 18 0.05
22 22 0.06
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.46
Consensus pattern (18 bp):
AAAAATTTTCGTGTTTTC
Found at i:1529523 original size:38 final size:36
Alignment explanation
Indices: 1529437--1529529 Score: 118
Period size: 38 Copynumber: 2.5 Consensus size: 36
1529427 ATTTTCGTGT
*
1529437 TTTCAAAAATTTTCGTG--TTTTCAAAAAATTCCATT
1 TTTC-AAAATTTTCGTGTTTTTTCAAAAAATTCCATA
*
1529472 TTTCAAAATTTTTCGTGTTTTTTTAAAAAATTTCCATA
1 TTTCAAAA-TTTTCGTGTTTTTTCAAAAAA-TTCCATA
1529510 TTTCTAAAATTTTCGTGTTT
1 TTTC-AAAATTTTCGTGTTT
1529530 AAAAAATTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
34 4 0.08
35 12 0.24
37 10 0.20
38 21 0.41
39 4 0.08
ACGTcount: A:0.30, C:0.12, G:0.06, T:0.52
Consensus pattern (36 bp):
TTTCAAAATTTTCGTGTTTTTTCAAAAAATTCCATA
Found at i:1529581 original size:53 final size:53
Alignment explanation
Indices: 1529517--1529824 Score: 155
Period size: 53 Copynumber: 5.8 Consensus size: 53
1529507 ATATTTCTAA
* *
1529517 AATTTTCGTGTTTAAAAAATT-TCGTATTTTCAAAATTTTTTATTTTTTTCAAC
1 AATTCTCGTGTTTAAAAAATTCTCGTATTTT-AAAATTTTTTATGTTTTTCAAC
* * ** *
1529570 AATTCTCGTGTTTCACAAATTCTCGTATTTTAAAATTTTTTATGTTTTAAAAAATA
1 AATTCTCGTGTTTAAAAAATTCTCGTATTTTAAAATTTTTTATGTTTT--TCAA-C
* * * * * * *
1529626 AATTTCTCGTGTTTCAAAAATTGTCATGTTTTAAAAATTTTCATGTTTCT-AA-
1 AA-TTCTCGTGTTTAAAAAATTCTCGTATTTTAAAATTTTTTATGTTTTTCAAC
* * * * * *
1529678 AATGT-TCGTATTTCAAAAAATCCTCGTGTTTTCAAAAATTCTCATG--TTTCAA-
1 AAT-TCTCGTGTTT-AAAAAATTCTCGTATTTT-AAAATTTTTTATGTTTTTCAAC
* ** * * * * * *
1529730 AAATCTTCGTGTTTTCAAAATTCTAGTGTTTCAAAAATTTTCATG-TTTTCAAA
1 AATTC-TCGTGTTTAAAAAATTCTCGTATTTTAAAATTTTTTATGTTTTTCAAC
* * * * *
1529783 AATTTCCCCTGTTTTCAAAAATTCTCGTATTTCAAAAATTTT
1 AA-TTCTCGTG-TTTAAAAAATTCTCGTATTTTAAAATTTTT
1529825 CTTTTTTTCA
Statistics
Matches: 203, Mismatches: 37, Indels: 29
0.75 0.14 0.11
Matches are distributed among these distances:
51 23 0.11
52 40 0.20
53 58 0.29
54 39 0.19
55 2 0.01
56 2 0.01
57 39 0.19
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (53 bp):
AATTCTCGTGTTTAAAAAATTCTCGTATTTTAAAATTTTTTATGTTTTTCAAC
Found at i:1529763 original size:16 final size:16
Alignment explanation
Indices: 1529707--1529765 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 16
1529697 ATCCTCGTGT
1529707 TTTCAAAAATTCTCA-TG
1 TTTC-AAAATTCT-AGTG
* *
1529724 TTTCAAAAATCTTCGTG
1 TTTCAAAATTC-TAGTG
1529741 TTTTCAAAATTCTAGTG
1 -TTTCAAAATTCTAGTG
1529758 TTTCAAAA
1 TTTCAAAA
1529766 ATTTTCATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
16 14 0.40
17 11 0.31
18 10 0.29
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.42
Consensus pattern (16 bp):
TTTCAAAATTCTAGTG
Found at i:1529914 original size:18 final size:18
Alignment explanation
Indices: 1529423--1529916 Score: 167
Period size: 18 Copynumber: 27.4 Consensus size: 18
1529413 GAAAAATCAT
*
1529423 AAAAATTTTCGTGTTTTC
1 AAAAAATTTCGTGTTTTC
*
1529441 AAAAATTTTCGTGTTTTC
1 AAAAAATTTCGTGTTTTC
* *
1529459 AAAAAATTCCAT-TTTTC
1 AAAAAATTTCGTGTTTTC
** *
1529476 AAAATTTTTCGTGTTTTTTT
1 AAAAAATTTCGTG--TTTTC
* *
1529496 AAAAAATTTCCAT-ATTTC
1 AAAAAATTT-CGTGTTTTC
* *
1529514 TAAAATTTTCGTG-TTT-
1 AAAAAATTTCGTGTTTTC
*
1529530 AAAAAATTTCGTATTTTC
1 AAAAAATTTCGTGTTTTC
** ** *
1529548 AAAATTTTTTATTTTTTTC
1 AAAA-AATTTCGTGTTTTC
*
1529567 -AACAATTCTCGTG-TTTC
1 AAAAAATT-TCGTGTTTTC
* *
1529584 -ACAAATTCTCGTATTTT-
1 AAAAAATT-TCGTGTTTTC
** ** *
1529601 AAAATTTTTTATGTTTTAAA
1 AAAAAATTTCGTGTTTT--C
1529621 AAATAAATTTC-TCGTGTTTC
1 AAA-AAATTTCGT-GT-TTTC
*
1529641 -AAAAATTGTCATGTTTT-
1 AAAAAATT-TCGTGTTTTC
* *
1529658 AAAAATTTTCATG-TTTC
1 AAAAAATTTCGTGTTTTC
* *
1529675 -TAAAATGTTCGT-ATTTC
1 AAAAAAT-TTCGTGTTTTC
*
1529692 AAAAAATCCTCGTGTTTTC
1 AAAAAAT-TTCGTGTTTTC
*
1529711 -AAAAATTCTCATG-TTTC
1 AAAAAATT-TCGTGTTTTC
1529728 -AAAAATCTTCGTGTTTTC
1 AAAAAAT-TTCGTGTTTTC
*
1529746 --AAAATTCTAGTG-TTTC
1 AAAAAATT-TCGTGTTTTC
* *
1529762 AAAAATTTTCATGTTTTC
1 AAAAAATTTCGTGTTTTC
*
1529780 -AAAAATTTCCCCTGTTTTC
1 AAAAAATTT--CGTGTTTTC
*
1529799 -AAAAATTCTCGT-ATTTC
1 AAAAAATT-TCGTGTTTTC
* * *
1529816 AAAAATTTTCTTTTTTTC
1 AAAAAATTTCGTGTTTTC
*
1529834 AAAAAAAAACTTCCGTGTTTT-
1 ---AAAAAA-TTTCGTGTTTTC
* *
1529855 -ATAAATCTCCGTGTTTTC
1 AAAAAAT-TTCGTGTTTTC
**
1529873 AAAAAATTCTCG-ACTTTC
1 AAAAAATT-TCGTGTTTTC
1529891 AAAAAATTTCGTGTTTTC
1 AAAAAATTTCGTGTTTTC
1529909 AAAAAATT
1 AAAAAATT
1529917 GACATTGTTT
Statistics
Matches: 354, Mismatches: 76, Indels: 92
0.68 0.15 0.18
Matches are distributed among these distances:
16 23 0.06
17 113 0.32
18 136 0.38
19 41 0.12
20 17 0.05
21 13 0.04
22 11 0.03
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.46
Consensus pattern (18 bp):
AAAAAATTTCGTGTTTTC
Found at i:1530040 original size:21 final size:21
Alignment explanation
Indices: 1529984--1530056 Score: 91
Period size: 19 Copynumber: 3.6 Consensus size: 21
1529974 CAAAATTTTT
1529984 GTGTTTTC-AAAATAAAATT-
1 GTGTTTTCAAAAATAAAATTC
1530003 GTGTTTT-AAAAATAAAATTC
1 GTGTTTTCAAAAATAAAATTC
*
1530023 GTGTTTTCAAAAAAAAAATTC
1 GTGTTTTCAAAAATAAAATTC
1530044 -TCGTGTTTCAAAA
1 GT-GT-TTTCAAAA
1530057 TTTTCGTGTT
Statistics
Matches: 48, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
19 18 0.38
20 8 0.17
21 14 0.29
22 8 0.17
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.38
Consensus pattern (21 bp):
GTGTTTTCAAAAATAAAATTC
Found at i:1530052 original size:22 final size:20
Alignment explanation
Indices: 1529988--1530056 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
1529978 ATTTTTGTGT
*
1529988 TTTC-AAAATAAAATT-GTG
1 TTTCAAAAAAAAAATTCGTG
* *
1530006 TTTTAAAAATAAAATTCGTG
1 TTTCAAAAAAAAAATTCGTG
1530026 TTTTCAAAAAAAAAATTCTCGTG
1 -TTTCAAAAAAAAAA-T-TCGTG
1530049 TTTCAAAA
1 TTTCAAAA
1530057 TTTTCGTGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
18 3 0.07
19 11 0.26
20 3 0.07
21 12 0.28
22 9 0.21
23 5 0.12
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.38
Consensus pattern (20 bp):
TTTCAAAAAAAAAATTCGTG
Found at i:1530056 original size:18 final size:17
Alignment explanation
Indices: 1530035--1530125 Score: 55
Period size: 18 Copynumber: 5.1 Consensus size: 17
1530025 GTTTTCAAAA
1530035 AAAAAATTCTCGTGTTTC
1 AAAAAATT-TCGTGTTTC
* *
1530053 -AAAATTTTCGTGTTTTTTTA
1 AAAAAATTTCGTG----TTTC
*
1530073 AAAAAAATTCGTGTTTC
1 AAAAAATTTCGTGTTTC
1530090 GAAAAAATGTT-GTGTTTC
1 -AAAAAAT-TTCGTGTTTC
1530108 --AAAATTCTCGTGTTTC
1 AAAAAATT-TCGTGTTTC
1530124 AA
1 AA
1530126 TTGGATCACG
Statistics
Matches: 56, Mismatches: 6, Indels: 22
0.67 0.07 0.26
Matches are distributed among these distances:
14 1 0.02
15 6 0.11
16 12 0.21
17 9 0.16
18 13 0.23
19 2 0.04
20 3 0.05
21 10 0.18
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (17 bp):
AAAAAATTTCGTGTTTC
Found at i:1530056 original size:20 final size:19
Alignment explanation
Indices: 1529930--1530111 Score: 65
Period size: 18 Copynumber: 8.9 Consensus size: 19
1529920 ATTGTTTCAT
1529930 AAATTTCCGTGTTTCAAAAA
1 AAATTT-CGTGTTTCAAAAA
*
1529950 AAATCCTCGTGTTTCATAATTTATCA
1 AAAT-TTCGTGTTTCA-AA---A--A
*
1529976 AAATTTTTGTGTTTTCAAAATA
1 AAA-TTTCGTG-TTTCAAAA-A
*
1529998 AAA-TT-GTGTTTTAAAAA
1 AAATTTCGTGTTTCAAAAA
*
1530015 TAAAATTCGTGTTTTCAAAAAAA
1 -AAATTTCGTG-TTTC--AAAAA
1530038 AAATTCTCGTGTTTC---AA
1 AAATT-TCGTGTTTCAAAAA
* *
1530055 AATTTTCGTGTTTTTTTAAAAA
1 AAATTTCGTG---TTTCAAAAA
*
1530077 AAA-TTCGTGTTTC-GAAA
1 AAATTTCGTGTTTCAAAAA
1530094 AAATGTT-GTGTTTCAAAA
1 AAAT-TTCGTGTTTCAAAA
1530112 TTCTCGTGTT
Statistics
Matches: 124, Mismatches: 13, Indels: 51
0.66 0.07 0.27
Matches are distributed among these distances:
16 5 0.04
17 13 0.10
18 20 0.16
19 12 0.10
20 18 0.15
21 12 0.10
22 16 0.13
23 11 0.09
24 1 0.01
26 10 0.08
27 6 0.05
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.42
Consensus pattern (19 bp):
AAATTTCGTGTTTCAAAAA
Found at i:1530058 original size:16 final size:16
Alignment explanation
Indices: 1530037--1530067 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1530027 TTTCAAAAAA
1530037 AAAATTCTCGTGTTTC
1 AAAATTCTCGTGTTTC
*
1530053 AAAATTTTCGTGTTT
1 AAAATTCTCGTGTTT
1530068 TTTTAAAAAA
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:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (16 bp):
AAAATTCTCGTGTTTC
Found at i:1530063 original size:39 final size:37
Alignment explanation
Indices: 1529973--1530094 Score: 97
Period size: 39 Copynumber: 3.2 Consensus size: 37
1529963 TCATAATTTA
* *
1529973 TCAAAATTTTTGTGTTTTCAAAATAAAA-TT-GTGTTT
1 TCAAAATTTTCGTGTTTTCAAAAAAAAATTTCGTG-TT
* *
1530009 TAAAAATAAAATTCGTGTTTTCAAAAAAAAAATTCTCGTGTT
1 TCAAAAT---TTTCGTGTTTTC-AAAAAAAAATT-TCGTGTT
**
1530051 TCAAAATTTTCGTGTTTTTTTAAAAAAAA-TTCGTGTT
1 TCAAAATTTTCGTG-TTTTCAAAAAAAAATTTCGTGTT
1530088 TCGAAAA
1 TC-AAAA
1530095 AATGTTGTGT
Statistics
Matches: 69, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
36 6 0.09
37 9 0.13
38 5 0.07
39 24 0.35
40 12 0.17
41 1 0.01
42 9 0.13
43 3 0.04
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.43
Consensus pattern (37 bp):
TCAAAATTTTCGTGTTTTCAAAAAAAAATTTCGTGTT
Found at i:1530096 original size:17 final size:17
Alignment explanation
Indices: 1530074--1530125 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
1530064 GTTTTTTTAA
1530074 AAAAAAT-TCGTGTTTC
1 AAAAAATGTCGTGTTTC
*
1530090 GAAAAAATGTTGTGTTTC
1 -AAAAAATGTCGTGTTTC
* *
1530108 -AAAATTCTCGTGTTTC
1 AAAAAATGTCGTGTTTC
1530124 AA
1 AA
1530126 TTGGATCACG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 13 0.45
17 8 0.28
18 8 0.28
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (17 bp):
AAAAAATGTCGTGTTTC
Found at i:1541999 original size:36 final size:36
Alignment explanation
Indices: 1541929--1541999 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
1541919 AAATTGACTC
* **
1541929 ATATTGCGAGAGGTGAGTTAGCTTTTTTTTTTTTTT
1 ATATTGCGAGAGGTGAGTTAGCTCTTTTAATTTTTT
1541965 ATATTGCGAGAGGTGAGTTAAGC-CTTTTAATTTTT
1 ATATTGCGAGAGGTGAGTT-AGCTCTTTTAATTTTT
1542000 GTTTTTCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 28 0.90
37 3 0.10
ACGTcount: A:0.21, C:0.07, G:0.23, T:0.49
Consensus pattern (36 bp):
ATATTGCGAGAGGTGAGTTAGCTCTTTTAATTTTTT
Found at i:1542394 original size:191 final size:191
Alignment explanation
Indices: 1541965--1542424 Score: 870
Period size: 190 Copynumber: 2.4 Consensus size: 191
1541955 TTTTTTTTTT
1541965 ATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCGAGAA
1 ATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCGAGAA
1542030 ATGA-TTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTTTAAAAAAATCAACTCATATTGCG
66 ATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTTTAAAAAAATCAACTCATATTGCG
1542094 AGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTATGTTTTAAATTGACTC
131 AGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTATGTTTTAAATTGACTC
1542155 ATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCGAGAA
1 ATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCGAGAA
1542220 ATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTTTAAAAAAATCAACTCATATTGCG
66 ATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTTTAAAAAAATCAACTCATATTGCG
1542285 AGAA-TGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTATGTTTTAAATTGACTC
131 AGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTATGTTTTAAATTGACTC
*
1542345 ATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAATCAACTCATATTGCAAGA
1 ATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC-AAAATCAACTCATATTGCGAGA
**
1542410 GGTGAGTTGAGCCTC
65 AATGAGTTGAGCCTC
1542425 GGCTCACATG
Statistics
Matches: 265, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
190 167 0.63
191 98 0.37
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.36
Consensus pattern (191 bp):
ATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCGAGAA
ATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTTTAAAAAAATCAACTCATATTGCG
AGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTATGTTTTAAATTGACTC
Found at i:1542464 original size:16 final size:17
Alignment explanation
Indices: 1542443--1542476 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1542433 TGCTGAGGTA
*
1542443 TTTTCAATTTATG-TTT
1 TTTTCAATCTATGCTTT
1542459 TTTTCAATCTATGCTTT
1 TTTTCAATCTATGCTTT
1542476 T
1 T
1542477 CAAAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTTCAATCTATGCTTT
Found at i:1542642 original size:13 final size:14
Alignment explanation
Indices: 1542626--1542656 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1542616 TCTTTTCAAA
1542626 TTCTG-TTTTTAAT
1 TTCTGTTTTTTAAT
1542639 TTCTGTTTTTTAAT
1 TTCTGTTTTTTAAT
1542653 TTCT
1 TTCT
1542657 ATGTTTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.13, C:0.10, G:0.06, T:0.71
Consensus pattern (14 bp):
TTCTGTTTTTTAAT
Found at i:1542681 original size:105 final size:104
Alignment explanation
Indices: 1542564--1542752 Score: 281
Period size: 105 Copynumber: 1.8 Consensus size: 104
1542554 TCTACTTTTC
* * *
1542564 AAATCAACTCATATTTCAAGAGGTGAGTTGAGTCTCAGGCCACACGCTGAGGTCTTTTCAAATTC
1 AAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGG--ACACGCTGAGGTATTTTCAAATTC
* * *
1542629 T-GTTTTTAATTTCTGTTTTTTAATTTCTATGTTTCAAAAA
64 TACTTTTCAATTTCTATTTTTTAATTTCTATGTTTCAAAAA
* *
1542669 AAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTA
1 AAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAAATTCTA
1542734 CTTTTCAATTTCTATTTTT
66 CTTTTCAATTTCTATTTTT
1542753 CAAAAATCAA
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
103 22 0.29
104 16 0.21
105 37 0.49
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (104 bp):
AAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAAATTCTA
CTTTTCAATTTCTATTTTTTAATTTCTATGTTTCAAAAA
Found at i:1542740 original size:14 final size:14
Alignment explanation
Indices: 1542721--1542755 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1542711 CGCTGAGGTA
1542721 TTTTCAATTTCTAC
1 TTTTCAATTTCTAC
*
1542735 TTTTCAATTTCTAT
1 TTTTCAATTTCTAC
1542749 TTTTCAA
1 TTTTCAA
1542756 AAATCAACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTCTAC
Found at i:1542818 original size:54 final size:55
Alignment explanation
Indices: 1542734--1542950 Score: 324
Period size: 54 Copynumber: 4.1 Consensus size: 55
1542724 TCAATTTCTA
1542734 CTTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
*
1542789 CTTTT-AATTTCTATTTTTCAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1542843 C--TT---TTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTTCTATTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* * *
1542894 CTTTTGCAAATTCT-GTTTTC-AAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
1 CTTTT-CAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1542948 CTT
1 CTT
1542951 GGCTCACGTG
Statistics
Matches: 150, Mismatches: 5, Indels: 15
0.88 0.03 0.09
Matches are distributed among these distances:
50 12 0.08
51 35 0.23
52 2 0.01
53 2 0.01
54 85 0.57
55 5 0.03
56 5 0.03
57 4 0.03
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (55 bp):
CTTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
Found at i:1542923 original size:105 final size:104
Alignment explanation
Indices: 1542742--1542950 Score: 341
Period size: 105 Copynumber: 2.0 Consensus size: 104
1542732 TACTTTTCAA
* *
1542742 TTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTATTTTT
1 TTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAAATTCTAGTTTT
*
1542807 CAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTT
66 CAAAAACCAACTCATATTGCGAGAAGTGAGTTGAGCCTT
1542846 TTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTGCAAATTCT-GT
1 TTTCTATTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT--AAATTCTAGT
*
1542910 TTTC-AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTT
63 TTTCAAAAACCAACTCATATTGCGAGAAGTGAGTTGAGCCTT
1542951 GGCTCACGTG
Statistics
Matches: 98, Mismatches: 4, Indels: 5
0.92 0.04 0.05
Matches are distributed among these distances:
104 12 0.12
105 75 0.77
106 5 0.05
107 6 0.06
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (104 bp):
TTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAAATTCTAGTTTT
CAAAAACCAACTCATATTGCGAGAAGTGAGTTGAGCCTT
Found at i:1543255 original size:30 final size:31
Alignment explanation
Indices: 1543221--1543322 Score: 122
Period size: 30 Copynumber: 3.4 Consensus size: 31
1543211 TTAAAAATAA
*
1543221 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
1543251 AAATTTCATTTTGACCCTTAAAC-TTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
1543281 AAATTTCACTTAGACCCCTAAAC-TTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTTC-TCT
1543311 AAATTTCATTTT
1 AAATTTCATTTT
1543323 AATCCTAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 4 0.06
30 57 0.92
31 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.44
Consensus pattern (31 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTCT
Found at i:1543604 original size:10 final size:10
Alignment explanation
Indices: 1543585--1543634 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
1543575 TTTTTCGAAG
*
1543585 GAAAAAAGAA
1 GAAAAGAGAA
1543595 GAAAAGAGAA
1 GAAAAGAGAA
1543605 GAAAAGAGAA
1 GAAAAGAGAA
* *
1543615 -AGAGGAGAA
1 GAAAAGAGAA
1543624 GAAAAGA-AA
1 GAAAAGAGAA
1543633 GA
1 GA
1543635 GTACCAGCGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
GAAAAGAGAA
Found at i:1543635 original size:17 final size:19
Alignment explanation
Indices: 1543588--1543630 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
1543578 TTCGAAGGAA
1543588 AAAAGAAGAAA-A-GAGAAG
1 AAAAG-AGAAAGAGGAGAAG
1543606 AAAAGAGAAAGAGGAGAAG
1 AAAAGAGAAAGAGGAGAAG
1543625 AAAAGA
1 AAAAGA
1543631 AAGAGTACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.22
18 6 0.26
19 12 0.52
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (19 bp):
AAAAGAGAAAGAGGAGAAG
Found at i:1543706 original size:3 final size:3
Alignment explanation
Indices: 1543700--1543734 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
1543690 GTGTAGGAGG
1543700 AGA AGA AGA AGA AGA AGA AGA AGAA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA AGA A
1543735 AGAAAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1543729 original size:10 final size:10
Alignment explanation
Indices: 1543700--1543748 Score: 66
Period size: 10 Copynumber: 5.1 Consensus size: 10
1543690 GTGTAGGAGG
1543700 AGAAG-AAGA
1 AGAAGAAAGA
1543709 AGAAG-AAGA
1 AGAAGAAAGA
1543718 AGAAGAAAGA
1 AGAAGAAAGA
1543728 AGAAGAAAGA
1 AGAAGAAAGA
* *
1543738 AAAAAAAAGA
1 AGAAGAAAGA
1543748 A
1 A
1543749 AAAAAATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
9 14 0.38
10 23 0.62
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (10 bp):
AGAAGAAAGA
Found at i:1543952 original size:14 final size:15
Alignment explanation
Indices: 1543913--1543953 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
1543903 AAACCAAAGC
1543913 AAAAAAAAGCAGCCCA
1 AAAAAAAAG-AGCCCA
1543929 AAAAGAAAAG-GCCCA
1 AAAA-AAAAGAGCCCA
1543944 AAAAAAAAGA
1 AAAAAAAAGA
1543954 AAAAACAGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 5 0.22
15 9 0.39
16 4 0.17
17 5 0.22
ACGTcount: A:0.68, C:0.17, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAGCCCA
Found at i:1544087 original size:7 final size:7
Alignment explanation
Indices: 1544065--1544144 Score: 90
Period size: 7 Copynumber: 11.0 Consensus size: 7
1544055 AGCAGGCCAG
1544065 GAAAAAA
1 GAAAAAA
*
1544072 G-AGAAA
1 GAAAAAA
1544078 GAAAAAA
1 GAAAAAA
1544085 GAAAAAA
1 GAAAAAA
*
1544092 GAAAGAA
1 GAAAAAA
1544099 GAAAAAA
1 GAAAAAA
*
1544106 GAAAAGAG
1 GAAAA-AA
1544114 GAAAAAA
1 GAAAAAA
1544121 GGAAAAAGAA
1 -G-AAAA-AA
1544131 GAAAAAA
1 GAAAAAA
1544138 GAAAAAA
1 GAAAAAA
1544145 AAGAGTTTCA
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
6 5 0.08
7 39 0.63
8 11 0.18
9 5 0.08
10 2 0.03
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:1544127 original size:36 final size:35
Alignment explanation
Indices: 1544065--1544149 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 35
1544055 AGCAGGCCAG
*
1544065 GAAAAAAGAGAA-A-GAAAAAAGAAAAAAGAAAGAA
1 GAAAAAAGAAAAGAGGAAAAAAGAAAAAAG-AAGAA
*
1544099 GAAAAAAGAAAAGAGGAAAAAAGGAAAAAGAAGAA
1 GAAAAAAGAAAAGAGGAAAAAAGAAAAAAGAAGAA
* *
1544134 AAAAGAAAAAAAAGAG
1 GAAA-AAAGAAAAGAG
1544150 TTTCAATTCG
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
34 11 0.25
35 9 0.20
36 24 0.55
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (35 bp):
GAAAAAAGAAAAGAGGAAAAAAGAAAAAAGAAGAA
Found at i:1544801 original size:18 final size:17
Alignment explanation
Indices: 1544727--1544889 Score: 159
Period size: 17 Copynumber: 9.4 Consensus size: 17
1544717 ATCAATTTTC
* *
1544727 CAAAATTTTTAGTGTCTT
1 CAAAAATTTTCGTGT-TT
*
1544745 CTAAAAATTTTTGTGTTT
1 C-AAAAATTTTCGTGTTT
1544763 CAAAAATTTTCGT-TTT
1 CAAAAATTTTCGTGTTT
*
1544779 CAAAAATTTCCGTGTTT
1 CAAAAATTTTCGTGTTT
*
1544796 CAAAAATTTTCGTATTTT
1 CAAAAATTTTCGT-GTTT
*
1544814 CAAAAATTTTCGTATTT
1 CAAAAATTTTCGTGTTT
** *
1544831 CAAAAATCCTCTTGTTTT
1 CAAAAATTTTCGTG-TTT
1544849 CAAAAA-TTTCGGTGTTT
1 CAAAAATTTTC-GTGTTT
**
1544866 TGAAAATTTTCGTGTTTT
1 CAAAAATTTTCGTG-TTT
1544884 CAAAAA
1 CAAAAA
1544890 AAAATCTCGT
Statistics
Matches: 120, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
16 15 0.12
17 51 0.43
18 42 0.35
19 12 0.10
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (17 bp):
CAAAAATTTTCGTGTTT
Found at i:1544821 original size:35 final size:35
Alignment explanation
Indices: 1544727--1544889 Score: 177
Period size: 35 Copynumber: 4.7 Consensus size: 35
1544717 ATCAATTTTC
* * * **
1544727 CAAAATTTTTAGTGTCTTCTAAAAATTTTTGTGTTT
1 CAAAAATTTTCGTGTTTTC-AAAAATTTCCGTGTTT
1544763 CAAAAATTTTC--GTTTTCAAAAATTTCCGTGTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTTCCGTGTTT
* * *
1544796 CAAAAATTTTCGTATTTTCAAAAATTTTCGTATTT
1 CAAAAATTTTCGTGTTTTCAAAAATTTCCGTGTTT
** * *
1544831 CAAAAATCCTCTTGTTTTCAAAAATTTCGGTGTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTTCCGTGTTT
**
1544866 TGAAAATTTTCGTGTTTTCAAAAA
1 CAAAAATTTTCGTGTTTTCAAAAA
1544890 AAAATCTCGT
Statistics
Matches: 105, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
33 25 0.24
34 5 0.05
35 66 0.63
36 9 0.09
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (35 bp):
CAAAAATTTTCGTGTTTTCAAAAATTTCCGTGTTT
Found at i:1549835 original size:21 final size:21
Alignment explanation
Indices: 1549802--1549843 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1549792 AAATTTCATA
1549802 TCCATAACCCTAAACTTTAAAC
1 TCCATAACCCTAAAC-TTAAAC
* *
1549824 TCCA-AACTCTAATCTTAAAC
1 TCCATAACCCTAAACTTAAAC
1549844 CTCGAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.33
21 8 0.44
22 4 0.22
ACGTcount: A:0.40, C:0.31, G:0.00, T:0.29
Consensus pattern (21 bp):
TCCATAACCCTAAACTTAAAC
Found at i:1550653 original size:12 final size:12
Alignment explanation
Indices: 1550632--1550663 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1550622 TTTCTTTCTT
1550632 TTTA-TTTTTTA
1 TTTATTTTTTTA
1550643 TTTATTTTTTTA
1 TTTATTTTTTTA
1550655 TTT-TTTTTT
1 TTTATTTTTT
1550664 GGGACCTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (12 bp):
TTTATTTTTTTA
Found at i:1553147 original size:192 final size:192
Alignment explanation
Indices: 1552820--1553212 Score: 786
Period size: 192 Copynumber: 2.0 Consensus size: 192
1552810 TGGTGTTATT
1552820 ACCCCGTTTAATTAAGATAAGGCGAGAGATAATCAGGTTGTGAACCGCGTGAAGGAGTTTATTTT
1 ACCCCGTTTAATTAAGATAAGGCGAGAGATAATCAGGTTGTGAACCGCGTGAAGGAGTTTATTTT
1552885 ATTTTTATCGTGATAAAATCTCGTTTGGACATTAGCAATGATAAAAACCACTTTTTAAAAAATAA
66 ATTTTTATCGTGATAAAATCTCGTTTGGACATTAGCAATGATAAAAACCACTTTTTAAAAAATAA
1552950 AAAATAAAAACCGCTATCCGGTTTTATAAAACCACTTTTCCTTTAGTCTTCTATAAATAAAG
131 AAAATAAAAACCGCTATCCGGTTTTATAAAACCACTTTTCCTTTAGTCTTCTATAAATAAAG
1553012 ACCCCGTTTAATTAAGATAAGGCGAGAGATAATCAGGTTGTGAACCGCGTGAAGGAGTTTATTTT
1 ACCCCGTTTAATTAAGATAAGGCGAGAGATAATCAGGTTGTGAACCGCGTGAAGGAGTTTATTTT
1553077 ATTTTTATCGTGATAAAATCTCGTTTGGACATTAGCAATGATAAAAACCACTTTTTAAAAAATAA
66 ATTTTTATCGTGATAAAATCTCGTTTGGACATTAGCAATGATAAAAACCACTTTTTAAAAAATAA
1553142 AAAATAAAAACCGCTATCCGGTTTTATAAAACCACTTTTCCTTTAGTCTTCTATAAATAAAG
131 AAAATAAAAACCGCTATCCGGTTTTATAAAACCACTTTTCCTTTAGTCTTCTATAAATAAAG
1553204 ACCCCGTTT
1 ACCCCGTTT
1553213 CATAGCTGCC
Statistics
Matches: 201, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
192 201 1.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (192 bp):
ACCCCGTTTAATTAAGATAAGGCGAGAGATAATCAGGTTGTGAACCGCGTGAAGGAGTTTATTTT
ATTTTTATCGTGATAAAATCTCGTTTGGACATTAGCAATGATAAAAACCACTTTTTAAAAAATAA
AAAATAAAAACCGCTATCCGGTTTTATAAAACCACTTTTCCTTTAGTCTTCTATAAATAAAG
Found at i:1565384 original size:141 final size:141
Alignment explanation
Indices: 1565130--1565409 Score: 420
Period size: 141 Copynumber: 2.0 Consensus size: 141
1565120 ATTTGATACC
* *** *
1565130 TTAAGCTAAGTTCATTAGAACTAGCCTAGAATTTCAAATTTTAGGCACGGCATAACCAGCAAATC
1 TTAAGCTAAGTTCATTAAAACTAGCCTAGAATTTCAAAAAATAGGCACGACATAACCAGCAAATC
* * *
1565195 AGTTCTTAACCTCTCATTCGCCATGACTCAATTTGATACCTTAAGCTAAGTTCAATCAGTTCAAG
66 AGTTCTTAACCTCTCATCCGCCATGACTCAATTTGATACCTCAAGCTAAGTTCAATCAGTTCAAC
1565260 TTCAATTAACT
131 TTCAATTAACT
* * *
1565271 TTAAGCTAA-TTCAGTTAAAACTAGCCTAGAGTTTCAAAAAATAGGCACTACATAGCCAAG-AAA
1 TTAAGCTAAGTTCA-TTAAAACTAGCCTAGAATTTCAAAAAATAGGCACGACATAACC-AGCAAA
*
1565334 TCAGTTCTTAACCTCTCATCCGCCATGATTCAATTTGATACCTCAAGCTAAGTTCAATCAGTTCA
64 TCAGTTCTTAACCTCTCATCCGCCATGACTCAATTTGATACCTCAAGCTAAGTTCAATCAGTTCA
1565399 ACTTCAATTAA
129 ACTTCAATTAA
1565410 AACTAGCTTA
Statistics
Matches: 125, Mismatches: 12, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
140 4 0.03
141 119 0.95
142 2 0.02
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (141 bp):
TTAAGCTAAGTTCATTAAAACTAGCCTAGAATTTCAAAAAATAGGCACGACATAACCAGCAAATC
AGTTCTTAACCTCTCATCCGCCATGACTCAATTTGATACCTCAAGCTAAGTTCAATCAGTTCAAC
TTCAATTAACT
Found at i:1566209 original size:23 final size:22
Alignment explanation
Indices: 1566183--1566225 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1566173 TTATCATAAT
1566183 ATTTTTTAATATTTATAAATTTA
1 ATTTTTTAATA-TTATAAATTTA
**
1566206 ATTTTTTTGTATTATAAATT
1 ATTTTTTAATATTATAAATT
1566226 AAATAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
ATTTTTTAATATTATAAATTTA
Found at i:1568880 original size:6 final size:6
Alignment explanation
Indices: 1568869--1568928 Score: 120
Period size: 6 Copynumber: 10.0 Consensus size: 6
1568859 GCTCTAAACA
1568869 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1568917 ATACAT ATACAT
1 ATACAT ATACAT
1568929 GAAGGTATAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:1570525 original size:28 final size:28
Alignment explanation
Indices: 1570478--1570535 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
1570468 TTTGGACTTA
** *
1570478 TTTTTTAATTTGGTACTTGAGCTTCTTC
1 TTTTTTAATTTGAAAATTGAGCTTCTTC
* *
1570506 TTTTTTAATTTGAAAATTGAGTTTTTTC
1 TTTTTTAATTTGAAAATTGAGCTTCTTC
1570534 TT
1 TT
1570536 ATCCCAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.19, C:0.09, G:0.12, T:0.60
Consensus pattern (28 bp):
TTTTTTAATTTGAAAATTGAGCTTCTTC
Found at i:1573758 original size:24 final size:24
Alignment explanation
Indices: 1573714--1573762 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
1573704 ATTATGAAAA
1573714 TAATAAAGGTTAAAATACAAACAC
1 TAATAAAGGTTAAAATACAAACAC
*
1573738 TAATAAAAGGTTGAAAT-CAAACAC
1 TAAT-AAAGGTTAAAATACAAACAC
1573762 T
1 T
1573763 TGACAGTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.55, C:0.12, G:0.10, T:0.22
Consensus pattern (24 bp):
TAATAAAGGTTAAAATACAAACAC
Found at i:1575180 original size:16 final size:16
Alignment explanation
Indices: 1575161--1575202 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
1575151 TTAAAACTTG
1575161 AAAAATATAAAGACAA
1 AAAAATATAAAGACAA
***
1575177 AAAAAT-TAAATTTAA
1 AAAAATATAAAGACAA
1575192 AAAAATATAAA
1 AAAAATATAAA
1575203 CTAAATTCGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (16 bp):
AAAAATATAAAGACAA
Found at i:1577489 original size:13 final size:13
Alignment explanation
Indices: 1577466--1577503 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
1577456 TTAATAAAAA
1577466 TAAAAATTATATAT-
1 TAAAAA-TATA-ATC
1577480 TAAAAATATAATC
1 TAAAAATATAATC
1577493 TAAAAATATAA
1 TAAAAATATAA
1577504 ATACATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 2 0.09
13 15 0.65
14 6 0.26
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (13 bp):
TAAAAATATAATC
Found at i:1583825 original size:16 final size:18
Alignment explanation
Indices: 1583804--1583838 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1583794 TTAATATTTT
1583804 TTTTAATT-GTAC-ATAA
1 TTTTAATTGGTACAATAA
1583820 TTTTAATTGGTACAATAA
1 TTTTAATTGGTACAATAA
1583838 T
1 T
1583839 AAATTCAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 4 0.24
18 5 0.29
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.49
Consensus pattern (18 bp):
TTTTAATTGGTACAATAA
Found at i:1594582 original size:14 final size:15
Alignment explanation
Indices: 1594563--1594591 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1594553 TATATATGCA
1594563 TTTTTTATT-TTTAT
1 TTTTTTATTGTTTAT
1594577 TTTTTTATTGTTTAT
1 TTTTTTATTGTTTAT
1594592 AACTAGCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (15 bp):
TTTTTTATTGTTTAT
Done.