Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold60
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: 3815296
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 18690 characters in sequence are not A, C, G, or T
File 7 of 21
Found at i:890206 original size:12 final size:12
Alignment explanation
Indices: 890189--890214 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
890179 AACTAAAAAC
890189 AAAAAATAAAGA
1 AAAAAATAAAGA
890201 AAAAAATAAAGA
1 AAAAAATAAAGA
890213 AA
1 AA
890215 TTAGAAAGGG
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:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (12 bp):
AAAAAATAAAGA
Found at i:892691 original size:12 final size:12
Alignment explanation
Indices: 892676--892701 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
892666 TATTGAGTAT
892676 TCTATTTGTCAC
1 TCTATTTGTCAC
892688 TCTATTTGTCAC
1 TCTATTTGTCAC
892700 TC
1 TC
892702 CTATGTTTGA
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:0.27, G:0.08, T:0.50
Consensus pattern (12 bp):
TCTATTTGTCAC
Found at i:894552 original size:23 final size:25
Alignment explanation
Indices: 894525--894570 Score: 62
Period size: 23 Copynumber: 1.9 Consensus size: 25
894515 TTATGATTCA
894525 ATTTATTATT-TTT-TA-ATATATTT
1 ATTTA-TATTATTTCTATATATATTT
894548 ATTTATATTATTTCTATATATAT
1 ATTTATATTATTTCTATATATAT
894571 ATTAATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.20
23 8 0.40
24 2 0.10
25 6 0.30
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (25 bp):
ATTTATATTATTTCTATATATATTT
Found at i:894648 original size:14 final size:14
Alignment explanation
Indices: 894618--894666 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
894608 TTATATTTGT
894618 AAATAA-TAATT--
1 AAATAATTAATTAA
*
894629 AAATAATTGATTAA
1 AAATAATTAATTAA
894643 AAATAATTAATTAA
1 AAATAATTAATTAA
894657 AAA-AATTAAT
1 AAATAATTAAT
894667 CGGAACCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
11 6 0.18
12 4 0.12
13 7 0.21
14 16 0.48
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (14 bp):
AAATAATTAATTAA
Found at i:897550 original size:17 final size:17
Alignment explanation
Indices: 897530--897566 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
897520 TGATTGAATG
*
897530 TTTAACATTTATAATTT
1 TTTAACATTAATAATTT
897547 TTTAACATTAATAATTT
1 TTTAACATTAATAATTT
897564 TTT
1 TTT
897567 TTCCTGCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTAACATTAATAATTT
Found at i:900498 original size:23 final size:23
Alignment explanation
Indices: 900472--900545 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
900462 AATTTATTAC
900472 TAATAAAAAATTAATATTTAATT
1 TAATAAAAAATTAATATTTAATT
*
900495 TAAT--AAAATTAAAATTTTTAA-T
1 TAATAAAAAATT--AATATTTAATT
* *
900517 TAATATAAAAA-TAAGATTAAATT
1 TAATA-AAAAATTAATATTTAATT
900540 TAATAA
1 TAATAA
900546 TATAAAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
21 6 0.15
22 12 0.29
23 18 0.44
24 1 0.02
25 4 0.10
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (23 bp):
TAATAAAAAATTAATATTTAATT
Found at i:900511 original size:50 final size:46
Alignment explanation
Indices: 900457--900562 Score: 108
Period size: 45 Copynumber: 2.3 Consensus size: 46
900447 TTAATATGAT
* * *
900457 AATTTAATTTATTACTAATAAAAAATTAATATTTAATTTAATAAAATTAA
1 AATTTAATTTATTAAT-AT-AAAAA-TAAGATTAAATTTAATAAAA-TAA
* *
900507 AATTT--TTAATTAATATAAAAATAAGATTAAATTTAATAATATAA
1 AATTTAATTTATTAATATAAAAATAAGATTAAATTTAATAAAATAA
*
900551 AATTTAAATTAT
1 AATTTAATTTAT
900563 CTCTCGTACA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
44 8 0.17
45 17 0.36
46 8 0.17
47 2 0.04
48 7 0.15
50 5 0.11
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (46 bp):
AATTTAATTTATTAATATAAAAATAAGATTAAATTTAATAAAATAA
Found at i:902887 original size:22 final size:23
Alignment explanation
Indices: 902846--902891 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
902836 TCCCCCTTAC
902846 TGAAAAAGGGTTTTGTTTTTTGT
1 TGAAAAAGGGTTTTGTTTTTTGT
902869 TGAAAAAGGGTTTTGTTTTTTGT
1 TGAAAAAGGGTTTTGTTTTTTGT
902892 AGAACCTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (23 bp):
TGAAAAAGGGTTTTGTTTTTTGT
Found at i:904949 original size:2 final size:2
Alignment explanation
Indices: 904942--904992 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
904932 TGAAATTAAA
904942 AT AT AT 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 AT AT AT
904984 AT AT AT AT A
1 AT AT AT AT A
904993 CTTACAAAGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:906885 original size:2 final size:2
Alignment explanation
Indices: 906878--906923 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
906868 AAGGGAAACA
906878 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
906920 TC TC
1 TC TC
906924 GTTGGGAGGC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:907751 original size:13 final size:13
Alignment explanation
Indices: 907733--907781 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
907723 CTTAAAAGTG
*
907733 ATATAATCATAAA
1 ATATAATAATAAA
*
907746 ATATAAAAATAAA
1 ATATAATAATAAA
*
907759 ATAAAAATAATTAAA
1 AT-ATAATAA-TAAA
907774 ATATAATA
1 ATATAATA
907782 TGATATAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 13 0.45
14 10 0.34
15 6 0.21
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (13 bp):
ATATAATAATAAA
Found at i:907779 original size:28 final size:29
Alignment explanation
Indices: 907742--907816 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 29
907732 GATATAATCA
907742 TAAAATATAAAAATAAAAT-AAAAATAAT
1 TAAAATATAAAAATAAAATAAAAAATAAT
* * *
907770 TAAAATAT-AATATGATATAAAAAATAAT
1 TAAAATATAAAAATAAAATAAAAAATAAT
* *
907798 AAAAATATGAAAATTAAAA
1 TAAAATAT-AAAAATAAAA
907817 ATTTTTATAC
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
27 7 0.19
28 24 0.67
30 5 0.14
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.27
Consensus pattern (29 bp):
TAAAATATAAAAATAAAATAAAAAATAAT
Found at i:909118 original size:23 final size:24
Alignment explanation
Indices: 909061--909119 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 24
909051 TTGCTCTAAC
909061 TTAATTTTTTTTAAAATATTCATAT
1 TTAA-TTTTTTTAAAATATTCATAT
* * *
909086 TTAATATTTTT-AGATATTGATA-
1 TTAATTTTTTTAAAATATTCATAT
909108 TTAAGTTTTTTT
1 TTAA-TTTTTTT
909120 TTAAAGGCCC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 4 0.14
23 15 0.52
24 6 0.21
25 4 0.14
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (24 bp):
TTAATTTTTTTAAAATATTCATAT
Found at i:916280 original size:165 final size:165
Alignment explanation
Indices: 915981--916489 Score: 928
Period size: 165 Copynumber: 3.1 Consensus size: 165
915971 ATTTGAAACC
*
915981 TTATTTCCAATCTAAAAAGATATACTCAGGCATCGCAATAACTTAAGTGCAAGAACTGTGCTGCT
1 TTATTTCCAATCTAAAAAGATATACTCAGGCATCGCAATACCTTAAGTGCAAGAACTGTGCTGCT
* *
916046 GAAATAGCAGTTTCCTCAGCTCAGGTTAGATTTTTATTTAGCTCCGATTAGATGTTTTCAATAAG
66 GAAATAGAAGTTTCCTCAGCTCAGGTTAGA-GTTTATTTAGCTCCGATTAGATGTTTTCAATAAG
916111 AAAAGTTAGGCTGAACCTTTTTCTTATTTAGACTTG
130 AAAAGTTAGGCTGAACCTTTTTCTTATTTAGACTTG
**
916147 TTATTTCCAATCTAAAAAGATATACTCAGATATCGCAATACCTTAAGTGCAAGAACTGTGCTGCT
1 TTATTTCCAATCTAAAAAGATATACTCAGGCATCGCAATACCTTAAGTGCAAGAACTGTGCTGCT
*
916212 GAAATAGAAGTTTCCTCAGCTCAGGTTAGAGTTTATTTGGCTCCGATTAGATGTTTTCAATAAGA
66 GAAATAGAAGTTTCCTCAGCTCAGGTTAGAGTTTATTTAGCTCCGATTAGATGTTTTCAATAAGA
916277 AAAGTTAGGCTGAACCTTTTTCTTATTTAGACTTG
131 AAAGTTAGGCTGAACCTTTTTCTTATTTAGACTTG
*
916312 TTATTTCCAATCTAAAAAGATATACTCAGGCATCGCAATACCTTAAGGGCAAGAACTGTGCTGCT
1 TTATTTCCAATCTAAAAAGATATACTCAGGCATCGCAATACCTTAAGTGCAAGAACTGTGCTGCT
916377 GAAATAGAAGTTTCCTCAGCTCAGGTTAGAGTTTATTTAGCTCCGATTAGATGTTTTCAATAAGA
66 GAAATAGAAGTTTCCTCAGCTCAGGTTAGAGTTTATTTAGCTCCGATTAGATGTTTTCAATAAGA
916442 AAAGTTAGGCTGAACCTTTTTCTTATTTAGACTTG
131 AAAGTTAGGCTGAACCTTTTTCTTATTTAGACTTG
*
916477 TTGTATTCCAATC
1 TTAT-TTCCAATC
916490 GTCATCACTG
Statistics
Matches: 331, Mismatches: 11, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
165 232 0.70
166 99 0.30
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (165 bp):
TTATTTCCAATCTAAAAAGATATACTCAGGCATCGCAATACCTTAAGTGCAAGAACTGTGCTGCT
GAAATAGAAGTTTCCTCAGCTCAGGTTAGAGTTTATTTAGCTCCGATTAGATGTTTTCAATAAGA
AAAGTTAGGCTGAACCTTTTTCTTATTTAGACTTG
Found at i:918696 original size:173 final size:173
Alignment explanation
Indices: 918407--918749 Score: 659
Period size: 173 Copynumber: 2.0 Consensus size: 173
918397 GGCGATCGCA
918407 ACAATCGCATGCACAGTTGAGTAGATCACCCTCAGCTGCGGTTGATGAAGGAGGACAAACACACA
1 ACAATCGCATGCACAGTTGAGTAGATCACCCTCAGCTGCGGTTGATGAAGGAGGACAAACACACA
918472 CAGGACCAGAACACTCACCAACAGAATAGGAAGAGAGAATAGGTCCTTTTCTATTCAAAATAAGA
66 CAGGACCAGAACACTCACCAACAGAATAGGAAGAGAGAATAGGTCCTTTTCTATTCAAAATAAGA
*
918537 GTCCTATACTCTTCTCAATGCCAGTAAAACCCAGTTCCTCCAT
131 GTCCTATACTCTTCTCAATGCCAGTAAAACCCAGGTCCTCCAT
918580 ACAATCGCATGCACAGTTGAGTAGATCACCCTCAGCTGCGGTTGATGAAGGAGGACAAACACACA
1 ACAATCGCATGCACAGTTGAGTAGATCACCCTCAGCTGCGGTTGATGAAGGAGGACAAACACACA
*
918645 CGGGACCAGAACACTCACCAACAGAATAGGAAGAGAGAATAGGTCCTTTTCTATTCAAAATAAGA
66 CAGGACCAGAACACTCACCAACAGAATAGGAAGAGAGAATAGGTCCTTTTCTATTCAAAATAAGA
*
918710 GTCCTATACTCTTCTCAATGCCAGTAAAACTCAGGTCCTC
131 GTCCTATACTCTTCTCAATGCCAGTAAAACCCAGGTCCTC
918750 TATATTATCA
Statistics
Matches: 167, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
173 167 1.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (173 bp):
ACAATCGCATGCACAGTTGAGTAGATCACCCTCAGCTGCGGTTGATGAAGGAGGACAAACACACA
CAGGACCAGAACACTCACCAACAGAATAGGAAGAGAGAATAGGTCCTTTTCTATTCAAAATAAGA
GTCCTATACTCTTCTCAATGCCAGTAAAACCCAGGTCCTCCAT
Found at i:923165 original size:52 final size:52
Alignment explanation
Indices: 923038--923166 Score: 141
Period size: 52 Copynumber: 2.5 Consensus size: 52
923028 TCAATCGTTT
* * * * *
923038 CCATGGTGTCAGCATTATTAATGACACCAAGTCACTCACATCCTAATCGCCA
1 CCATGGCGTCACCATTATTAGTGGCACAAAGTCACTCACATCCTAATCGCCA
* * * ** *
923090 CCATGGCATAACCATTATCAGTGGCACAAAGTCACTCTGATTCTAATCGCCA
1 CCATGGCGTCACCATTATTAGTGGCACAAAGTCACTCACATCCTAATCGCCA
* *
923142 CCATGGCGTCATCACTATTAGTGGC
1 CCATGGCGTCACCATTATTAGTGGC
923167 GCCAAGCCAC
Statistics
Matches: 61, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (52 bp):
CCATGGCGTCACCATTATTAGTGGCACAAAGTCACTCACATCCTAATCGCCA
Found at i:923188 original size:52 final size:52
Alignment explanation
Indices: 923077--923191 Score: 131
Period size: 52 Copynumber: 2.2 Consensus size: 52
923067 AGTCACTCAC
* * *
923077 ATCCTAATCGCCACCATGGCATAACCATTATCAGTGGCACAAAGTCACTCTG
1 ATCCTAATCGCCACCATGGCATAACCACTATCAGTGGCACAAAGCCACTCTA
* * * * * * * *
923129 ATTCTAATCGCCACCATGGCGTCATCACTATTAGTGGCGCCAAGCCACTTTA
1 ATCCTAATCGCCACCATGGCATAACCACTATCAGTGGCACAAAGCCACTCTA
923181 ATCCTAATCGC
1 ATCCTAATCGC
923192 GACTATGACA
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.25
Consensus pattern (52 bp):
ATCCTAATCGCCACCATGGCATAACCACTATCAGTGGCACAAAGCCACTCTA
Found at i:929527 original size:743 final size:742
Alignment explanation
Indices: 928103--929560 Score: 2650
Period size: 743 Copynumber: 2.0 Consensus size: 742
928093 CTATAAGATG
928103 CTAATTTAGCTAGTGTTTTTTCTGTAACAGTTAATGTTTTTGTGGATGCCTCACCATTGGTGACA
1 CTAATTTAGCTAGTGTTTTTTCTGTAACAGTTAATGTTTTTGTGGATGCCTCACCATTGGTGACA
928168 TCAGTGCTAGATGGCTACAATGTCTGTGTTGGGTAAAAACGCAATAAAATAAGAAGATTAAAGCA
66 TCAGTGCTAGATGGCTACAATGTCTGTGTTGGGTAAAAACGCAATAAAATAAGAAGATTAAAGCA
928233 AAAAAAACAAGAATACACTAGATTTACATGGTTCGATCAATATGACCTATGTCCATGTTGATGAG
131 AAAAAAACAAGAATACACTAGATTTACATGGTTCGATCAATATGACCTATGTCCATGTTGATGAG
* * *
928298 AATCAAGGAAGGTCCATTGAAAACAAAGCCCTGAAGGCGTTGGAATGGTTTCAAGGACCAATGAC
196 AACCAAGAAAGGTCCATTGAAAACAAAACCCTGAAGGCGTTGGAATGGTTTCAAGGACCAATGAC
*
928363 AAGGGCAAAGGGAAGGAGGATAAAGGAAGACCTAAAGAATATGGTTGCTGCCCTATTTGAAAGTA
261 AAGGGCAAAGGCAAGGAGGATAAAGGAAGACCTAAAGAATATGGTTGCTGCCCTATTTGAAAGTA
928428 GACTCAATTTAAAGTTAGGAGAGCCCAAGCTAGTCAATTGCATATATTTGAAAGATATGGACTCC
326 GACTCAATTTAAAGTTAGGAGAGCCCAAGCTAGTCAATTGCATATATTTGAAAGATATGGACTCC
* * *
928493 AATGGATTAATTTAGGACTTGGGTTATTTTGTAATAAAAGGCATGTTGGTTGTGACTTGCTTTGA
391 AATAGATTAAATTAGGACTTGGGTTATTTTGTAATAAAAGGCATGCTGGTTGTGACTTGCTTTGA
928558 GCTTTATTTAGTATAAAAACTTGTTATTTGGGTTAGACTAAGAGTTGGGCTTGTTAGCATAATAA
456 GCTTTATTTAGTATAAAAACTTGTTATTTGGGTTAGACTAAGAGTTGGGCTTGTTAGCATAATAA
* *
928623 GCCCCTTAGGGTTTGCGTTAACTATGGCTTATTAGGGCATATATAAGCTCTTGTAAACAGATTTG
521 GCCCCTTAGGGTTTGCGTTAACTATGGCTTATGAGGGCATATATAAGCTCTTATAAACAGATTTG
928688 AAAGGAGGCAGACAATGATATTTGAAAATTAAATACATTTTATGTGAGAGTGTGATTCTTAAGTT
586 AAAGGAGGCAGACAATGATATTTGAAAATTAAATACATTTTATGTGAGAGTGTGATTCTTAAGTT
* * * * * *
928753 ATTAAGTGAGTCAATTTTTTTGGATTTTATCAAGAGGTCAAGACTTTTGTGATGGTCATTCCTTT
651 ATTAAGTGAGCCAATTTTTCTGGATTTTATCAAGAGGCCAAGACTCTTGTGATGATAATTCCTTT
928818 AGCTAGTGTTTTTGTTAACTATGGCTT
716 AGCTAGTGTTTTTGTTAACTATGGCTT
928845 CTAATTTAGCTAGTGTTTTTTCTGTAACAGTTAATGTTTTTGTGGATGCCTCACCATTGGTGACA
1 CTAATTTAGCTAGTGTTTTTTCTGTAACAGTTAATGTTTTTGTGGATGCCTCACCATTGGTGACA
928910 TCAGTGCTAGATGGCTACAATGTCTGTGTTGGGTAAAAACGCAATAAAATAAGAAGATTAAAGCG
66 TCAGTGCTAGATGGCTACAATGTCTGTGTTGGGTAAAAACGCAATAAAATAAGAAGATTAAAGC-
*
928975 AAAAAAAATAAGAATACACTAGATTTACATGGTTCGATCAATATGACCTATGTCCATGTTGATGA
130 AAAAAAAACAAGAATACACTAGATTTACATGGTTCGATCAATATGACCTATGTCCATGTTGATGA
929040 GAACCAAGAAAGGTCCATTGAAAACAAAACCCTGAAGGCGTTGGAATGGTTTCAAGGACCAATGA
195 GAACCAAGAAAGGTCCATTGAAAACAAAACCCTGAAGGCGTTGGAATGGTTTCAAGGACCAATGA
929105 CAAGGGCAAAGGCAAGGAGGATAAAGGAAGACCTAAAGAATATGGTTGCTGCCCTATTTGAAAGT
260 CAAGGGCAAAGGCAAGGAGGATAAAGGAAGACCTAAAGAATATGGTTGCTGCCCTATTTGAAAGT
** *
929170 AGACTCAATTTGGAGTTAGGAGAGCCCAAGCTAGTCAATTTCATATATTTGAAAGATAT-GAGCT
325 AGACTCAATTTAAAGTTAGGAGAGCCCAAGCTAGTCAATTGCATATATTTGAAAGATATGGA-CT
*
929234 CCAATAGATTAAATTAGGACTTGGGTTATTTTGTAATAAAGGGCATGCTGGTTGTGACTTGCTTT
389 CCAATAGATTAAATTAGGACTTGGGTTATTTTGTAATAAAAGGCATGCTGGTTGTGACTTGCTTT
*
929299 GGGCTTTATTTAGTATAAAAACTTGTTATTTGGGTTTA-ACTAAGAGTTGGGCTTGTTAGCATAA
454 GAGCTTTATTTAGTATAAAAACTTGTTATTTGGG-TTAGACTAAGAGTTGGGCTTGTTAGCATAA
*
929363 TAAGCCCCTTAGGGTTTGTGTTAACTATGGCTTATGAGGGCATATATAAGCTCTTATAAACAGAT
518 TAAGCCCCTTAGGGTTTGCGTTAACTATGGCTTATGAGGGCATATATAAGCTCTTATAAACAGAT
*
929428 TTGAAAGGAGGCAGACAATGATATTTGAAAATTAAATACATTTTGTGTGAGAGTGTGATTCTTAA
583 TTGAAAGGAGGCAGACAATGATATTTGAAAATTAAATACATTTTATGTGAGAGTGTGATTCTTAA
* *
929493 GTTCTTGAGTGAGCCAATTTTTCTGGATTTTATCAAGAGGCCAAGACTCTTGTGATGATAATTCC
648 GTTATTAAGTGAGCCAATTTTTCTGGATTTTATCAAGAGGCCAAGACTCTTGTGATGATAATTCC
929558 TTT
713 TTT
929561 TGGCTTATCA
Statistics
Matches: 688, Mismatches: 25, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
742 131 0.19
743 554 0.81
744 3 0.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (742 bp):
CTAATTTAGCTAGTGTTTTTTCTGTAACAGTTAATGTTTTTGTGGATGCCTCACCATTGGTGACA
TCAGTGCTAGATGGCTACAATGTCTGTGTTGGGTAAAAACGCAATAAAATAAGAAGATTAAAGCA
AAAAAAACAAGAATACACTAGATTTACATGGTTCGATCAATATGACCTATGTCCATGTTGATGAG
AACCAAGAAAGGTCCATTGAAAACAAAACCCTGAAGGCGTTGGAATGGTTTCAAGGACCAATGAC
AAGGGCAAAGGCAAGGAGGATAAAGGAAGACCTAAAGAATATGGTTGCTGCCCTATTTGAAAGTA
GACTCAATTTAAAGTTAGGAGAGCCCAAGCTAGTCAATTGCATATATTTGAAAGATATGGACTCC
AATAGATTAAATTAGGACTTGGGTTATTTTGTAATAAAAGGCATGCTGGTTGTGACTTGCTTTGA
GCTTTATTTAGTATAAAAACTTGTTATTTGGGTTAGACTAAGAGTTGGGCTTGTTAGCATAATAA
GCCCCTTAGGGTTTGCGTTAACTATGGCTTATGAGGGCATATATAAGCTCTTATAAACAGATTTG
AAAGGAGGCAGACAATGATATTTGAAAATTAAATACATTTTATGTGAGAGTGTGATTCTTAAGTT
ATTAAGTGAGCCAATTTTTCTGGATTTTATCAAGAGGCCAAGACTCTTGTGATGATAATTCCTTT
AGCTAGTGTTTTTGTTAACTATGGCTT
Found at i:929908 original size:18 final size:17
Alignment explanation
Indices: 929867--929900 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
929857 AGTTTTTTTC
*
929867 AAGAATATAAAAAAAGA
1 AAGAAAATAAAAAAAGA
929884 AAGAAAATAAAAAAAGA
1 AAGAAAATAAAAAAAGA
929901 GAGGAAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (17 bp):
AAGAAAATAAAAAAAGA
Found at i:930702 original size:33 final size:33
Alignment explanation
Indices: 930647--930729 Score: 112
Period size: 33 Copynumber: 2.5 Consensus size: 33
930637 TAGCTCTGAA
* * *
930647 AGAGAAAGAAAAGATAAAAGGGATGATAGGAGG
1 AGAGATAGAAGAGATAAAAGGGATGATAGGAAG
* * *
930680 AGGGATAGTAGAGATAAGAGGGATGATAGGAAG
1 AGAGATAGAAGAGATAAAAGGGATGATAGGAAG
930713 AGAGATAGAAGAGATAA
1 AGAGATAGAAGAGATAA
930730 TAAAGAGATG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.51, C:0.00, G:0.37, T:0.12
Consensus pattern (33 bp):
AGAGATAGAAGAGATAAAAGGGATGATAGGAAG
Found at i:941156 original size:2 final size:2
Alignment explanation
Indices: 941149--941175 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
941139 AAGGAGAATT
941149 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
941176 TTTTGTTCAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:944046 original size:31 final size:31
Alignment explanation
Indices: 944009--944070 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
943999 TCTATTTTTG
944009 TTTGATT-AAATTT-TACTGTTAAAATTTAATT
1 TTTGATTGAAATTTAT-C-GTTAAAATTTAATT
*
944040 TTTGATTGAAATTTATCGTTAAACTTTAATT
1 TTTGATTGAAATTTATCGTTAAAATTTAATT
944071 ATGTATGGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 20 0.71
32 7 0.25
33 1 0.04
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (31 bp):
TTTGATTGAAATTTATCGTTAAAATTTAATT
Found at i:944727 original size:2 final size:2
Alignment explanation
Indices: 944715--944753 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
944705 CCAATCAAAC
* * *
944715 AT AT AT GT AT AT AT AT AT AT AT AT AT AT GT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
944754 GAAACAGCTG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
AT
Found at i:945207 original size:1 final size:1
Alignment explanation
Indices: 945203--945227 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
945193 TGGTTTTTAA
945203 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
945228 AAAAGATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:945602 original size:2 final size:2
Alignment explanation
Indices: 945595--945632 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
945585 AAAGCTTGCA
945595 AT 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 AT
945633 GGATTAGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:946838 original size:27 final size:26
Alignment explanation
Indices: 946776--946841 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 26
946766 TTTAATGTTA
946776 ATATT-TATTAAAATTATAATAATAT
1 ATATTATATTAAAATTATAATAATAT
*
946801 TTATTATATTAATAATTATAATAA-AT
1 ATATTATATTAA-AATTATAATAATAT
946827 ATGA-TATAATTAAAA
1 AT-ATTAT-ATTAAAA
946842 AAATTATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
25 4 0.11
26 14 0.40
27 17 0.49
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (26 bp):
ATATTATATTAAAATTATAATAATAT
Found at i:947106 original size:2 final size:2
Alignment explanation
Indices: 947099--947125 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
947089 CTGTTGTGAT
947099 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
947126 GGGTTTTAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:949876 original size:2 final size:2
Alignment explanation
Indices: 949869--949908 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
949859 GAGTGGTCAA
949869 AT AT 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 AT AT
949909 TAGCTCTATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:950968 original size:2 final size:2
Alignment explanation
Indices: 950961--950994 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
950951 GTTTCTCATC
950961 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
950995 ATATATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:950999 original size:2 final size:2
Alignment explanation
Indices: 950994--951020 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
950984 TCTCTCTCTC
950994 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
951021 TTTTTTTATC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:951411 original size:14 final size:14
Alignment explanation
Indices: 951392--951443 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
951382 ATTTTATATT
951392 TATATAAATTTTAA
1 TATATAAATTTTAA
951406 TATATAGATAATTTTATA
1 TATAT--A-AATTTTA-A
951424 TTATATAAATTTTAA
1 -TATATAAATTTTAA
*
951439 AATAT
1 TATAT
951444 TTATTTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
14 9 0.28
15 1 0.03
16 8 0.25
17 8 0.25
18 1 0.03
19 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (14 bp):
TATATAAATTTTAA
Found at i:951411 original size:16 final size:16
Alignment explanation
Indices: 951382--951443 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
951372 TATTTAAAAT
*
951382 ATTTTATATTTATATAA
1 ATTTTA-ATATATATAA
*
951399 ATTTTAATATATAGATA
1 ATTTTAATATATATA-A
951416 ATTTT-ATATTATATAA
1 ATTTTAATA-TATATAA
*
951432 ATTTTAAAATAT
1 ATTTTAATATAT
951444 TTATTTTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
16 19 0.50
17 19 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
ATTTTAATATATATAA
Found at i:951522 original size:28 final size:29
Alignment explanation
Indices: 951462--951522 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
951452 ATATCATAAT
**
951462 TATATTACTTTTCATATTATTTTATATTT
1 TATATTACTTTTCATATTATTTTATATCA
*
951491 TATATTACCTTTT-A-ATTATTTTTTATCA
1 TATATTA-CTTTTCATATTATTTTATATCA
951519 TATA
1 TATA
951523 ACCAAATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 15 0.54
29 8 0.29
30 5 0.18
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (29 bp):
TATATTACTTTTCATATTATTTTATATCA
Found at i:951943 original size:19 final size:20
Alignment explanation
Indices: 951921--951958 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
951911 AAAATATTTA
951921 TTTT-ATATAATAA-TAAAAT
1 TTTTAATAT-ATAATTAAAAT
951940 TTTTAATATATAATTAAAA
1 TTTTAATATATAATTAAAA
951959 ATTTAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTTAATATATAATTAAAAT
Found at i:951957 original size:20 final size:19
Alignment explanation
Indices: 951921--951958 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
951911 AAAATATTTA
951921 TTTTATATAATAATAAAAT
1 TTTTATATAATAATAAAAT
951940 TTTTA-ATATATAATTAAAA
1 TTTTATATA-ATAA-TAAAA
951959 ATTTAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.18
19 9 0.53
20 5 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTTATATAATAATAAAAT
Found at i:952585 original size:25 final size:26
Alignment explanation
Indices: 952539--952591 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
952529 AATTGAAAAA
* *
952539 TTTTAAAAATTTATTATATATTTTAT
1 TTTTAAAAATTAATTATATATTTAAT
* *
952565 TTTTTAAAATTAATT-TTTATTTAAT
1 TTTTAAAAATTAATTATATATTTAAT
952590 TT
1 TT
952592 AAATAATATC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (26 bp):
TTTTAAAAATTAATTATATATTTAAT
Found at i:953953 original size:9 final size:11
Alignment explanation
Indices: 953922--953950 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
953912 AAATTAAAAA
953922 ATTATTTTTAT
1 ATTATTTTTAT
953933 ATTATTTTTAT
1 ATTATTTTTAT
953944 ATT-TTTT
1 ATTATTTT
953951 ATAATTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
ATTATTTTTAT
Found at i:954477 original size:24 final size:26
Alignment explanation
Indices: 954450--954501 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
954440 ATTGATTAAA
954450 AATAAAAATATTTT-AAAAT-TTTTT
1 AATAAAAATATTTTCAAAATATTTTT
* *
954474 AATAAATATATTTTCAACATATTTTT
1 AATAAAAATATTTTCAAAATATTTTT
954500 AA
1 AA
954502 GAAATTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 13 0.54
25 4 0.17
26 7 0.29
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (26 bp):
AATAAAAATATTTTCAAAATATTTTT
Found at i:954506 original size:26 final size:24
Alignment explanation
Indices: 954457--954506 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
954447 AAAAATAAAA
*
954457 ATATTTTAAAATTTTTTAATAAAT
1 ATATTTTAAAATTTTTTAAGAAAT
*
954481 ATATTTTCAACATATTTTTAAGAAAT
1 ATATTTT-AAAAT-TTTTTAAGAAAT
954507 TTAATAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 4 0.18
26 11 0.50
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (24 bp):
ATATTTTAAAATTTTTTAAGAAAT
Found at i:957891 original size:19 final size:18
Alignment explanation
Indices: 957845--957890 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
957835 TATTATAAAC
957845 ATTATATATAATGTATAT
1 ATTATATATAATGTATAT
*
957863 A-TATATATATATGTGTA-
1 ATTATATATA-ATGTATAT
957880 ATTATTATATA
1 ATTA-TATATA
957891 TTTATATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 9 0.38
18 9 0.38
19 6 0.25
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (18 bp):
ATTATATATAATGTATAT
Found at i:958159 original size:18 final size:17
Alignment explanation
Indices: 958127--958160 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
958117 AGATAATTAA
958127 TTATATATAAAATTATG
1 TTATATATAAAATTATG
*
958144 TTATATAATTAAATTAT
1 TTATAT-ATAAAATTAT
958161 AATAAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TTATATATAAAATTATG
Found at i:958679 original size:14 final size:15
Alignment explanation
Indices: 958647--958697 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 15
958637 GCTTCTAACC
*
958647 ATAAATATATTAAAT
1 ATAAATATATTAAAA
958662 ATAAATAT-TTAAAA
1 ATAAATATATTAAAA
*
958676 ATAATTA-ATTAATTAA
1 ATAAATATATTAA--AA
958692 ATAAAT
1 ATAAAT
958698 TAAAATTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 15 0.50
15 8 0.27
16 7 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
ATAAATATATTAAAA
Found at i:958741 original size:23 final size:23
Alignment explanation
Indices: 958709--958788 Score: 71
Period size: 23 Copynumber: 3.6 Consensus size: 23
958699 AAAATTTTAT
958709 ATTTAATATATTATCAATAAATAA
1 ATTT-ATATATTATCAATAAATAA
958733 ATTTATATAATTAT-AATAAATAA
1 ATTTATAT-ATTATCAATAAATAA
* * *
958756 A-ATA-ATATTA-CATAAAAATAT
1 ATTTATATATTATCA-ATAAATAA
958777 ATTTATAT-TTAT
1 ATTTATATATTAT
958789 TTTTAATTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
20 5 0.11
21 9 0.20
22 7 0.15
23 16 0.35
24 9 0.20
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (23 bp):
ATTTATATATTATCAATAAATAA
Found at i:958758 original size:24 final size:24
Alignment explanation
Indices: 958709--958756 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 24
958699 AAAATTTTAT
958709 ATTTAATATATTATCAATAAATAA
1 ATTTAATATATTATCAATAAATAA
958733 ATTT-ATATAATTAT-AATAAATAA
1 ATTTAATAT-ATTATCAATAAATAA
958756 A
1 A
958757 ATAATATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
ATTTAATATATTATCAATAAATAA
Found at i:959831 original size:1 final size:1
Alignment explanation
Indices: 959825--959849 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
959815 ACAGTTACAA
959825 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
959850 AACAAAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:962985 original size:11 final size:11
Alignment explanation
Indices: 962971--963081 Score: 56
Period size: 11 Copynumber: 10.3 Consensus size: 11
962961 TAAATTTTTT
*
962971 ATTATTTTTAA
1 ATTAATTTTAA
* *
962982 ATTAAATTTAT
1 ATTAATTTTAA
*
962993 TTTAATTTTAA
1 ATTAATTTTAA
963004 ATT-ATTTTAA
1 ATTAATTTTAA
963014 ATTTAA--TTAA
1 A-TTAATTTTAA
* *
963024 TTTACATATTAA
1 ATTA-ATTTTAA
963036 ATTTAA-TTT-A
1 A-TTAATTTTAA
*
963046 ATTAAATTTAA
1 ATTAATTTTAA
*
963057 AATAA--TTAA
1 ATTAATTTTAA
963066 ATTTAATATTTAA
1 A-TTAAT-TTTAA
963079 ATT
1 ATT
963082 TATCAAGTTT
Statistics
Matches: 76, Mismatches: 12, Indels: 23
0.68 0.11 0.21
Matches are distributed among these distances:
9 12 0.16
10 21 0.28
11 27 0.36
12 8 0.11
13 8 0.11
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (11 bp):
ATTAATTTTAA
Found at i:963004 original size:22 final size:23
Alignment explanation
Indices: 962960--963007 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
962950 TTGTTTTTTT
* *
962960 TTAAATTTTTTATTATTTTTAAA
1 TTAAATTTATTATTAATTTTAAA
962983 TTAAATTTATT-TTAATTTTAAA
1 TTAAATTTATTATTAATTTTAAA
963005 TTA
1 TTA
963008 TTTTAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TTAAATTTATTATTAATTTTAAA
Found at i:963018 original size:22 final size:22
Alignment explanation
Indices: 962976--963048 Score: 67
Period size: 22 Copynumber: 3.1 Consensus size: 22
962966 TTTTTATTAT
*
962976 TTTTAAATTAAATTTATTTTAA
1 TTTTAAATTAAATTTAATTTAA
*
962998 TTTTAAATT-ATTTTAAATTTAA
1 TTTTAAATTAAATTT-AATTTAA
963020 TTAATTTACATATTAAATTTAATTTAA
1 -T--TTTA-A-ATTAAATTTAATTTAA
963047 TT
1 TT
963049 AAATTTAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
21 4 0.10
22 15 0.37
23 1 0.02
24 1 0.02
25 4 0.10
26 2 0.05
27 10 0.24
28 4 0.10
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTAAATTAAATTTAATTTAA
Found at i:963027 original size:15 final size:15
Alignment explanation
Indices: 962977--963127 Score: 62
Period size: 15 Copynumber: 9.9 Consensus size: 15
962967 TTTTATTATT
* *
962977 TTTAAATTAAATTTAT
1 TTTAAATTTAA-TTAA
* *
962993 TTTAATTTTAAATTAT
1 TTTAAATTT-AATTAA
963009 TTTAAATTTAATTAA
1 TTTAAATTTAATTAA
*
963024 TTTACA--T-ATTAAA
1 TTTAAATTTAATT-AA
963037 TTT-AATTTAATTAAA
1 TTTAAATTTAATT-AA
*
963052 TTTAAA-ATAATTAAA
1 TTTAAATTTAATT-AA
*
963067 TTTAATATTTAAATTTA
1 TTTAA-ATTT-AATTAA
* * * *
963084 -TCAAGTTTAATCAT
1 TTTAAATTTAATTAA
* *
963098 TTTAAATTTAAATCAT
1 TTTAAATTT-AATTAA
*
963114 TTTAAATTAAATTA
1 TTTAAATTTAATTA
963128 TTAATTTTTT
Statistics
Matches: 106, Mismatches: 18, Indels: 23
0.72 0.12 0.16
Matches are distributed among these distances:
12 4 0.04
13 6 0.06
14 4 0.04
15 45 0.42
16 39 0.37
17 4 0.04
18 4 0.04
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.52
Consensus pattern (15 bp):
TTTAAATTTAATTAA
Found at i:963034 original size:27 final size:26
Alignment explanation
Indices: 962978--963081 Score: 87
Period size: 27 Copynumber: 4.1 Consensus size: 26
962968 TTTATTATTT
*
962978 TTAAA-TTAAATTTATTTTAATTTTAAA
1 TTAAATTTAAATTTA-ATTAA-TTTAAA
*
963005 TT-ATTTTAAATTTAATTAATTTACATA
1 TTAAATTTAAATTTAATTAATTTA-A-A
963032 TTAAATTT-AATTTAATTAAATTTAAA
1 TTAAATTTAAATTTAATT-AATTTAAA
*
963058 AT-AA-TTAAATTTAA-T-ATTTAAA
1 TTAAATTTAAATTTAATTAATTTAAA
963080 TT
1 TT
963082 TATCAAGTTT
Statistics
Matches: 66, Mismatches: 5, Indels: 17
0.75 0.06 0.19
Matches are distributed among these distances:
22 8 0.12
24 3 0.05
25 13 0.20
26 8 0.12
27 24 0.36
28 10 0.15
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (26 bp):
TTAAATTTAAATTTAATTAATTTAAA
Found at i:963036 original size:32 final size:33
Alignment explanation
Indices: 962971--963056 Score: 90
Period size: 32 Copynumber: 2.7 Consensus size: 33
962961 TAAATTTTTT
* *
962971 ATTATTTTTAAATTAAATTTATTTTAATTTTAA
1 ATTATTTTTAAATTAAATTTAATTTAATATTAA
*
963004 ATTA-TTTTAAATTTAA-TTAATTTACATATTAA
1 ATTATTTTTAAATTAAATTTAATTTA-ATATTAA
*
963036 ATT-TAATTT-AATTAAATTTAA
1 ATTAT-TTTTAAATTAAATTTAA
963057 AATAATTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
31 7 0.16
32 26 0.59
33 11 0.25
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (33 bp):
ATTATTTTTAAATTAAATTTAATTTAATATTAA
Found at i:963076 original size:7 final size:6
Alignment explanation
Indices: 962977--963083 Score: 63
Period size: 6 Copynumber: 18.7 Consensus size: 6
962967 TTTTATTATT
* * *
962977 TTTAAA -TTAAA TTT-AT TTTAAT TTTAAA -TT-AT TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
963020 -TT-AA TTTACA TATTAAA TTT-AA TTT-AA -TTAAA TTTAAAA TAATTAAA
1 TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA TTTAAA TTT-AAA T--TTAAA
963067 TTTAATA TTTAAA TTTA
1 TTTAA-A TTTAAA TTTA
963084 TCAAGTTTAA
Statistics
Matches: 82, Mismatches: 6, Indels: 26
0.72 0.05 0.23
Matches are distributed among these distances:
4 7 0.09
5 26 0.32
6 28 0.34
7 15 0.18
8 4 0.05
9 2 0.02
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:963113 original size:16 final size:15
Alignment explanation
Indices: 963092--963125 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
963082 TATCAAGTTT
963092 AATCATTTTAAATTTA
1 AATCATTTTAAA-TTA
963108 AATCATTTTAAATTA
1 AATCATTTTAAATTA
963123 AAT
1 AAT
963126 TATTAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (15 bp):
AATCATTTTAAATTA
Found at i:963152 original size:22 final size:21
Alignment explanation
Indices: 963113--963155 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
963103 ATTTAAATCA
*
963113 TTTTAAATTAAATTATTAATT
1 TTTTAAATTAAATAATTAATT
*
963134 TTTTTAATTAAATAAATTAATT
1 TTTTAAATTAAAT-AATTAATT
963156 AAATTTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTAAATTAAATAATTAATT
Found at i:963168 original size:26 final size:26
Alignment explanation
Indices: 963115--963182 Score: 66
Period size: 26 Copynumber: 2.5 Consensus size: 26
963105 TTAAATCATT
* **
963115 TTAAATTAAATT-ATTAATTTTTTTAA
1 TTAAA-TAAATTAATTAAATTTTAAAA
963141 TTAAATAAATTAATTAAATTTTAAAA
1 TTAAATAAATTAATTAAATTTTAAAA
963167 TTGAAATCAAAATTAA
1 TT-AAAT--AAATTAA
963183 CTAATTATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 6 0.17
26 18 0.51
27 4 0.11
29 7 0.20
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (26 bp):
TTAAATAAATTAATTAAATTTTAAAA
Found at i:963990 original size:4 final size:4
Alignment explanation
Indices: 963981--964017 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
963971 GAATGAAGAG
*
963981 GGAA GGAA GGAA GGAA GGAA GGAA GAAA GGAA GGAA G
1 GGAA GGAA GGAA GGAA GGAA GGAA GGAA GGAA GGAA G
964018 CCAAAAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (4 bp):
GGAA
Found at i:973317 original size:20 final size:19
Alignment explanation
Indices: 973279--973320 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
973269 AAGATCAGAT
*
973279 TAAAAAAATATAAATTATG
1 TAAAAAAATATAAAATATG
*
973298 TAAAAAATTATAAAAATATG
1 TAAAAAAATAT-AAAATATG
973318 TAA
1 TAA
973321 CATAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (19 bp):
TAAAAAAATATAAAATATG
Found at i:974375 original size:22 final size:22
Alignment explanation
Indices: 974337--974378 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
974327 CTTATTATGT
974337 AATTTTTTATATATTTATATTA
1 AATTTTTTATATATTTATATTA
*
974359 AATTTATTT-TATTTTTATAT
1 AATTT-TTTATATATTTATAT
974379 CATAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
AATTTTTTATATATTTATATTA
Found at i:974378 original size:28 final size:28
Alignment explanation
Indices: 974341--974416 Score: 70
Period size: 28 Copynumber: 2.8 Consensus size: 28
974331 TTATGTAATT
***
974341 TTTTATATATTTATATTAAATTTATTTTA
1 TTTT-TATATTTATATTAAATTTAAAATA
*
974370 TTTTTATA-TCATAATTAAATTTAAAATA
1 TTTTTATATTTAT-ATTAAATTTAAAATA
974398 -TTTTAT-TTTATA-TAAATTT
1 TTTTTATATTTATATTAAATTT
974417 TAATACGTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
25 7 0.17
26 1 0.03
27 12 0.30
28 16 0.40
29 4 0.10
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTTTATATTTATATTAAATTTAAAATA
Found at i:974530 original size:17 final size:18
Alignment explanation
Indices: 974473--974547 Score: 62
Period size: 17 Copynumber: 4.0 Consensus size: 18
974463 TCATATCGTA
* *
974473 TTTATATTTTTTTATGTT
1 TTTATAATTATTTATGTT
* * *
974491 ATATTATATTTTAATTATTTT
1 -T-TTATA-ATTATTTATGTT
974512 TTTATAA-TATTTATGTT
1 TTTATAATTATTTATGTT
974529 TTTATAATTATTTGATGTT
1 TTTATAATTATTT-ATGTT
974548 CAAAATTATC
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
17 15 0.33
18 5 0.11
19 11 0.24
20 6 0.13
21 9 0.20
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTATAATTATTTATGTT
Found at i:974998 original size:24 final size:24
Alignment explanation
Indices: 974948--974998 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
974938 TACGTTTGTC
** * **
974948 TATTTATATTGTATTATATTATTA
1 TATTTATATCATAATATATTAAAA
974972 TATTTATATCATAATATATTAAAA
1 TATTTATATCATAATATATTAAAA
974996 TAT
1 TAT
974999 AAAAAAATTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
TATTTATATCATAATATATTAAAA
Found at i:975700 original size:2 final size:2
Alignment explanation
Indices: 975693--975719 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
975683 GGTTCAAAAT
975693 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
975720 TCTCATGTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:976888 original size:21 final size:21
Alignment explanation
Indices: 976864--976906 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
976854 GTGTTTAATA
*
976864 TTTAATTATTTTGAT-ATAAAT
1 TTTAAATATTTT-ATAATAAAT
976885 TTTAAATATTTTATAATAAAT
1 TTTAAATATTTTATAATAAAT
976906 T
1 T
976907 ATATTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTAAATATTTTATAATAAAT
Found at i:976946 original size:27 final size:27
Alignment explanation
Indices: 976891--976943 Score: 74
Period size: 25 Copynumber: 2.0 Consensus size: 27
976881 AAATTTTAAA
976891 TATTTTATAATAAATTATATTTATATT
1 TATTTTATAATAAATTATATTTATATT
* *
976918 TATTTTAT-ATAGATT-TTTTTATATT
1 TATTTTATAATAAATTATATTTATATT
976943 T
1 T
976944 TTAAAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 10 0.42
26 6 0.25
27 8 0.33
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (27 bp):
TATTTTATAATAAATTATATTTATATT
Found at i:977645 original size:40 final size:39
Alignment explanation
Indices: 977601--977701 Score: 157
Period size: 40 Copynumber: 2.5 Consensus size: 39
977591 CATAATATAA
977601 AATTAAAATTAATTATTTTTAAAAAATAATTATACAAATC
1 AATT-AAATTAATTATTTTTAAAAAATAATTATACAAATC
***
977641 AATTAAATTAATTATTTTATAAAAAATAATTATATTGATC
1 AATTAAATTAATTATTTT-TAAAAAATAATTATACAAATC
977681 AATTAAATTAATTATTTTTAA
1 AATTAAATTAATTATTTTTAA
977702 CCTTTCCCTT
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
39 17 0.30
40 40 0.70
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (39 bp):
AATTAAATTAATTATTTTTAAAAAATAATTATACAAATC
Found at i:978078 original size:22 final size:22
Alignment explanation
Indices: 978045--978094 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
978035 AAATAATTTT
978045 TTTTAAATATTTAATAAGTTATAA
1 TTTTAAAT-TTTAAT-AGTTATAA
*
978069 TTTTAAATTTTAATATTTATAA
1 TTTTAAATTTTAATAGTTATAA
978091 TTTT
1 TTTT
978095 TTTTTTCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 11 0.44
23 6 0.24
24 8 0.32
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
TTTTAAATTTTAATAGTTATAA
Found at i:978349 original size:25 final size:27
Alignment explanation
Indices: 978277--978342 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 27
978267 TAAAATTTTT
978277 TTATTAA-ATTTAATTATAAAAATATATAA
1 TTATTAATA-TTAA-TAT-AAAATATATAA
*
978306 TTATTAATATTAATGTAAAATATAT-A
1 TTATTAATATTAATATAAAATATATAA
978332 TTA-TAATATTA
1 TTATTAATATTA
978343 TCATAAATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 8 0.23
26 4 0.11
27 9 0.26
28 2 0.06
29 11 0.31
30 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
TTATTAATATTAATATAAAATATATAA
Found at i:978354 original size:27 final size:26
Alignment explanation
Indices: 978292--978342 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
978282 AAATTTAATT
978292 ATAAAAATATATAATTATTAATATTA
1 ATAAAAATATATAATTATTAATATTA
*
978318 ATGTAAAATATAT-ATTA-TAATATTA
1 AT-AAAAATATATAATTATTAATATTA
978343 TCATAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 8 0.35
26 6 0.26
27 9 0.39
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (26 bp):
ATAAAAATATATAATTATTAATATTA
Found at i:978824 original size:2 final size:2
Alignment explanation
Indices: 978817--978843 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
978807 GGTTTTGTTC
978817 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
978844 AGTGAATGTG
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:981171 original size:26 final size:25
Alignment explanation
Indices: 981104--981184 Score: 67
Period size: 26 Copynumber: 3.1 Consensus size: 25
981094 ATGCACGTAG
981104 AATTTTGAATA-A-ATAAAAAATATTT
1 AATTTT-AATATATATAAAAAAT-TTT
* *
981129 AATTATTTATTTAATATAAAAAATTTT
1 AATT-TTAATAT-ATATAAAAAATTTT
* *
981156 AATTTTAAATATATATTAAAAATATT
1 AATTTT-AATATATATAAAAAATTTT
981182 AAT
1 AAT
981185 ATTTTTTGAT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
25 6 0.13
26 19 0.42
27 11 0.24
28 9 0.20
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (25 bp):
AATTTTAATATATATAAAAAATTTT
Found at i:984518 original size:14 final size:14
Alignment explanation
Indices: 984501--984527 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
984491 ATAATTATTT
984501 AAATATAATATAAA
1 AAATATAATATAAA
984515 AAATATAATATAA
1 AAATATAATATAA
984528 TATGAATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATATAATATAAA
Found at i:984562 original size:19 final size:19
Alignment explanation
Indices: 984534--984613 Score: 59
Period size: 18 Copynumber: 4.5 Consensus size: 19
984524 ATAATATGAA
*
984534 TATATGAATATTTTAAATTT
1 TATAT-AATATATTAAATTT
984554 TATAT-A-ATATT-AA--T
1 TATATAATATATTAAATTT
*
984568 TAT-TAAT-TATTAAAATT
1 TATATAATATATTAAATTT
*
984585 TATATAA-ATATAAAACTTT
1 TATATAATATATTAAA-TTT
984604 TATATAATAT
1 TATATAATAT
984614 TTATTATTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 18
0.70 0.04 0.26
Matches are distributed among these distances:
13 1 0.02
14 9 0.19
15 2 0.04
16 2 0.04
17 8 0.17
18 10 0.21
19 9 0.19
20 7 0.15
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (19 bp):
TATATAATATATTAAATTT
Found at i:984587 original size:31 final size:33
Alignment explanation
Indices: 984522--984591 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 33
984512 AAAAAATATA
* *
984522 ATATAATATGAATATATGAATATTTTAAATTTT
1 ATATAATATGAATATATGAATATATTAAAATTT
* *
984555 ATATAATATTAAT-TATTAAT-TATTAAAATTT
1 ATATAATATGAATATATGAATATATTAAAATTT
984586 ATATAA
1 ATATAA
984592 ATATAAAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 15 0.45
32 6 0.18
33 12 0.36
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (33 bp):
ATATAATATGAATATATGAATATATTAAAATTT
Found at i:984696 original size:2 final size:2
Alignment explanation
Indices: 984689--984729 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
984679 AGCAATGCAA
984689 TC TC TC TC 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 TC TC TC TC T
984730 GTCTAGTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:992132 original size:156 final size:156
Alignment explanation
Indices: 991844--992136 Score: 478
Period size: 156 Copynumber: 1.9 Consensus size: 156
991834 CGTTTAGTGT
* *
991844 TATATATATATATACTTTTAGACCAGAGATGTTCAAGTATAACATGGATTAGAAACTATGTTTAA
1 TATATATATATACACTTTTAGACCAGAGATGTTCAAGCATAACATGGATTAGAAACTATGTTTAA
* * *
991909 GTAGAAGAATTTTAATTCCATTAGGAGTTTTGAATTGTATTAGAAGTATAAAATCTAATTATGAT
66 GTAGAAGAATTTTAATTCCATGAGGAGTTTAGAATTCTATTAGAAGTATAAAATCTAATTATGAT
991974 TATTACATTTTAGTGTAATATATATA
131 TATTACATTTTAGTGTAATATATATA
** *
992000 TATATATATATACACTTTTAGATTAGAGATGTTCGAGCATAACATGGATTAGAAACTATGTTTAA
1 TATATATATATACACTTTTAGACCAGAGATGTTCAAGCATAACATGGATTAGAAACTATGTTTAA
* ** *
992065 GTAGAGGTTTTTTAATTCCATGAGGAGTTTAGAATTCTATTAGAAGTATAAAATCTAATTATTAT
66 GTAGAAGAATTTTAATTCCATGAGGAGTTTAGAATTCTATTAGAAGTATAAAATCTAATTATGAT
992130 TATTACA
131 TATTACA
992137 AATTAATAAA
Statistics
Matches: 125, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
156 125 1.00
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (156 bp):
TATATATATATACACTTTTAGACCAGAGATGTTCAAGCATAACATGGATTAGAAACTATGTTTAA
GTAGAAGAATTTTAATTCCATGAGGAGTTTAGAATTCTATTAGAAGTATAAAATCTAATTATGAT
TATTACATTTTAGTGTAATATATATA
Found at i:992344 original size:19 final size:19
Alignment explanation
Indices: 992320--992356 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
992310 CTAATAATAA
992320 AAAATTTAATTATAAAATT
1 AAAATTTAATTATAAAATT
992339 AAAATTTAATTATAAAAT
1 AAAATTTAATTATAAAAT
992357 AAAGTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAATTTAATTATAAAATT
Found at i:996241 original size:39 final size:39
Alignment explanation
Indices: 996187--996263 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
996177 AGTATCTTGA
* *
996187 TCCTTCTTTCATTTTCTTTGTTTTGCCCTGCATCCAAAG
1 TCCTTCTTTCATTTTCTTTGTTTGGCACTGCATCCAAAG
996226 TCCTTCTTTCATTTTCTTTGTTTGGCACTGCATCCAAA
1 TCCTTCTTTCATTTTCTTTGTTTGGCACTGCATCCAAA
996264 CTTGAATCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.14, C:0.27, G:0.10, T:0.48
Consensus pattern (39 bp):
TCCTTCTTTCATTTTCTTTGTTTGGCACTGCATCCAAAG
Found at i:997269 original size:25 final size:25
Alignment explanation
Indices: 997235--997286 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
997225 AATGTAAAAA
997235 CTTACCATCTTTACTGGCCAATTTG
1 CTTACCATCTTTACTGGCCAATTTG
997260 CTTACCATCTTTACTGGCCAATTTG
1 CTTACCATCTTTACTGGCCAATTTG
997285 CT
1 CT
997287 AGGCCGGCAT
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:0.19, C:0.29, G:0.12, T:0.40
Consensus pattern (25 bp):
CTTACCATCTTTACTGGCCAATTTG
Found at i:998181 original size:2 final size:2
Alignment explanation
Indices: 998174--998210 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
998164 CACCAAAATA
998174 TC TC 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 TC TC T
998211 ATATATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:998215 original size:2 final size:2
Alignment explanation
Indices: 998210--998245 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
998200 TCTCTCTCTC
998210 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
998246 CACACGCATT
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):
TA
Found at i:998331 original size:17 final size:18
Alignment explanation
Indices: 998285--998331 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
998275 AGTATTATTT
998285 TTTATATTATTTATTATA
1 TTTATATTATTTATTATA
998303 TTT-TAATTATTT-TTATA
1 TTTAT-ATTATTTATTATA
*
998320 TTTATATCATTT
1 TTTATATTATTT
998332 CAAAGATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTATATTATTTATTATA
Found at i:998903 original size:20 final size:20
Alignment explanation
Indices: 998878--998931 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 20
998868 GGATTGATAA
998878 AAAAAATTAATTTAATCAAT
1 AAAAAATTAATTTAATCAAT
* *
998898 AAAAAATTATATTAAATTAAT
1 AAAAAATTA-ATTTAATCAAT
998919 AAAAAATTAATTT
1 AAAAAATTAATTT
998932 TATGTTAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 12 0.40
21 18 0.60
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAAAATTAATTTAATCAAT
Found at i:999031 original size:21 final size:22
Alignment explanation
Indices: 999005--999047 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
998995 AAATAGTACA
999005 TTATTAA-ATTAAATATATTTT
1 TTATTAATATTAAATATATTTT
*
999026 TTATTAATTATTTAATATATTT
1 TTATTAA-TATTAAATATATTT
999048 GATACATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
23 12 0.63
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATTAATATTAAATATATTTT
Found at i:1002269 original size:20 final size:19
Alignment explanation
Indices: 1002222--1002272 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
1002212 TAAGATTTAA
*
1002222 ATTATAATTATAAATTTATT
1 ATTATAATTAT-ATTTTATT
1002242 -TT-TAATTATATTTTATTT
1 ATTATAATTATATTTTA-TT
1002260 ATTATAATTATAT
1 ATTATAATTATAT
1002273 AATTATAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 5 0.19
18 9 0.33
19 4 0.15
20 9 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTATAATTATATTTTATT
Found at i:1002277 original size:14 final size:14
Alignment explanation
Indices: 1002221--1002281 Score: 51
Period size: 14 Copynumber: 4.6 Consensus size: 14
1002211 ATAAGATTTA
1002221 AATTATAATTATA-
1 AATTATAATTATAT
*
1002234 AATT-T-ATT-TTT
1 AATTATAATTATAT
*
1002245 AATTAT-ATTTTATT
1 AATTATAATTATA-T
*
1002259 TATTATAATTATAT
1 AATTATAATTATAT
1002273 AATTATAAT
1 AATTATAAT
1002282 AAATAACAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
10 1 0.03
11 7 0.18
12 5 0.13
13 5 0.13
14 15 0.39
15 5 0.13
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
AATTATAATTATAT
Found at i:1002766 original size:20 final size:20
Alignment explanation
Indices: 1002743--1002820 Score: 59
Period size: 20 Copynumber: 3.8 Consensus size: 20
1002733 CTCCTGTAAT
*
1002743 TTTTTATAACTTTTGTAACG
1 TTTTTATAACTTTTATAACG
* * **
1002763 TTTTTTTAA-TATTTTTAATT
1 TTTTTATAACT-TTTATAACG
*
1002783 TTTTTGATAAATTTTATAACG
1 TTTTT-ATAACTTTTATAACG
*
1002804 TCTTTATAAACTTTTAT
1 TTTTTAT-AACTTTTAT
1002821 GATGAGTTTG
Statistics
Matches: 44, Mismatches: 10, Indels: 7
0.72 0.16 0.11
Matches are distributed among these distances:
19 1 0.02
20 21 0.48
21 21 0.48
22 1 0.02
ACGTcount: A:0.28, C:0.06, G:0.05, T:0.60
Consensus pattern (20 bp):
TTTTTATAACTTTTATAACG
Found at i:1006211 original size:20 final size:21
Alignment explanation
Indices: 1006163--1006214 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
1006153 ATTATAAAAT
**
1006163 TTATTAAAAATATATTTAGTG
1 TTATTAAAAATATATTTAAAG
*
1006184 TTATTAAAATTATATTTAAAG
1 TTATTAAAAATATATTTAAAG
*
1006205 TTATAAAAAA
1 TTATTAAAAA
1006215 ATTATTATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (21 bp):
TTATTAAAAATATATTTAAAG
Found at i:1006236 original size:21 final size:21
Alignment explanation
Indices: 1006212--1006342 Score: 69
Period size: 21 Copynumber: 6.2 Consensus size: 21
1006202 AAGTTATAAA
1006212 AAAATTATTATAAATATTATC
1 AAAATTATTATAAATATTATC
* *
1006233 AAAATTA-TATAAAAAAGTATC
1 AAAATTATTAT-AAATATTATC
1006254 AAAATCATATTA-AAA-ATTA-C
1 AAAAT--TATTATAAATATTATC
*
1006274 -AACTTA-TATGAAA-ATTTATTTC
1 AAAATTATTAT-AAATA-TTA--TC
* * *
1006296 AAAATTTATAAAAAATATTATT
1 AAAA-TTATTATAAATATTATC
* *
1006318 AAAATTATTTTAAATATTATG
1 AAAATTATTATAAATATTATC
1006339 AAAA
1 AAAA
1006343 CAAGTAGAAA
Statistics
Matches: 84, Mismatches: 12, Indels: 28
0.68 0.10 0.23
Matches are distributed among these distances:
16 2 0.02
17 2 0.02
18 4 0.05
19 6 0.07
20 4 0.05
21 40 0.48
22 9 0.11
23 4 0.05
24 11 0.13
25 2 0.02
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (21 bp):
AAAATTATTATAAATATTATC
Found at i:1009479 original size:151 final size:147
Alignment explanation
Indices: 1009215--1009490 Score: 358
Period size: 151 Copynumber: 1.9 Consensus size: 147
1009205 AATTAAGAAG
* * * *
1009215 TTTACATTAATAAGGAATTAATGGTTAATAATAAAATAAATAAAATTACTCAATGTTTTAATTTT
1 TTTACATTAATAAAGAATTAATGATTAATAAGAAAATAAATAAAATTACTCAATATTTTAATTTT
* ** * * *
1009280 AATAAAAAACTATTAATTAATTAAGGACATAGTAATTAATATTATAAATTATTAAGGGTAAATAT
66 AATAAAAAACAATTAATTAATTAAAAAAATAATAATTAATATTATAAATTATCAAGGGTAAATAT
1009345 GTTATTCACTATTTGAT
131 GTTATTCACTATTTGAT
* *
1009362 TTTACATTAATAAATAATTCAA-GATTAATAAGGAAATAAAT-AAATTACTCAATATTTTAATTT
1 TTTACATTAATAAAGAATT-AATGATTAATAAGAAAATAAATAAAATTACTCAATATTTTAATTT
* *
1009425 TAATAAGAAAATTATCAATTTATTAATTAAAAAAATAATAGTTAATATTATAAATTATCAAGGGT
65 TAAT-A-AAAA--A-CAATTAATTAATTAAAAAAATAATAATTAATATTATAAATTATCAAGGGT
1009490 A
125 A
1009491 TAACTATGAA
Statistics
Matches: 109, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
146 25 0.23
147 34 0.31
148 6 0.06
150 1 0.01
151 43 0.39
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.39
Consensus pattern (147 bp):
TTTACATTAATAAAGAATTAATGATTAATAAGAAAATAAATAAAATTACTCAATATTTTAATTTT
AATAAAAAACAATTAATTAATTAAAAAAATAATAATTAATATTATAAATTATCAAGGGTAAATAT
GTTATTCACTATTTGAT
Found at i:1011086 original size:18 final size:18
Alignment explanation
Indices: 1011065--1011115 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
1011055 GTTTTTTTAA
*
1011065 TTATAATCTTTTTAGTAT
1 TTATAATCTTTTTAATAT
* *
1011083 TTATTATCTTTAATAATAT
1 TTATAATCTTT-TTAATAT
1011102 TTA-AATCATTTTTA
1 TTATAATC-TTTTTA
1011116 TAACCTGTAG
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (18 bp):
TTATAATCTTTTTAATAT
Found at i:1012033 original size:10 final size:10
Alignment explanation
Indices: 1012018--1012071 Score: 63
Period size: 10 Copynumber: 5.1 Consensus size: 10
1012008 TGTTAATGTG
1012018 ATTTTTTATA
1 ATTTTTTATA
1012028 ATTTTTTATA
1 ATTTTTTATA
1012038 ATTTTTTAATA
1 ATTTTTT-ATA
*
1012049 TTTTTTGTAATA
1 ATTTTT-T-ATA
*
1012061 TTTTTTTATA
1 ATTTTTTATA
1012071 A
1 A
1012072 CAATTGTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
10 20 0.50
11 9 0.22
12 11 0.28
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:1012043 original size:20 final size:22
Alignment explanation
Indices: 1012018--1012071 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
1012008 TGTTAATGTG
1012018 ATTTTTTATAATTTTT-T-ATA
1 ATTTTTTATAATTTTTGTAATA
*
1012038 ATTTTTTAATATTTTTTGTAATA
1 ATTTTTT-ATAATTTTTGTAATA
*
1012061 TTTTTTTATAA
1 ATTTTTTATAA
1012072 CAATTGTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 7 0.25
21 8 0.29
22 4 0.14
23 9 0.32
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (22 bp):
ATTTTTTATAATTTTTGTAATA
Found at i:1012123 original size:23 final size:22
Alignment explanation
Indices: 1012093--1012149 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
1012083 TTTTATAACC
*
1012093 TTTTTATAATAATTGCAGCTTTT
1 TTTTTATAATAATTGCAAC-TTT
* *
1012116 TTTTTATAAT-TTTGTAACTTT
1 TTTTTATAATAATTGCAACTTT
1012137 TTTTTATAA-AATT
1 TTTTTATAATAATT
1012150 TGTAATCTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 14 0.48
22 5 0.17
23 10 0.34
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.61
Consensus pattern (22 bp):
TTTTTATAATAATTGCAACTTT
Found at i:1012137 original size:21 final size:22
Alignment explanation
Indices: 1012113--1012154 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1012103 AATTGCAGCT
*
1012113 TTTTTTTTAT-AATTTTGTAAC
1 TTTTTTTTATAAAATTTGTAAC
1012134 TTTTTTTTATAAAATTTGTAA
1 TTTTTTTTATAAAATTTGTAA
1012155 TCTCTTGGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (22 bp):
TTTTTTTTATAAAATTTGTAAC
Found at i:1014897 original size:42 final size:42
Alignment explanation
Indices: 1014836--1014927 Score: 175
Period size: 42 Copynumber: 2.2 Consensus size: 42
1014826 CAATGCAACG
1014836 CAAGCTCTGAATTCTAGCTAATTAGCTTGTAGCTGTTAACCA
1 CAAGCTCTGAATTCTAGCTAATTAGCTTGTAGCTGTTAACCA
*
1014878 CTAGCTCTGAATTCTAGCTAATTAGCTTGTAGCTGTTAACCA
1 CAAGCTCTGAATTCTAGCTAATTAGCTTGTAGCTGTTAACCA
1014920 CAAGCTCT
1 CAAGCTCT
1014928 AAATAAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (42 bp):
CAAGCTCTGAATTCTAGCTAATTAGCTTGTAGCTGTTAACCA
Found at i:1016145 original size:16 final size:15
Alignment explanation
Indices: 1016075--1016145 Score: 52
Period size: 16 Copynumber: 4.4 Consensus size: 15
1016065 ATATGAAAAT
*
1016075 AATTAATAAAAATTTA
1 AATTAA-AAAAAATTA
* *
1016091 GATTAAAAATAATTA
1 AATTAAAAAAAATTA
* *
1016106 ATATTAAAAAAATAAATC
1 A-ATT-AAAAAA-AATTA
1016124 AATTAAGAAAAAATTA
1 AATTAA-AAAAAATTA
1016140 AATTAA
1 AATTAA
1016146 CACGGACTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
15 7 0.17
16 19 0.45
17 12 0.29
18 4 0.10
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (15 bp):
AATTAAAAAAAATTA
Found at i:1016350 original size:142 final size:138
Alignment explanation
Indices: 1016048--1016367 Score: 367
Period size: 142 Copynumber: 2.3 Consensus size: 138
1016038 ATAACACTAT
* * * * *
1016048 GTCAATATCTTAATTTAATATGAAAATAATTAATAAAAATTTAGATTAAAAATAATTAATATTAA
1 GTCAATATATTAATTTAATA-AAAAATAATTAATAAAAACTTAGACTAAAAATAATTAATAATAA
** * *
1016113 AAAAATAAATCAATTAAGAAAAAATTAAATTAACACGGACTTTAAGGTTAGTAAAAAATAATAAA
65 AAAAATAAATCAATTAAGAAAAAATTAAATTAACAAAGACTTCAAGATTAGTAAAAAATAATAAA
1016178 TAAAGATTA
130 TAAAGATTA
* * * * * * *
1016187 ATTAATATTTTACTTCAATAAAAAATCATTAATAAAAACTTAGACTAAAAATTAGTTAATAAATA
1 GTCAATATATTAATTTAATAAAAAATAATTAATAAAAACTTAGACTAAAAA-TAATTAAT-AATA
* *
1016252 AAAATATACAA-CAATTTAAGAAAAAA-TAACATTAATAAAGACTTCAAGATTCA-TAAGAAAAT
64 AAAAAATA-AATCAA-TTAAGAAAAAATTAA-ATTAACAAAGACTTCAAGATT-AGTAA-AAAAT
1016314 AATAAATAAAGATTA
124 AATAAATAAAGATTA
*
1016329 GTCAATATATTAATTTAATAAAAATTAATTAATTAAAAA
1 GTCAATATATTAATTTAATAAAAAATAATTAA-TAAAAA
1016368 TCTATTAATA
Statistics
Matches: 149, Mismatches: 24, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
138 27 0.18
139 22 0.15
140 16 0.11
141 32 0.21
142 46 0.31
143 6 0.04
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.32
Consensus pattern (138 bp):
GTCAATATATTAATTTAATAAAAAATAATTAATAAAAACTTAGACTAAAAATAATTAATAATAAA
AAAATAAATCAATTAAGAAAAAATTAAATTAACAAAGACTTCAAGATTAGTAAAAAATAATAAAT
AAAGATTA
Found at i:1016405 original size:15 final size:16
Alignment explanation
Indices: 1016385--1016414 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1016375 ATATTTATAA
1016385 AAAAATTTTA-ATTAG
1 AAAAATTTTATATTAG
1016400 AAAAATTTTATATTA
1 AAAAATTTTATATTA
1016415 ATAAAGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
AAAAATTTTATATTAG
Found at i:1024735 original size:17 final size:17
Alignment explanation
Indices: 1024713--1024757 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1024703 TTTTAATTAT
* *
1024713 TTATATTTGATGTATAA
1 TTATATTTAATATATAA
1024730 TTATATTTAATATATAA
1 TTATATTTAATATATAA
*
1024747 TTATATATAAT
1 TTATATTTAAT
1024758 GATAAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (17 bp):
TTATATTTAATATATAA
Found at i:1024821 original size:17 final size:17
Alignment explanation
Indices: 1024785--1024834 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
1024775 TTAATTAATT
*
1024785 TTTAAATATATAAA-AAA
1 TTTAAA-ATATAAATATA
1024802 TTTAAAATATAAATATA
1 TTTAAAATATAAATATA
*
1024819 TTT-ATAT-TAAATATA
1 TTTAAAATATAAATATA
1024834 T
1 T
1024835 ATCTTTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 9 0.30
16 10 0.33
17 11 0.37
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTAAAATATAAATATA
Found at i:1029966 original size:20 final size:23
Alignment explanation
Indices: 1029936--1029976 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
1029926 ATAGCTTTAG
1029936 AAAAGAGGAAA-AAA-AAAAAAA
1 AAAAGAGGAAAGAAAGAAAAAAA
1029957 AAAAGA-GAAAGAAAGAAAAA
1 AAAAGAGGAAAGAAAGAAAAA
1029977 CTAAGGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 9 0.50
22 5 0.28
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (23 bp):
AAAAGAGGAAAGAAAGAAAAAAA
Found at i:1032831 original size:38 final size:38
Alignment explanation
Indices: 1032780--1032857 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
1032770 AGGAACTGTA
1032780 AGAAATATTAAAGAGAAAGAGTTATAAGATAGATTTTG
1 AGAAATATTAAAGAGAAAGAGTTATAAGATAGATTTTG
1032818 AGAAATATTAAAGAGAAAGAGTTATAAGATAGATTTTG
1 AGAAATATTAAAGAGAAAGAGTTATAAGATAGATTTTG
1032856 AG
1 AG
1032858 GTACGAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.22, T:0.28
Consensus pattern (38 bp):
AGAAATATTAAAGAGAAAGAGTTATAAGATAGATTTTG
Found at i:1033171 original size:15 final size:15
Alignment explanation
Indices: 1033151--1033188 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
1033141 ATTATTTTGA
1033151 AAAAATTAAAT-AAAT
1 AAAAA-TAAATAAAAT
1033166 AAAAATAAATAAAAT
1 AAAAATAAATAAAAT
1033181 -AAAATAAA
1 AAAAATAAA
1033189 AATTTGTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAAATAAATAAAAT
Found at i:1033173 original size:10 final size:10
Alignment explanation
Indices: 1033158--1033191 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
1033148 TGAAAAAATT
1033158 AAATAAATAA
1 AAATAAATAA
1033168 AAATAAAT-A
1 AAATAAATAA
1033177 AAATAAAATAA
1 AAAT-AAATAA
1033188 AAAT
1 AAAT
1033192 TTGTATCTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.23
10 12 0.55
11 5 0.23
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
AAATAAATAA
Found at i:1036155 original size:23 final size:22
Alignment explanation
Indices: 1036113--1036156 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
1036103 TTTTTAAATA
1036113 TAAATAAAAAAATTAAATTTTGT
1 TAAATAAAAAAATT-AATTTTGT
1036136 TAAATATATAAAAATT-ATTTT
1 TAAATA-A-AAAAATTAATTTT
1036157 AAAATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
24 1 0.05
25 7 0.37
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAATAAAAAAATTAATTTTGT
Found at i:1037098 original size:2 final size:2
Alignment explanation
Indices: 1037091--1037118 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1037081 AGGTTTCATA
1037091 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
1037119 GAATGTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1038806 original size:17 final size:17
Alignment explanation
Indices: 1038786--1038849 Score: 74
Period size: 17 Copynumber: 3.7 Consensus size: 17
1038776 CAATCACAGA
*
1038786 TTTTAAAATTTATATAT
1 TTTTAAAAATTATATAT
* *
1038803 TTTTAAAAATCATAAAAT
1 TTTTAAAAATTAT-ATAT
*
1038821 TTTTAAAAATTACATAT
1 TTTTAAAAATTATATAT
*
1038838 TTTTAAGAATTA
1 TTTTAAAAATTA
1038850 CAGATTTCTG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
17 25 0.64
18 14 0.36
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (17 bp):
TTTTAAAAATTATATAT
Found at i:1044202 original size:17 final size:17
Alignment explanation
Indices: 1044171--1044217 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
1044161 GATCAACATC
1044171 AATCACAGA-TTTTAAG
1 AATCACAGATTTTTAAG
*
1044187 AATCACATATTTTTAAG
1 AATCACAGATTTTTAAG
*
1044204 AATTACAGATTTTT
1 AATCACAGATTTTT
1044218 GTAATCACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 8 0.30
17 19 0.70
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (17 bp):
AATCACAGATTTTTAAG
Found at i:1044231 original size:16 final size:16
Alignment explanation
Indices: 1044171--1044232 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
1044161 GATCAACATC
* *
1044171 AATCACAGATTTTAAG
1 AATCACATATTTTTAG
1044187 AATCACATATTTTTAAG
1 AATCACATATTTTT-AG
* *
1044204 AATTACAGATTTTT-G
1 AATCACATATTTTTAG
1044219 TAATCACATATTTT
1 -AATCACATATTTT
1044233 CAACCCATTG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
15 1 0.03
16 23 0.61
17 14 0.37
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (16 bp):
AATCACATATTTTTAG
Found at i:1047709 original size:20 final size:19
Alignment explanation
Indices: 1047667--1047712 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1047657 ATTTTTTTTA
1047667 TATTTAT-ATTTAAATTAT
1 TATTTATAATTTAAATTAT
**
1047685 TATTTATAATTTTTATTATT
1 TATTTATAATTTAAATTA-T
1047705 TATTTATA
1 TATTTATA
1047713 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 7 0.29
19 8 0.33
20 9 0.38
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTTATAATTTAAATTAT
Found at i:1048067 original size:30 final size:30
Alignment explanation
Indices: 1048024--1048081 Score: 75
Period size: 29 Copynumber: 1.9 Consensus size: 30
1048014 TAATCAACTA
1048024 TTTAATAACATAAAATTAA-TAATCGAAATAC
1 TTTAATAACAT-AAATTAATTAAT-GAAATAC
*
1048055 TTTAA-AATATAAATTAATTAATGAAAT
1 TTTAATAACATAAATTAATTAATGAAAT
1048082 TTAAATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 12 0.48
30 8 0.32
31 5 0.20
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.36
Consensus pattern (30 bp):
TTTAATAACATAAATTAATTAATGAAATAC
Found at i:1048758 original size:318 final size:312
Alignment explanation
Indices: 1048185--1048788 Score: 897
Period size: 318 Copynumber: 1.9 Consensus size: 312
1048175 CATCAACTGC
*
1048185 ACCAACAAACACAATAAATAACTTGTAATATAAGAAAAAATCTCAAAAATTAAAAAAAAATTAAA
1 ACCAACAAACACAATAAATAACTTGTAATATAAGAAAAAATCCCAAAAATTAAAAAAAAA-TAAA
* * *
1048250 ACTTATTAGAAGCAAATAATTTGATAGGAGAAGAAACCTCAATTAAAAATAAAGTTATGATAACA
65 ACTTATTAGAAGCAAATAATTTGATAGGAAAAAAAACCTCAATGAAAAATAAAGTTATGATAACA
* *
1048315 TTTAAATATAATAATTATAAGATGAAGTAAAAAAAAATAAGCATTTTATACCTAAACTACCAATA
130 TTTAAATATAATAATTATAAGATGAAGTAAAAAAAAATAAACATTTTATACCTAAACCACCAATA
* *
1048380 ACCTTTCACTGATAAACCTAGTACATGAAAATAAATCATAAAATTAATAAAAGACCATATCCTAT
195 ACCTTTCACTGATAAACATAGTACATGAAAATAAACCATAAAATTAATAAAAGACCATATCCTAT
* *
1048445 GCACACAGAATATGTTCAGATACAAAGTAGAAGTTAATACCTTTCCTTCACATA
260 ACACACAAAATATGTTCA-ATACAAAGTAGAAGTTAATACCTTTCCTTCACATA
* * * *
1048499 ACCAACAAACATAATAAATAATTTGTAATATAAGAAAAAATCCCAATAATTAAAAACAAAA-AAG
1 ACCAACAAACACAATAAATAACTTGTAATATAAGAAAAAATCCCAAAAATTAAAAA-AAAATAAA
* * **
1048563 ACTTGTTAGAAGCAAATAATTTGCTAGGAAAAAAAACCTCAATGAAAAATGGAGTTATGATAACA
65 ACTTATTAGAAGCAAATAATTTGATAGGAAAAAAAACCTCAATGAAAAATAAAGTTATGATAACA
*
1048628 TTTAAATATAATAATTATTAGATGAAGTAATAAAAAAAAGAATAAACATTTTATACCTAAACCAC
130 TTTAAATATAATAATTATAAGATGAAG---T-AAAAAAA-AATAAACATTTTATACCTAAACCAC
* * *
1048693 CAATAACCTTTCATTGATAAA-ATTGTTACATGAAAATAAACCATGAAATTAATAAAAGACCATA
190 CAATAACCTTTCACTGATAAACATAG-TACATGAAAATAAACCATAAAATTAATAAAAGACCATA
* *
1048757 TCTTATATACACAAAATATGTTCAATACAAAG
254 TCCTATACACACAAAATATGTTCAATACAAAG
1048789 CAGTTATTAT
Statistics
Matches: 259, Mismatches: 24, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
313 86 0.33
314 52 0.20
315 4 0.02
316 1 0.00
317 17 0.07
318 99 0.38
ACGTcount: A:0.52, C:0.13, G:0.08, T:0.26
Consensus pattern (312 bp):
ACCAACAAACACAATAAATAACTTGTAATATAAGAAAAAATCCCAAAAATTAAAAAAAAATAAAA
CTTATTAGAAGCAAATAATTTGATAGGAAAAAAAACCTCAATGAAAAATAAAGTTATGATAACAT
TTAAATATAATAATTATAAGATGAAGTAAAAAAAAATAAACATTTTATACCTAAACCACCAATAA
CCTTTCACTGATAAACATAGTACATGAAAATAAACCATAAAATTAATAAAAGACCATATCCTATA
CACACAAAATATGTTCAATACAAAGTAGAAGTTAATACCTTTCCTTCACATA
Found at i:1049431 original size:6 final size:6
Alignment explanation
Indices: 1049409--1049448 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
1049399 TTTTTCTATT
*
1049409 TTTTTC TTTAT- TTTTTC TTTTTC TTTTTC TCTTTTC TTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC T-TTTTC TTTT
1049449 GATTACTAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 4 0.13
6 20 0.67
7 6 0.20
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:1049435 original size:13 final size:12
Alignment explanation
Indices: 1049395--1049448 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 12
1049385 TTCATTTCCC
1049395 TTTTTTTTTCTAT
1 TTTTTTTTTCT-T
*
1049408 TTTTTTCTTTATT
1 TTTTTT-TTTCTT
1049421 TTTTCTTTTTCTT
1 TTTT-TTTTTCTT
*
1049434 TTTCTCTTTTCTT
1 TTT-TTTTTTCTT
1049447 TT
1 TT
1049449 GATTACTAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
13 28 0.80
14 7 0.20
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTTTTTCTT
Found at i:1049448 original size:12 final size:11
Alignment explanation
Indices: 1049389--1049448 Score: 52
Period size: 11 Copynumber: 5.3 Consensus size: 11
1049379 TTTTTTTTCA
*
1049389 TTTCCCTTTTT
1 TTTCTCTTTTT
1049400 TTT-TCTATTTT
1 TTTCTCT-TTTT
1049411 TTTCT-TTATTT
1 TTTCTCTT-TTT
*
1049422 TTTCTTTTTCTT
1 TTTCTCTTT-TT
1049434 TTTCTCTTTTCT
1 TTTCTCTTTT-T
1049446 TTT
1 TTT
1049449 GATTACTAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
10 3 0.07
11 21 0.51
12 17 0.41
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTCTCTTTTT
Found at i:1049448 original size:25 final size:26
Alignment explanation
Indices: 1049394--1049448 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
1049384 TTTCATTTCC
*
1049394 CTTTTTTTTTCTATTTTTTTCTTTAT
1 CTTTTTTTTTCTATTTTTCTCTTTAT
*
1049420 -TTTTTCTTTT-TCTTTTTCTCTTT-T
1 CTTTTT-TTTTCTATTTTTCTCTTTAT
1049444 CTTTT
1 CTTTT
1049449 GATTACTAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
24 1 0.04
25 20 0.80
26 4 0.16
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.82
Consensus pattern (26 bp):
CTTTTTTTTTCTATTTTTCTCTTTAT
Found at i:1050337 original size:21 final size:21
Alignment explanation
Indices: 1050313--1050352 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1050303 TATCCAATTC
*
1050313 AAATCGAAGAAAAAACTCTCT
1 AAATCAAAGAAAAAACTCTCT
1050334 AAATCAAAGAAAAAACTCT
1 AAATCAAAGAAAAAACTCT
1050353 AAATGTAGTA
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:0.57, C:0.17, G:0.07, T:0.17
Consensus pattern (21 bp):
AAATCAAAGAAAAAACTCTCT
Found at i:1054979 original size:5 final size:5
Alignment explanation
Indices: 1054952--1054993 Score: 54
Period size: 5 Copynumber: 9.0 Consensus size: 5
1054942 TTAATTATTT
*
1054952 TAAAA -AAAA TTAAA T-AAA T-AAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
1054994 ATTTGCATCT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
4 12 0.35
5 22 0.65
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:1057904 original size:23 final size:22
Alignment explanation
Indices: 1057862--1057905 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
1057852 TTTTTAAATA
1057862 TAAATAAAAAAATTAAATTTTGT
1 TAAATAAAAAAATT-AATTTTGT
1057885 TAAATATATAAAAATT-ATTTT
1 TAAATA-A-AAAAATTAATTTT
1057906 AAAATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
24 1 0.05
25 7 0.37
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAATAAAAAAATTAATTTTGT
Found at i:1060555 original size:17 final size:17
Alignment explanation
Indices: 1060533--1060596 Score: 74
Period size: 17 Copynumber: 3.7 Consensus size: 17
1060523 CAATCACAGC
*
1060533 TTTTAAAATTTATATAT
1 TTTTAAAAATTATATAT
* *
1060550 TTTTAAAAATCATAAAAT
1 TTTTAAAAATTAT-ATAT
*
1060568 TTTTAAAAATTACATAT
1 TTTTAAAAATTATATAT
*
1060585 TTTTAAGAATTA
1 TTTTAAAAATTA
1060597 CAGATTTCTG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
17 25 0.64
18 14 0.36
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (17 bp):
TTTTAAAAATTATATAT
Done.