Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold64
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: 7997333
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 95991 characters in sequence are not A, C, G, or T
File 5 of 45
Found at i:936316 original size:2 final size:2
Alignment explanation
Indices: 936309--936341 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
936299 AGTACAGTCT
936309 TA TA TA 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 TA TA TA T
936342 CTTTGCCCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:942260 original size:18 final size:18
Alignment explanation
Indices: 942233--942277 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
942223 ACATATACCG
*
942233 TTAAATTAT-ATTTAAGAA
1 TTAAAATATAATTTAA-AA
942251 TTAAAATATAATTTAAAA
1 TTAAAATATAATTTAAAA
*
942269 ATAAAATAT
1 TTAAAATAT
942278 TTGATTGTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
TTAAAATATAATTTAAAA
Found at i:942741 original size:11 final size:11
Alignment explanation
Indices: 942721--942753 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
942711 TTGTTTATGG
942721 TAAAGTTTAAA
1 TAAAGTTTAAA
*
942732 TAATGTTTAAA
1 TAAAGTTTAAA
942743 TAAAGTTTAAA
1 TAAAGTTTAAA
942754 GTTTAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (11 bp):
TAAAGTTTAAA
Found at i:945992 original size:196 final size:196
Alignment explanation
Indices: 945631--946023 Score: 616
Period size: 196 Copynumber: 2.0 Consensus size: 196
945621 TTCAAGCAAC
*
945631 TTGTTTAGGGTCATGTCTTCCATGGAGTTCGTACTAATTTTTCCTGCTTTGAGATGGCTAGTTCA
1 TTGTTTAGGGTCATGTCTTCCATGGAGTTAGTACTAATTTTTCCTGCTTTGAGATGGCTAGTTCA
* *
945696 AGGGCCAAAAAGAAACGATGCCTTTGCCCACTTCTGTCCCAGCTCTCAAGAGCAATCCTGCAGGT
66 AGGGCCAAAAAGAAAAGATGCCTTTGCCCACTTCTGTCCCAACTCTCAAGAGCAATCCTGCAGGT
945761 TAACAGAGTAAATTATTTAGTACTTACGGTTGATTCTCGTTTTAACTCATTTTCATGG-TTTCAA
131 TAACAGAGTAAATTATTTAGTACTTACGGTTGATTCTCGTTTTAACTCATTTTCATGGCTTT-AA
945825 AT
195 AT
* ** *
945827 TTGTTTAGGGTCATGTCTTCCATGGAGTTAGTATTGGTTTTTCCTGTTTTGAGAT-GCTAGTTC-
1 TTGTTTAGGGTCATGTCTTCCATGGAGTTAGTACTAATTTTTCCTGCTTTGAGATGGCTAGTTCA
*
945890 AGTGGCCAAAAAGGAAAAGATGCCATTTGCCCACTTCTGTCCCAACT-TCCAAGAGCAATGCTGC
66 AG-GGCCAAAAA-GAAAAGATGCC-TTTGCCCACTTCTGTCCCAACTCT-CAAGAGCAATCCTGC
* *
945954 AGGTTAACAGAGTGAATTATTTAGTACTT-TGGTTGATTCTCGTTTTAACTCATTTTCATGGCTT
127 AGGTTAACAGAGTAAATTATTTAGTACTTACGGTTGATTCTCGTTTTAACTCATTTTCATGGCTT
946018 TAAAT
192 TAAAT
946023 T
1 T
946024 GACGCAACAT
Statistics
Matches: 182, Mismatches: 10, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
194 2 0.01
195 17 0.09
196 97 0.53
197 66 0.36
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (196 bp):
TTGTTTAGGGTCATGTCTTCCATGGAGTTAGTACTAATTTTTCCTGCTTTGAGATGGCTAGTTCA
AGGGCCAAAAAGAAAAGATGCCTTTGCCCACTTCTGTCCCAACTCTCAAGAGCAATCCTGCAGGT
TAACAGAGTAAATTATTTAGTACTTACGGTTGATTCTCGTTTTAACTCATTTTCATGGCTTTAAA
T
Found at i:946387 original size:2 final size:2
Alignment explanation
Indices: 946380--946404 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
946370 AACTTCGATA
946380 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 A
946405 CACACACTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:948912 original size:2 final size:2
Alignment explanation
Indices: 948907--948944 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
948897 GCGCGCGTGC
*
948907 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GC GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
948945 TTTGTGCATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.03, G:0.50, T:0.47
Consensus pattern (2 bp):
GT
Found at i:964686 original size:2 final size:2
Alignment explanation
Indices: 964679--964719 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
964669 CCTTCGTCTT
* *
964679 TA TA TA TA CA TA TA TA CA 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 TA TA TA TA TA TA TA T
964720 TGTAGAAGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:965024 original size:28 final size:29
Alignment explanation
Indices: 964970--965029 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
964960 CATGTCTTTA
964970 TTTAAATGTTATGTCTTTACATAACAA-T
1 TTTAAATGTTATGTCTTTACATAACAACT
*
964998 TTTAAATGTTGTGTTCTTT-CA-ACACAACT
1 TTTAAATGTTATG-TCTTTACATA-ACAACT
965027 TTT
1 TTT
965030 TGATGCAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 1 0.04
28 18 0.64
29 9 0.32
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.48
Consensus pattern (29 bp):
TTTAAATGTTATGTCTTTACATAACAACT
Found at i:965096 original size:17 final size:17
Alignment explanation
Indices: 965077--965110 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
965067 AAATATTAAT
965077 AAATAAATAATATAATTA
1 AAATAAA-AATATAATTA
965095 AAATAAAAATATAATT
1 AAATAAAAATATAATT
965111 GCATTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATAAAAATATAATTA
Found at i:965684 original size:2 final size:2
Alignment explanation
Indices: 965667--965702 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
965657 TTATTTAAAA
* *
965667 AT AT AA AT AC 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
965703 CAATGAATCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:965815 original size:3 final size:3
Alignment explanation
Indices: 965807--965846 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
965797 AATTACGAGT
*
965807 TTA TTA TTA TT- TT- TTA TTT TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
965847 AAAACATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:965868 original size:24 final size:24
Alignment explanation
Indices: 965828--965873 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
965818 TTTTATTTTT
*
965828 ATTATTATTATTATTATTAAAAAC
1 ATTATTATTATTATTATGAAAAAC
*
965852 ATTATT-TTTTTACTTATGAAAA
1 ATTATTATTATTA-TTATGAAAA
965874 TGGCAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.52
Consensus pattern (24 bp):
ATTATTATTATTATTATGAAAAAC
Found at i:970088 original size:2 final size:2
Alignment explanation
Indices: 970081--970112 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
970071 AGACTAATTA
970081 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
970113 TATTAATCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:972552 original size:14 final size:14
Alignment explanation
Indices: 972533--972565 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
972523 TTTCCATACA
972533 CACACACACACACG
1 CACACACACACACG
*
972547 CACACACACACATG
1 CACACACACACACG
972561 CACAC
1 CACAC
972566 TTACAACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.42, C:0.48, G:0.06, T:0.03
Consensus pattern (14 bp):
CACACACACACACG
Found at i:974329 original size:64 final size:64
Alignment explanation
Indices: 974225--974355 Score: 208
Period size: 64 Copynumber: 2.0 Consensus size: 64
974215 AAGAATGTTG
* * * * *
974225 AAAGTAAGACAAGGTGGAAAATATAGGATTTTATTTGACTTGGGTAATATTTTTCTTCCTACCA
1 AAAGTAAGACAAGGTGGAAAATATAGGATTTCATTAGACTTGGGTAATATATATCTTCCTACAA
*
974289 AAAGTAAGATAAGGTGGAAAATATAGGATTTCATTAGACTTGGGTAATATATATCTTCCTACAA
1 AAAGTAAGACAAGGTGGAAAATATAGGATTTCATTAGACTTGGGTAATATATATCTTCCTACAA
974353 AAA
1 AAA
974356 AAGGGGGGGG
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (64 bp):
AAAGTAAGACAAGGTGGAAAATATAGGATTTCATTAGACTTGGGTAATATATATCTTCCTACAA
Found at i:975245 original size:26 final size:26
Alignment explanation
Indices: 975195--975246 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
975185 TATACGACAA
*
975195 TGGTTCGGTTAAAATGCAACGAAAAC
1 TGGTTCGGTTAAAATGAAACGAAAAC
*
975221 TGGTTCGGTTAAAATGGAAACAAAAA
1 TGGTTCGGTTAAAAT-GAAACGAAAA
975247 TATGTTGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (26 bp):
TGGTTCGGTTAAAATGAAACGAAAAC
Found at i:975366 original size:19 final size:19
Alignment explanation
Indices: 975342--975379 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
975332 TTGGCCGATG
975342 TTTTTTGTTTTTAGTTTTT
1 TTTTTTGTTTTTAGTTTTT
* *
975361 TTTTTTTTTTTTGGTTTTT
1 TTTTTTGTTTTTAGTTTTT
975380 CTATAGAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.03, C:0.00, G:0.11, T:0.87
Consensus pattern (19 bp):
TTTTTTGTTTTTAGTTTTT
Found at i:975912 original size:16 final size:17
Alignment explanation
Indices: 975881--975914 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
975871 TCTCCTCTCT
975881 CTTTATATAGTATTTTAA
1 CTTTATATAG-ATTTTAA
975899 CTTTATATAG-TTTTAA
1 CTTTATATAGATTTTAA
975915 ACATGGGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (17 bp):
CTTTATATAGATTTTAA
Found at i:979043 original size:180 final size:180
Alignment explanation
Indices: 978741--979079 Score: 678
Period size: 180 Copynumber: 1.9 Consensus size: 180
978731 TGTTGCAAGG
978741 GAGGAGGTATTGGCAAAAGCCATAATAAAAAGGTCTGGTTTAAGGAGGAGCTCATTGTGTTTTAG
1 GAGGAGGTATTGGCAAAAGCCATAATAAAAAGGTCTGGTTTAAGGAGGAGCTCATTGTGTTTTAG
978806 CATGTATCACTCTCAAAATTTCACATGTCTGGCAAGCCTGGCATGTTATATGCCCAAAATAGATT
66 CATGTATCACTCTCAAAATTTCACATGTCTGGCAAGCCTGGCATGTTATATGCCCAAAATAGATT
978871 TCTTTTCATTGATTAACATGTCCTATTTGGCAACCTGGCATGTCCTATTT
131 TCTTTTCATTGATTAACATGTCCTATTTGGCAACCTGGCATGTCCTATTT
978921 GAGGAGGTATTGGCAAAAGCCATAATAAAAAGGTCTGGTTTAAGGAGGAGCTCATTGTGTTTTAG
1 GAGGAGGTATTGGCAAAAGCCATAATAAAAAGGTCTGGTTTAAGGAGGAGCTCATTGTGTTTTAG
978986 CATGTATCACTCTCAAAATTTCACATGTCTGGCAAGCCTGGCATGTTATATGCCCAAAATAGATT
66 CATGTATCACTCTCAAAATTTCACATGTCTGGCAAGCCTGGCATGTTATATGCCCAAAATAGATT
979051 TCTTTTCATTGATTAACATGTCCTATTTG
131 TCTTTTCATTGATTAACATGTCCTATTTG
979080 AGTTGCATAT
Statistics
Matches: 159, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
180 159 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (180 bp):
GAGGAGGTATTGGCAAAAGCCATAATAAAAAGGTCTGGTTTAAGGAGGAGCTCATTGTGTTTTAG
CATGTATCACTCTCAAAATTTCACATGTCTGGCAAGCCTGGCATGTTATATGCCCAAAATAGATT
TCTTTTCATTGATTAACATGTCCTATTTGGCAACCTGGCATGTCCTATTT
Found at i:981846 original size:59 final size:59
Alignment explanation
Indices: 981751--981864 Score: 194
Period size: 59 Copynumber: 1.9 Consensus size: 59
981741 GGCAAGTTGG
*
981751 GTAGCACTACTTTCTGACTGAAAAAGGTGACTGTTGATAAAAGAAAAGCTCTCTTCCTT
1 GTAGCACTACTTTCTGACTGAAAAAGGTGACAGTTGATAAAAGAAAAGCTCTCTTCCTT
*
981810 GTAGCACTACTTTCTGACTGGCAAAA-GTGACAGTTGATAAAAGAAAAGCTCTCTT
1 GTAGCACTACTTTCTGACT-GAAAAAGGTGACAGTTGATAAAAGAAAAGCTCTCTT
981865 TCTTTTTTAG
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
59 47 0.90
60 5 0.10
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29
Consensus pattern (59 bp):
GTAGCACTACTTTCTGACTGAAAAAGGTGACAGTTGATAAAAGAAAAGCTCTCTTCCTT
Found at i:983236 original size:2 final size:2
Alignment explanation
Indices: 983229--983262 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
983219 TCCATCTTAC
*
983229 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
983263 CCATCTTACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:985636 original size:2 final size:2
Alignment explanation
Indices: 985629--985656 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
985619 TTTCATGACA
985629 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
985657 TATTGTTAAA
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:988384 original size:19 final size:19
Alignment explanation
Indices: 988341--988384 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
988331 TCCTTATGAA
*
988341 AAATATAAATATCAGATAT
1 AAATATATATATCAGATAT
*
988360 AAATATATAT-T-TGATAT
1 AAATATATATATCAGATAT
988377 AAATATAT
1 AAATATAT
988385 TTAAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 13 0.57
18 1 0.04
19 9 0.39
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (19 bp):
AAATATATATATCAGATAT
Found at i:991237 original size:3 final size:3
Alignment explanation
Indices: 991229--991263 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
991219 TTGTTTAATA
991229 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
991264 ATCATCACTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:992268 original size:2 final size:2
Alignment explanation
Indices: 992263--992289 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
992253 AAATGAACTC
992263 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
992290 AATCCAATGC
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:1002814 original size:16 final size:16
Alignment explanation
Indices: 1002774--1002829 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
1002764 TAAATTCATA
1002774 AAATATAAATTATTAAT
1 AAATATAAATTATT-AT
* *
1002791 GTAATATAATTTATTAT
1 -AAATATAAATTATTAT
* *
1002808 AAATATAAAATATTTT
1 AAATATAAATTATTAT
1002824 AAATAT
1 AAATAT
1002830 GATTATAACA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
16 18 0.56
17 2 0.06
18 12 0.38
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (16 bp):
AAATATAAATTATTAT
Found at i:1002848 original size:30 final size:27
Alignment explanation
Indices: 1002803--1002873 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 27
1002793 AATATAATTT
* *
1002803 ATTATAAATATAAAATATTTTAAATATG
1 ATTATAAATATAAAATATATT-AATATA
1002831 ATTATAACATAATAAAATATATTAATATA
1 ATTATAA-AT-ATAAAATATATTAATATA
*
1002860 ATTATGATATATAA
1 ATTAT-AAATATAA
1002874 CTTAGCAGAC
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 11 0.30
29 14 0.38
30 12 0.32
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (27 bp):
ATTATAAATATAAAATATATTAATATA
Found at i:1004388 original size:49 final size:49
Alignment explanation
Indices: 1004316--1004410 Score: 172
Period size: 49 Copynumber: 1.9 Consensus size: 49
1004306 ATAGAGATAA
*
1004316 TAATCCAAATTCTATAAACAAGCTCATTGACAAACTTATAAGCAAATTT
1 TAATCCAAATTCTAAAAACAAGCTCATTGACAAACTTATAAGCAAATTT
*
1004365 TAATCCGAATTCTAAAAACAAGCTCATTGACAAACTTATAAGCAAA
1 TAATCCAAATTCTAAAAACAAGCTCATTGACAAACTTATAAGCAAA
1004411 ACCAGCTGTG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.46, C:0.19, G:0.07, T:0.27
Consensus pattern (49 bp):
TAATCCAAATTCTAAAAACAAGCTCATTGACAAACTTATAAGCAAATTT
Found at i:1007580 original size:3 final size:3
Alignment explanation
Indices: 1007572--1007608 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
1007562 AAATTAAATG
*
1007572 AAT AAT AAT AAT AAT AA- AAG AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1007609 ACGGGTAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:1007594 original size:20 final size:20
Alignment explanation
Indices: 1007566--1007609 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1007556 TATGCCAAAT
*
1007566 TAAATGAATAATAATAATAA
1 TAAAAGAATAATAATAATAA
1007586 TAAAAGAATAATAATAATAA
1 TAAAAGAATAATAATAATAA
1007606 TAAA
1 TAAA
1007610 CGGGTAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (20 bp):
TAAAAGAATAATAATAATAA
Found at i:1009184 original size:2 final size:2
Alignment explanation
Indices: 1009179--1009203 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1009169 TTTATAATTC
1009179 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 A
1009204 AGCTTTTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1011788 original size:25 final size:26
Alignment explanation
Indices: 1011740--1011790 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
1011730 TTTATATATT
*
1011740 TTTTAATTTAATTAAAATTATTATAA
1 TTTTAATATAATTAAAATTATTATAA
1011766 TTTTAATATAA-TAAAA-TATTTATAA
1 TTTTAATATAATTAAAATTA-TTATAA
1011791 ACTTTAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 2 0.09
25 11 0.48
26 10 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
TTTTAATATAATTAAAATTATTATAA
Found at i:1011796 original size:26 final size:26
Alignment explanation
Indices: 1011741--1011798 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
1011731 TTATATATTT
* *
1011741 TTTAATTTAATTAAAATTATTATAAT
1 TTTAATATAATTAAAATTATTATAAC
1011767 TTTAATATAA-TAAAA-TATTTATAAAC
1 TTTAATATAATTAAAATTA-TTAT-AAC
1011793 TTTAAT
1 TTTAAT
1011799 TATTTATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 2 0.07
25 9 0.32
26 17 0.61
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
TTTAATATAATTAAAATTATTATAAC
Found at i:1016931 original size:24 final size:25
Alignment explanation
Indices: 1016904--1016952 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1016894 AAATATATTT
* *
1016904 ATTTTTTATAT-AATTTTTAGAAAA
1 ATTTTTAATATAAATTTTGAGAAAA
*
1016928 ATTTTTAATTTAAATTTTGAGAAAA
1 ATTTTTAATATAAATTTTGAGAAAA
1016953 GCTAATTTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (25 bp):
ATTTTTAATATAAATTTTGAGAAAA
Found at i:1018128 original size:2 final size:2
Alignment explanation
Indices: 1018121--1018146 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1018111 TTATTGCGCA
1018121 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
1018147 TTCACTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1025773 original size:65 final size:65
Alignment explanation
Indices: 1025690--1025811 Score: 199
Period size: 65 Copynumber: 1.9 Consensus size: 65
1025680 AAATGCAATA
* * *
1025690 GGTTATGGAGCAAATTGAATTCCAATACCAAAAGAAATCAGATTGTAAATCATGGTTCACAATTG
1 GGTTATGAAGCAAATTGAAATCCAATACCAAAAGAAATCAGATTGTAAATCAAGGTTCACAATTG
* *
1025755 GGTTATGAAGCAAGTTGAAATCCAATACCAAGAGAAATCAGATTGTAAATCAAGGTT
1 GGTTATGAAGCAAATTGAAATCCAATACCAAAAGAAATCAGATTGTAAATCAAGGTT
1025812 TAATTGTTCA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
65 52 1.00
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (65 bp):
GGTTATGAAGCAAATTGAAATCCAATACCAAAAGAAATCAGATTGTAAATCAAGGTTCACAATTG
Found at i:1029805 original size:4 final size:4
Alignment explanation
Indices: 1029796--1029824 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1029786 CCTAACTTAG
1029796 AATA AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA AATA A
1029825 GAAAAGGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:1031014 original size:2 final size:2
Alignment explanation
Indices: 1031007--1031040 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1030997 TAATAAAATG
*
1031007 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1031041 AAACAATGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1031883 original size:13 final size:13
Alignment explanation
Indices: 1031845--1031887 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
1031835 ATTTTTTAAA
1031845 TATATAAAA-ATT
1 TATATAAAATATT
*
1031857 TAAATTAAATATATT
1 TATA-TAAA-ATATT
1031872 TATATAAAATATT
1 TATATAAAATATT
1031885 TAT
1 TAT
1031888 TCATTTACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 3 0.12
13 12 0.46
14 5 0.19
15 6 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TATATAAAATATT
Found at i:1037419 original size:22 final size:20
Alignment explanation
Indices: 1037383--1037458 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
1037373 AAATTATATT
*
1037383 ATTATATTAAT-ATATAAAAA
1 ATTATATAAATAATAT-AAAA
* *
1037403 ATTATATAATATAATATTATA
1 ATTATATAA-ATAATATAAAA
* *
1037424 A-TATAAAAATAATATAAAT
1 ATTATATAAATAATATAAAA
1037443 ATTATATAAA-AATATA
1 ATTATATAAATAATATA
1037459 TATTCGTAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
19 15 0.33
20 21 0.47
21 5 0.11
22 4 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTATATAAATAATATAAAA
Found at i:1037437 original size:11 final size:11
Alignment explanation
Indices: 1037421--1037460 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
1037411 ATATAATATT
1037421 ATAATATAAAA
1 ATAATATAAAA
*
1037432 ATAATATAAAT
1 ATAATATAAAA
*
1037443 ATTATATAAAA
1 ATAATATAAAA
1037454 AT-ATATA
1 ATAATATA
1037461 TTCGTAAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 5 0.19
11 21 0.81
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:1037457 original size:30 final size:30
Alignment explanation
Indices: 1037373--1037458 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 30
1037363 CCATTTTTGG
* *
1037373 AAAT-TATATTATTATATTAATATATAAAA
1 AAATATATAATATTATATTAAAATATAAAA
* * *
1037402 AATTATATAATATAATATTATAATATAAAA
1 AAATATATAATATTATATTAAAATATAAAA
*
1037432 ATAATATA-AATATTATATAAAAATATA
1 A-AATATATAATATTATATTAAAATATA
1037459 TATTCGTAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 3 0.07
30 38 0.83
31 5 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
AAATATATAATATTATATTAAAATATAAAA
Found at i:1038725 original size:40 final size:42
Alignment explanation
Indices: 1038653--1038756 Score: 101
Period size: 41 Copynumber: 2.6 Consensus size: 42
1038643 TATATATTTT
* * * * *
1038653 ATAAT-TAAATGAAATAAAAATATTTCTTAATT-ATTAAAT-
1 ATAATCTAAATCAAATAAAATTAATTCTAAATTAATAAAATA
1038692 ATATATCTAAATCAAATAAAATTAATT-TAAATTAATAAAATA
1 ATA-ATCTAAATCAAATAAAATTAATTCTAAATTAATAAAATA
* *
1038734 ATAATTTAATTCAAAT-AAATTAA
1 ATAATCTAAATCAAATAAAATTAA
1038757 ACTTATTATT
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
39 3 0.06
40 14 0.26
41 34 0.63
42 3 0.06
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (42 bp):
ATAATCTAAATCAAATAAAATTAATTCTAAATTAATAAAATA
Found at i:1039893 original size:22 final size:22
Alignment explanation
Indices: 1039852--1039904 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
1039842 TTTATCAAAT
*
1039852 TAAATTATATTAAAAATTTTAAA
1 TAAATTA-AATAAAAATTTTAAA
* *
1039875 TAAATTAAATAAAATTTTTAAT
1 TAAATTAAATAAAAATTTTAAA
1039897 TAAATTAA
1 TAAATTAA
1039905 TTTATTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 20 0.74
23 7 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAATTAAATAAAAATTTTAAA
Found at i:1039912 original size:17 final size:18
Alignment explanation
Indices: 1039875--1039922 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
1039865 AAATTTTAAA
1039875 TAAATTAAATAAAATTTT
1 TAAATTAAATAAAATTTT
*
1039893 T-AATTAAAT-TAATTTAT
1 TAAATTAAATAAAATTT-T
1039910 TAAATTAATATAA
1 TAAATTAA-ATAA
1039923 TAATATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
16 5 0.21
17 10 0.42
18 7 0.29
19 2 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAAATTAAATAAAATTTT
Found at i:1040064 original size:33 final size:32
Alignment explanation
Indices: 1040004--1040090 Score: 88
Period size: 33 Copynumber: 2.7 Consensus size: 32
1039994 CATATATTAT
* * *
1040004 AATTATATTTTAAATTATTATATATTTTAATAA
1 AATTATAATTTATATTATTATAAATTTTAAT-A
1040037 AATTAATAATTTATATTA-TATAAATTTTAATA
1 AATT-ATAATTTATATTATTATAAATTTTAATA
*
1040069 TATTTATATATTTATATT-TTAT
1 -AATTATA-ATTTATATTATTAT
1040091 TTTTATTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
32 4 0.09
33 31 0.67
34 11 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (32 bp):
AATTATAATTTATATTATTATAAATTTTAATA
Found at i:1040081 original size:18 final size:18
Alignment explanation
Indices: 1039984--1040081 Score: 62
Period size: 17 Copynumber: 5.5 Consensus size: 18
1039974 AAAATTTATA
* *
1039984 TATATTTTTTCATATATT
1 TATATATTTTAATATATT
1040002 ATAATTATATTTTAA-AT-TAT
1 -T-A-TATATTTTAATATAT-T
* *
1040022 TATATATTTTAATAAAAT
1 TATATATTTTAATATATT
* *
1040040 TA-ATAATTT-ATAT-TA
1 TATATATTTTAATATATT
*
1040055 TATAAATTTTAATATATT
1 TATATATTTTAATATATT
1040073 TATATATTT
1 TATATATTT
1040082 ATATTTTATT
Statistics
Matches: 59, Mismatches: 12, Indels: 17
0.67 0.14 0.19
Matches are distributed among these distances:
15 2 0.03
16 8 0.14
17 20 0.34
18 14 0.24
19 3 0.05
20 4 0.07
21 8 0.14
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATATTTTAATATATT
Found at i:1040087 original size:24 final size:23
Alignment explanation
Indices: 1039980--1040101 Score: 67
Period size: 24 Copynumber: 5.3 Consensus size: 23
1039970 AATAAAAATT
* * * *
1039980 TATATATATTTTTTCATATATTA
1 TATATTTATATTTTAATATTTTA
1040003 TA-A-TTATATTTTAA-ATTATTA
1 TATATTTATATTTTAATATT-TTA
** *
1040024 TATATTTTAATAAAATTAATAATTTA
1 TATA-TTT-AT-ATTTTAATATTTTA
* *
1040050 TATTATATAAATTTTAATATATTTA
1 TA-TATTTATATTTTAATAT-TTTA
1040075 TATATTTATATTTT-AT-TTTTA
1 TATATTTATATTTTAATATTTTA
1040096 T-TATTT
1 TATATTT
1040102 TTATAATTAT
Statistics
Matches: 76, Mismatches: 14, Indels: 21
0.68 0.13 0.19
Matches are distributed among these distances:
20 7 0.09
21 18 0.24
22 3 0.04
23 4 0.05
24 19 0.25
25 9 0.12
26 12 0.16
27 4 0.05
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (23 bp):
TATATTTATATTTTAATATTTTA
Found at i:1040530 original size:2 final size:2
Alignment explanation
Indices: 1040518--1040551 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
1040508 ATTGGTGTTA
*
1040518 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1040552 CACACGTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1042113 original size:14 final size:16
Alignment explanation
Indices: 1042086--1042117 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
1042076 TTTAATTTAA
1042086 TTTAATTAATAATTTT
1 TTTAATTAATAATTTT
1042102 TTTAA-TAA-AATTTT
1 TTTAATTAATAATTTT
1042116 TT
1 TT
1042118 ATTTAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTAATTAATAATTTT
Found at i:1042406 original size:32 final size:32
Alignment explanation
Indices: 1042365--1042476 Score: 100
Period size: 32 Copynumber: 3.5 Consensus size: 32
1042355 TGACATGAAC
1042365 CCGAAATGACCTGAATCCATAATAACTCAAAT
1 CCGAAATGACCTGAATCCATAATAACTCAAAT
** * * * *
1042397 CCGAAATGACCAAAATCCAAAATATCCCCAA-
1 CCGAAATGACCTGAATCCATAATAACTCAAAT
* * * * * *
1042428 CCTAAAATGACCCGAACCCGTAATGACTCGAAT
1 CC-GAAATGACCTGAATCCATAATAACTCAAAT
1042461 CCGAAATGACCTGAAT
1 CCGAAATGACCTGAAT
1042477 AATTAACCCG
Statistics
Matches: 59, Mismatches: 19, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
31 2 0.03
32 55 0.93
33 2 0.03
ACGTcount: A:0.42, C:0.29, G:0.12, T:0.18
Consensus pattern (32 bp):
CCGAAATGACCTGAATCCATAATAACTCAAAT
Found at i:1042476 original size:16 final size:16
Alignment explanation
Indices: 1042352--1042476 Score: 53
Period size: 16 Copynumber: 7.8 Consensus size: 16
1042342 CCGAACTCGA
* *
1042352 AAATGACATGAACCCG
1 AAATGACCTGAATCCG
1042368 AAATGACCTGAATCC-
1 AAATGACCTGAATCCG
* *
1042383 ATAAT-AACTCAAATCCG
1 A-AATGACCT-GAATCCG
** *
1042400 AAATGACCAAAATCCA
1 AAATGACCTGAATCCG
** *
1042416 AAAT-ATCCCCAA-CCTA
1 AAATGA-CCTGAATCC-G
* *
1042432 AAATGACCCGAACCCG
1 AAATGACCTGAATCCG
*
1042448 TAATGA-CTCGAATCCG
1 AAATGACCT-GAATCCG
1042464 AAATGACCTGAAT
1 AAATGACCTGAAT
1042477 AATTAACCCG
Statistics
Matches: 84, Mismatches: 15, Indels: 20
0.71 0.13 0.17
Matches are distributed among these distances:
15 8 0.10
16 68 0.81
17 8 0.10
ACGTcount: A:0.43, C:0.27, G:0.12, T:0.18
Consensus pattern (16 bp):
AAATGACCTGAATCCG
Found at i:1043417 original size:16 final size:16
Alignment explanation
Indices: 1043395--1043433 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1043385 TAATAGATGA
1043395 AAAAAATAAAGTAAAT
1 AAAAAATAAAGTAAAT
* * *
1043411 TAAAAATAGAGTGAAT
1 AAAAAATAAAGTAAAT
1043427 AAAAAAT
1 AAAAAAT
1043434 TAAATTCCAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (16 bp):
AAAAAATAAAGTAAAT
Found at i:1046790 original size:57 final size:57
Alignment explanation
Indices: 1046721--1046833 Score: 226
Period size: 57 Copynumber: 2.0 Consensus size: 57
1046711 ATATAATAAT
1046721 AAATATATTAATTTAACTATAATAAATATGAATAGTCAAAAACTTGATTTACTTTAC
1 AAATATATTAATTTAACTATAATAAATATGAATAGTCAAAAACTTGATTTACTTTAC
1046778 AAATATATTAATTTAACTATAATAAATATGAATAGTCAAAAACTTGATTTACTTTA
1 AAATATATTAATTTAACTATAATAAATATGAATAGTCAAAAACTTGATTTACTTTA
1046834 ATGATAATAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.39
Consensus pattern (57 bp):
AAATATATTAATTTAACTATAATAAATATGAATAGTCAAAAACTTGATTTACTTTAC
Found at i:1047045 original size:40 final size:40
Alignment explanation
Indices: 1046959--1047063 Score: 115
Period size: 40 Copynumber: 2.6 Consensus size: 40
1046949 TTGAGCGGCC
* * * *
1046959 ACCAAATCTGTTTTTCTTCCTGTTTCTGGTTCGAGTGACA
1 ACCAAATCTGTTTTTCTTCCCGTTTCTGCTTCAAGAGACA
* *
1046999 ACCAAATCTATTTTTCTTCCCGTTTCTGCTTCAAGCAG-CG
1 ACCAAATCTGTTTTTCTTCCCGTTTCTGCTTCAAG-AGACA
*
1047039 ATCAAATCTGTTTTT-TTCCCAGTTT
1 ACCAAATCTGTTTTTCTTCCC-GTTT
1047064 TGTTCTAAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
39 5 0.09
40 49 0.89
41 1 0.02
ACGTcount: A:0.19, C:0.25, G:0.13, T:0.43
Consensus pattern (40 bp):
ACCAAATCTGTTTTTCTTCCCGTTTCTGCTTCAAGAGACA
Found at i:1047345 original size:15 final size:14
Alignment explanation
Indices: 1047305--1047354 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 14
1047295 TAAGTAGTTA
1047305 TATTTTAAAAATAAT
1 TATTTTAAAAA-AAT
1047320 ATATTTTTAAAAAAAT
1 -TA-TTTTAAAAAAAT
*
1047336 TATTTGTAAATAAAT
1 TATTT-TAAAAAAAT
1047351 TATT
1 TATT
1047355 AAAAAATGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
14 3 0.10
15 14 0.45
16 5 0.16
17 9 0.29
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
TATTTTAAAAAAAT
Found at i:1048225 original size:31 final size:31
Alignment explanation
Indices: 1048187--1048259 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
1048177 CGAAATAATT
*
1048187 TAAATTTAAAATGATTCAAACTTAAAATATC
1 TAAATTTAAAATAATTCAAACTTAAAATATC
* * *
1048218 TAAATTTAAAATAATTTAAATTTAAAATATT
1 TAAATTTAAAATAATTCAAACTTAAAATATC
1048249 TAAATTTAAAA
1 TAAATTTAAAA
1048260 ATTTAAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (31 bp):
TAAATTTAAAATAATTCAAACTTAAAATATC
Found at i:1048228 original size:15 final size:16
Alignment explanation
Indices: 1048156--1048300 Score: 116
Period size: 16 Copynumber: 8.8 Consensus size: 16
1048146 GGATCAACTC
*
1048156 AAATTCAAAATAATTT
1 AAATTTAAAATAATTT
* * **
1048172 GAACTCGAAATAATTT
1 AAATTTAAAATAATTT
* *
1048188 AAATTTAAAATGATTC
1 AAATTTAAAATAATTT
* *
1048204 AAACTTAAAAT-ATCT
1 AAATTTAAAATAATTT
1048219 AAATTTAAAATAATTT
1 AAATTTAAAATAATTT
1048235 AAATTTAAAATATTTAAATTT
1 AAATTT-AAA-A--T-AATTT
1048256 AAAAATTTAAAATAATTT
1 --AAATTTAAAATAATTT
*
1048274 -AATTTAAAATAATCT
1 AAATTTAAAATAATTT
1048289 -AATTTAAAATAA
1 AAATTTAAAATAA
1048301 ATTTCACGTG
Statistics
Matches: 106, Mismatches: 15, Indels: 17
0.77 0.11 0.12
Matches are distributed among these distances:
15 38 0.36
16 42 0.40
17 3 0.03
18 6 0.06
19 1 0.01
20 1 0.01
21 6 0.06
22 3 0.03
23 6 0.06
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (16 bp):
AAATTTAAAATAATTT
Found at i:1048261 original size:23 final size:23
Alignment explanation
Indices: 1048235--1048282 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
1048225 AAAATAATTT
1048235 AAATTTAAAAT-ATTTAAATTTAA
1 AAATTTAAAATAATTT-AATTTAA
1048258 AAATTTAAAATAATTTAATTTAA
1 AAATTTAAAATAATTTAATTTAA
1048281 AA
1 AA
1048283 TAATCTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATTTAAAATAATTTAATTTAA
Found at i:1048293 original size:38 final size:39
Alignment explanation
Indices: 1048219--1048297 Score: 126
Period size: 38 Copynumber: 2.1 Consensus size: 39
1048209 TAAAATATCT
*
1048219 AAATTTAAAATAATTTAAATTTAAAATATTTAAATTTAA
1 AAATTTAAAATAATTTAAATTTAAAATATCTAAATTTAA
1048258 AAATTTAAAATAATTT-AATTTAAAATAATCT-AATTTAA
1 AAATTTAAAATAATTTAAATTTAAAAT-ATCTAAATTTAA
1048296 AA
1 AA
1048298 TAAATTTCAC
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
38 19 0.50
39 19 0.50
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (39 bp):
AAATTTAAAATAATTTAAATTTAAAATATCTAAATTTAA
Found at i:1050185 original size:3 final size:3
Alignment explanation
Indices: 1050177--1050208 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1050167 CATGACAATA
1050177 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1050209 CCGAGAGGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1054873 original size:2 final size:2
Alignment explanation
Indices: 1054868--1054892 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1054858 TTCATATATA
1054868 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
1054893 ACATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1054900 original size:2 final size:2
Alignment explanation
Indices: 1054895--1054922 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1054885 GTGTGTGTAC
1054895 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
1054923 TATCAACAGA
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:1055657 original size:3 final size:3
Alignment explanation
Indices: 1055649--1055679 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1055639 TGTTTTTGTT
*
1055649 TTC TTC TTC TTT TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1055680 CGAGCAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:1061831 original size:18 final size:20
Alignment explanation
Indices: 1061789--1061832 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 20
1061779 TTTAGTATAT
*
1061789 AATTATATTAAAAATTATTAA
1 AATTATATTAAAAA-TATAAA
1061810 AATTATA-TAAAAA-ATAAA
1 AATTATATTAAAAATATAAA
1061828 AATTA
1 AATTA
1061833 AATATTATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 9 0.41
20 6 0.27
21 7 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AATTATATTAAAAATATAAA
Found at i:1064809 original size:2 final size:2
Alignment explanation
Indices: 1064802--1064840 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1064792 TTTTTATTTG
1064802 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
1064841 ATCTCATTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1068109 original size:2 final size:2
Alignment explanation
Indices: 1068104--1068137 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1068094 ACACACACGC
1068104 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
1068138 CAAACAAATT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1069405 original size:19 final size:20
Alignment explanation
Indices: 1069377--1069416 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1069367 TTATTAATTT
*
1069377 AAATT-TTTTATTAAATAAA
1 AAATTATTTAATTAAATAAA
*
1069396 AAATTATTTAATTAATTAAA
1 AAATTATTTAATTAAATAAA
1069416 A
1 A
1069417 TTTTTTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATTATTTAATTAAATAAA
Found at i:1069418 original size:18 final size:18
Alignment explanation
Indices: 1069346--1069423 Score: 50
Period size: 18 Copynumber: 4.1 Consensus size: 18
1069336 TATTTATAAA
*
1069346 AATTGATTAAAGATTATTT
1 AATTAATTAAA-ATTATTT
*
1069365 GATTATTAATTTAAATT-TTT
1 -A--ATTAATTAAAATTATTT
* *
1069385 TATTAAATAAAAAATTATTT
1 AATT-AAT-TAAAATTATTT
*
1069405 AATTAATTAAAATTTTTT
1 AATTAATTAAAATTATTT
1069423 A
1 A
1069424 TAAATATCAA
Statistics
Matches: 45, Mismatches: 8, Indels: 12
0.69 0.12 0.18
Matches are distributed among these distances:
17 3 0.07
18 13 0.29
19 8 0.18
20 10 0.22
21 3 0.07
22 8 0.18
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (18 bp):
AATTAATTAAAATTATTT
Found at i:1071618 original size:2 final size:2
Alignment explanation
Indices: 1071611--1071639 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1071601 AAAGTCCCCA
1071611 AT 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 AT A
1071640 ATAAGGTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1075148 original size:79 final size:79
Alignment explanation
Indices: 1075017--1075162 Score: 265
Period size: 79 Copynumber: 1.8 Consensus size: 79
1075007 GAAGTGAGAA
1075017 TTTTGCCAGGGAATCAGAGATATATCAGTCAAAATTCTGAATTATTGTTTAAGTAATAAAAAGAT
1 TTTTGCCAGGGAATCAGAGATATATCAGTCAAAATTCTGAATTATTGTTTAAGTAATAAAAAGAT
1075082 TAAATTGCATATTC
66 TAAATTGCATATTC
* * *
1075096 TTTTGTCAGGGAATCAGAGATATATCATTCAAAATTTTGAATTATTGTTTAAGTAATAAAAAGAT
1 TTTTGCCAGGGAATCAGAGATATATCAGTCAAAATTCTGAATTATTGTTTAAGTAATAAAAAGAT
1075161 TA
66 TA
1075163 TGGTCTTGTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 64 1.00
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (79 bp):
TTTTGCCAGGGAATCAGAGATATATCAGTCAAAATTCTGAATTATTGTTTAAGTAATAAAAAGAT
TAAATTGCATATTC
Found at i:1076303 original size:3 final size:3
Alignment explanation
Indices: 1076295--1076344 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
1076285 TTTTAAACTA
1076295 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1076343 TA
1 TA
1076345 CTGTATTTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1077014 original size:21 final size:21
Alignment explanation
Indices: 1076978--1077033 Score: 76
Period size: 23 Copynumber: 2.6 Consensus size: 21
1076968 AAAAATAAAA
1076978 TACATATTTATATATATGACAT
1 TACATATTTATATATA-GACAT
* *
1077000 TACATTATTTATATATATATAT
1 TACA-TATTTATATATAGACAT
1077022 TACATATTTATA
1 TACATATTTATA
1077034 GCTAATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 8 0.26
22 11 0.35
23 12 0.39
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (21 bp):
TACATATTTATATATAGACAT
Found at i:1077389 original size:3 final size:3
Alignment explanation
Indices: 1077381--1077412 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1077371 AAAAGAAAAT
1077381 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1077413 CTAAAAGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1082736 original size:33 final size:33
Alignment explanation
Indices: 1082694--1082759 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
1082684 GACTGTTCCC
1082694 CTGAGAATACAACAGAAAATTCAAGTAGAGCAT
1 CTGAGAATACAACAGAAAATTCAAGTAGAGCAT
1082727 CTGAGAATACAACAGAAAATTCAAGTAGAGCAT
1 CTGAGAATACAACAGAAAATTCAAGTAGAGCAT
1082760 GTAATCAGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.48, C:0.15, G:0.18, T:0.18
Consensus pattern (33 bp):
CTGAGAATACAACAGAAAATTCAAGTAGAGCAT
Found at i:1083269 original size:2 final size:2
Alignment explanation
Indices: 1083262--1083292 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1083252 CTATCCAACA
1083262 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1083293 TAAGATCTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1086129 original size:65 final size:65
Alignment explanation
Indices: 1086023--1086170 Score: 206
Period size: 65 Copynumber: 2.3 Consensus size: 65
1086013 TACTACCCAG
* * * *
1086023 GGACACAAGCCACTCTCCCTCTAATAATGGCACCCACCTCATACTAACCAGGGAGGACCTTTGAA
1 GGACACAAGCCACTCTCCCTCCAATAATGGCACACACCTCATACTAACCAAGGAGGACCATTGAA
* * * * *
1086088 GGACACAAGCCACTTTCCCTCCAATAGTGGCACACAGCTCATACTACCCAAGGAGGACCATTGAG
1 GGACACAAGCCACTCTCCCTCCAATAATGGCACACACCTCATACTAACCAAGGAGGACCATTGAA
*
1086153 GGACACAAGCCACACTCC
1 GGACACAAGCCACTCTCC
1086171 TAATAGTGGC
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
65 72 1.00
ACGTcount: A:0.31, C:0.34, G:0.18, T:0.16
Consensus pattern (65 bp):
GGACACAAGCCACTCTCCCTCCAATAATGGCACACACCTCATACTAACCAAGGAGGACCATTGAA
Found at i:1086198 original size:62 final size:63
Alignment explanation
Indices: 1086021--1086347 Score: 204
Period size: 65 Copynumber: 5.3 Consensus size: 63
1086011 CATACTACCC
* * * *
1086021 AGGGACACAAGCCACTCTCCCTCTAATAATGGCACCCA-CCTCATACTAACCAGGGAGGACCTTT
1 AGGGACACAAGCCACTCT-CC-CTAATAGTGGCA-CCAGCCTCATACTACCCAAGGAGGACCATT
1086085 G
63 G
* *
1086086 AAGGACACAAGCCACTTTCCCTCCAATAGTGGCACACAG-CTCATACTACCCAAGGAGGACCATT
1 AGGGACACAAGCCACTCTCCCT--AATAGTGGCAC-CAGCCTCATACTACCCAAGGAGGACCATT
1086150 G
63 G
* **
1086151 AGGGACACAAGCCACACT-CCTAATAGTGGCACTTGCCTCATACTACCC-A-G-GGACACA---
1 AGGGACACAAGCCACTCTCCCTAATAGTGGCACCAGCCTCATACTACCCAAGGAGGAC-CATTG
* * * * * * *
1086208 A--G-C-C-A--CTCTCCCTCTAATAGTGGCAATCA-CCTCATACTTGCCTAGGGAGGACCATTG
1 AGGGACACAAGCCACTCTCCCTAATAGTGGC-ACCAGCCTCATAC-TACCCAAGGAGGACCATTG
* * * * *
1086265 AAGGACACAAGCCGCTTTCCCTCTAATAGTGGCA-CACGCCTCATACTACCTAAGGAGGACCTTT
1 AGGGACACAAGCCACTCT-CC-CTAATAGTGGCACCA-GCCTCATACTACCCAAGGAGGACCATT
*
1086329 A
63 G
* *
1086330 AGGGATATAAGCCACTCT
1 AGGGACACAAGCCACTCT
1086348 TGCTTTATTA
Statistics
Matches: 202, Mismatches: 34, Indels: 52
0.70 0.12 0.18
Matches are distributed among these distances:
50 3 0.01
51 19 0.09
52 5 0.02
53 1 0.00
54 4 0.02
55 5 0.02
57 2 0.01
59 5 0.02
60 4 0.02
61 3 0.01
62 24 0.12
63 2 0.01
64 11 0.05
65 95 0.47
66 19 0.09
ACGTcount: A:0.30, C:0.32, G:0.19, T:0.20
Consensus pattern (63 bp):
AGGGACACAAGCCACTCTCCCTAATAGTGGCACCAGCCTCATACTACCCAAGGAGGACCATTG
Found at i:1086212 original size:178 final size:179
Alignment explanation
Indices: 1085963--1086344 Score: 561
Period size: 178 Copynumber: 2.1 Consensus size: 179
1085953 CGACCTAGGA
* * * *
1085963 AGGACCATTAAAGGACTCAAACCACTCTCCTAATAGCGGCACCAGCCTCATACTACCCAGGGACA
1 AGGACCATTAAGGGACACAAGCCACACTCCTAATAGCGGCACCAGCCTCATACTACCCAGGGACA
* *
1086028 CAAGCCACTCTCCCTCTAATAATGGCACCCACCTCATACTAACC-AGGGAGGACCTTTGAAGGAC
66 CAAGCCACTCTCCCTCTAATAATGGCAACCACCTCATACTAACCTAGGGAGGACCATTGAAGGAC
1086092 ACAAGCCACTTTCCCTCCAATAGTGGCACACAG-CTCATACTACCCAAGG
131 ACAAGCCACTTTCCCTCCAATAGTGGCACAC-GCCTCATACTACCCAAGG
* * **
1086141 AGGACCATTGAGGGACACAAGCCACACTCCTAATAGTGGCACTTGCCTCATACTACCCAGGGACA
1 AGGACCATTAAGGGACACAAGCCACACTCCTAATAGCGGCACCAGCCTCATACTACCCAGGGACA
* * **
1086206 CAAGCCACTCTCCCTCTAATAGTGGCAATCACCTCATACTTGCCTAGGGAGGACCATTGAAGGAC
66 CAAGCCACTCTCCCTCTAATAATGGCAACCACCTCATACTAACCTAGGGAGGACCATTGAAGGAC
* * *
1086271 ACAAGCCGCTTTCCCTCTAATAGTGGCACACGCCTCATACTACCTAAGG
131 ACAAGCCACTTTCCCTCCAATAGTGGCACACGCCTCATACTACCCAAGG
* * *
1086320 AGGACCTTTAAGGGATATAAGCCAC
1 AGGACCATTAAGGGACACAAGCCAC
1086345 TCTTGCTTTA
Statistics
Matches: 181, Mismatches: 21, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
178 97 0.54
179 84 0.46
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.19
Consensus pattern (179 bp):
AGGACCATTAAGGGACACAAGCCACACTCCTAATAGCGGCACCAGCCTCATACTACCCAGGGACA
CAAGCCACTCTCCCTCTAATAATGGCAACCACCTCATACTAACCTAGGGAGGACCATTGAAGGAC
ACAAGCCACTTTCCCTCCAATAGTGGCACACGCCTCATACTACCCAAGG
Found at i:1086227 original size:113 final size:116
Alignment explanation
Indices: 1086088--1086314 Score: 300
Period size: 113 Copynumber: 2.0 Consensus size: 116
1086078 GACCTTTGAA
* *
1086088 GGACACAAGCCACTTTCCCTCCAATAGTGGCACA-CAGCTCATAC-TACCCAAGGAGGACCATTG
1 GGACACAAGCCACTCTCCCTCCAATAGTGGCA-ATCACCTCATACTTACCCAAGGAGGACCATTG
* * **
1086151 AGGGACACAAGCCAC-ACTC-CTAATAGTGGCACTTGCCTCATACTACCCAG
65 AAGGACACAAGCCACTACCCTCTAATAGTGGCACACGCCTCATACTACCCAG
* * * *
1086201 GGACACAAGCCACTCTCCCTCTAATAGTGGCAATCACCTCATACTTGCCTAGGGAGGACCATTGA
1 GGACACAAGCCACTCTCCCTCCAATAGTGGCAATCACCTCATACTTACCCAAGGAGGACCATTGA
* *
1086266 AGGACACAAGCCGCTTTCCCTCTAATAGTGGCACACGCCTCATACTACC
66 AGGACACAAGCCAC-TACCCTCTAATAGTGGCACACGCCTCATACTACC
1086315 TAAGGAGGAC
Statistics
Matches: 97, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
112 1 0.01
113 39 0.40
114 29 0.30
116 2 0.02
117 26 0.27
ACGTcount: A:0.29, C:0.33, G:0.19, T:0.19
Consensus pattern (116 bp):
GGACACAAGCCACTCTCCCTCCAATAGTGGCAATCACCTCATACTTACCCAAGGAGGACCATTGA
AGGACACAAGCCACTACCCTCTAATAGTGGCACACGCCTCATACTACCCAG
Found at i:1086241 original size:51 final size:48
Alignment explanation
Indices: 1086151--1086245 Score: 127
Period size: 51 Copynumber: 1.9 Consensus size: 48
1086141 AGGACCATTG
* **
1086151 AGGGACACAAGCCACACTCCTAATAGTGGCACTTGCCTCATACTACCC
1 AGGGACACAAGCCACACTCCTAATAGTGGCAATCACCTCATACTACCC
*
1086199 AGGGACACAAGCCACTCTCCCTCTAATAGTGGCAATCACCTCATACT
1 AGGGACACAAGCCACACT--C-CTAATAGTGGCAATCACCTCATACT
1086246 TGCCTAGGGA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
48 17 0.43
50 1 0.03
51 22 0.55
ACGTcount: A:0.29, C:0.35, G:0.16, T:0.20
Consensus pattern (48 bp):
AGGGACACAAGCCACACTCCTAATAGTGGCAATCACCTCATACTACCC
Found at i:1086286 original size:66 final size:65
Alignment explanation
Indices: 1086201--1086347 Score: 181
Period size: 66 Copynumber: 2.2 Consensus size: 65
1086191 TACTACCCAG
* *
1086201 GGACACAAGCCACTCTCCCTCTAATAGTGGCA-ATCACCTCATACTTGCCTAGGGAGGACCATTG
1 GGACACAAGCCACTCTCCCTCTAATAGTGGCACA-CACCTCATAC-TACCTAAGGAGGACCATTG
1086265 AA
64 AA
* * * *
1086267 GGACACAAGCCGCTTTCCCTCTAATAGTGGCACACGCCTCATACTACCTAAGGAGGACC-TTTAA
1 GGACACAAGCCACTCTCCCTCTAATAGTGGCACACACCTCATACTACCTAAGGAGGACCATTGAA
* *
1086331 GGGATATAAGCCACTCT
1 -GGACACAAGCCACTCT
1086348 TGCTTTATTA
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
64 4 0.06
65 25 0.36
66 39 0.57
67 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.22
Consensus pattern (65 bp):
GGACACAAGCCACTCTCCCTCTAATAGTGGCACACACCTCATACTACCTAAGGAGGACCATTGAA
Found at i:1090200 original size:22 final size:22
Alignment explanation
Indices: 1090172--1090248 Score: 70
Period size: 21 Copynumber: 3.5 Consensus size: 22
1090162 ATTTTACATA
1090172 TTATTATATATATATCTTATTT
1 TTATTATATATATATCTTATTT
* * *
1090194 TTATTAT-TTTATATCATATTA
1 TTATTATATATATATCTTATTT
1090215 TT-TTATATATTATAT-TTAATTAT
1 TTATTATATA-TATATCTT-ATT-T
*
1090238 TTTTTATATAT
1 TTATTATATAT
1090249 TTATATATTA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 4 0.09
21 15 0.34
22 15 0.34
23 3 0.07
24 7 0.16
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (22 bp):
TTATTATATATATATCTTATTT
Found at i:1090258 original size:22 final size:23
Alignment explanation
Indices: 1090191--1090259 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 23
1090181 ATATATCTTA
*
1090191 TTTTTAT-TATTTTATATCA-TAT
1 TTTTTATATA-TTTATATAATTAT
*
1090213 TATTTTATATATTATATTTAATTAT
1 T-TTTTATATATT-TATATAATTAT
1090238 TTTTTATATATTTATAT-ATTAT
1 TTTTTATATATTTATATAATTAT
1090260 CTAAAATAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
22 6 0.15
23 12 0.30
24 18 0.45
25 4 0.10
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTTATATATTTATATAATTAT
Found at i:1091031 original size:2 final size:2
Alignment explanation
Indices: 1091024--1091052 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1091014 TAAAAGCAAA
1091024 AT 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 AT A
1091053 ACACAACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1091220 original size:21 final size:22
Alignment explanation
Indices: 1091180--1091220 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1091170 TTGGAAAGTA
*
1091180 AATCATGACCTTTTACTTTTCT
1 AATCATGACCTTTTAATTTTCT
*
1091202 AATCATGA-TTTTTAATTTT
1 AATCATGACCTTTTAATTTT
1091221 GTTTCTCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.27, C:0.15, G:0.05, T:0.54
Consensus pattern (22 bp):
AATCATGACCTTTTAATTTTCT
Found at i:1093881 original size:22 final size:22
Alignment explanation
Indices: 1093839--1093879 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1093829 ATTATTTTAC
*
1093839 TAAATATTTTTTAAAATAAATA
1 TAAATAATTTTTAAAATAAATA
1093861 TAAATAATTTTT-AAATAAA
1 TAAATAATTTTTAAAATAAA
1093880 ATTACATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TAAATAATTTTTAAAATAAATA
Found at i:1098888 original size:18 final size:17
Alignment explanation
Indices: 1098865--1098901 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
1098855 TCATTATAAC
*
1098865 AAAAATTAATTAATATTA
1 AAAAATTAAATAA-ATTA
1098883 AAAAATTAAATAAATTA
1 AAAAATTAAATAAATTA
1098900 AA
1 AA
1098902 TTAAACTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAAATTAAATAAATTA
Found at i:1102389 original size:105 final size:105
Alignment explanation
Indices: 1102271--1102480 Score: 420
Period size: 105 Copynumber: 2.0 Consensus size: 105
1102261 CTCCATGCCT
1102271 TAATATAATATCTAATGCATGTGCCCTTGATATTGCACACCTGCTAAAATGTCCTATGTTAAAAT
1 TAATATAATATCTAATGCATGTGCCCTTGATATTGCACACCTGCTAAAATGTCCTATGTTAAAAT
1102336 TAAGATTGGCCAATCGTGCAGTTGCTTCTGCATAAGTAGC
66 TAAGATTGGCCAATCGTGCAGTTGCTTCTGCATAAGTAGC
1102376 TAATATAATATCTAATGCATGTGCCCTTGATATTGCACACCTGCTAAAATGTCCTATGTTAAAAT
1 TAATATAATATCTAATGCATGTGCCCTTGATATTGCACACCTGCTAAAATGTCCTATGTTAAAAT
1102441 TAAGATTGGCCAATCGTGCAGTTGCTTCTGCATAAGTAGC
66 TAAGATTGGCCAATCGTGCAGTTGCTTCTGCATAAGTAGC
1102481 CTTCTCAACA
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 105 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (105 bp):
TAATATAATATCTAATGCATGTGCCCTTGATATTGCACACCTGCTAAAATGTCCTATGTTAAAAT
TAAGATTGGCCAATCGTGCAGTTGCTTCTGCATAAGTAGC
Found at i:1103877 original size:54 final size:54
Alignment explanation
Indices: 1103788--1103893 Score: 158
Period size: 54 Copynumber: 2.0 Consensus size: 54
1103778 TTTCTCAAGC
* * *
1103788 CCATAAGTAAATTTTACGTGTCTATTTGCACAAATGAGCTGAAATAGTATTAGG
1 CCATAAGTAAATTTTACATGTCTATTTGCACAAATGAGCTAAAATAGGATTAGG
* * *
1103842 CCATGAGTAACTTTTACATGTCTATTTGCATAAATGAGCTAAAATAGGATTA
1 CCATAAGTAAATTTTACATGTCTATTTGCACAAATGAGCTAAAATAGGATTA
1103894 CCAGAAAACA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (54 bp):
CCATAAGTAAATTTTACATGTCTATTTGCACAAATGAGCTAAAATAGGATTAGG
Found at i:1106827 original size:12 final size:12
Alignment explanation
Indices: 1106810--1106847 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
1106800 ATTAGAGATG
1106810 AATAAAATAATA
1 AATAAAATAATA
*
1106822 AATAAAAT-ATG
1 AATAAAATAATA
1106833 AATAAAA-AATA
1 AATAAAATAATA
1106844 AATA
1 AATA
1106848 GTATTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 15 0.65
12 8 0.35
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (12 bp):
AATAAAATAATA
Found at i:1106838 original size:11 final size:12
Alignment explanation
Indices: 1106807--1106839 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1106797 GAGATTAGAG
1106807 ATGAATAAAATA
1 ATGAATAAAATA
*
1106819 ATAAATAAAAT-
1 ATGAATAAAATA
1106830 ATGAATAAAA
1 ATGAATAAAA
1106840 AATAAATAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (12 bp):
ATGAATAAAATA
Found at i:1107228 original size:25 final size:25
Alignment explanation
Indices: 1107200--1107256 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
1107190 TAAAATCATA
* *
1107200 TAAAAATACATATTTATAAATT-ATT
1 TAAAAATACAAATTTA-AAATTAAAT
* *
1107225 TAAAAAAATAAATTTAAAATTAAAT
1 TAAAAATACAAATTTAAAATTAAAT
1107250 TAAAAAT
1 TAAAAAT
1107257 TTTTAACCAC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (25 bp):
TAAAAATACAAATTTAAAATTAAAT
Found at i:1107324 original size:38 final size:38
Alignment explanation
Indices: 1107272--1107346 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
1107262 ACCACCAATC
*
1107272 AAATTTAAATTAAATTTACTAATAATTAATCATTAATT
1 AAATCTAAATTAAATTTACTAATAATTAATCATTAATT
* *
1107310 AAATCTAAATTAAATTTATTAATCATTAATCATTAAT
1 AAATCTAAATTAAATTTACTAATAATTAATCATTAAT
1107347 CATCAATCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (38 bp):
AAATCTAAATTAAATTTACTAATAATTAATCATTAATT
Found at i:1108342 original size:3 final size:3
Alignment explanation
Indices: 1108334--1108366 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1108324 TATTAACCTC
1108334 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1108367 GTAGAAGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1115509 original size:30 final size:30
Alignment explanation
Indices: 1115475--1115536 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
1115465 AATTATTACG
* ** * *
1115475 TAATTGTCAATTTGTTAAAACTATGGGCCT
1 TAATTGCCAATTTACTAAAACCAGGGGCCT
1115505 TAATTGCCAATTTACTAAAACCAGGGGCCT
1 TAATTGCCAATTTACTAAAACCAGGGGCCT
1115535 TA
1 TA
1115537 TTTTCTCAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (30 bp):
TAATTGCCAATTTACTAAAACCAGGGGCCT
Found at i:1115960 original size:8 final size:8
Alignment explanation
Indices: 1115947--1116003 Score: 55
Period size: 8 Copynumber: 7.1 Consensus size: 8
1115937 ATTGAATATT
1115947 TTTAAATA
1 TTTAAATA
1115955 TTTAAATA
1 TTTAAATA
1115963 TTT-AA-A
1 TTTAAATA
*
1115969 TTTAAATTT
1 TTTAAA-TA
* *
1115978 TTTAATTT
1 TTTAAATA
1115986 TTTAAAATA
1 TTT-AAATA
1115995 TTTAAATA
1 TTTAAATA
1116003 T
1 T
1116004 ATTTATATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
6 4 0.10
7 4 0.10
8 22 0.54
9 11 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
TTTAAATA
Found at i:1116088 original size:17 final size:16
Alignment explanation
Indices: 1116066--1116114 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 16
1116056 AAAAAAAAAT
1116066 ATTTATTAGATATTTAA
1 ATTTATTA-ATATTTAA
1116083 ATTTATTTAATATTTAA
1 ATTTA-TTAATATTTAA
1116100 ATTTATTTAATATTT
1 ATTTA-TTAATATTT
1116115 TTTAAATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 28 0.90
18 3 0.10
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (16 bp):
ATTTATTAATATTTAA
Found at i:1116089 original size:21 final size:20
Alignment explanation
Indices: 1116065--1116122 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 20
1116055 TAAAAAAAAA
1116065 TATTTATTAGATATTTAAATT
1 TATTTATTA-ATATTTAAATT
1116086 TA--T-TTAATATTTAAATT
1 TATTTATTAATATTTAAATT
* * *
1116103 TATTTAATATTTTTTAAATT
1 TATTTATTAATATTTAAATT
1116123 AATATAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
17 13 0.42
18 3 0.10
19 2 0.06
20 11 0.35
21 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TATTTATTAATATTTAAATT
Found at i:1116091 original size:10 final size:10
Alignment explanation
Indices: 1116076--1116122 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
1116066 ATTTATTAGA
1116076 TATTTAAATT
1 TATTTAAATT
1116086 TATTT-AA--
1 TATTTAAATT
1116093 TATTTAAATT
1 TATTTAAATT
1116103 TATTTAATATT
1 TATTTAA-ATT
1116114 T-TTTAAATT
1 TATTTAAATT
1116123 AATATAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
7 5 0.15
8 2 0.06
9 5 0.15
10 17 0.52
11 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATTTAAATT
Found at i:1116120 original size:20 final size:20
Alignment explanation
Indices: 1116078--1116136 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 20
1116068 TTATTAGATA
1116078 TTTAAATTTATTTAATA---
1 TTTAAATTTATTTAATATTT
1116095 TTTAAATTTATTTAATATTT
1 TTTAAATTTATTTAATATTT
* * *
1116115 TTTAAATTAATATAAAATTT
1 TTTAAATTTATTTAATATTT
1116135 TT
1 TT
1116137 AAAAAATTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
17 17 0.47
20 19 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTAAATTTATTTAATATTT
Found at i:1116222 original size:13 final size:15
Alignment explanation
Indices: 1116194--1116228 Score: 56
Period size: 13 Copynumber: 2.5 Consensus size: 15
1116184 ATTATTTACA
1116194 TAAATAAATCAAATT
1 TAAATAAATCAAATT
1116209 TAAA-AAAT-AAATT
1 TAAATAAATCAAATT
1116222 TAAATAA
1 TAAATAA
1116229 TTAATATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 9 0.47
14 6 0.32
15 4 0.21
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAATAAATCAAATT
Found at i:1116276 original size:15 final size:15
Alignment explanation
Indices: 1116253--1116293 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 15
1116243 ATCAAAATCA
1116253 AAATAATTTAAATATT
1 AAAT-ATTTAAATATT
1116269 AAATATTTAAA-ATT
1 AAATATTTAAATATT
*
1116283 -TATATTTAAAT
1 AAATATTTAAAT
1116294 CATTTTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 9 0.39
14 3 0.13
15 7 0.30
16 4 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AAATATTTAAATATT
Found at i:1116282 original size:22 final size:22
Alignment explanation
Indices: 1116257--1116298 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1116247 AAATCAAAAT
1116257 AATTTAAATATTAAAT-ATTTAA
1 AATTTAAAT-TTAAATCATTTAA
*
1116279 AATTTATATTTAAATCATTT
1 AATTTAAATTTAAATCATTT
1116299 TTAATATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
AATTTAAATTTAAATCATTTAA
Found at i:1121592 original size:27 final size:27
Alignment explanation
Indices: 1121524--1121588 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
1121514 TTACATGTTA
* *
1121524 TAATTATTTTTAAAATA-TTATATATT
1 TAATTAATTTTAATATATTTATATATT
*
1121550 TAATTAATTTTAATATATTTATGTATT
1 TAATTAATTTTAATATATTTATATATT
1121577 TATATTATATTT
1 TA-ATTA-ATTT
1121589 ATATTATGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 15 0.45
27 10 0.30
28 4 0.12
29 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (27 bp):
TAATTAATTTTAATATATTTATATATT
Found at i:1124520 original size:29 final size:29
Alignment explanation
Indices: 1124478--1124534 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
1124468 AATGCATAAG
** *
1124478 TTTCAATTGGAGGATATCTTCTTCCTGGC
1 TTTCAATTAAAGGAAATCTTCTTCCTGGC
1124507 TTTCAATTAAAGGAAATCTTCTTCCTGG
1 TTTCAATTAAAGGAAATCTTCTTCCTGG
1124535 GTAACCTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (29 bp):
TTTCAATTAAAGGAAATCTTCTTCCTGGC
Found at i:1126651 original size:2 final size:2
Alignment explanation
Indices: 1126639--1126674 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1126629 TGTCATTGAA
*
1126639 AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1126675 CAAAAAAGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1127093 original size:65 final size:63
Alignment explanation
Indices: 1127021--1127189 Score: 169
Period size: 65 Copynumber: 2.6 Consensus size: 63
1127011 TATTTATTAT
* *
1127021 AATTAAAAATTAAATAAAATAATAATATATTTAATTTTTAAAATTTTTTATTAATTATAATTTA
1 AATTTAAAATTAAATTAAAT-ATAATATATTTAATTTTTAAAATTTTTTATTAATTATAATTTA
* * * * * * *
1127085 AATTTAAAATGAGTATTTAATATAGATATA-TTAATTTTATAAATTTTTTTATTTATTGTACTTT
1 AATTTAAAATTA-AATTAAATATA-ATATATTTAATTTT-TAAAATTTTTTATTAATTATAATTT
1127149 A
63 A
* * *
1127150 AATTTGATATTAATATTAAATATAAGTATATGTAATTTTT
1 AATTTAAAATTAA-ATTAAATATAA-TATATTTAATTTTT
1127190 TTATTTAAAA
Statistics
Matches: 84, Mismatches: 15, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
64 22 0.26
65 55 0.65
66 7 0.08
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (63 bp):
AATTTAAAATTAAATTAAATATAATATATTTAATTTTTAAAATTTTTTATTAATTATAATTTA
Found at i:1127352 original size:9 final size:8
Alignment explanation
Indices: 1127324--1127353 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1127314 AAACCTTCAT
1127324 TTTTTTTA
1 TTTTTTTA
1127332 TTTTTTTA
1 TTTTTTTA
*
1127340 TTTTTTAA
1 TTTTTTTA
1127348 TTTTTT
1 TTTTTT
1127354 CAGGTTCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTTA
Found at i:1128014 original size:7 final size:7
Alignment explanation
Indices: 1128002--1128031 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
1127992 AAATCATAAT
1128002 TTTAAAA
1 TTTAAAA
1128009 TTTAAAA
1 TTTAAAA
1128016 TTTAAAA
1 TTTAAAA
1128023 TTTAAAA
1 TTTAAAA
1128030 TT
1 TT
1128032 ATTAAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
TTTAAAA
Found at i:1128103 original size:27 final size:26
Alignment explanation
Indices: 1128051--1128103 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
1128041 TATTTTTTAA
* *
1128051 AAAATATTATATAAATTAATTAAATT
1 AAAATATTATATAAAATAACTAAATT
* *
1128077 AAAATTTTAATATAAAATAACTCAATT
1 AAAATATT-ATATAAAATAACTAAATT
1128104 GCATCTTATG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.40
Consensus pattern (26 bp):
AAAATATTATATAAAATAACTAAATT
Found at i:1130220 original size:2 final size:2
Alignment explanation
Indices: 1130213--1130241 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1130203 TAATTTAATG
1130213 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1130242 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1130246 original size:2 final size:2
Alignment explanation
Indices: 1130241--1130276 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1130231 ACACACACAC
1130241 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
1130277 TCCAATAGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1139003 original size:18 final size:19
Alignment explanation
Indices: 1138967--1139016 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
1138957 ATTATATAAA
*
1138967 TATTATGATA-TTATGTTTT
1 TATTATTATATTTA-GTTTT
*
1138986 TA-TATTA-ATTTATTTTT
1 TATTATTATATTTAGTTTT
1139003 TATTATTATATTTA
1 TATTATTATATTTA
1139017 ATATTATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 7 0.27
18 12 0.46
19 7 0.27
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (19 bp):
TATTATTATATTTAGTTTT
Found at i:1139014 original size:15 final size:16
Alignment explanation
Indices: 1138975--1139015 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1138965 AATATTATGA
*
1138975 TATTATGTTTTTATAT
1 TATTATATTTTTATAT
1138991 TAATT-TATTTTT-TAT
1 T-ATTATATTTTTATAT
1139006 TATTATATTT
1 TATTATATTT
1139016 AATATTATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
14 3 0.14
15 9 0.41
16 7 0.32
17 3 0.14
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (16 bp):
TATTATATTTTTATAT
Found at i:1144329 original size:2 final size:2
Alignment explanation
Indices: 1144322--1144353 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1144312 TCTAATTCAC
1144322 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
1144354 ACGTAGATGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1146137 original size:19 final size:18
Alignment explanation
Indices: 1146104--1146155 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
1146094 AAACTCCATC
*
1146104 TAATAATTTTTAAATCAA
1 TAATTATTTTTAAATCAA
*
1146122 TAATTATTTATTAAATTAA
1 TAATTATTT-TTAAATCAA
*
1146141 -ATTTATTTTTTAAAT
1 TAATTA-TTTTTAAAT
1146156 ATATATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 18 0.62
19 11 0.38
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
TAATTATTTTTAAATCAA
Found at i:1148063 original size:14 final size:15
Alignment explanation
Indices: 1148044--1148074 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1148034 AACGCGACAC
1148044 TAATTTTTTT-ATTT
1 TAATTTTTTTAATTT
1148058 TAATTTTTTTAATTT
1 TAATTTTTTTAATTT
1148073 TA
1 TA
1148075 CAGTAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TAATTTTTTTAATTT
Found at i:1149040 original size:2 final size:2
Alignment explanation
Indices: 1149033--1149061 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1149023 CATGAACGAA
1149033 AT 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 AT A
1149062 ATAAACGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1149510 original size:12 final size:12
Alignment explanation
Indices: 1149493--1149539 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
1149483 CCTTTTTTTT
1149493 TTCTAATTTTAA
1 TTCTAATTTTAA
* *
1149505 TACTAATTCTAA
1 TTCTAATTTTAA
* *
1149517 TTCCAATTTCAA
1 TTCTAATTTTAA
1149529 TTCTAATTTTA
1 TTCTAATTTTA
1149540 TTTATTATTT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.34, C:0.15, G:0.00, T:0.51
Consensus pattern (12 bp):
TTCTAATTTTAA
Done.