Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015354.1 Kokia drynarioides strain JFW-HI SEQ_130401, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1324750
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 502 characters in sequence are not A, C, G, or T
File 3 of 4
Found at i:786996 original size:22 final size:23
Alignment explanation
Indices: 786948--786996 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
786938 CGCATAATTT
*
786948 TTTAAAAAACCTTATTTTCGTAA
1 TTTAAAAAAACTTATTTTCGTAA
* *
786971 -TTAAAAAAATTTA-TTTGGTAA
1 TTTAAAAAAACTTATTTTCGTAA
786992 TTTAA
1 TTTAA
786997 TTAGAAACGT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (23 bp):
TTTAAAAAAACTTATTTTCGTAA
Found at i:788301 original size:24 final size:24
Alignment explanation
Indices: 788273--788324 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
788263 GGCTTCCAAT
* *
788273 TTTTTTCAGGTTTCTCGAGTTTGGA
1 TTTTTACAGGTTTCTC-AGATTGGA
**
788298 TTTTTACATTTTTCTCAGATTGGA
1 TTTTTACAGGTTTCTCAGATTGGA
788322 TTT
1 TTT
788325 GGGATTTGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.15, C:0.12, G:0.17, T:0.56
Consensus pattern (24 bp):
TTTTTACAGGTTTCTCAGATTGGA
Found at i:788436 original size:6 final size:6
Alignment explanation
Indices: 788425--788452 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
788415 AGGATGAAGT
788425 TTTGGA TTTGGA TTTGGA TTTGGA TTTG
1 TTTGGA TTTGGA TTTGGA TTTGGA TTTG
788453 AGCTTTCTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.32, T:0.54
Consensus pattern (6 bp):
TTTGGA
Found at i:790567 original size:24 final size:24
Alignment explanation
Indices: 790481--790555 Score: 116
Period size: 24 Copynumber: 3.1 Consensus size: 24
790471 AGAAATAATC
* *
790481 TTTCAGTTAAA-TTCTGTTTATTTG
1 TTTCAATTAAACTT-TGTTTATTTA
790505 TTTCAATTAAACTTTGTTTATTTA
1 TTTCAATTAAACTTTGTTTATTTA
790529 TTTCAATTAAACTTTGTTTATTTA
1 TTTCAATTAAACTTTGTTTATTTA
790553 TTT
1 TTT
790556 GAGTCAAACT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
24 46 0.96
25 2 0.04
ACGTcount: A:0.25, C:0.08, G:0.07, T:0.60
Consensus pattern (24 bp):
TTTCAATTAAACTTTGTTTATTTA
Found at i:799185 original size:18 final size:18
Alignment explanation
Indices: 799164--799202 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
799154 TTTCCAATAG
799164 TAATTTTAGTAATAGTTA
1 TAATTTTAGTAATAGTTA
** *
799182 TAATTTTTTTAATTGTTA
1 TAATTTTAGTAATAGTTA
799200 TAA
1 TAA
799203 ATATTATTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (18 bp):
TAATTTTAGTAATAGTTA
Found at i:811415 original size:14 final size:16
Alignment explanation
Indices: 811391--811422 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
811381 GAGTTGTTTG
811391 AAAGCAT-AAAAATAA
1 AAAGCATAAAAAATAA
811406 AAAG-ATAAAAAATAA
1 AAAGCATAAAAAATAA
811421 AA
1 AA
811423 TAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 2 0.12
15 14 0.88
ACGTcount: A:0.78, C:0.03, G:0.06, T:0.12
Consensus pattern (16 bp):
AAAGCATAAAAAATAA
Found at i:812757 original size:5 final size:6
Alignment explanation
Indices: 812732--812756 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
812722 AGCAACTAAC
812732 AAGAAA AAGAAA AAGAAA AAGAAA A
1 AAGAAA AAGAAA AAGAAA AAGAAA A
812757 GTGAGCTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:821495 original size:16 final size:16
Alignment explanation
Indices: 821474--821508 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
821464 TGGCTCTAAG
*
821474 GAAAAGAAAAGAAAGA
1 GAAAAGAAAAGAAAAA
*
821490 GAAAAGACAAGAAAAA
1 GAAAAGAAAAGAAAAA
821506 GAA
1 GAA
821509 GCACAAAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.74, C:0.03, G:0.23, T:0.00
Consensus pattern (16 bp):
GAAAAGAAAAGAAAAA
Found at i:823204 original size:21 final size:21
Alignment explanation
Indices: 823180--823241 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
823170 ACCCCAGAAG
823180 ATGGTGATCTAATTTAGCAAC
1 ATGGTGATCTAATTTAGCAAC
* * ** **
823201 ATGGAGGTCTAACCCTAG-AGG
1 ATGGTGATCTAA-TTTAGCAAC
823222 ATGGTGATCTAATTTAGCAA
1 ATGGTGATCTAATTTAGCAA
823242 GGACACAACA
Statistics
Matches: 28, Mismatches: 11, Indels: 4
0.65 0.26 0.09
Matches are distributed among these distances:
20 3 0.11
21 22 0.79
22 3 0.11
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (21 bp):
ATGGTGATCTAATTTAGCAAC
Found at i:823225 original size:42 final size:42
Alignment explanation
Indices: 823158--823241 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
823148 AGTTAGTTAC
823158 CATGGAGGTCTAACCCCAGAAGATGGTGATCTAATTTAGCAA
1 CATGGAGGTCTAACCCCAGAAGATGGTGATCTAATTTAGCAA
* *
823200 CATGGAGGTCTAACCCTAGAGGATGGTGATCTAATTTAGCAA
1 CATGGAGGTCTAACCCCAGAAGATGGTGATCTAATTTAGCAA
823242 GGACACAACA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (42 bp):
CATGGAGGTCTAACCCCAGAAGATGGTGATCTAATTTAGCAA
Found at i:836475 original size:18 final size:18
Alignment explanation
Indices: 836452--836498 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
836442 TAGCCTGATC
*
836452 AGATGCAATCACATACTT
1 AGATGCAATCACATAATT
836470 AGATGCAATCACATAATT
1 AGATGCAATCACATAATT
836488 AGATGCAATCA
1 AGATGCAATCA
836499 TATGTTGGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.26
Consensus pattern (18 bp):
AGATGCAATCACATAATT
Found at i:836568 original size:6 final size:6
Alignment explanation
Indices: 836557--836581 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
836547 TAGCATCAGT
836557 AACAGC AACAGC AACAGC AACAGC A
1 AACAGC AACAGC AACAGC AACAGC A
836582 GTATTCTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.32, G:0.16, T:0.00
Consensus pattern (6 bp):
AACAGC
Found at i:859074 original size:18 final size:18
Alignment explanation
Indices: 859051--859102 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
859041 TGCAGCCTGG
*
859051 TCAGATGCAATCACATAT
1 TCAGATGCAATCACATAA
* *
859069 TCAGATGTAGTCACATAA
1 TCAGATGCAATCACATAA
*
859087 TCAGATGCAACCACAT
1 TCAGATGCAATCACAT
859103 TGTCAAATGC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.25
Consensus pattern (18 bp):
TCAGATGCAATCACATAA
Found at i:872524 original size:30 final size:28
Alignment explanation
Indices: 872485--872583 Score: 81
Period size: 30 Copynumber: 3.4 Consensus size: 28
872475 AAAATTTTTT
872485 ATTTGACCCTTAATTTTTCTAAAAATTTAG
1 ATTTGACCCTTAA-TTTTC-AAAAATTTAG
* * ** *
872515 ATTTAACCCTCGAACTTCCCAAAAATTTGG
1 ATTTGACCCT-TAA-TTTTCAAAAATTTAG
* * *
872545 ATTTTACCCCTAAATTTTCCAAAATTTAG
1 ATTTGA-CCCTTAATTTTCAAAAATTTAG
872574 ATTTGACCCT
1 ATTTGACCCT
872584 CGAACTTCTC
Statistics
Matches: 54, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
28 4 0.07
29 16 0.30
30 25 0.46
31 9 0.17
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.39
Consensus pattern (28 bp):
ATTTGACCCTTAATTTTCAAAAATTTAG
Found at i:872563 original size:60 final size:59
Alignment explanation
Indices: 872467--872630 Score: 168
Period size: 59 Copynumber: 2.8 Consensus size: 59
872457 TTCACCCCTA
* * ** * *
872467 AACTTCCTAAAATTTTTTATTTGACCCTTAATTTTTCTAAAAATTTAGATTTAACCCTCG
1 AACTTCCCAAAAATTTGAATTTGACCCCTAAATTTTC-AAAAATTTAGATTTAACCCTCG
* * * *
872527 AACTTCCCAAAAATTTGGATTTTACCCCTAAATTTTCCAAAATTTAGATTTGACCCTCG
1 AACTTCCCAAAAATTTGAATTTGACCCCTAAATTTTCAAAAATTTAGATTTAACCCTCG
* * * * *
872586 AACTTCTCAAAAAATTGAATTT-AGCCCCCAAACTTTCCAAAATTT
1 AACTTCCCAAAAATTTGAATTTGA-CCCCTAAATTTTCAAAAATTT
872631 CATTTTGACC
Statistics
Matches: 89, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
58 1 0.01
59 58 0.65
60 30 0.34
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.38
Consensus pattern (59 bp):
AACTTCCCAAAAATTTGAATTTGACCCCTAAATTTTCAAAAATTTAGATTTAACCCTCG
Found at i:872596 original size:29 final size:29
Alignment explanation
Indices: 872501--872597 Score: 97
Period size: 29 Copynumber: 3.3 Consensus size: 29
872491 CCCTTAATTT
*
872501 TTCTAAAAATTTAGATTTAACCCTCGAAC
1 TTCTCAAAATTTAGATTTAACCCTCGAAC
* * * * *
872530 TTCCCAAAAATTTGGATTTTACCC-CTAAA
1 TTCTC-AAAATTTAGATTTAACCCTCGAAC
* *
872559 TTTTCCAAAATTTAGATTTGACCCTCGAAC
1 TTCT-CAAAATTTAGATTTAACCCTCGAAC
872589 TTCTCAAAA
1 TTCTCAAAA
872598 AATTGAATTT
Statistics
Matches: 52, Mismatches: 13, Indels: 6
0.73 0.18 0.08
Matches are distributed among these distances:
29 29 0.56
30 23 0.44
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.35
Consensus pattern (29 bp):
TTCTCAAAATTTAGATTTAACCCTCGAAC
Found at i:872642 original size:59 final size:59
Alignment explanation
Indices: 872506--872630 Score: 180
Period size: 59 Copynumber: 2.1 Consensus size: 59
872496 AATTTTTCTA
* * * * *
872506 AAAATTTAGATTTAACCCTCGAACTTCCCAAAAATTTGGATTTTACCCCTAAATTTTCC
1 AAAATTTAGATTTGACCCTCGAACTTCCCAAAAAATTGGAATTTACCCCCAAACTTTCC
*
872565 AAAATTTAGATTTGACCCTCGAACTTCTCAAAAAATT-GAATTTAGCCCCCAAACTTTCC
1 AAAATTTAGATTTGACCCTCGAACTTCCCAAAAAATTGGAATTTA-CCCCCAAACTTTCC
872624 AAAATTT
1 AAAATTT
872631 CATTTTGACC
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 6 0.10
59 53 0.90
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.34
Consensus pattern (59 bp):
AAAATTTAGATTTGACCCTCGAACTTCCCAAAAAATTGGAATTTACCCCCAAACTTTCC
Found at i:874059 original size:14 final size:16
Alignment explanation
Indices: 874030--874062 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
874020 CTGTATTTTG
874030 TTTTCATATTGACTTT
1 TTTTCATATTGACTTT
874046 TTTTCAT-TTG-CTTT
1 TTTTCATATTGACTTT
874060 TTT
1 TTT
874063 ATTTTTGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 3 0.18
16 7 0.41
ACGTcount: A:0.12, C:0.12, G:0.06, T:0.70
Consensus pattern (16 bp):
TTTTCATATTGACTTT
Found at i:875771 original size:2 final size:2
Alignment explanation
Indices: 875766--875796 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
875756 TATATATATA
875766 TG TG TG 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 TG TG TG T
875797 AAATTTGGGT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:882878 original size:17 final size:19
Alignment explanation
Indices: 882851--882886 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
882841 ATTAATTTTA
882851 TTTACTTAATTT-TTTATT
1 TTTACTTAATTTGTTTATT
882869 TTTA-TTAATTTGTTTATT
1 TTTACTTAATTTGTTTATT
882887 GTTCTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.72
Consensus pattern (19 bp):
TTTACTTAATTTGTTTATT
Found at i:886083 original size:215 final size:215
Alignment explanation
Indices: 885712--886139 Score: 811
Period size: 215 Copynumber: 2.0 Consensus size: 215
885702 CAACGCAACT
885712 TAAGAAGAGAAGCTTATTGCAATCCTGGAAGAACATAAGAAAGCCATAGCCTAGAGCATCGCAAA
1 TAAGAAGAGAAGCTTATTGCAATCCTGGAAGAACATAAGAAAGCCATAGCCTAGAGCATCGCAAA
*
885777 CATCAAAGGCATCAGTCCTTCTTTCTGTATGGATAAGATAAGGTTAGAAGAAGAAGGGAAGCAAT
66 CATCAAAGGCATCAGTCCTTCTTTCTGCATGGATAAGATAAGGTTAGAAGAAGAAGGGAAGCAAT
885842 CCATTAAGCAACGAAGATGACTCAATGAGAAAATGAAAGAAGTGGTAAAGAAAGAAATCATCAAA
131 CCATTAAGCAACGAAGATGACTCAATGAGAAAATGAAAGAAGTGGTAAAGAAAGAAATCATCAAA
*
885907 TGGTTAGATGCGGGCATACA
196 TGCTTAGATGCGGGCATACA
*
885927 TAAGAAGAGAAGCTTATTGCAATCCTGGAAGAACATAAGAAAGCTATAGCCTAGAGCATCGCAAA
1 TAAGAAGAGAAGCTTATTGCAATCCTGGAAGAACATAAGAAAGCCATAGCCTAGAGCATCGCAAA
*
885992 CATCAGAGGCATCAGTCCTTCTTTCTGCATGGATAAGATAAGGTTAGAAGAAGAAGGGAAGCAAT
66 CATCAAAGGCATCAGTCCTTCTTTCTGCATGGATAAGATAAGGTTAGAAGAAGAAGGGAAGCAAT
*
886057 CCATTAAGTAACGAAGATGACTCAATGAGAAAATGAAAGAAGTGGTAAAGAAAGAAATCATCAAA
131 CCATTAAGCAACGAAGATGACTCAATGAGAAAATGAAAGAAGTGGTAAAGAAAGAAATCATCAAA
886122 TGCTTAGATGCGGGCATA
196 TGCTTAGATGCGGGCATA
886140 ATATACCCTA
Statistics
Matches: 208, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
215 208 1.00
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (215 bp):
TAAGAAGAGAAGCTTATTGCAATCCTGGAAGAACATAAGAAAGCCATAGCCTAGAGCATCGCAAA
CATCAAAGGCATCAGTCCTTCTTTCTGCATGGATAAGATAAGGTTAGAAGAAGAAGGGAAGCAAT
CCATTAAGCAACGAAGATGACTCAATGAGAAAATGAAAGAAGTGGTAAAGAAAGAAATCATCAAA
TGCTTAGATGCGGGCATACA
Found at i:890623 original size:21 final size:21
Alignment explanation
Indices: 890593--890640 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
890583 GAAGTAAATC
* *
890593 AAGAAGATGAGAAA-GAGGAGG
1 AAGAAAATGA-AAACGAGAAGG
890614 AAGAAAATGAAAACGAGAAGG
1 AAGAAAATGAAAACGAGAAGG
890635 AAGAAA
1 AAGAAA
890641 CAGAGCCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.60, C:0.02, G:0.33, T:0.04
Consensus pattern (21 bp):
AAGAAAATGAAAACGAGAAGG
Found at i:902034 original size:123 final size:123
Alignment explanation
Indices: 901809--902063 Score: 352
Period size: 123 Copynumber: 2.1 Consensus size: 123
901799 AATACCATCA
* * * * **
901809 ATGGGGTTTGAAGTTTCACTCATATTGAGTTTCGTTTCATTGATTTGGTCTACTTCTCTGTATCT
1 ATGGAGTTTGAAGTTTCACTCACATTGAGCTTCGCTTCATTGATTCAGTCTACTTCTCTGTATCT
* * ** *
901874 CATCAGGAAGGTGACCACTTCATTGTTTTGACCCACTTCTTTGTGTCTCATCAGGAAG
66 CATCAGGAAGATGACCACTTCATTCTTTTGACCCACTTCTTTGTACCTCATCAGAAAG
901932 ATGGAGTTTGAAGTTAT-ACTCACATTGAGCTTCGCTTCATTGATTCAGTCTACTTCTCTGTATC
1 ATGGAGTTTGAAGTT-TCACTCACATTGAGCTTCGCTTCATTGATTCAGTCTACTTCTCTGTATC
* ** *
901996 TCATCAGGAAGATGACCGCTTCATTCTTTTGATTCACTTCTTTGTACCTTATCAGAAAG
65 TCATCAGGAAGATGACCACTTCATTCTTTTGACCCACTTCTTTGTACCTCATCAGAAAG
902055 ATGGA-TTTG
1 ATGGAGTTTG
902064 GTCCACTCCT
Statistics
Matches: 116, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
122 4 0.03
123 111 0.96
124 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.40
Consensus pattern (123 bp):
ATGGAGTTTGAAGTTTCACTCACATTGAGCTTCGCTTCATTGATTCAGTCTACTTCTCTGTATCT
CATCAGGAAGATGACCACTTCATTCTTTTGACCCACTTCTTTGTACCTCATCAGAAAG
Found at i:902257 original size:78 final size:76
Alignment explanation
Indices: 902099--902259 Score: 216
Period size: 78 Copynumber: 2.1 Consensus size: 76
902089 AAGATAATTG
* * *
902099 CTTCATCATTTTGATCCACTTCTCTGTATTTCATCAAGAAGATGAGGGTTTGAAGTTTCACTCAC
1 CTTCATTATTTTGATCCACTTCTCTATATTTCATCAAGAAGATGAGAGTTTGAAGTTTCACTCAC
**
902164 ATTGAGCTTTG
66 ATTGAGCTTCA
* * *
902175 CTTCATTATTTTGGTCCACTTCTCTATATCTCATCATCAGGAAGATG-GAGTTTGAAGTTTTACT
1 CTTCATTATTTTGATCCACTTCTCTATAT-T--TCATCAAGAAGATGAGAGTTTGAAGTTTCACT
902239 CACATTGAGCTTCA
63 CACATTGAGCTTCA
902253 CTTCATT
1 CTTCATT
902260 GATTCGGTCT
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
76 26 0.35
77 1 0.01
78 34 0.46
79 13 0.18
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (76 bp):
CTTCATTATTTTGATCCACTTCTCTATATTTCATCAAGAAGATGAGAGTTTGAAGTTTCACTCAC
ATTGAGCTTCA
Found at i:902418 original size:85 final size:85
Alignment explanation
Indices: 902273--902428 Score: 222
Period size: 85 Copynumber: 1.8 Consensus size: 85
902263 TCGGTCTACT
* * * *
902273 TCTGTATCTCATCAAGAAGATGACCACTTCATTATTTTAATCCAGTTCTGTATATCTCATCAGGA
1 TCTGTATATCATCAAGAAGATGACCACTTCATCATTTTAATCAACTTCTGTATATCTCATCAGGA
902338 AGATGAATTTGATCCACTTC
66 AGATGAATTTGATCCACTTC
* * * * * *
902358 TCTGTATATCATCAAGAAGATGATCACTTCATCATTTTGATCAACTTTTTTGTATTTCATCAGGA
1 TCTGTATATCATCAAGAAGATGACCACTTCATCATTTTAATCAACTTCTGTATATCTCATCAGGA
902423 AGATGA
66 AGATGA
902429 GGGTTTGAAG
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
85 61 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (85 bp):
TCTGTATATCATCAAGAAGATGACCACTTCATCATTTTAATCAACTTCTGTATATCTCATCAGGA
AGATGAATTTGATCCACTTC
Found at i:902427 original size:285 final size:287
Alignment explanation
Indices: 901921--902493 Score: 835
Period size: 285 Copynumber: 2.0 Consensus size: 287
901911 TCTTTGTGTC
*
901921 TCATCAGGAAGATGGAGTTTGAAGTTATACTCACATTGAGCTTCGCTTCATTGATTCAGTCTACT
1 TCATCAGGAAGATGGAGTTTGAAGTTATACTCACATTGAGCTTCACTTCATTGATTCAGTCTACT
* * * * * * * *
901986 TCTCTGTATCTCATCAGGAAGATGACCGCTTCATTCTTTTGATTCACTTCTTTGTACCTTATCAG
66 TCTCTGTATCTCATCAAGAAGATGACCACTTCATTATTTTAATCCACTTCTGTATACCTCATCAG
* * * * * * ** *
902051 AAAGATGGATTTGGTCCACTCCTTTGTATCTTATCAGGAAGATAATTGCTTCATCATTTTGATCC
131 AAAGATGAATTTGATCCACTCCTCTGTATATCATCAAGAAGATAATCACTTCATCATTTTGATCA
**
902116 ACTTCTCTGTATTTCATCAAGAAGATGAGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCAT
196 ACTTCTCTGTATTTCATCAAGAAGATGAGGGTTTGAAGTTTCACTCACATTGAGCTTCACTTCAT
902181 TATTTTGGTCCACTTCTCTATATCTCA
261 TATTTTGGTCCACTTCTCTATATCTCA
* *
902208 TCATCAGGAAGATGGAGTTTGAAGTTTTACTCACATTGAGCTTCACTTCATTGATTCGGTCTAC-
1 TCATCAGGAAGATGGAGTTTGAAGTTATACTCACATTGAGCTTCACTTCATTGATTCAGTCTACT
* *
902272 T-TCTGTATCTCATCAAGAAGATGACCACTTCATTATTTTAATCCAGTTCTGTATATCTCATCAG
66 TCTCTGTATCTCATCAAGAAGATGACCACTTCATTATTTTAATCCACTTCTGTATACCTCATCAG
* * *
902336 GAAGATGAATTTGATCCACTTCTCTGTATATCATCAAGAAGATGATCACTTCATCATTTTGATCA
131 AAAGATGAATTTGATCCACTCCTCTGTATATCATCAAGAAGATAATCACTTCATCATTTTGATCA
* * *
902401 ACTTTTTTGTATTTCATCAGGAAGATGAGGGTTTGAAGTTTCACTCACATTGAGCTTCACTTCAT
196 ACTTCTCTGTATTTCATCAAGAAGATGAGGGTTTGAAGTTTCACTCACATTGAGCTTCACTTCAT
* * *
902466 TGTTTTGGTCTACTTCTCTGTATCTCA
261 TATTTTGGTCCACTTCTCTATATCTCA
902493 T
1 T
902494 TAGGAAGATG
Statistics
Matches: 253, Mismatches: 33, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
285 191 0.75
286 1 0.00
287 61 0.24
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (287 bp):
TCATCAGGAAGATGGAGTTTGAAGTTATACTCACATTGAGCTTCACTTCATTGATTCAGTCTACT
TCTCTGTATCTCATCAAGAAGATGACCACTTCATTATTTTAATCCACTTCTGTATACCTCATCAG
AAAGATGAATTTGATCCACTCCTCTGTATATCATCAAGAAGATAATCACTTCATCATTTTGATCA
ACTTCTCTGTATTTCATCAAGAAGATGAGGGTTTGAAGTTTCACTCACATTGAGCTTCACTTCAT
TATTTTGGTCCACTTCTCTATATCTCA
Found at i:902578 original size:124 final size:124
Alignment explanation
Indices: 902353--902596 Score: 362
Period size: 124 Copynumber: 2.0 Consensus size: 124
902343 AATTTGATCC
* * * *
902353 ACTTCTCTGTATATCATCAAGAAGATGATCACTTCATCATTTTGATCAACTTTTTTGTATTTCAT
1 ACTTCTCTGTATATCATCAAGAAGATGATCACTTCATCATTTTGATCAACTTCTCTATATCTCAT
* *
902418 CAGGAAGATGAGGGTTTGAAGTTTCACTCACATTGAGCTTCACTTCATTGTTTTGGTCT
66 CAGGAAGATGAGGGTTTGAAGTTTCACTCACATTGAGCTCCACTTCATTATTTTGGTCT
* * * * *
902477 ACTTCTCTGTATCTCATTAGGAAGATGATCGCTTCATCATTTTGATCCACTTCTCTATATCTCAT
1 ACTTCTCTGTATATCATCAAGAAGATGATCACTTCATCATTTTGATCAACTTCTCTATATCTCAT
* **
902542 CAGGAAGATGGGGGTTTGAAGTTTCACTCATGTTGAGCTCCACTTCATTATTTTG
66 CAGGAAGATGAGGGTTTGAAGTTTCACTCACATTGAGCTCCACTTCATTATTTTG
902597 ATCCACTGTA
Statistics
Matches: 106, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
124 106 1.00
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (124 bp):
ACTTCTCTGTATATCATCAAGAAGATGATCACTTCATCATTTTGATCAACTTCTCTATATCTCAT
CAGGAAGATGAGGGTTTGAAGTTTCACTCACATTGAGCTCCACTTCATTATTTTGGTCT
Found at i:902694 original size:46 final size:46
Alignment explanation
Indices: 902626--902862 Score: 175
Period size: 45 Copynumber: 5.2 Consensus size: 46
902616 AGATAATAGT
* *
902626 TTCAATCTGCCCCTT-TTAACTTAAGGGCGAAAGATTGGATGATGAC
1 TTCAATCTG-CCCTTCTTGACTTAAGGGCAAAAGATTGGATGATGAC
* * * *
902672 TTCAATTTGCCCTTCTTGACTTAGGGGTAAAAGATTGGATGATGGC
1 TTCAATCTGCCCTTCTTGACTTAAGGGCAAAAGATTGGATGATGAC
* * * *
902718 TTCAATCTGCCCTTCTTGAC-TAGGGGTAGAAGATTGGAATG-TGGC
1 TTCAATCTGCCCTTCTTGACTTAAGGGCAAAAGATTGG-ATGATGAC
* * * * * * * *
902763 TTTAATTTGCCCCTATTGA-TTCAGGGTAAATGATTGGAATG-TGGC
1 TTCAATCTGCCCTTCTTGACTTAAGGGCAAAAGATTGG-ATGATGAC
* * * *
902808 TTTC-ATCTGCCCTTCTTGA-AT-AGGTGTAAAAGATTGGAAGATGGC
1 -TTCAATCTGCCCTTCTTGACTTAAGG-GCAAAAGATTGGATGATGAC
902853 TTCAATCTGC
1 TTCAATCTGC
902863 AACATGGTCG
Statistics
Matches: 161, Mismatches: 23, Indels: 15
0.81 0.12 0.08
Matches are distributed among these distances:
44 8 0.05
45 95 0.59
46 58 0.36
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (46 bp):
TTCAATCTGCCCTTCTTGACTTAAGGGCAAAAGATTGGATGATGAC
Found at i:902763 original size:45 final size:46
Alignment explanation
Indices: 902655--902862 Score: 241
Period size: 45 Copynumber: 4.6 Consensus size: 46
902645 CTTAAGGGCG
* *
902655 AAAGATTGG-ATGATGACTTCAATTTGCCCTTCTTGACTTAGGGGTA
1 AAAGATTGGAATGATGGCTTCAATCTGCCCTTCTTGAC-TAGGGGTA
902701 AAAGATTGG-ATGATGGCTTCAATCTGCCCTTCTTGACTAGGGGTA
1 AAAGATTGGAATGATGGCTTCAATCTGCCCTTCTTGACTAGGGGTA
* * * * * *
902746 GAAGATTGGAATG-TGGCTTTAATTTGCCCCTATTGATTCA-GGGTA
1 AAAGATTGGAATGATGGCTTCAATCTGCCCTTCTTGACT-AGGGGTA
* * *
902791 AATGATTGGAATG-TGGCTTTC-ATCTGCCCTTCTTGAATAGGTGTA
1 AAAGATTGGAATGATGGC-TTCAATCTGCCCTTCTTGACTAGGGGTA
902836 AAAGATTGGAA-GATGGCTTCAATCTGC
1 AAAGATTGGAATGATGGCTTCAATCTGC
902863 AACATGGTCG
Statistics
Matches: 139, Mismatches: 17, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
44 5 0.04
45 93 0.67
46 41 0.29
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.34
Consensus pattern (46 bp):
AAAGATTGGAATGATGGCTTCAATCTGCCCTTCTTGACTAGGGGTA
Found at i:903225 original size:49 final size:49
Alignment explanation
Indices: 903179--903430 Score: 174
Period size: 49 Copynumber: 5.2 Consensus size: 49
903169 TGCGGCTTTG
* * *
903179 ATCTTTCCTTTCACATCTCTACGGTATAAGGTTCGTCGTTGTGGCTTCCA
1 ATCTTTCCTTTCACATCTCTAAGGTATAAGATTCATCGTTGTGGCTT-CA
* * * *
903229 CAT-TTCCCTCTT-A-ATCTTTAAGGTATAAAATTCACCGTTGTGGCTTCA
1 -ATCTTTCCT-TTCACATCTCTAAGGTATAAGATTCATCGTTGTGGCTTCA
* * * * *
903277 ATCTTTCCCTTCACATCACTAAGGTATAAGGTTTATCGTTGTAGCTTCA
1 ATCTTTCCTTTCACATCTCTAAGGTATAAGATTCATCGTTGTGGCTTCA
* * * ** * * * *
903326 ACCTCTCCTATCAC-TCTCTAAGGTATAAGATTCGCCATTATGACTTTA
1 ATCTTTCCTTTCACATCTCTAAGGTATAAGATTCATCGTTGTGGCTTCA
* * ** * *
903374 ATCTCTTCC-TTCACAT-TCTTATGGTACAAGATTCGCCATTGCGGCTTCA
1 ATCT-TTCCTTTCACATCTC-TAAGGTATAAGATTCATCGTTGTGGCTTCA
903423 ATCTTTCC
1 ATCTTTCC
903431 CATCTCGTCT
Statistics
Matches: 155, Mismatches: 39, Indels: 17
0.73 0.18 0.08
Matches are distributed among these distances:
47 4 0.03
48 44 0.28
49 97 0.63
50 6 0.04
51 4 0.03
ACGTcount: A:0.22, C:0.26, G:0.13, T:0.38
Consensus pattern (49 bp):
ATCTTTCCTTTCACATCTCTAAGGTATAAGATTCATCGTTGTGGCTTCA
Found at i:904331 original size:16 final size:17
Alignment explanation
Indices: 904312--904348 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
904302 TTCTATTTCC
904312 TTTTCT-TTC-CTTTATT
1 TTTTCTCTTCTCTTT-TT
904328 TTTTCTCTTCTCTTTTT
1 TTTTCTCTTCTCTTTTT
904345 TTTT
1 TTTT
904349 TAGTAAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.32
17 9 0.47
18 4 0.21
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTCTCTTCTCTTTTT
Found at i:905230 original size:18 final size:19
Alignment explanation
Indices: 905189--905232 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
905179 TCATCGCGAA
*
905189 TTTTCCTTCTTTTCTTCGC
1 TTTTCTTTCTTTTCTTCGC
905208 TTTTCTTTCTCTTT-TTC-C
1 TTTTCTTTCT-TTTCTTCGC
905226 TTTTCTT
1 TTTTCTT
905233 GGGTTTTAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 12 0.52
20 3 0.13
ACGTcount: A:0.00, C:0.27, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTTCTTTCTTTTCTTCGC
Found at i:909173 original size:13 final size:13
Alignment explanation
Indices: 909155--909179 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
909145 AATTAAACCA
909155 AAAATTAAAAATT
1 AAAATTAAAAATT
909168 AAAATTAAAAAT
1 AAAATTAAAAAT
909180 AAATTTGGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAATTAAAAATT
Found at i:913202 original size:39 final size:39
Alignment explanation
Indices: 913148--913227 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
913138 GAAGGAGATA
913148 AATATCAAGGAGTAAAGAATTTAAATCCAAAAATCTCTC
1 AATATCAAGGAGTAAAGAATTTAAATCCAAAAATCTCTC
913187 AATATCAAGGAGTAAAGAATTTAAATCCAAAAATCTCTC
1 AATATCAAGGAGTAAAGAATTTAAATCCAAAAATCTCTC
913226 AA
1 AA
913228 ATCTTCAAGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (39 bp):
AATATCAAGGAGTAAAGAATTTAAATCCAAAAATCTCTC
Found at i:917512 original size:15 final size:15
Alignment explanation
Indices: 917492--917524 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
917482 TACTTTGCAA
917492 TGCTCCTTCCCTCTT
1 TGCTCCTTCCCTCTT
917507 TGCTCCTTCCCTCTT
1 TGCTCCTTCCCTCTT
917522 TGC
1 TGC
917525 GTAGGATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.45, G:0.09, T:0.45
Consensus pattern (15 bp):
TGCTCCTTCCCTCTT
Found at i:917763 original size:18 final size:18
Alignment explanation
Indices: 917742--917789 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
917732 GTCCTTGCAT
**
917742 TTGTGGTTGCAAACTTGA
1 TTGTGGTTGCAAACAAGA
* * *
917760 TTGTGGTGGTAATCAAGA
1 TTGTGGTTGCAAACAAGA
917778 TTGTGGTTGCAA
1 TTGTGGTTGCAA
917790 TTGACTATGT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.23, C:0.08, G:0.31, T:0.38
Consensus pattern (18 bp):
TTGTGGTTGCAAACAAGA
Found at i:922552 original size:36 final size:36
Alignment explanation
Indices: 922512--922610 Score: 137
Period size: 36 Copynumber: 2.8 Consensus size: 36
922502 AAGGTCATGC
*
922512 TTACTACCTGTTGACCCAAAGATCA-GAATGCTCATT
1 TTACTCCCTGTTGACCCAAAGATCATG-ATGCTCATT
* *
922548 TTACTCCCTGTTGACCCAAAGGTCATGTTGCTCATT
1 TTACTCCCTGTTGACCCAAAGATCATGATGCTCATT
* *
922584 TTACTCCCTGTTGACCTAAAGGTCATG
1 TTACTCCCTGTTGACCCAAAGATCATG
922611 CCTGTTACCA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 57 0.98
37 1 0.02
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.33
Consensus pattern (36 bp):
TTACTCCCTGTTGACCCAAAGATCATGATGCTCATT
Found at i:923329 original size:10 final size:10
Alignment explanation
Indices: 923314--923342 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
923304 CTTTAACATG
923314 AAAATTACTA
1 AAAATTACTA
923324 AAAATTACTA
1 AAAATTACTA
923334 AAAATTACT
1 AAAATTACT
923343 TTATAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAATTACTA
Found at i:927990 original size:36 final size:36
Alignment explanation
Indices: 927943--928041 Score: 153
Period size: 36 Copynumber: 2.8 Consensus size: 36
927933 AAGGTCATGC
* *
927943 TTACTGCCTGTTGACCCAAAGATCATGATGCTCATT
1 TTACTCCCTGTTGACCCAAAGGTCATGATGCTCATT
* *
927979 TTACTCCCTGTTGACCTAAAGGTCATGTTGCTCATT
1 TTACTCCCTGTTGACCCAAAGGTCATGATGCTCATT
*
928015 TTACTCTCTGTTGACCCAAAGGTCATG
1 TTACTCCCTGTTGACCCAAAGGTCATG
928042 CTTGTTACTA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.35
Consensus pattern (36 bp):
TTACTCCCTGTTGACCCAAAGGTCATGATGCTCATT
Found at i:932198 original size:21 final size:22
Alignment explanation
Indices: 932149--932198 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
932139 AAACAACTCA
*
932149 TGAAAC-AGTGCAGACTTCTAC
1 TGAAACAAGTGAAGACTTCTAC
*
932170 -CAATACAAGTGAAG-CTTCTAC
1 TGAA-ACAAGTGAAGACTTCTAC
932191 TGAAACAA
1 TGAAACAA
932199 ATCATGCTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 6
0.72 0.09 0.19
Matches are distributed among these distances:
20 2 0.09
21 13 0.57
22 8 0.35
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (22 bp):
TGAAACAAGTGAAGACTTCTAC
Found at i:932843 original size:36 final size:36
Alignment explanation
Indices: 932802--932893 Score: 103
Period size: 36 Copynumber: 2.6 Consensus size: 36
932792 AAGGTCATGC
* **
932802 CTACTCCCTGTTGACCCAAAGATCGTGATGGTCATT
1 CTACTCCCTGTTGACCCAAAGATCATGATGCACATT
** ** *
932838 CTACTCCCCATTGACTTAAAGGTCATGATGCACATT
1 CTACTCCCTGTTGACCCAAAGATCATGATGCACATT
*
932874 TTACTCCCTGTTGACCCAAA
1 CTACTCCCTGTTGACCCAAA
932894 TGTCATACCT
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.30
Consensus pattern (36 bp):
CTACTCCCTGTTGACCCAAAGATCATGATGCACATT
Found at i:936668 original size:41 final size:41
Alignment explanation
Indices: 936621--936702 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
936611 CTTCAACACT
936621 TACCTTTTCATTACCTAGGAGCTTTTTCTTACTTGTGCATA
1 TACCTTTTCATTACCTAGGAGCTTTTTCTTACTTGTGCATA
936662 TACCTTTTCATTACCTAGGAGCTTTTTCTTACTTGTGCATA
1 TACCTTTTCATTACCTAGGAGCTTTTTCTTACTTGTGCATA
936703 ATTCCTTTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.20, C:0.22, G:0.12, T:0.46
Consensus pattern (41 bp):
TACCTTTTCATTACCTAGGAGCTTTTTCTTACTTGTGCATA
Found at i:940681 original size:18 final size:18
Alignment explanation
Indices: 940654--940700 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
940644 CAACTAAAGT
* *
940654 AAAATGAAATGTAATGAC
1 AAAATAAAATGCAATGAC
940672 AAAATAAAATGCAATGAC
1 AAAATAAAATGCAATGAC
940690 --AATAAAATGCA
1 AAAATAAAATGCA
940701 TGCAAACTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 11 0.41
18 16 0.59
ACGTcount: A:0.60, C:0.09, G:0.13, T:0.19
Consensus pattern (18 bp):
AAAATAAAATGCAATGAC
Found at i:948732 original size:14 final size:15
Alignment explanation
Indices: 948715--948747 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
948705 CAAAAGAAAT
948715 AAAAGAAA-ATAAAC
1 AAAAGAAAGATAAAC
*
948729 AAAAGAAAGTTAAAC
1 AAAAGAAAGATAAAC
948744 AAAA
1 AAAA
948748 ATTTAAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.76, C:0.06, G:0.09, T:0.09
Consensus pattern (15 bp):
AAAAGAAAGATAAAC
Found at i:950705 original size:13 final size:13
Alignment explanation
Indices: 950680--950715 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
950670 AACAGTTTTA
950680 AAAATACAGAAAAT
1 AAAATA-AGAAAAT
950694 AAAATAAGAAAAT
1 AAAATAAGAAAAT
950707 AAATATAAG
1 AAA-ATAAG
950716 TTTGTAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.17
Consensus pattern (13 bp):
AAAATAAGAAAAT
Found at i:967139 original size:30 final size:28
Alignment explanation
Indices: 967102--967183 Score: 92
Period size: 30 Copynumber: 2.9 Consensus size: 28
967092 TAGAAATTAT
*
967102 AAAATTATTAATATTATAAAAAAATATGA
1 AAAATTATTAAAATTATAAAAAAATA-GA
* * * *
967131 AAGAATTATAAAAATTTTAAACATATAGA
1 AA-AATTATTAAAATTATAAAAAAATAGA
*
967160 AAAGTTATTAAAATTATAAAAAAA
1 AAAATTATTAAAATTATAAAAAAA
967184 ACTATAGAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
28 17 0.40
29 6 0.14
30 19 0.45
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (28 bp):
AAAATTATTAAAATTATAAAAAAATAGA
Found at i:967151 original size:9 final size:9
Alignment explanation
Indices: 967076--967257 Score: 71
Period size: 9 Copynumber: 18.9 Consensus size: 9
967066 GTAAAATACG
*
967076 AAAATTACA
1 AAAATTATA
**
967085 AAAAAAATA
1 AAAATTATA
*
967094 GAAATTAT-
1 AAAATTATA
*
967102 AAAATTATT
1 AAAATTATA
*
967111 AATATTATAA
1 AAAATTAT-A
*
967121 AAAAATATGA
1 AAAATTAT-A
967131 AAGAATTATA
1 AA-AATTATA
*
967141 AAAATTTTA
1 AAAATTATA
*
967150 AACA-TATA
1 AAAATTATA
*
967158 GAAAAGTTATT
1 -AAAA-TTATA
967169 AAAATTATAAAA
1 AAAATTAT---A
*
967181 AAAACTATAGAA
1 AAAA-T-TA-TA
967193 AAAAGTTATA
1 AAAA-TTATA
*
967203 GAAAATTATT
1 -AAAATTATA
*
967213 AAAATGATA
1 AAAATTATA
*
967222 AAAAGTATA
1 AAAATTATA
* *
967231 AGAATTGTTA
1 AAAATT-ATA
*
967241 AATATTATA
1 AAAATTATA
967250 AAAATTAT
1 AAAATTAT
967258 TTAAAAAGTT
Statistics
Matches: 125, Mismatches: 34, Indels: 28
0.67 0.18 0.15
Matches are distributed among these distances:
8 10 0.08
9 61 0.49
10 27 0.22
11 14 0.11
12 10 0.08
13 1 0.01
14 2 0.02
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.31
Consensus pattern (9 bp):
AAAATTATA
Found at i:967196 original size:13 final size:13
Alignment explanation
Indices: 967169--967207 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
967159 AAAAGTTATT
967169 AAAATTATA-AAA
1 AAAATTATAGAAA
*
967181 AAAACTATAGAAA
1 AAAATTATAGAAA
*
967194 AAAGTTATAGAAA
1 AAAATTATAGAAA
967207 A
1 A
967208 TTATTAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 8 0.35
13 15 0.65
ACGTcount: A:0.69, C:0.03, G:0.08, T:0.21
Consensus pattern (13 bp):
AAAATTATAGAAA
Found at i:967230 original size:28 final size:29
Alignment explanation
Indices: 967192--967257 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 29
967182 AAACTATAGA
967192 AAAAAGTTATAGAAAATTATTAAA-ATGAT
1 AAAAAGTTATA-AAAATTATTAAATATGAT
* * *
967221 AAAAAG-TATAAGAATTGTTAAATATTAT
1 AAAAAGTTATAAAAATTATTAAATATGAT
967249 AAAAA-TTAT
1 AAAAAGTTAT
967258 TTAAAAAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 10 0.31
28 16 0.50
29 6 0.19
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (29 bp):
AAAAAGTTATAAAAATTATTAAATATGAT
Found at i:968592 original size:153 final size:153
Alignment explanation
Indices: 968282--968582 Score: 514
Period size: 153 Copynumber: 2.0 Consensus size: 153
968272 GATTAAATCT
968282 TTTTGTAAAGCGATTCTTAAAAAAATTAGGGTTTAAGGACTAAAATGTGAAAATGATGAAAATAT
1 TTTTGTAAAGCGATTCTTAAAAAAATTAGGGTTTAAGGACTAAAATGTGAAAATGATGAAAATAT
* *
968347 ATGTATTGTTATGAAAATGATTGTGTGTAGCGGTTGGGTAGACACCCTAAGGAATTCAGTTATGG
66 ATGTATTGTTATGAAAATGATTGTGTGTAGCGATTGGGTAGACACCCTAAGGAATTCAGCTATGG
968412 TTGGTTGTATAAGAGAAAAAATA
131 TTGGTTGTATAAGAGAAAAAATA
* * ** *
968435 TTTTGTAAAGTGATTCTTGATGAAATTAGGGTTTAATGACTAAAATGTGAAAATGATGAAAATAT
1 TTTTGTAAAGCGATTCTTAAAAAAATTAGGGTTTAAGGACTAAAATGTGAAAATGATGAAAATAT
968500 ATGTATTGTTATGAAAATGATTGTGTGTAGCGATTGGGTAGACACCCTAAGGAATTC-GACTATG
66 ATGTATTGTTATGAAAATGATTGTGTGTAGCGATTGGGTAGACACCCTAAGGAATTCAG-CTATG
*
968564 GTTGGTTGTGTAAGAGAAA
130 GTTGGTTGTATAAGAGAAA
968583 TGTTATTTTG
Statistics
Matches: 139, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
152 1 0.01
153 138 0.99
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.34
Consensus pattern (153 bp):
TTTTGTAAAGCGATTCTTAAAAAAATTAGGGTTTAAGGACTAAAATGTGAAAATGATGAAAATAT
ATGTATTGTTATGAAAATGATTGTGTGTAGCGATTGGGTAGACACCCTAAGGAATTCAGCTATGG
TTGGTTGTATAAGAGAAAAAATA
Found at i:969946 original size:21 final size:21
Alignment explanation
Indices: 969916--969969 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
969906 GAAGTTTTTA
* *
969916 GTATCAGTAGAAG-CGTGACTT
1 GTATCGGTAGAAGTCCT-ACTT
*
969937 GTTTCGGTAGAAGTCCTACTT
1 GTATCGGTAGAAGTCCTACTT
969958 GTATCGGTAGAA
1 GTATCGGTAGAA
969970 TTATTTTAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGTCCTACTT
Found at i:973536 original size:23 final size:23
Alignment explanation
Indices: 973506--973554 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
973496 GAATAGAATG
973506 CTTCAACTTGTTCTTTATTTCCT
1 CTTCAACTTGTTCTTTATTTCCT
973529 CTTCAACTTGTTCTTTATTTCCT
1 CTTCAACTTGTTCTTTATTTCCT
973552 CTT
1 CTT
973555 AAGCATTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.12, C:0.27, G:0.04, T:0.57
Consensus pattern (23 bp):
CTTCAACTTGTTCTTTATTTCCT
Found at i:987509 original size:24 final size:25
Alignment explanation
Indices: 987459--987510 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
987449 CCCATAAAAG
* * *
987459 AAAAGAGAAAGAAATAAAATTTGAT
1 AAAAGAGAAAAAAATAAAATATAAT
*
987484 AAAA-AGAAAAAAATATAATATAAT
1 AAAAGAGAAAAAAATAAAATATAAT
987508 AAA
1 AAA
987511 TGTTGTATTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (25 bp):
AAAAGAGAAAAAAATAAAATATAAT
Found at i:996193 original size:36 final size:36
Alignment explanation
Indices: 996153--996227 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
996143 AGATATTGGC
996153 CTTTGGGCGTCACCCTCTTCTTTCTTC-TTCTTTCTT
1 CTTTGGGCGTCACCCTCTTCTTTCTTCTTTC-TTCTT
996189 CTTTGGGCGTCACCCTCTTCTTTCTTCTTTCTTCTT
1 CTTTGGGCGTCACCCTCTTCTTTCTTCTTTCTTCTT
996225 CTT
1 CTT
996228 CTTTTTCTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 35 0.92
37 3 0.08
ACGTcount: A:0.03, C:0.33, G:0.11, T:0.53
Consensus pattern (36 bp):
CTTTGGGCGTCACCCTCTTCTTTCTTCTTTCTTCTT
Found at i:996210 original size:3 final size:3
Alignment explanation
Indices: 996204--996254 Score: 75
Period size: 3 Copynumber: 16.3 Consensus size: 3
996194 GGCGTCACCC
*
996204 TCT TCTT TCT TCTT TCT TCT TCT TCT TTT TCT TCT TCT TCT TCT TCT
1 TCT TC-T TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
996251 TCT T
1 TCT T
996255 GTCTTTGCAC
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 38 0.86
4 6 0.14
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TCT
Found at i:1008774 original size:20 final size:20
Alignment explanation
Indices: 1008751--1008789 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1008741 ACTAAGTAAT
*
1008751 AAATAGGTTGAGTAAGGTTA
1 AAATAGGTTAAGTAAGGTTA
* *
1008771 AAATGGGTTAATTAAGGTT
1 AAATAGGTTAAGTAAGGTT
1008790 TAATAATGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.33
Consensus pattern (20 bp):
AAATAGGTTAAGTAAGGTTA
Found at i:1015408 original size:16 final size:16
Alignment explanation
Indices: 1015387--1015417 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1015377 TTGTGGATCC
1015387 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
1015403 CATTTTATCTTTATT
1 CATTTTACCTTTATT
1015418 TTCACATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:1020857 original size:20 final size:20
Alignment explanation
Indices: 1020795--1020863 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
1020785 AAGCTCGGTG
* * *
1020795 GTATCGATATTTTTACATGA
1 GTATCGATAATTTTAAATAA
*
1020815 GTATTGAT-ATTTTCATAA-AA
1 GTATCGATAATTTT-A-AATAA
*
1020835 GTATCGATAATTTTAAATCA
1 GTATCGATAATTTTAAATAA
1020855 GTATCGATA
1 GTATCGATA
1020864 CCAAACTGCA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 6 0.15
20 27 0.69
21 6 0.15
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (20 bp):
GTATCGATAATTTTAAATAA
Found at i:1022031 original size:18 final size:19
Alignment explanation
Indices: 1022010--1022054 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
1022000 CAAATTCTTC
*
1022010 TTCTTTCTCTC-TTTCTCT
1 TTCTTCCTCTCTTTTCTCT
1022028 TTCTTCCTCTCTTTTCTC-
1 TTCTTCCTCTCTTTTCTCT
1022046 TTCTTCCTC
1 TTCTTCCTC
1022055 AACACCCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (19 bp):
TTCTTCCTCTCTTTTCTCT
Found at i:1038766 original size:19 final size:16
Alignment explanation
Indices: 1038741--1038785 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 16
1038731 TTAATCATTT
1038741 GAAAAAGAAACAAAATGA
1 GAAAAAGAAACAAAA--A
*
1038759 GAAAAAAGAAAGAAAAA
1 G-AAAAAGAAACAAAAA
1038776 GAAAAAGAAA
1 GAAAAAGAAA
1038786 GAAGTTTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 9 0.36
17 2 0.08
18 1 0.04
19 13 0.52
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (16 bp):
GAAAAAGAAACAAAAA
Found at i:1044209 original size:21 final size:21
Alignment explanation
Indices: 1044183--1044226 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1044173 ACTCGTTTTC
*
1044183 TTACTCATGATTCTTTTGTTT
1 TTACTCATGATTCTTTTCTTT
**
1044204 TTACTCATTTTTCTTTTCTTT
1 TTACTCATGATTCTTTTCTTT
1044225 TT
1 TT
1044227 TATTTTTCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.11, C:0.16, G:0.05, T:0.68
Consensus pattern (21 bp):
TTACTCATGATTCTTTTCTTT
Found at i:1046921 original size:13 final size:12
Alignment explanation
Indices: 1046905--1046943 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
1046895 TTCTTTTTAT
*
1046905 TTTTTATTTTTCC
1 TTTTTAATTTT-C
1046918 TTTTTAATTTTC
1 TTTTTAATTTTC
1046930 TTTTTAATCTTTC
1 TTTTTAAT-TTTC
1046943 T
1 T
1046944 CGTTCCCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTAATTTTC
Found at i:1046934 original size:20 final size:20
Alignment explanation
Indices: 1046897--1046934 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1046887 TATAAAATTT
*
1046897 CTTTTTATTTTTTATTTTTC
1 CTTTTTATTTTCTATTTTTC
1046917 CTTTTTAATTTTCT-TTTT
1 CTTTTT-ATTTTCTATTTT
1046935 AATCTTTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (20 bp):
CTTTTTATTTTCTATTTTTC
Found at i:1048030 original size:19 final size:19
Alignment explanation
Indices: 1048006--1048045 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1047996 CTTTTCAAAA
*
1048006 AACCTAGAAATGTTGAATG
1 AACCTAGAAATGTCGAATG
1048025 AACCTAGAAATGTCGAATG
1 AACCTAGAAATGTCGAATG
1048044 AA
1 AA
1048046 TTCAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.23
Consensus pattern (19 bp):
AACCTAGAAATGTCGAATG
Found at i:1051959 original size:16 final size:16
Alignment explanation
Indices: 1051938--1051973 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1051928 AAATAATCCC
*
1051938 AAAATTACAAGTCTCA
1 AAAATTAAAAGTCTCA
1051954 AAAATTAAAAGTCTCA
1 AAAATTAAAAGTCTCA
1051970 AAAA
1 AAAA
1051974 CACTTTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.58, C:0.14, G:0.06, T:0.22
Consensus pattern (16 bp):
AAAATTAAAAGTCTCA
Found at i:1066625 original size:24 final size:25
Alignment explanation
Indices: 1066572--1066625 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
1066562 TAGGGTCTTT
**
1066572 TAAAAACTTTAAAATTATTTTATAA
1 TAAAAACTTTAAAATTATTAAATAA
*
1066597 -AAAAAATTTAAAATT-TTAAATTAA
1 TAAAAACTTTAAAATTATTAAA-TAA
1066621 TAAAA
1 TAAAA
1066626 GTAAAATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
23 3 0.12
24 17 0.71
25 4 0.17
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (25 bp):
TAAAAACTTTAAAATTATTAAATAA
Found at i:1085211 original size:22 final size:22
Alignment explanation
Indices: 1085183--1085229 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
1085173 TAAGTCAGAT
1085183 TTGCACACTAAAACTGTTAATA
1 TTGCACACTAAAACTGTTAATA
1085205 TTGCACACTAAAACTGTTAATA
1 TTGCACACTAAAACTGTTAATA
1085227 TTG
1 TTG
1085230 TTAATGCAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (22 bp):
TTGCACACTAAAACTGTTAATA
Found at i:1121381 original size:22 final size:21
Alignment explanation
Indices: 1121331--1121382 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
1121321 TCATTTGAAA
*
1121331 AAGGAAAATGAGAAAAAAAAG
1 AAGGAAAAAGAGAAAAAAAAG
**
1121352 AAACAAAAAGA-AAAGAGAAAAG
1 AAGGAAAAAGAGAAA-A-AAAAG
1121374 AAGGAAAAA
1 AAGGAAAAA
1121383 TGCTTGCTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
20 3 0.12
21 9 0.38
22 12 0.50
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.02
Consensus pattern (21 bp):
AAGGAAAAAGAGAAAAAAAAG
Found at i:1126389 original size:56 final size:56
Alignment explanation
Indices: 1126328--1126439 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
1126318 AGTATAATAG
1126328 ATAGATGAAAATCTATCAGATATCGATCCCACAAGGATGGCTGCTTATGTTTTTAA
1 ATAGATGAAAATCTATCAGATATCGATCCCACAAGGATGGCTGCTTATGTTTTTAA
1126384 ATAGATGAAAATCTATCAGATATCGATCCCACAAGGATGGCTGCTTATGTTTTTAA
1 ATAGATGAAAATCTATCAGATATCGATCCCACAAGGATGGCTGCTTATGTTTTTAA
1126440 TTGTAGATGC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (56 bp):
ATAGATGAAAATCTATCAGATATCGATCCCACAAGGATGGCTGCTTATGTTTTTAA
Found at i:1127586 original size:18 final size:20
Alignment explanation
Indices: 1127549--1127588 Score: 57
Period size: 18 Copynumber: 2.0 Consensus size: 20
1127539 AGCATCACTG
1127549 AGTTAGAAAATGCACTTACTA
1 AGTTAGAAAATG-ACTTACTA
1127570 AGTTA-AAAATG-CTTACTA
1 AGTTAGAAAATGACTTACTA
1127588 A
1 A
1127589 AAAATGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
20 6 0.32
21 5 0.26
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (20 bp):
AGTTAGAAAATGACTTACTA
Found at i:1138491 original size:19 final size:19
Alignment explanation
Indices: 1138463--1138500 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1138453 TAAACAAAAT
*
1138463 CGAAATATAAATAAAACAA
1 CGAAAAATAAATAAAACAA
*
1138482 CGAAAAATAAATAACACAA
1 CGAAAAATAAATAAAACAA
1138501 ATGTAAAGAA
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:0.68, C:0.13, G:0.05, T:0.13
Consensus pattern (19 bp):
CGAAAAATAAATAAAACAA
Found at i:1142581 original size:3 final size:3
Alignment explanation
Indices: 1142575--1142599 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1142565 AATACTACTA
1142575 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
1142600 CCTTGCATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:1147906 original size:59 final size:59
Alignment explanation
Indices: 1147814--1147938 Score: 232
Period size: 59 Copynumber: 2.1 Consensus size: 59
1147804 CAATGCCTTA
1147814 TGTCTTCCCTAAACACCTCAATATGCACAAATATTAATTTTATCACATAATCTCAAAAT
1 TGTCTTCCCTAAACACCTCAATATGCACAAATATTAATTTTATCACATAATCTCAAAAT
*
1147873 TGTCTTCCCTAAACACCTCGATATGCACAAATATTAATTTTATCACATAATCTCAAAAT
1 TGTCTTCCCTAAACACCTCAATATGCACAAATATTAATTTTATCACATAATCTCAAAAT
*
1147932 TATCTTC
1 TGTCTTC
1147939 TATCATATAT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 64 1.00
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (59 bp):
TGTCTTCCCTAAACACCTCAATATGCACAAATATTAATTTTATCACATAATCTCAAAAT
Found at i:1149689 original size:28 final size:28
Alignment explanation
Indices: 1149649--1149721 Score: 128
Period size: 28 Copynumber: 2.6 Consensus size: 28
1149639 ATCAGAACTA
1149649 TTGACCCAAAGGTCATGCTTACTACCTC
1 TTGACCCAAAGGTCATGCTTACTACCTC
* *
1149677 TTGACCCAAAGGTCATGCTTACTACTTG
1 TTGACCCAAAGGTCATGCTTACTACCTC
1149705 TTGACCCAAAGGTCATG
1 TTGACCCAAAGGTCATG
1149722 ATGCTCATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (28 bp):
TTGACCCAAAGGTCATGCTTACTACCTC
Found at i:1158105 original size:27 final size:25
Alignment explanation
Indices: 1158065--1158131 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 25
1158055 GACTTAAACG
* * *
1158065 AAAATAAATTTAAAGATG-ATTTATA
1 AAAATAAACTTAAACATGAATCT-TA
1158090 CAAAATGAAACTTAAACATGAATCTTA
1 -AAAAT-AAACTTAAACATGAATCTTA
1158117 AAAATAAAACTTAAA
1 AAAAT-AAACTTAAA
1158132 TCTCAATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
26 19 0.54
27 13 0.37
28 3 0.09
ACGTcount: A:0.58, C:0.07, G:0.06, T:0.28
Consensus pattern (25 bp):
AAAATAAACTTAAACATGAATCTTA
Found at i:1158441 original size:18 final size:19
Alignment explanation
Indices: 1158418--1158453 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1158408 TTAAAAAGCC
*
1158418 TAATTTG-ATTTTAGGGAT
1 TAATTTGAAATTTAGGGAT
1158436 TAATTTGAAATTTAGGGA
1 TAATTTGAAATTTAGGGA
1158454 ATTTTGAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (19 bp):
TAATTTGAAATTTAGGGAT
Found at i:1159219 original size:14 final size:14
Alignment explanation
Indices: 1159200--1159226 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1159190 CCAAACTTGA
1159200 ACTGTTCACCGTTC
1 ACTGTTCACCGTTC
1159214 ACTGTTCACCGTT
1 ACTGTTCACCGTT
1159227 GATCATTGAC
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:0.15, C:0.33, G:0.15, T:0.37
Consensus pattern (14 bp):
ACTGTTCACCGTTC
Found at i:1164126 original size:12 final size:13
Alignment explanation
Indices: 1164100--1164132 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
1164090 GATATGCATG
1164100 AAAACTAAAACTA
1 AAAACTAAAACTA
1164113 AAAACTAAAA-TA
1 AAAACTAAAACTA
1164125 AAAACTAA
1 AAAACTAA
1164133 CTCAATTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.73, C:0.12, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAACTAAAACTA
Found at i:1179083 original size:15 final size:16
Alignment explanation
Indices: 1179058--1179087 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1179048 ATTGAAAATT
1179058 ACTTAAAAACCTAATG
1 ACTTAAAAACCTAATG
1179074 ACTT-AAAACCTAAT
1 ACTTAAAAACCTAAT
1179088 CCTAAATTCA
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:0.50, C:0.20, G:0.03, T:0.27
Consensus pattern (16 bp):
ACTTAAAAACCTAATG
Found at i:1189912 original size:21 final size:21
Alignment explanation
Indices: 1189869--1189912 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1189859 CAATACAAGG
* *
1189869 GAATTATAATCAACATTAGCA
1 GAATTACAATCAACATAAGCA
* *
1189890 GAATTACAATCAGCATAATCA
1 GAATTACAATCAACATAAGCA
1189911 GA
1 GA
1189913 TGCATCCATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.25
Consensus pattern (21 bp):
GAATTACAATCAACATAAGCA
Found at i:1196489 original size:17 final size:17
Alignment explanation
Indices: 1196467--1196517 Score: 84
Period size: 17 Copynumber: 3.0 Consensus size: 17
1196457 TGTTAGTAAG
1196467 CATTGTCATTGCATTTT
1 CATTGTCATTGCATTTT
*
1196484 CATTGTCATTGCATTTC
1 CATTGTCATTGCATTTT
*
1196501 CATTATCATTGCATTTT
1 CATTGTCATTGCATTTT
1196518 AGTGCATTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.51
Consensus pattern (17 bp):
CATTGTCATTGCATTTT
Found at i:1198039 original size:22 final size:22
Alignment explanation
Indices: 1198011--1198059 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
1198001 CTCTCAAGGG
1198011 AGAATCGACGTAGGGAAGATGC
1 AGAATCGACGTAGGGAAGATGC
1198033 AGAATCGACGTAGGGAAGATGC
1 AGAATCGACGTAGGGAAGATGC
1198055 AGAAT
1 AGAAT
1198060 AGCTCTTGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.39, C:0.12, G:0.35, T:0.14
Consensus pattern (22 bp):
AGAATCGACGTAGGGAAGATGC
Found at i:1205307 original size:20 final size:20
Alignment explanation
Indices: 1205284--1205322 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1205274 ATTTAAGTAC
*
1205284 AAATT-TATTCTTTTATAATT
1 AAATTATATT-TTTGATAATT
1205304 AAATTATATTTTTGATAAT
1 AAATTATATTTTTGATAAT
1205323 AATTACTACG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (20 bp):
AAATTATATTTTTGATAATT
Found at i:1206727 original size:36 final size:36
Alignment explanation
Indices: 1206687--1206898 Score: 307
Period size: 36 Copynumber: 5.9 Consensus size: 36
1206677 CTGTCGTGAA
* *
1206687 AGTAAATATGTGGGTATGTTATTCATTCCATGAGAT
1 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAC
* * * *
1206723 AGTAATTATTTGTGTATGTTATTCATGCCATGTGAC
1 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAC
*
1206759 AGTAAATGTGTGGGTATGTTATTCATGCCATGAGAC
1 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAC
* * * * *
1206795 AGTAAATATGTAGGTAGGTTATTCATGTCATGTGAT
1 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAC
*
1206831 AGTAAATATGTGGGTGTGTTATTCATGCCATGAGAC
1 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAC
1206867 AGTAAATATGTGGGTATGTTATTCATGCCATG
1 AGTAAATATGTGGGTATGTTATTCATGCCATG
1206899 TGATAGTGAA
Statistics
Matches: 152, Mismatches: 24, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 152 1.00
ACGTcount: A:0.28, C:0.09, G:0.25, T:0.38
Consensus pattern (36 bp):
AGTAAATATGTGGGTATGTTATTCATGCCATGAGAC
Found at i:1207272 original size:66 final size:66
Alignment explanation
Indices: 1207161--1207285 Score: 173
Period size: 66 Copynumber: 1.9 Consensus size: 66
1207151 GGGAAATAAG
* * * *
1207161 GAGAGTGTTAGCTTTATCCTTCACTTTTAGGACATGTTTGGCTCTATGAGTCTTTTGGTTTGTTT
1 GAGAGTGTTAGCTTTATCCTTCACTTATAGGAAATGTTCGACTCTATGAGTCTTTTGGTTTGTTT
1207226 A
66 A
*
1207227 GAGAGTGTTAG-TTATATGCTTCACTTAT-GCGAAATGTTCGACTCTATGAGTCTTTTGGT
1 GAGAGTGTTAGCTT-TATCCTTCACTTATAG-GAAATGTTCGACTCTATGAGTCTTTTGGT
1207286 GTGATTGGAG
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
65 3 0.06
66 49 0.94
ACGTcount: A:0.19, C:0.14, G:0.23, T:0.44
Consensus pattern (66 bp):
GAGAGTGTTAGCTTTATCCTTCACTTATAGGAAATGTTCGACTCTATGAGTCTTTTGGTTTGTTT
A
Found at i:1207428 original size:23 final size:22
Alignment explanation
Indices: 1207374--1207480 Score: 128
Period size: 23 Copynumber: 4.8 Consensus size: 22
1207364 TTAAATGTGC
* *
1207374 TAAATATTACTGTGATTATGCT
1 TAAATATTAATGTGATTTTGCT
*
1207396 TGAATATTAATGTGATTTGTGCT
1 TAAATATTAATGTGATTT-TGCT
*
1207419 TAAA-AGTTAATGTGATTTATGTT
1 TAAATA-TTAATGTGATTT-TGCT
1207442 TAAATATTAATGTGAATTTT-CT
1 TAAATATTAATGTG-ATTTTGCT
1207464 TAAATATTAATGTGATT
1 TAAATATTAATGTGATT
1207481 AATGTTGAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
21 3 0.04
22 31 0.42
23 35 0.47
24 5 0.07
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.48
Consensus pattern (22 bp):
TAAATATTAATGTGATTTTGCT
Found at i:1207501 original size:45 final size:46
Alignment explanation
Indices: 1207369--1207493 Score: 154
Period size: 45 Copynumber: 2.8 Consensus size: 46
1207359 TATCATTAAA
*
1207369 TGTGC-TAAATATTACTGTGATTATGCTTG-AATATTAATGTG-ATT
1 TGTGCTTAAATATTAATGTGATTATG-TTGAAATATTAATGTGAATT
*
1207413 TGTGCTTAAA-AGTTAATGTGATTTATGTTTAAATATTAATGTGAATT
1 TGTGCTTAAATA-TTAATGTGA-TTATGTTGAAATATTAATGTGAATT
1207460 T-T-CTTAAATATTAATGTGATTAATGTTGAAATAT
1 TGTGCTTAAATATTAATGTGATT-ATGTTGAAATAT
1207494 CCATGTGACT
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
44 8 0.11
45 40 0.56
46 19 0.27
47 4 0.06
ACGTcount: A:0.34, C:0.04, G:0.16, T:0.46
Consensus pattern (46 bp):
TGTGCTTAAATATTAATGTGATTATGTTGAAATATTAATGTGAATT
Found at i:1207523 original size:10 final size:10
Alignment explanation
Indices: 1207504--1207533 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1207494 CCATGTGACT
1207504 AATGTAATTA
1 AATGTAATTA
*
1207514 AATGTGATTA
1 AATGTAATTA
1207524 AATGTAATTA
1 AATGTAATTA
1207534 GTATGTGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (10 bp):
AATGTAATTA
Found at i:1212513 original size:14 final size:15
Alignment explanation
Indices: 1212477--1212514 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1212467 TTAAAACAAC
*
1212477 ACAAAGAAAAGTGAA
1 ACAAATAAAAGTGAA
1212492 ACAAATAAAAGT-AA
1 ACAAATAAAAGTGAA
*
1212506 ATAAATAAA
1 ACAAATAAA
1212515 TGCATCGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.71, C:0.05, G:0.11, T:0.13
Consensus pattern (15 bp):
ACAAATAAAAGTGAA
Found at i:1235026 original size:21 final size:21
Alignment explanation
Indices: 1234997--1235036 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1234987 TTATAATACA
1234997 AAAAAAGAAAAGAAAAAGAGG
1 AAAAAAGAAAAGAAAAAGAGG
* *
1235018 AAAAGAGAAAAGAAGAAGA
1 AAAAAAGAAAAGAAAAAGA
1235037 AAGAAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (21 bp):
AAAAAAGAAAAGAAAAAGAGG
Found at i:1235276 original size:42 final size:42
Alignment explanation
Indices: 1235230--1235309 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
1235220 TCAAAAAAAT
* *
1235230 GAGACAGCTTTTAAAAATCAGCAAGCATCATTTCATGGTCTC
1 GAGACAGCTTTGAAAAATCAACAAGCATCATTTCATGGTCTC
*
1235272 GAGACAGCTTTGAAAAATCAACAAGTATCATTTCATGG
1 GAGACAGCTTTGAAAAATCAACAAGCATCATTTCATGG
1235310 CCTTGAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (42 bp):
GAGACAGCTTTGAAAAATCAACAAGCATCATTTCATGGTCTC
Found at i:1239551 original size:37 final size:37
Alignment explanation
Indices: 1239517--1239591 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
1239507 TATTGCGGTG
* * *
1239517 ATAGTTTTGGGTGCAATATGGAAGTGCTCATGCGGCA
1 ATAGATTTGGGCGCAATATAGAAGTGCTCATGCGGCA
* *
1239554 ATAGATTTGGGCGCAATCTAGAAGTGCTCATGCAGCA
1 ATAGATTTGGGCGCAATATAGAAGTGCTCATGCGGCA
1239591 A
1 A
1239592 CATTAGTAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.27
Consensus pattern (37 bp):
ATAGATTTGGGCGCAATATAGAAGTGCTCATGCGGCA
Found at i:1240648 original size:17 final size:17
Alignment explanation
Indices: 1240609--1240657 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
1240599 ATATATATGG
* **
1240609 AAATGTAATGACAATTT
1 AAATGTAGTGACAATAA
*
1240626 AGATGTAGTGACAATAA
1 AAATGTAGTGACAATAA
*
1240643 AAATGTAGGGACAAT
1 AAATGTAGTGACAAT
1240658 TATACTATAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.47, C:0.06, G:0.20, T:0.27
Consensus pattern (17 bp):
AAATGTAGTGACAATAA
Found at i:1241354 original size:12 final size:12
Alignment explanation
Indices: 1241337--1241361 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1241327 TTTGTCTCAA
1241337 CATCTTTTTCTT
1 CATCTTTTTCTT
1241349 CATCTTTTTCTT
1 CATCTTTTTCTT
1241361 C
1 C
1241362 CTCCACATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (12 bp):
CATCTTTTTCTT
Found at i:1243764 original size:26 final size:26
Alignment explanation
Indices: 1243721--1243774 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
1243711 ATTTTGGGCG
1243721 CAATTCTGGACACATTCATGCAACGA
1 CAATTCTGGACACATTCATGCAACGA
* ** *
1243747 CAATTCTGTACATGTTCATGCAGCGA
1 CAATTCTGGACACATTCATGCAACGA
1243773 CA
1 CA
1243775 TTCCTGGGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (26 bp):
CAATTCTGGACACATTCATGCAACGA
Found at i:1243918 original size:37 final size:37
Alignment explanation
Indices: 1243877--1243953 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 37
1243867 AAAATATTCC
* * ** *
1243877 TGCGGCGACAGTTTTGGGTGCAATCTGGAAGTGCTCA
1 TGCGGCAAAAGTTTTGGGCACAATCTAGAAGTGCTCA
1243914 TGCGGCAAAAGTTTTGGGCACAATCTAGAAGTGCTCA
1 TGCGGCAAAAGTTTTGGGCACAATCTAGAAGTGCTCA
1243951 TGC
1 TGC
1243954 AGAGACATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.26
Consensus pattern (37 bp):
TGCGGCAAAAGTTTTGGGCACAATCTAGAAGTGCTCA
Found at i:1248082 original size:15 final size:15
Alignment explanation
Indices: 1248064--1248101 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
1248054 TCGAAAAAAA
1248064 AAAAGAAAAAAATCG
1 AAAAGAAAAAAATCG
*
1248079 AAAAGAAAAAAATTG
1 AAAAGAAAAAAATCG
1248094 -AAAGAAAA
1 AAAAGAAAA
1248102 TTGAATTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.76, C:0.03, G:0.13, T:0.08
Consensus pattern (15 bp):
AAAAGAAAAAAATCG
Found at i:1248097 original size:29 final size:27
Alignment explanation
Indices: 1248057--1248131 Score: 80
Period size: 29 Copynumber: 2.7 Consensus size: 27
1248047 ATTTTGTTCG
1248057 AAAAAAAA-AAAGAAAAAAATCGAAAA
1 AAAAAAAAGAAAGAAAAAAATCGAAAA
* * *
1248083 GAAAAAAATTGAAAGAAAATTGAATTGAAAA
1 -AAAAAAA-AGAAAGAAAA--AAATCGAAAA
1248114 AAAAAAAAGAAAGAAAAA
1 AAAAAAAAGAAAGAAAAA
1248132 GAAAAAAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
27 7 0.18
29 17 0.44
30 7 0.18
31 8 0.21
ACGTcount: A:0.77, C:0.01, G:0.12, T:0.09
Consensus pattern (27 bp):
AAAAAAAAGAAAGAAAAAAATCGAAAA
Found at i:1253553 original size:209 final size:210
Alignment explanation
Indices: 1253035--1254865 Score: 2434
Period size: 210 Copynumber: 8.8 Consensus size: 210
1253025 GAGCGAATCA
* * * * **
1253035 AAACAAGTGATGCAGTCATCTTCCTAATGAGATACTAAAAAGTAGACCAAATCAAAGAAGTCAAA
1 AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAAAGAAACCAAA
* * * *
1253100 GCTCAATGTGAGCAAAACTTCAAACCCCAGCATCCTGATGAGATACTGAGCAGCAGGTCGAAGCA
66 GCTCAATGTGAGCAAAACTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
*
1253165 ATAAAATGGTCAACTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
131 ATAAAATGGTCAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
*
1253230 TAGAGAAGCGGATTG
196 CAGAGAAGCGGATTG
* *
1253245 AAACAAGTGACGCGGTCATCTTCCTGATGAGATATTGAGAAGTAGACCAAATCAAAGAAACCAAA
1 AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAAAGAAACCAAA
* * * *
1253310 GCTCAATGTGAGCAAAACTTTGAA-CCTCAGCTTCCTAATGAGATACTAAGAAGCAGGTCAAAGC
66 GCTCAATGTGAGCAAAACTTCGAACCCT-AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
*
1253374 AATAAAATGGTCAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCTTCTTCC-GATGAGAT
130 AATAAAATGGTCAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAT
1253438 ACAGAGAAGCGGATTG
195 ACAGAGAAGCGGATTG
** * * * *
1253454 AAACAAGTGATGCAATTATCTTCCTGTTGAGATACTGAGAAGTAGATCAAATCAAAGAAGCCAAA
1 AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAAAGAAACCAAA
* * *
1253519 GTTCAATGTGAGCAAAACTGCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTTGAAGCA
66 GCTCAATGTGAGCAAAACTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
* * *
1253584 ATAAAATGGTCAGCTTCCTAATGAGATACTGAGAAGTTGACCAAATTCGTCTTCTTGATGAGATA
131 ATAAAATGGTCAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
*
1253649 CAGAGAAGCTGATTG
196 CAGAGAAGCGGATTG
1253664 AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAAAGAAACCAAA
1 AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAAAGAAACCAAA
* * *
1253729 GCTCAATGTGAGCAAAACTTCGAATCCC-AGCTTCCTAATGAGATACTAAGAAGCAAGTCGAAGC
66 GCTCAATGTGAGCAAAACTTCGAA-CCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
*
1253793 AATAAAATGGTCAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCC-GATGAGAT
130 AATAAAATGGTCAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAT
1253857 ACAGAGAAGCGGATTG
195 ACAGAGAAGCGGATTG
* * *
1253873 AAACAAGTGATGCAGTTATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAAAGAAGCCAAA
1 AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAAAGAAACCAAA
1253938 GCTCAATGTGAGCAAAACTTCGAACCCTAGCTTCC---TGAGATACTGAGAAGCAGGTCGAAGCA
66 GCTCAATGTGAGCAAAACTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
* *
1254000 ATAAAATGGTCAGCTTCCTGGTGAGATATTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
131 ATAAAATGGTCAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
* *
1254065 TAGAGAAGTGGATTG
196 CAGAGAAGCGGATTG
* *
1254080 AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACC-AG
1 AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAAAGAAACCAAA
* * * * * *
1254144 GCTCAAAGTTAGCAAATCTTTGAACCCCAGC-TCTCTGATGAGATACTAAGAAGCAGGTCGAAGC
66 GCTCAATGTGAGCAAAACTTCGAACCCTAGCTTC-CTGATGAGATACTGAGAAGCAGGTCGAAGC
* * * * * * * *
1254208 AATAAAATGGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCTTGATGAGAC
130 AATAAAATGGTCAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAT
* **
1254273 ACAGAGAAGTGGATCA
195 ACAGAGAAGCGGATTG
* * * *
1254289 AAACAAGTGATGTGGTCATCTTCCTGATTAGATACTGAGAAGTAGACCAAATCAACGAAACCAAG
1 AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAAAGAAACCAAA
* * * * *
1254354 GCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAACCA
66 GCTCAATGTGAGCAAAACTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
* * * * * * * * *
1254419 ATAAAGCT-GTTAGGTTCCTGATGAGATGCAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGAC
131 ATAAA-ATGGTCAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAT
* * **
1254483 ACAAAGAAGTGGATCA
195 ACAGAGAAGCGGATTG
* * *
1254499 AAACAAGTGATGCGGTCATCTTCCTGATGAGATATTGAGAAGTAGA-CAAATCAATGAAA-CAAG
1 AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAAAGAAACCAAA
* * * * *
1254562 GCTTAAAGTGAGCAAATCTTTGAA-CCTCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAACC
66 GCTCAATGTGAGCAAAACTTCGAACCCT-AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
* * * * * * * *
1254626 AATAAAACGGTTACCTTCTTGATGAGATACAGAGAAGTGAACCAGATTCGTCTTCCTAATGAGAT
130 AATAAAATGGTCAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAT
* **
1254691 ACA-AGGAAGTGGATCA
195 ACAGA-GAAGCGGATTG
* * * *
1254707 AAACAAGTGTTGCTGTCATCTTCCTGATGAGATACTGAAAAGTAGACCAAATCAATGAAACCCAA
1 AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAAAGAAA-CCAA
* ** * * * *
1254772 AGCTCGATGTGAGTTAAACTTTGAACCCTAGCATCCTAATGAGATACTGAGAAGCAGGTCAAAGC
65 AGCTCAATGTGAGCAAAACTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAG-
*
1254837 CAA-AAAGTGGTC-GTCTTCCTGATGAGATA
129 CAATAAAATGGTCAG-CTTCCTGATGAGATA
1254866 TAAGGAAGAA
Statistics
Matches: 1458, Mismatches: 141, Indels: 43
0.89 0.09 0.03
Matches are distributed among these distances:
205 2 0.00
206 105 0.07
207 83 0.06
208 175 0.12
209 480 0.33
210 529 0.36
211 78 0.05
212 6 0.00
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.23
Consensus pattern (210 bp):
AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAAAGAAACCAAA
GCTCAATGTGAGCAAAACTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
ATAAAATGGTCAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
CAGAGAAGCGGATTG
Found at i:1253813 original size:419 final size:419
Alignment explanation
Indices: 1253020--1254865 Score: 2539
Period size: 419 Copynumber: 4.4 Consensus size: 419
1253010 GATCATAGGG
* * * * *
1253020 CAGAGGAGCGAATCAAAACAAGTGATGCAGTCATCTTCCTAATGAGATACTAAAAAGTAGACCAA
1 CAGAGAAGCGGATCAAAACAAGTGATGCAGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAA
* * * *
1253085 ATCAAAGAAGTCAAAGCTCAATGTGAGCAAAACTTCAAACCCCAGCATCCTGATGAGATACTGAG
66 ATCAAAGAAGCCAAAGCTCAATGTGAGCAAAACTTCGAACCCTAGCTTCCTGATGAGATACTGAG
* *
1253150 CAGCAGGTCGAAGCAATAAAATGGTCAACTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGT
131 AAGCAGGTCGAAGCAATAAAATGGTCAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGT
* * * *
1253215 CTTCCTGATGAGATATAGAGAAGCGGATTGAAACAAGTGACGCGGTCATCTTCCTGATGAGATAT
196 CTTCCTGATGAGATACAGAGAAGTGGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATAC
*
1253280 TGAGAAGTAGACCAAATCAAAGAAACCAAAGCTCAATGTGAGCAAAACTTTGAACCTCAGCTTCC
261 TGAGAAGTAGACCAAATCAAAGAAACCAAAGCTCAAAGTGAGCAAAACTTTGAACCTCAGCTTCC
* * *
1253345 TAATGAGATACTAAGAAGCAGGTCAAAGCAATAAAATGGTCAGCTTCCTGATGAGATACTGAGAA
326 TAATGAGATACTAAGAAGCAGGTCGAAGCAATAAAATGGTCACCTTCCTGATGAGATACAGAGAA
* *
1253410 GTGGACCAAATTCTTCTTCCGATGAGATA
391 GTGAACCAAATTCGTCTTCCGATGAGATA
** * * * *
1253439 CAGAGAAGCGGATTGAAACAAGTGATGCAATTATCTTCCTGTTGAGATACTGAGAAGTAGATCAA
1 CAGAGAAGCGGATCAAAACAAGTGATGCAGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAA
* *
1253504 ATCAAAGAAGCCAAAGTTCAATGTGAGCAAAACTGCGAACCCTAGCTTCCTGATGAGATACTGAG
66 ATCAAAGAAGCCAAAGCTCAATGTGAGCAAAACTTCGAACCCTAGCTTCCTGATGAGATACTGAG
* * *
1253569 AAGCAGGTTGAAGCAATAAAATGGTCAGCTTCCTAATGAGATACTGAGAAGTTGACCAAATTCGT
131 AAGCAGGTCGAAGCAATAAAATGGTCAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGT
*
1253634 CTTCTTGATGAGATACAGAGAAGCT-GATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATA
196 CTTCCTGATGAGATACAGAGAAG-TGGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATA
* *
1253698 CTGAGAAGTAGACCAAATCAAAGAAACCAAAGCTCAATGTGAGCAAAACTTCGAATCC-CAGCTT
260 CTGAGAAGTAGACCAAATCAAAGAAACCAAAGCTCAAAGTGAGCAAAACTTTGAA-CCTCAGCTT
* * *
1253762 CCTAATGAGATACTAAGAAGCAAGTCGAAGCAATAAAATGGTCAGCTTCCTGATGAGATACTGAG
324 CCTAATGAGATACTAAGAAGCAGGTCGAAGCAATAAAATGGTCACCTTCCTGATGAGATACAGAG
* *
1253827 AAGTGGACCAAATTCATCTTCCGATGAGATA
389 AAGTGAACCAAATTCGTCTTCCGATGAGATA
** *
1253858 CAGAGAAGCGGATTGAAACAAGTGATGCAGTTATCTTCCTGATGAGATACTGAGAAGTAGACCAA
1 CAGAGAAGCGGATCAAAACAAGTGATGCAGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAA
1253923 ATCAAAGAAGCCAAAGCTCAATGTGAGCAAAACTTCGAACCCTAGCTTCC---TGAGATACTGAG
66 ATCAAAGAAGCCAAAGCTCAATGTGAGCAAAACTTCGAACCCTAGCTTCCTGATGAGATACTGAG
* *
1253985 AAGCAGGTCGAAGCAATAAAATGGTCAGCTTCCTGGTGAGATATTGAGAAGTGGACCAAATTCGT
131 AAGCAGGTCGAAGCAATAAAATGGTCAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGT
*
1254050 CTTCCTGATGAGATATAGAGAAGTGGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATAC
196 CTTCCTGATGAGATACAGAGAAGTGGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATAC
* * * * *
1254115 TGAGAAGTAGACCAAATCAATGAAACC-AGGCTCAAAGTTAGCAAATCTTTGAACCCCAGC-TCT
261 TGAGAAGTAGACCAAATCAAAGAAACCAAAGCTCAAAGTGAGCAAAACTTTGAACCTCAGCTTC-
* *
1254178 CTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAATGGTTACCTTCCTGATGAGATACAGAGA
325 CTAATGAGATACTAAGAAGCAGGTCGAAGCAATAAAATGGTCACCTTCCTGATGAGATACAGAGA
* * * *
1254243 AGTGAACCAGATCCGTCTTCTTGATGAGACA
390 AGTGAACCAAATTCGTCTTC-CGATGAGATA
* ** *
1254274 CAGAGAAGTGGATCAAAACAAGTGATGTGGTCATCTTCCTGATTAGATACTGAGAAGTAGACCAA
1 CAGAGAAGCGGATCAAAACAAGTGATGCAGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAA
* * * * * *
1254339 ATCAACGAAACCAAGGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAG
66 ATCAAAGAAGCCAAAGCTCAATGTGAGCAAAACTTCGAACCCTAGCTTCCTGATGAGATACTGAG
* * * * * * * * * *
1254404 AAGCAGGTCAAACCAATAAAGCT-GTTAGGTTCCTGATGAGATGCAGAGAAGTGAACCAGATCCG
131 AAGCAGGTCGAAGCAATAAA-ATGGTCAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCG
* * **
1254468 TCTTCCTGATGAGACACAAAGAAGTGGATCAAAACAAGTGATGCGGTCATCTTCCTGATGAGATA
195 TCTTCCTGATGAGATACAGAGAAGTGGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATA
* * * * *
1254533 TTGAGAAGTAGA-CAAATCAATGAAA-CAAGGCTTAAAGTGAGCAAATCTTTGAACCTCAGCTTC
260 CTGAGAAGTAGACCAAATCAAAGAAACCAAAGCTCAAAGTGAGCAAAACTTTGAACCTCAGCTTC
* * * * * *
1254596 CTGATGAGATACTGAGAAGCAGGTCGAACCAATAAAACGGTTACCTTCTTGATGAGATACAGAGA
325 CTAATGAGATACTAAGAAGCAGGTCGAAGCAATAAAATGGTCACCTTCCTGATGAGATACAGAGA
* *
1254661 AGTGAACCAGATTCGTCTTCCTAATGAGATA
390 AGTGAACCAAATTCGTCTTCC-GATGAGATA
* * * *
1254692 CA-AGGAAGTGGATCAAAACAAGTGTTGCTGTCATCTTCCTGATGAGATACTGAAAAGTAGACCA
1 CAGA-GAAGCGGATCAAAACAAGTGATGCAGTCATCTTCCTGATGAGATACTGAGAAGTAGACCA
* * * ** * * *
1254756 AATCAATGAAACCCAAAGCTCGATGTGAGTTAAACTTTGAACCCTAGCATCCTAATGAGATACTG
65 AATCAAAG-AAGCCAAAGCTCAATGTGAGCAAAACTTCGAACCCTAGCTTCCTGATGAGATACTG
* *
1254821 AGAAGCAGGTCAAAGCCAA-AAAGTGGTC-GTCTTCCTGATGAGATA
129 AGAAGCAGGTCGAAG-CAATAAAATGGTCAG-CTTCCTGATGAGATA
1254866 TAAGGAAGAA
Statistics
Matches: 1285, Mismatches: 124, Indels: 36
0.89 0.09 0.02
Matches are distributed among these distances:
414 4 0.00
415 102 0.08
416 269 0.21
417 2 0.00
418 196 0.15
419 706 0.55
420 6 0.00
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (419 bp):
CAGAGAAGCGGATCAAAACAAGTGATGCAGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAA
ATCAAAGAAGCCAAAGCTCAATGTGAGCAAAACTTCGAACCCTAGCTTCCTGATGAGATACTGAG
AAGCAGGTCGAAGCAATAAAATGGTCAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGT
CTTCCTGATGAGATACAGAGAAGTGGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATAC
TGAGAAGTAGACCAAATCAAAGAAACCAAAGCTCAAAGTGAGCAAAACTTTGAACCTCAGCTTCC
TAATGAGATACTAAGAAGCAGGTCGAAGCAATAAAATGGTCACCTTCCTGATGAGATACAGAGAA
GTGAACCAAATTCGTCTTCCGATGAGATA
Found at i:1255293 original size:34 final size:34
Alignment explanation
Indices: 1255257--1255340 Score: 125
Period size: 34 Copynumber: 2.5 Consensus size: 34
1255247 AATTTTGGAT
* *
1255257 TTTTAAATTTTAATTTA-TTTAAGTTTAAATTTA
1 TTTTAAATTTAAACTTATTTTAAGTTTAAATTTA
*
1255290 TTTTAAATTTAAACTTATTTTGAGTTTAAATTTA
1 TTTTAAATTTAAACTTATTTTAAGTTTAAATTTA
*
1255324 TTTTAAATTAAAACTTA
1 TTTTAAATTTAAACTTA
1255341 ATTAAGAGTC
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 15 0.33
34 31 0.67
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (34 bp):
TTTTAAATTTAAACTTATTTTAAGTTTAAATTTA
Found at i:1255300 original size:17 final size:17
Alignment explanation
Indices: 1255257--1255332 Score: 100
Period size: 17 Copynumber: 4.5 Consensus size: 17
1255247 AATTTTGGAT
*
1255257 TTTTAAATTTTAATTTA
1 TTTTAAATTTAAATTTA
*
1255274 -TTTAAGTTTAAATTTA
1 TTTTAAATTTAAATTTA
*
1255290 TTTTAAATTTAAACTTA
1 TTTTAAATTTAAATTTA
* *
1255307 TTTTGAGTTTAAATTTA
1 TTTTAAATTTAAATTTA
1255324 TTTTAAATT
1 TTTTAAATT
1255333 AAAACTTAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
16 14 0.29
17 35 0.71
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.59
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:1256069 original size:3 final size:3
Alignment explanation
Indices: 1256063--1256089 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1256053 TTCATTAAAT
1256063 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1256090 CAAAAAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1257318 original size:59 final size:56
Alignment explanation
Indices: 1257210--1257464 Score: 226
Period size: 59 Copynumber: 4.4 Consensus size: 56
1257200 AAGTCCTTGT
* * * *
1257210 AACTCTCCAAAAATTATATTTTGACCCCCAAACTTTTAAAAATTACATTTTGACCCTCA
1 AACT-TCCAAAAATTACATTTTG-CCCTCAAACTTCTAAAAATTACATTTT-ACCCTCG
* *
1257269 AACTTCTCATAAATTACATTTTGCCCTTAAACTTCTAAAAATTACCATTTTACCCTCG
1 AACTTC-CAAAAATTACATTTTGCCCTCAAACTTCTAAAAATTA-CATTTTACCCTCG
** * *
1257327 AACTTCCAAAAAATCCCATTTTTACCCTCGAACTTCTAAAAATTAACATTTTACCCTCG
1 AACTTCC-AAAAATTACA-TTTTGCCCTCAAACTTCTAAAAATT-ACATTTTACCCTCG
* * * * * *
1257386 AATTTCCAAAAATTCCATTTTTAACCC-CAAACTTTTTGAAAATTACCATTTTACCC-CC
1 AACTTCCAAAAATTACA-TTTT-GCCCTCAAAC-TTCTAAAAATTA-CATTTTACCCTCG
* *
1257444 AATTTCCAAAAATTCCATTTT
1 AACTTCCAAAAATTACATTTT
1257465 TAACCTTGAA
Statistics
Matches: 170, Mismatches: 18, Indels: 18
0.83 0.09 0.09
Matches are distributed among these distances:
57 5 0.03
58 76 0.45
59 88 0.52
60 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (56 bp):
AACTTCCAAAAATTACATTTTGCCCTCAAACTTCTAAAAATTACATTTTACCCTCG
Found at i:1257465 original size:58 final size:59
Alignment explanation
Indices: 1257215--1257498 Score: 269
Period size: 58 Copynumber: 4.9 Consensus size: 59
1257205 CTTGTAACTC
** * * * * *
1257215 TCCAAAAATTATATTTTGACCCCCAAACTTT-TAAAAATTA-CATTTTGACCCTCAAACT
1 TCCAAAAATTCCATTTTTAACCCCGAACTTTCTAAAAATTACCATTTT-ACCCTCGAATT
* * * ** *
1257273 TCTCATAAATTACA-TTTT-GCCCTTAAAC-TTCTAAAAATTACCATTTTACCCTCGAACT
1 TC-CAAAAATTCCATTTTTAACCC-CGAACTTTCTAAAAATTACCATTTTACCCTCGAATT
* *
1257331 TCCAAAAAATCCCATTTTT-ACCCTCGAAC-TTCTAAAAATTAACATTTTACCCTCGAATT
1 TCC-AAAAATTCCATTTTTAACCC-CGAACTTTCTAAAAATTACCATTTTACCCTCGAATT
* * * *
1257390 TCCAAAAATTCCATTTTTAACCCCAAACTTTTTGAAAATTACCATTTTACCC-CCAATT
1 TCCAAAAATTCCATTTTTAACCCCGAACTTTCTAAAAATTACCATTTTACCCTCGAATT
** *
1257448 TCCAAAAATTCCATTTTTAACCTTGAACTTTCAAAAAATTACCATTTTACC
1 TCCAAAAATTCCATTTTTAACCCCGAACTTTCTAAAAATTACCATTTTACC
1257499 TCCGGGCATC
Statistics
Matches: 192, Mismatches: 26, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
57 6 0.03
58 105 0.55
59 81 0.42
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.36
Consensus pattern (59 bp):
TCCAAAAATTCCATTTTTAACCCCGAACTTTCTAAAAATTACCATTTTACCCTCGAATT
Found at i:1257499 original size:29 final size:29
Alignment explanation
Indices: 1257240--1257500 Score: 166
Period size: 29 Copynumber: 9.0 Consensus size: 29
1257230 TTGACCCCCA
*
1257240 AACTTT-TAAAAATTA-CATTTTGACCCTCA
1 AACTTTCTAAAAATTACCATTTT-A-CCTCG
* * **
1257269 AAC-TTCTCATAAATTA-CATTTTGCCCTTA
1 AACTTTCT-AAAAATTACCATTTT-ACCTCG
1257298 AAC-TTCTAAAAATTACCATTTTACCCTCG
1 AACTTTCTAAAAATTACCATTTTA-CCTCG
* * *
1257327 AAC-TTCCAAAAAATCCCATTTTTACCCTCG
1 AACTTTCTAAAAATTACCA-TTTTA-CCTCG
*
1257357 AAC-TTCTAAAAATTAACATTTTACCCTCG
1 AACTTTCTAAAAATTACCATTTTA-CCTCG
* * *
1257386 AA-TTTCCAAAAATT-CCATTTTTAACCCCA
1 AACTTTCTAAAAATTACCA-TTTT-ACCTCG
* * * *
1257415 AACTTTTTGAAAATTACCATTTTACCCCC
1 AACTTTCTAAAAATTACCATTTTACCTCG
* *
1257444 AA-TTTCCAAAAATT-CCATTTTTAACCTTG
1 AACTTTCTAAAAATTACCA-TTTT-ACCTCG
*
1257473 AACTTTCAAAAAATTACCATTTTACCTC
1 AACTTTCTAAAAATTACCATTTTACCTC
1257501 CGGGCATCCA
Statistics
Matches: 188, Mismatches: 30, Indels: 28
0.76 0.12 0.11
Matches are distributed among these distances:
27 3 0.02
28 24 0.13
29 87 0.46
30 68 0.36
31 6 0.03
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (29 bp):
AACTTTCTAAAAATTACCATTTTACCTCG
Found at i:1262275 original size:95 final size:95
Alignment explanation
Indices: 1262154--1262341 Score: 295
Period size: 95 Copynumber: 2.0 Consensus size: 95
1262144 TGCGTAATTC
* * * *
1262154 TCAAATTAATTCATAATTAAGTAAAGCTTAGGGATAAAATTGAGCTGAAAATAAAATTTTGGGGC
1 TCAAATTAATTCATAATTAAGCAAAGCTTAGGAACAAAATTAAGCTGAAAATAAAATTTTGGGGC
* *
1262219 TAAATTAAGAATTTTAGGATTTAATTATTT
66 TAAATTAAGAATTTCAGAATTTAATTATTT
* * *
1262249 TCAAGTTAATTCGTAATTAAGCAAAGCTTAGGAACAAAATTAAGCTGAAAATAAAATTTTGGGGT
1 TCAAATTAATTCATAATTAAGCAAAGCTTAGGAACAAAATTAAGCTGAAAATAAAATTTTGGGGC
1262314 TAAATTAAGAATTTCAGAATTTAATTAT
66 TAAATTAAGAATTTCAGAATTTAATTAT
1262342 AAAACGGGTT
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
95 84 1.00
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.35
Consensus pattern (95 bp):
TCAAATTAATTCATAATTAAGCAAAGCTTAGGAACAAAATTAAGCTGAAAATAAAATTTTGGGGC
TAAATTAAGAATTTCAGAATTTAATTATTT
Found at i:1263124 original size:32 final size:32
Alignment explanation
Indices: 1263068--1263138 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
1263058 CGCCTATTGA
*
1263068 TCGACTCAACCCATTGACCAGAGTTGATCGA-
1 TCGACCCAACCCATTGACCAGAGTTGATCGAC
* *
1263099 TCCGACCCAATCCATTGACCCGAGTTGATCGAC
1 T-CGACCCAACCCATTGACCAGAGTTGATCGAC
1263132 TCGACCC
1 TCGACCC
1263139 GTTAACTTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
31 1 0.03
32 33 0.94
33 1 0.03
ACGTcount: A:0.25, C:0.35, G:0.18, T:0.21
Consensus pattern (32 bp):
TCGACCCAACCCATTGACCAGAGTTGATCGAC
Found at i:1264826 original size:164 final size:163
Alignment explanation
Indices: 1264553--1264883 Score: 576
Period size: 164 Copynumber: 2.0 Consensus size: 163
1264543 TCAGACTTAA
*
1264553 ATATGGGCTTAAAATTGTCCAAATTTGCTCATATTTGCAAAAAAACTAATCCAAATTTATTTTAG
1 ATATGGGCTTAAAATTGACCAAATTTGCTCATATTTGCAAAAAAACTAATCCAAATTTATTTTAG
*
1264618 GACAGATCATATTATTTTTTTAATTTTTTTTAAAAATATTTATATTATATTATTTTAATATTTAA
66 GACAGATCATATTATTTTTTTAAATTTTTTTAAAAATATTTATATTATATTATTTTAATATTTAA
1264683 TAATTTTTTACATTTTTTATTTATTGAAATTTTTT
131 TAATTTTTTACA-TTTTT-TTTATTGAAATTTTTT
*
1264718 ATATGGGCTTAAAATTGACCAAATTTGCTCATATTTGC-AAAAGACTAA-CCTAAATTTATTTTA
1 ATATGGGCTTAAAATTGACCAAATTTGCTCATATTTGCAAAAAAACTAATCC-AAATTTATTTTA
* *
1264781 GGACAGGTCATATTATTTTTTTAAATTTTTTTAAAAATGTTTATATTATATTATTTTAATATTTA
65 GGACAGATCATATTATTTTTTTAAATTTTTTTAAAAATATTTATATTATATTATTTTAATATTTA
1264846 ATAATTTTTTACATTTTTTTTATTGAAATTTTTT
130 ATAATTTTTTACATTTTTTTTATTGAAATTTTTT
1264880 ATAT
1 ATAT
1264884 AATCATCTTA
Statistics
Matches: 160, Mismatches: 5, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
162 20 0.12
163 7 0.04
164 96 0.60
165 37 0.23
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (163 bp):
ATATGGGCTTAAAATTGACCAAATTTGCTCATATTTGCAAAAAAACTAATCCAAATTTATTTTAG
GACAGATCATATTATTTTTTTAAATTTTTTTAAAAATATTTATATTATATTATTTTAATATTTAA
TAATTTTTTACATTTTTTTTATTGAAATTTTTT
Found at i:1265581 original size:89 final size:89
Alignment explanation
Indices: 1265477--1265707 Score: 226
Period size: 89 Copynumber: 2.7 Consensus size: 89
1265467 AATCTTAACT
* *** * * * * *
1265477 TTTTTAAAAAAAGCAATTGAGTTTTTGTATTTTTTTTGCATTCACTTG-GATATTTTAATTTTCA
1 TTTTTAAAAAAAGCAATTAAGTCCCTGTATTTTTTTTGCACTCAATTGAG-TACTTGAACTTTCA
* * *
1265541 AAATACGTGAAAAAGACTCTCAAAC
65 AAATACATCAAAAAGACCCTCAAAC
* *
1265566 TTTTTCAAAAAAGCAATTAAGTCCCTGTCTTTTTTTTGCACTCAATTGAGTACTTGAACTTTCAA
1 TTTTTAAAAAAAGCAATTAAGTCCCTGTATTTTTTTTGCACTCAATTGAGTACTTGAACTTTCAA
*
1265631 AATACATCAAAAAGGCCCTCAAAC
66 AATACATCAAAAAGACCCTCAAAC
* *
1265655 --TTAAAAAAACAGCAATTAAG-CCC--T-TTTTTTTTACACTCAATTTGA-TACTTGAA
1 TTTTTAAAAAA-AGCAATTAAGTCCCTGTATTTTTTTTGCACTCAA-TTGAGTACTTGAA
1265708 TCGCCTTTAA
Statistics
Matches: 121, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
84 23 0.19
85 5 0.04
87 10 0.08
88 10 0.08
89 72 0.60
90 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (89 bp):
TTTTTAAAAAAAGCAATTAAGTCCCTGTATTTTTTTTGCACTCAATTGAGTACTTGAACTTTCAA
AATACATCAAAAAGACCCTCAAAC
Found at i:1265832 original size:8 final size:8
Alignment explanation
Indices: 1265821--1265921 Score: 58
Period size: 8 Copynumber: 11.2 Consensus size: 8
1265811 ATTAAATTTT
1265821 AATTAAAA
1 AATTAAAA
1265829 AATTAAAA
1 AATTAAAA
*
1265837 ATTATAAAA
1 AAT-TAAAA
*
1265846 AAATAAAA
1 AATTAAAA
1265854 ACATTATAAA
1 A-ATTA-AAA
1265864 AGATTATAAA
1 A-ATTA-AAA
1265874 AATGGTAAAA
1 AAT--TAAAA
**
1265884 TTTTATAAAA
1 -AAT-TAAAA
1265894 ATATTAAAA
1 A-ATTAAAA
*
1265903 AATTATAA
1 AATTAAAA
1265911 AATATAAAA
1 AAT-TAAAA
1265920 AA
1 AA
1265922 ACCATAAAAT
Statistics
Matches: 73, Mismatches: 12, Indels: 15
0.73 0.12 0.15
Matches are distributed among these distances:
8 25 0.34
9 23 0.32
10 22 0.30
11 3 0.04
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (8 bp):
AATTAAAA
Found at i:1265864 original size:10 final size:9
Alignment explanation
Indices: 1265821--1266002 Score: 76
Period size: 9 Copynumber: 19.7 Consensus size: 9
1265811 ATTAAATTTT
1265821 AATTA-AAA
1 AATTATAAA
1265829 AA-T-TAAA
1 AATTATAAA
1265836 AATTATAAA
1 AATTATAAA
*
1265845 AA-AATAAAA
1 AATTAT-AAA
1265854 ACATTATAAA
1 A-ATTATAAA
1265864 AGATTATAAA
1 A-ATTATAAA
**
1265874 AATGGTAAA
1 AATTATAAA
*
1265883 ATTTTATAAA
1 A-ATTATAAA
1265893 AA-TATTAAAA
1 AATTA-T-AAA
1265903 AATTAT-AA
1 AATTATAAA
*
1265911 AATATAAAAA
1 AAT-TATAAA
**
1265921 AACCAT-AA
1 AATTATAAA
1265929 AATT-TAATA
1 AATTATAA-A
*
1265938 AAGTTGTAAGAA
1 AA-TTAT-A-AA
1265950 AATTATAAA
1 AATTATAAA
* *
1265959 AAATGTAAA
1 AATTATAAA
*
1265968 GAAATAT-AA
1 -AATTATAAA
1265977 AATTCATAAAA
1 AATT-AT-AAA
1265988 AATTATAAA
1 AATTATAAA
1265997 AATTAT
1 AATTAT
1266003 CGTACAAAAA
Statistics
Matches: 132, Mismatches: 20, Indels: 43
0.68 0.10 0.22
Matches are distributed among these distances:
7 7 0.05
8 20 0.15
9 46 0.35
10 40 0.30
11 14 0.11
12 4 0.03
13 1 0.01
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.29
Consensus pattern (9 bp):
AATTATAAA
Found at i:1265882 original size:19 final size:19
Alignment explanation
Indices: 1265824--1265921 Score: 73
Period size: 19 Copynumber: 5.4 Consensus size: 19
1265814 AAATTTTAAT
*
1265824 TAAAAAATTA-AAAATTA-
1 TAAAAAATTATAAAAATAG
*
1265841 TAAAAAAATA-AAAACATTA-
1 TAAAAAATTATAAAA-A-TAG
* *
1265860 TAAAAGATTATAAAAATGG
1 TAAAAAATTATAAAAATAG
** *
1265879 TAAAATTTTATAAAAATAT
1 TAAAAAATTATAAAAATAG
1265898 TAAAAAATTAT-AAAATA-
1 TAAAAAATTATAAAAATAG
1265915 TAAAAAA
1 TAAAAAA
1265922 ACCATAAAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
17 20 0.30
18 7 0.11
19 35 0.53
20 4 0.06
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (19 bp):
TAAAAAATTATAAAAATAG
Found at i:1265930 original size:47 final size:45
Alignment explanation
Indices: 1265838--1266002 Score: 118
Period size: 47 Copynumber: 3.5 Consensus size: 45
1265828 AAATTAAAAA
* * ***
1265838 TTATAAAAAAATAAAAACATTATAAAAGATTATAAAAATGGTAAAATT
1 TTATAAAAAATTAAAAA-ATTATAAAATA-TA-AAAAAACATAAAATT
1265886 TTATAAAAATATTAAAAAATTATAAAATATAAAAAAACCATAAAATT
1 TTATAAAAA-ATTAAAAAATTATAAAATATAAAAAAA-CATAAAATT
* ** * * *
1265933 TAAT-AAAGTTGTAAGAAAATTATAAAAAATGTAAAGAAATATAAAA-T
1 TTATAAAAAAT-TAA-AAAATTAT--AAAATATAAAAAAACATAAAATT
*
1265980 TCATAAAAAATTATAAAAATTAT
1 TTATAAAAAATTA-AAAAATTAT
1266003 CGTACAAAAA
Statistics
Matches: 95, Mismatches: 14, Indels: 17
0.75 0.11 0.13
Matches are distributed among these distances:
45 1 0.01
46 11 0.12
47 34 0.36
48 30 0.32
49 19 0.20
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (45 bp):
TTATAAAAAATTAAAAAATTATAAAATATAAAAAAACATAAAATT
Found at i:1265991 original size:11 final size:10
Alignment explanation
Indices: 1265833--1266002 Score: 82
Period size: 10 Copynumber: 17.9 Consensus size: 10
1265823 TTAAAAAATT
1265833 AAAAATTATA
1 AAAAATTATA
1265843 AAAAA--ATA
1 AAAAATTATA
1265851 AAAACATTATA
1 AAAA-ATTATA
*
1265862 AAAGATTAT-
1 AAAAATTATA
**
1265871 AAAAATGGTA
1 AAAAATTATA
**
1265881 AAATTTTAT-
1 AAAAATTATA
1265890 AAAAA-TATTA
1 AAAAATTA-TA
1265900 AAAAATTATA
1 AAAAATTATA
*
1265910 AAATA-TA-A
1 AAAAATTATA
**
1265918 AAAAACCAT-
1 AAAAATTATA
1265927 -AAAATT-TA
1 AAAAATTATA
* *
1265935 ATAAAGTTGTA
1 A-AAAATTATA
1265946 AGAAAATTATA
1 A-AAAATTATA
1265957 AAAAATGTA-A
1 AAAAAT-TATA
*
1265967 AGAAA-TAT-
1 AAAAATTATA
1265975 -AAAATTCATA
1 AAAAATT-ATA
1265985 AAAAATTAT-
1 AAAAATTATA
1265994 AAAAATTAT
1 AAAAATTAT
1266003 CGTACAAAAA
Statistics
Matches: 120, Mismatches: 21, Indels: 39
0.67 0.12 0.22
Matches are distributed among these distances:
7 4 0.03
8 21 0.17
9 25 0.21
10 43 0.36
11 27 0.22
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (10 bp):
AAAAATTATA
Found at i:1266042 original size:11 final size:11
Alignment explanation
Indices: 1266022--1266054 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1266012 AGAAGCATTT
1266022 TATAATTTTTA
1 TATAATTTTTA
*
1266033 TATAACTTTTA
1 TATAATTTTTA
1266044 T-TAATTTTTA
1 TATAATTTTTA
1266054 T
1 T
1266055 TTTTTATCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (11 bp):
TATAATTTTTA
Found at i:1266218 original size:18 final size:18
Alignment explanation
Indices: 1266172--1266220 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
1266162 TTCTGATATA
1266172 TTTTATAATTTTTATCATT
1 TTTTATAA-TTTTATCATT
* *
1266191 TTATAAAATTTTA-CAATT
1 TTTTATAATTTTATC-ATT
1266209 TTTTATAATTTT
1 TTTTATAATTTT
1266221 TTGTCACATG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 1 0.04
18 18 0.72
19 6 0.24
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTATAATTTTATCATT
Found at i:1268314 original size:84 final size:84
Alignment explanation
Indices: 1268174--1268427 Score: 483
Period size: 84 Copynumber: 3.0 Consensus size: 84
1268164 AAAGTTTTGA
1268174 AAAACAAATCAC-ACACCACTATTACCTTTTCAGTTAATTGTTCATCCGGCCAGAGCCCTCCAAA
1 AAAACAAATCACAACACCACTATTACCTTTTCAGTTAATTGTTCATCCGGCCAGAGCCCTCCAAA
1268238 GCCCTTTGTAACTATTTCC
66 GCCCTTTGTAACTATTTCC
1268257 AAAACAAATCACAACACCACTATTACCTTTTCAGTTAATTGTTCATCCGGCCAGAGCCCTCCAAA
1 AAAACAAATCACAACACCACTATTACCTTTTCAGTTAATTGTTCATCCGGCCAGAGCCCTCCAAA
1268322 GCCCTTTGTAACTATTTCC
66 GCCCTTTGTAACTATTTCC
*
1268341 AAAACAAAACACAACACCACTATTACCTTTTCAGTTAATTGTTCATCCGGCCAGAGCCCTCCAAA
1 AAAACAAATCACAACACCACTATTACCTTTTCAGTTAATTGTTCATCCGGCCAGAGCCCTCCAAA
*
1268406 GCCCTTTGTAACTCTTTCC
66 GCCCTTTGTAACTATTTCC
1268425 AAA
1 AAA
1268428 GTTCCAAAAC
Statistics
Matches: 168, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
83 12 0.07
84 156 0.93
ACGTcount: A:0.31, C:0.31, G:0.09, T:0.28
Consensus pattern (84 bp):
AAAACAAATCACAACACCACTATTACCTTTTCAGTTAATTGTTCATCCGGCCAGAGCCCTCCAAA
GCCCTTTGTAACTATTTCC
Found at i:1285196 original size:17 final size:18
Alignment explanation
Indices: 1285165--1285202 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1285155 CAAGGACAAG
* *
1285165 AAAAGAAAGAGGAAGGAC
1 AAAAGAAAGAAGAAGCAC
1285183 AAAAGAAA-AAGAAGCAC
1 AAAAGAAAGAAGAAGCAC
1285200 AAA
1 AAA
1285203 GAGGAGTGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.68, C:0.08, G:0.24, T:0.00
Consensus pattern (18 bp):
AAAAGAAAGAAGAAGCAC
Found at i:1285339 original size:17 final size:16
Alignment explanation
Indices: 1285302--1285340 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
1285292 ACATGCATCT
1285302 CATTTTATTGTCATTG
1 CATTTTATTGTCATTG
* *
1285318 TATTTTAGTTGTCGTTG
1 CATTTTA-TTGTCATTG
1285335 CATTTT
1 CATTTT
1285341 CAGTGTTAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.15, C:0.10, G:0.15, T:0.59
Consensus pattern (16 bp):
CATTTTATTGTCATTG
Done.