Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 91 of 185
Found at i:28543159 original size:287 final size:286
Alignment explanation
Indices: 28542633--28543228 Score: 933
Period size: 287 Copynumber: 2.1 Consensus size: 286
28542623 TGAAGTCATT
* * *
28542633 ACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTACAACTACAAATTATGGTAAATCT
1 ACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAACTACAAATTACGGCAAATCT
* * *
28542698 TATCTTCCTGAAGTTACAGTGGGCAGATTGAAGCCACCAACCTTATCTCCCTGAAGTGGTAGTGG
66 TATCTTCCTGAAGTTACAGTGGGCAAATTGAAGCCACCAACCTTATCTCCCTGAAGTGGCAGCGG
* * *
28542763 AGCAGACTGAAGACAGCGAATCTTATTTCCCTGGTGTTGCAGTGGAACAGATTAAAAGTTACAAA
131 AGCAAACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAAGCTACAAA
* * *
28542828 TTGCAGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTGCC
196 TTACAGCAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCC
**
28542893 TGAAGTTCCAGCGGAGCAGACTGAAG
261 TGAAGTTCCAGCAAAGCAGACTGAAG
* * * *
28542919 ACAGTGAATCTTATTTCCCTGGCGTTGCAGTGGAATAGATTAAAAGCTACAAATTGCGGCGAATC
1 ACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAA-CTACAAATTACGGCAAATC
* * *
28542984 TTATCTTCCTGAAGTTGCAGTGGAGCAAATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGC
65 TTATCTTCCTGAAGTTACAGTGG-GCAAATTGAAGCCACCAACCTTATCTCCCTGAAGTGGCAGC
* *
28543049 GGAGCAAACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAATAGATT-AAAGCTACA
129 GGAGCAAACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAAGCTACA
*
28543113 AATTACGGCAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTC
194 AATTACAGCAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTC
*
28543178 CCTGAAGTTGCAGCAAAGCAGACTGAAG
259 CCTGAAGTTCCAGCAAAGCAGACTGAAG
*
28543206 ACAGCGAATCTTATTTCCTTGGC
1 ACAGCGAATCTTATTTCCCTGGC
28543229 TACAAATTAT
Statistics
Matches: 281, Mismatches: 27, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
286 42 0.15
287 152 0.54
288 87 0.31
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (286 bp):
ACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAACTACAAATTACGGCAAATCT
TATCTTCCTGAAGTTACAGTGGGCAAATTGAAGCCACCAACCTTATCTCCCTGAAGTGGCAGCGG
AGCAAACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAAGCTACAAA
TTACAGCAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCC
TGAAGTTCCAGCAAAGCAGACTGAAG
Found at i:28543178 original size:143 final size:144
Alignment explanation
Indices: 28542633--28543228 Score: 937
Period size: 144 Copynumber: 4.2 Consensus size: 144
28542623 TGAAGTCATT
* * *
28542633 ACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTACAA-CTACAAATTATGGTAAATC
1 ACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAAGCTACAAATTACGGCAAATC
* * * * *
28542697 TTATCTTCCTGAAGTTACAGTGG-GCAGATTGAAGCCACCAACCTTATCTCCCTGAAGTGGTAGT
66 TTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGC
28542761 GGAGCAGACTGAAG
131 GGAGCAGACTGAAG
* * * * *
28542775 ACAGCGAATCTTATTTCCCTGGTGTTGCAGTGGAACAGATTAAAAGTTACAAATTGCAGCGAATC
1 ACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAAGCTACAAATTACGGCAAATC
* *
28542840 TTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTGCCTGAAGTTCCAGC
66 TTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGC
28542905 GGAGCAGACTGAAG
131 GGAGCAGACTGAAG
* * * *
28542919 ACAGTGAATCTTATTTCCCTGGCGTTGCAGTGGAATAGATTAAAAGCTACAAATTGCGGCGAATC
1 ACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAAGCTACAAATTACGGCAAATC
*
28542984 TTATCTTCCTGAAGTTGCAGTGGAGCAAATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGC
66 TTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGC
*
28543049 GGAGCAAACTGAAG
131 GGAGCAGACTGAAG
* *
28543063 ACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAATAGATT-AAAGCTACAAATTACGGCAAATC
1 ACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAAGCTACAAATTACGGCAAATC
28543127 TTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGC
66 TTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGC
**
28543192 AAAGCAGACTGAAG
131 GGAGCAGACTGAAG
*
28543206 ACAGCGAATCTTATTTCCTTGGC
1 ACAGCGAATCTTATTTCCCTGGC
28543229 TACAAATTAT
Statistics
Matches: 419, Mismatches: 33, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
142 43 0.10
143 153 0.37
144 223 0.53
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (144 bp):
ACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAAGCTACAAATTACGGCAAATC
TTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGC
GGAGCAGACTGAAG
Found at i:28543260 original size:120 final size:120
Alignment explanation
Indices: 28543107--28543340 Score: 353
Period size: 120 Copynumber: 1.9 Consensus size: 120
28543097 ATAGATTAAA
*
28543107 GCTACAAATTACGGCAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCT
1 GCTACAAATTACGGCAAATCTTATCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGCCACCAGCCT
*
28543172 TATCTCCCTGAAGTTGCAGCAAAGCAGACTGAAGACAGCGAATCTTATTTCCTTG
66 TATCTCCCTCAAGTTGCAGCAAAGCAGACTGAAGACAGCGAATCTTATTTCCTTG
* * * * *
28543227 GCTACAAATTATGG-AGGATCTTATCTTCCTGAAGTTGCAGTGAAGTAGATTGGAGCCTCCAGCC
1 GCTACAAATTACGGCA-AATCTTATCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGCCACCAGCC
* ** *
28543291 TTATCTCCTTCAAGTTGCAGCGGAGCAGACTGAAGACAGTGAATCTTATT
65 TTATCTCCCTCAAGTTGCAGCAAAGCAGACTGAAGACAGCGAATCTTATT
28543341 ACCCTGGCGT
Statistics
Matches: 102, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
119 1 0.01
120 101 0.99
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.27
Consensus pattern (120 bp):
GCTACAAATTACGGCAAATCTTATCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGCCACCAGCCT
TATCTCCCTCAAGTTGCAGCAAAGCAGACTGAAGACAGCGAATCTTATTTCCTTG
Found at i:28544828 original size:3 final size:3
Alignment explanation
Indices: 28544820--28544876 Score: 69
Period size: 3 Copynumber: 19.0 Consensus size: 3
28544810 TAAACCTCAG
* * * *
28544820 ATT ATT ATT ATT GTT ATT ATT ATT ATT ATC ATT ATC ATT ATC ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
28544868 AAT ATT ATT
1 ATT ATT ATT
28544877 CTTAGATTGT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:28546548 original size:28 final size:28
Alignment explanation
Indices: 28546508--28546564 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
28546498 TGTTATGGTG
28546508 AAGAAGCAAATCTATTCTGAATTTTTGT
1 AAGAAGCAAATCTATTCTGAATTTTTGT
28546536 AAGAAGCAAATCTATTCTGAATTTTTGT
1 AAGAAGCAAATCTATTCTGAATTTTTGT
28546564 A
1 A
28546565 CTGGCTTGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.39
Consensus pattern (28 bp):
AAGAAGCAAATCTATTCTGAATTTTTGT
Found at i:28552838 original size:68 final size:68
Alignment explanation
Indices: 28552727--28552940 Score: 290
Period size: 68 Copynumber: 3.2 Consensus size: 68
28552717 GAATTGACAG
* *
28552727 GTAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGA-AATGTTT
1 GTAAGACCATAGCTGGGTTATGGCACTATGAATGTAAGACCATGGTTGGACCAT-GACAATGTTT
28552791 ATAT
65 ATAT
* *
28552795 GTAAGACCATAGCTGGGCTATGGCACTATGAATGTAAGGCCATGGTTGGACCATGACAATGTTTA
1 GTAAGACCATAGCTGGGTTATGGCACTATGAATGTAAGACCATGGTTGGACCATGACAATGTTTA
28552860 TAT
66 TAT
* ** ** * *
28552863 GTAATACCATAGCTGGGTTATGGCACTACAAATGTAAGACCATGGCAGGGCCATGACAA--TTCA
1 GTAAGACCATAGCTGGGTTATGGCACTATGAATGTAAGACCATGGTTGGACCATGACAATGTTTA
*
28552926 TGT
66 TAT
28552929 GTAAGACCATAG
1 GTAAGACCATAG
28552941 TTGAACTATG
Statistics
Matches: 130, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
66 16 0.12
67 2 0.02
68 112 0.86
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (68 bp):
GTAAGACCATAGCTGGGTTATGGCACTATGAATGTAAGACCATGGTTGGACCATGACAATGTTTA
TAT
Found at i:28554129 original size:40 final size:40
Alignment explanation
Indices: 28554075--28554160 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
28554065 GCGTTTTCTT
28554075 AAAAACACTACTATAGATCAAGCATTAGCAGCACTTTTTG
1 AAAAACACTACTATAGATCAAGCATTAGCAGCACTTTTTG
* * * * * * * *
28554115 AAAATCACTGCTATAGGTCGATCATTAGCGGCACTTTCTA
1 AAAAACACTACTATAGATCAAGCATTAGCAGCACTTTTTG
28554155 AAAAAC
1 AAAAAC
28554161 GCCGCAAAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (40 bp):
AAAAACACTACTATAGATCAAGCATTAGCAGCACTTTTTG
Found at i:28554269 original size:40 final size:40
Alignment explanation
Indices: 28554211--28554396 Score: 228
Period size: 40 Copynumber: 4.7 Consensus size: 40
28554201 AGCTTTAGAG
*
28554211 GCATTAGTGGCGCTTTTTGAAAAACGCCGCTATAGATCGA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATCGA
* * * * *
28554251 GCTTTAGTGGCGCTTTTTGAGAAACGCTGCTATAGGTCGA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATCGA
* * * * *
28554291 CCATTAGCGACGCTTTTTGAAAAACGCCACTGTAGGTCGA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATCGA
* * * *
28554331 GCATTAGCAGCGCTTCTTGAAAAACGCGGCTATATATCGA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATCGA
*
28554371 GTATTAGCGGCGCTTTTTGAAAAACG
1 GCATTAGCGGCGCTTTTTGAAAAACG
28554397 TCGCAAAAAA
Statistics
Matches: 122, Mismatches: 24, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 122 1.00
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.28
Consensus pattern (40 bp):
GCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATCGA
Found at i:28554314 original size:155 final size:155
Alignment explanation
Indices: 28554024--28554318 Score: 387
Period size: 155 Copynumber: 1.9 Consensus size: 155
28554014 TGGCGATCGT
* * *
28554024 ACAACGCCATCGTTTTATGTTGAGCTTTAGTGGCATTAGCGGCGTTTTCTTAAAAACACTACTAT
1 ACAACGCCATCGTTTTATGTTGAGCTTTAGAGGCATTAGCGGCGTTTTCTGAAAAACACCACTAT
* *
28554089 AGATCAAGCATTAGCAGCACTTTTTGAAAATCACTGCTATAGGTCGATCATTAGCGGCACTTTCT
66 AGATCAAGCATTAGCAGCACTTTTTGAAAATCACTGCTATAGGTCGACCATTAGCGACACTTTCT
28554154 AAAAAACGCCGCAAAATAATTAAGC
131 AAAAAACGCCGCAAAATAATTAAGC
** * * *
28554179 ACAACGCTGTCGTTTTATGTTGAGCTTTAGAGGCATTAGTGGCGCTTTT-TGAAAAACGCCGCTA
1 ACAACGCCATCGTTTTATGTTGAGCTTTAGAGGCATTAGCGGCG-TTTTCTGAAAAACACCACTA
* * ** * * *
28554243 TAGATCGAGCTTTAGTGGCGCTTTTTGAGAAA-CGCTGCTATAGGTCGACCATTAGCGACGCTTT
65 TAGATCAAGCATTAGCAGCACTTTTTGA-AAATCACTGCTATAGGTCGACCATTAGCGACACTTT
* *
28554307 TTGAAAAACGCC
129 CTAAAAAACGCC
28554319 ACTGTAGGTC
Statistics
Matches: 119, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
155 112 0.94
156 7 0.06
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.30
Consensus pattern (155 bp):
ACAACGCCATCGTTTTATGTTGAGCTTTAGAGGCATTAGCGGCGTTTTCTGAAAAACACCACTAT
AGATCAAGCATTAGCAGCACTTTTTGAAAATCACTGCTATAGGTCGACCATTAGCGACACTTTCT
AAAAAACGCCGCAAAATAATTAAGC
Found at i:28554637 original size:7 final size:7
Alignment explanation
Indices: 28554616--28554759 Score: 78
Period size: 7 Copynumber: 20.3 Consensus size: 7
28554606 TTAATTATCA
*
28554616 TTATAGT
1 TTATGGT
*
28554623 TTAGGGT
1 TTATGGT
28554630 TTATGGT
1 TTATGGT
*
28554637 TTAGGGT
1 TTATGGT
*
28554644 ATATGGT
1 TTATGGT
28554651 TTA-GGCT
1 TTATGG-T
*
28554658 TTAAGGT
1 TTATGGT
*
28554665 TTAAGAGT
1 TTATG-GT
28554673 TACTAT--T
1 T--TATGGT
*
28554680 TTAAGGT
1 TTATGGT
*
28554687 TTATGGA
1 TTATGGT
*
28554694 TTACGGT
1 TTATGGT
* *
28554701 TTAGGGA
1 TTATGGT
28554708 TTATGGT
1 TTATGGT
28554715 TTATGGT
1 TTATGGT
**
28554722 TTACAGT
1 TTATGGT
*
28554729 TTAAAGGT
1 TT-ATGGT
*
28554737 TTAGGGT
1 TTATGGT
*
28554744 TTAGGGT
1 TTATGGT
28554751 TTATGGT
1 TTATGGT
28554758 TT
1 TT
28554760 CAAGGTTTAG
Statistics
Matches: 106, Mismatches: 23, Indels: 16
0.73 0.16 0.11
Matches are distributed among these distances:
5 2 0.02
6 2 0.02
7 90 0.85
8 10 0.09
10 2 0.02
ACGTcount: A:0.22, C:0.03, G:0.28, T:0.47
Consensus pattern (7 bp):
TTATGGT
Found at i:28554638 original size:14 final size:14
Alignment explanation
Indices: 28554616--28554818 Score: 113
Period size: 14 Copynumber: 14.2 Consensus size: 14
28554606 TTAATTATCA
*
28554616 TTATAGTTTAGGGT
1 TTATGGTTTAGGGT
28554630 TTATGGTTTAGGGT
1 TTATGGTTTAGGGT
* *
28554644 ATATGGTTTAGGCT
1 TTATGGTTTAGGGT
* *
28554658 TTAAGGTTTAAGAGT
1 TTATGGTTT-AGGGT
*
28554673 TACTAT--TTTAAGGT
1 T--TATGGTTTAGGGT
* *
28554687 TTATGGATTACGGT
1 TTATGGTTTAGGGT
* * *
28554701 TTAGGGATTATGGT
1 TTATGGTTTAGGGT
**
28554715 TTATGGTTTACAGT
1 TTATGGTTTAGGGT
*
28554729 TTAAAGGTTTAGGGT
1 TT-ATGGTTTAGGGT
* *
28554744 TTAGGGTTTATGGT
1 TTATGGTTTAGGGT
* *
28554758 TTCAAGGTTTAGGGG
1 TT-ATGGTTTAGGGT
* * * *
28554773 ATAGGGGATAAGGGT
1 TTA-TGGTTTAGGGT
* *
28554788 TAAAGGTTTAGGGT
1 TTATGGTTTAGGGT
*
28554802 TTAGGGTTTAGGGT
1 TTATGGTTTAGGGT
28554816 TTA
1 TTA
28554819 GATTAATTAG
Statistics
Matches: 143, Mismatches: 38, Indels: 16
0.73 0.19 0.08
Matches are distributed among these distances:
12 3 0.02
14 102 0.71
15 36 0.25
17 2 0.01
ACGTcount: A:0.23, C:0.02, G:0.32, T:0.42
Consensus pattern (14 bp):
TTATGGTTTAGGGT
Found at i:28554751 original size:29 final size:28
Alignment explanation
Indices: 28554712--28554811 Score: 101
Period size: 29 Copynumber: 3.5 Consensus size: 28
28554702 TAGGGATTAT
*
28554712 GGTTTATGGTTTACAGTTTAAAGGTTTAG
1 GGTTTAGGGTTTA-AGTTTAAAGGTTTAG
* *
28554741 GGTTTAGGGTTTATGGTTTCAAGGTTTAG
1 GGTTTAGGGTTTA-AGTTTAAAGGTTTAG
** ** *
28554770 GGGATAGGGGATAAGGGTTAAAGGTTTAG
1 GGTTTAGGGTTTAA-GTTTAAAGGTTTAG
28554799 GGTTTAGGGTTTA
1 GGTTTAGGGTTTA
28554812 GGGTTTAGAT
Statistics
Matches: 55, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.23, C:0.02, G:0.36, T:0.39
Consensus pattern (28 bp):
GGTTTAGGGTTTAAGTTTAAAGGTTTAG
Found at i:28554802 original size:7 final size:7
Alignment explanation
Indices: 28554792--28554819 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
28554782 AAGGGTTAAA
28554792 GGTTTAG
1 GGTTTAG
28554799 GGTTTAG
1 GGTTTAG
28554806 GGTTTAG
1 GGTTTAG
28554813 GGTTTAG
1 GGTTTAG
28554820 ATTAATTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (7 bp):
GGTTTAG
Found at i:28555509 original size:23 final size:24
Alignment explanation
Indices: 28555478--28555531 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
28555468 TATAAAAAAT
* *
28555478 AAAATAAAAGTTTTTTAGCAGA-A
1 AAAACAAAAGATTTTTAGCAGAGA
*
28555501 AAAACAAAAGATTTTTAGCAGAGC
1 AAAACAAAAGATTTTTAGCAGAGA
28555525 AAAACAA
1 AAAACAA
28555532 TGTTGTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 20 0.74
24 7 0.26
ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22
Consensus pattern (24 bp):
AAAACAAAAGATTTTTAGCAGAGA
Found at i:28560563 original size:43 final size:43
Alignment explanation
Indices: 28560482--28560740 Score: 225
Period size: 43 Copynumber: 6.0 Consensus size: 43
28560472 CTTTTTGCGA
* ** *
28560482 CATTTGTGATAAAAAGCGTCGCTAAATATCATGTTCTTTAGTGG
1 CATTTGTGAT-AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGG
* * ** *
28560526 CATTTGTGATAAAAGTGCCACTAAAGGTCATACTCTTTAGCGA
1 CATTTGTGATAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGG
* * * * *
28560569 CGTTTTTAATAAAAGTGCCGCTAAAAGTCATGTTCTTTAGCGG
1 CATTTGTGATAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGG
* * ** * *
28560612 CGTTTGTGGTAAAAGCGTTGGTAAATGTCATGTTCTTTA-CTGG
1 CATTTGTGATAAAAGCGCCGCTAAAGGTCATGTTCTTTAGC-GG
* * * *
28560655 CATTTGTGATAAAAGCGTCGCTAAAGGTCCTGTTATTTAGTGG
1 CATTTGTGATAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGG
* * * * *
28560698 CGTTTCTGGT-GAAGCGCCGCTAAAGGTCATGTTTTTTAGCGG
1 CATTTGTGATAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGG
28560740 C
1 C
28560741 GTTTTTTCAC
Statistics
Matches: 172, Mismatches: 41, Indels: 6
0.79 0.19 0.03
Matches are distributed among these distances:
42 29 0.17
43 133 0.77
44 10 0.06
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (43 bp):
CATTTGTGATAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGG
Found at i:28560649 original size:86 final size:86
Alignment explanation
Indices: 28560493--28560746 Score: 253
Period size: 86 Copynumber: 3.0 Consensus size: 86
28560483 ATTTGTGATA
* * * * *
28560493 AAAAGCGTCGCTAAATA-TCATGTTCTTTAGTGGCATTTGTGATAAAAGTGCCACTAAAGGTCAT
1 AAAAGCGCCGCTAAA-AGTCATGTTCTTTAGTGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCAT
** *
28560557 ACTCTTTAGCGACGTTTTTAAT
65 GTTCTTTAGCGGCGTTTTTAAT
* * ** * *
28560579 AAAAGTGCCGCTAAAAGTCATGTTCTTTAGCGGCGTTTGTGGTAAAAGCGTTGGTAAATGTCATG
1 AAAAGCGCCGCTAAAAGTCATGTTCTTTAGTGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCATG
* * *
28560644 TTCTTTA-CTGGCATTTGTGAT
66 TTCTTTAGC-GGCGTTTTTAAT
* * * * * *
28560665 AAAAGCGTCGCTAAAGGTCCTGTTATTTAGTGGCGTTTCTGGT-GAAGCGCCGCTAAAGGTCATG
1 AAAAGCGCCGCTAAAAGTCATGTTCTTTAGTGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCATG
*
28560729 TTTTTTAGCGGCGTTTTT
66 TTCTTTAGCGGCGTTTTT
28560747 TCACATAAAC
Statistics
Matches: 133, Mismatches: 32, Indels: 7
0.77 0.19 0.04
Matches are distributed among these distances:
85 31 0.23
86 102 0.77
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (86 bp):
AAAAGCGCCGCTAAAAGTCATGTTCTTTAGTGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCATG
TTCTTTAGCGGCGTTTTTAAT
Found at i:28560694 original size:129 final size:129
Alignment explanation
Indices: 28560484--28560744 Score: 317
Period size: 129 Copynumber: 2.0 Consensus size: 129
28560474 TTTTGCGACA
* *
28560484 TTTGTGATAAAAAGCGTCGCTAAATATCATGTTCTTTAGTGGCATTTGTGATAAAAGTGCCACTA
1 TTTGTGATAAAAAGCGTCGCTAAATATCATGTTCTTTACTGGCATTTGTGATAAAAGCGCCACTA
* * *
28560549 AAGGTCATACTCTTTAGCGACGTTTTTAATAAAAGTGCCGCTAAAAGTCATGTTCTTTAGCGGCG
66 AAGGTCATACTATTTAGCGACGTTTCTAAT-AAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCG
* * * * * *
28560614 TTTGTGGT-AAAAGCGTTGGTAAATGTCATGTTCTTTACTGGCATTTGTGATAAAAGCGTCGCTA
1 TTTGTGATAAAAAGCGTCGCTAAATATCATGTTCTTTACTGGCATTTGTGATAAAAGCGCCACTA
* ** * * ** * * *
28560678 AAGGTCCTGTTATTTAGTGGCGTTTCTGGTGAAGCGCCGCTAAAGGTCATGTTTTTTAGCGGCG
66 AAGGTCATACTATTTAGCGACGTTTCTAATAAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCG
28560742 TTT
1 TTT
28560745 TTTCACATAA
Statistics
Matches: 110, Mismatches: 21, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
128 33 0.30
129 70 0.64
130 7 0.06
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (129 bp):
TTTGTGATAAAAAGCGTCGCTAAATATCATGTTCTTTACTGGCATTTGTGATAAAAGCGCCACTA
AAGGTCATACTATTTAGCGACGTTTCTAATAAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCG
Found at i:28565970 original size:50 final size:50
Alignment explanation
Indices: 28565895--28566130 Score: 296
Period size: 50 Copynumber: 4.7 Consensus size: 50
28565885 GTAAAGAGAT
28565895 CCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGA
1 CCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGA
* * *
28565945 CCCATGTAAGACCATGTCTTGGACATGGCGTTGGTACCGAGATGAGAGGT
1 CCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGA
* *
28565995 CCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGGT
1 CCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGA
** * * * * * *
28566045 CCCCCGTAAGACCATGTCTAGGACATGACATGGGCACCTATATGAGA--A
1 CCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGA
* * *
28566093 CTCTCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 C-C-CATGTAAGACCATGTCTGGGACATGGCGTTGGCA
28566131 GTATAAGAAA
Statistics
Matches: 162, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
48 1 0.01
49 1 0.01
50 160 0.99
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (50 bp):
CCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGA
Found at i:28569074 original size:101 final size:99
Alignment explanation
Indices: 28568937--28569127 Score: 256
Period size: 101 Copynumber: 1.9 Consensus size: 99
28568927 AATTAACAGG
* * * ** *
28568937 TAAGACCATAACTGGGTTATGGCACTACGAACGTAAGGCCATGGTTGGACCATGACAATGTTTAT
1 TAAGACCATAACTAGGTTATGGCACTACAAACGTAAGACCATGGCAGGACCATGACAATG--CAT
* *
28569002 ATGTAATACCATAGTTGGGCTATGGCATTCTGATGA
64 ATGTAAGACCATAGTTGGACTATGGCATTCTGATGA
* * * *
28569038 TAAGACCATAACTAGGTTATGGCACTACAAATGTAAGACCATGGCAGGGCCATGGCAATGCATGT
1 TAAGACCATAACTAGGTTATGGCACTACAAACGTAAGACCATGGCAGGACCATGACAATGCATAT
28569103 GTAAGACCATAGTTGGACTATGGCA
66 GTAAGACCATAGTTGGACTATGGCA
28569128 CAAAAAGAAC
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
99 26 0.33
101 52 0.67
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (99 bp):
TAAGACCATAACTAGGTTATGGCACTACAAACGTAAGACCATGGCAGGACCATGACAATGCATAT
GTAAGACCATAGTTGGACTATGGCATTCTGATGA
Found at i:28573079 original size:18 final size:18
Alignment explanation
Indices: 28573058--28573094 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
28573048 CTTCTTTTTA
28573058 TTTTTCATCTTCAGCAAC
1 TTTTTCATCTTCAGCAAC
*
28573076 TTTTTCTTCTTCAGCAAC
1 TTTTTCATCTTCAGCAAC
28573094 T
1 T
28573095 ACTTCGTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.27, G:0.05, T:0.49
Consensus pattern (18 bp):
TTTTTCATCTTCAGCAAC
Found at i:28581132 original size:934 final size:935
Alignment explanation
Indices: 28579329--28582390 Score: 4906
Period size: 934 Copynumber: 3.3 Consensus size: 935
28579319 ACTTGCTCTA
* * *
28579329 AGTAGATGTATTCCCATAACTGAATGTCGCAGCATTTTGTCTAGCATTCTAAGTTCCCCAAAATG
1 AGTAGATGTATTCCCATATCTGAATGTCGCAGCATTTTGTCTAGCATTCTGAGTTCCCCAAAATA
* * * *
28579394 GTTAGTTGCGTGCAGAGTTGTTGTAGGAGTTACCATAAGAATTGTCGCGGATGTAATAATATAAC
66 GTTGGTTGCGTGCAAAGTTGTTGTAAGAGTTACCATAAGAATTGTTGCGGATGTAATAATATAAC
* *
28579459 AGGCATTCTCTGTATGTTGTGGTCAATCTTCATAGCTATGGTTGTCACTACAAATCTCACAACAA
131 AGGCATTCTCTGCATATTGTGGTCAATCTTCATAGCTATGGTTGTCACTACAAATCTCACAACAA
*
28579524 AAAGTAGGAACATCAACTTGTTGAGCGACTTG--T--CT--AACGCCACTAGTCTATTGCATATT
196 AAAGTAGGAACATCAACTTGTTGAGCGACTTGTATAGGTGCAACGCCACTAGTCTATTGCATATT
*
28579583 TTTAATCATGTTTGGGAT-AGAAGAAACTTGAGCACTTAGTGCGGTTATTGCATCCAATTCAATA
261 TTTAATCATGTTTGTG-TGAGAAGAAACTTGAGCACTTAGTGCGGTTATTGCATCCAATTCAATA
28579647 ACTCCTGGAGTAGTTTTTGCTTGTGCAGCTATGGAGATAAGGTATTGATAATCATTCTGAGCAAT
325 ACTCCTGGAGTAGTTTTTGCTTGTGCAGCTATGGAGATAAGGTATTGATAATCATTCTGAGCAAT
* *
28579712 TCTCTCAAGAATTCTCACAGCATCATTATAAGTACAATCCAACAGAGGTCCATTGGCAGATGCAT
390 TCTCTCAAGAATTCTCACAGCATCATTATAAGTACAATTCAACAGAGGTCCATTGGCTGATGCAT
* * * * *
28579777 TGACAAGTTTCCTTGTATATGAATTCAACCCATTATAAAAATATCAATTTGGGTTTCTAGTTGAA
455 CGACAAGTTTCCTTGTATATGAATTCAGCCCATTATAAAAATCTCAATTTGTGTTTCTGGTTGAA
* * * * *
28579842 TGTCGTGCATGGGACAAAGTCGAAGTAAAGATTTATAATTTTCTCATGTGGTGTGAAGATTATGA
520 TGTCGTGCATGGGACAAAGTCAAAGTAAAGATTTATAATGTTCCCATGTGGTGTGAAGATTTTCA
* *
28579907 TCATCCAGCTGATGGTAAGTAGTAATATCATTTTGAAGACGAGCATTCATTGTTGGCGGGTTAAA
585 TCATCCAGCTGATGGTAAGTAGTAATATCATTTTGAAGACAAGCATTCATTGTTGGTGGGTTAAA
***
28579972 TCACAAAACAAACTGTGTTACTAGTGCATCCCAAGAAGTAATTGATTTAGTAGGTAGCCCAAAAA
650 TCACAAAACAAACTGTGTTACTAGTGCATCCCAAGAAGTAATTGATCCGGTAGGTAGCCCAAAAA
** * * * * *
28580037 ATGAAGTACTGGATCTTCTCTCTAAGGAATAAGGAAATAATTGCATCTTCAAGGCATCATCAAGA
715 ACCAAGTACGGGCTCTTCCCTATAAGGAATAAGGAAATAATTGCATCTTCAAGGCATCATCAGGA
*
28580102 TATCATAAGGAATAAGGATATATCGATCCTACAGGGATGGTTGTCTTTTTTCTATTAGTGTCGAT
780 TATCATAAGGAATAAGGATATATCGATCCCACAGGGATGGTTGTCTTTTTTCTATTAGTGTCGAT
28580167 GCAATAACTAGATAGAAACAAGATAAATTGTGAGGATAGTTGTCAGAGCAACAACTTGAAAACAA
845 GCAATAACTAGATAGAAACAAGATAAATTGTGAGGATAGTTGTCAGAGCAACAACTTGAAAACAA
*
28580232 TAAAATAAAATTTGATAATTGCCCTTG
910 TAAAATAAAATATGATAATTGCCC-TG
* * * *
28580259 -GTAGATGTATTCCCATATCTGAATGTAGCAGCATTTTGTCTAGCATTTTGACTTCCCCAAAATG
1 AGTAGATGTATTCCCATATCTGAATGTCGCAGCATTTTGTCTAGCATTCTGAGTTCCCCAAAATA
* *
28580323 GTTGGTTGTGTGCAAAGTTGTTGTAAGAGTTACCATAAGAATTGTTGCGGATGTACTAATATAAC
66 GTTGGTTGCGTGCAAAGTTGTTGTAAGAGTTACCATAAGAATTGTTGCGGATGTAATAATATAAC
* * * *
28580388 AGGCATTCTTTGCATATTGTGGTCAATTTTCATAGCTATAGTTGTCACTACAAATCTCAGAACAA
131 AGGCATTCTCTGCATATTGTGGTCAATCTTCATAGCTATGGTTGTCACTACAAATCTCACAACAA
*
28580453 AAAGTAGGAACATCAACTTGTTGAGCGACTTGCATAGGTGCAACGCCACTAGTCTATTGCAT-TT
196 AAAGTAGGAACATCAACTTGTTGAGCGACTTGTATAGGTGCAACGCCACTAGTCTATTGCATATT
*
28580517 TTTAATCATGTTTGTGTGAGAAGAAACTTGAGCACTTAGTGCGGTTATTGCATCCAATTCCATAA
261 TTTAATCATGTTTGTGTGAGAAGAAACTTGAGCACTTAGTGCGGTTATTGCATCCAATTCAATAA
* *
28580582 CTCCTGGACTAGTTTTTGCTTGTGCAACTATGGAGATAAGGTATTGATAATCATTCTGAGCAATT
326 CTCCTGGAGTAGTTTTTGCTTGTGCAGCTATGGAGATAAGGTATTGATAATCATTCTGAGCAATT
* *
28580647 CTCTCGAGAATTCTCACAGCATCATTATAAGTACAATTCAACAGAAGTCCATTGGCTGATGCATC
391 CTCTCAAGAATTCTCACAGCATCATTATAAGTACAATTCAACAGAGGTCCATTGGCTGATGCATC
*
28580712 GACAAGTTTCCTTGTATATGAATTCAGCCCATTATAAAAATCTCAATTTGTGTTTTTGGTTGAAT
456 GACAAGTTTCCTTGTATATGAATTCAGCCCATTATAAAAATCTCAATTTGTGTTTCTGGTTGAAT
* *
28580777 GTCGTACAGGGGACAAAGTCAAAGTAAAGATTTATAATGTTCCCATGTGGTGTGAAGATTTTCAT
521 GTCGTGCATGGGACAAAGTCAAAGTAAAGATTTATAATGTTCCCATGTGGTGTGAAGATTTTCAT
* * *
28580842 CATCCAGCTGACGGTAAGTAGTAATATCATTTTGAAGACAAGCATTTATTGTTGGTGAGTTAAAT
586 CATCCAGCTGATGGTAAGTAGTAATATCATTTTGAAGACAAGCATTCATTGTTGGTGGGTTAAAT
*
28580907 CACAAAACAAACTGTGGTACTAGTGCATCCCAAGAAGTAATTGATCCGGTAGGTAGCCCAAAAAA
651 CACAAAACAAACTGTGTTACTAGTGCATCCCAAGAAGTAATTGATCCGGTAGGTAGCCCAAAAAA
28580972 CCAAGTACGGGCTCTTCCCTATAAGGAATAAGGAAATAATTGCATCTTCAAGGCATCATCAGGAT
716 CCAAGTACGGGCTCTTCCCTATAAGGAATAAGGAAATAATTGCATCTTCAAGGCATCATCAGGAT
* * * ***
28581037 ATCATAAGGATTAATGATATATCGATCCCACAGGGATGGTTGTTTTTTTTCTCGAAGTGTCGATG
781 ATCATAAGGAATAAGGATATATCGATCCCACAGGGATGGTTGTCTTTTTTCTATTAGTGTCGATG
* * *
28581102 CAATAACTAGATAGAAACAGGATAAATTGTGAGGATAGTTATCAGAGCAACAACTTGAGAACAAT
846 CAATAACTAGATAGAAACAAGATAAATTGTGAGGATAGTTGTCAGAGCAACAACTTGAAAACAAT
28581167 AAAATAAAATATGATAATTGCCCTG
911 AAAATAAAATATGATAATTGCCCTG
*
28581192 AGTAGATGTATTCCCATATATGAATGTCGCAGCATTTTGTCTAGCATTCTGAGTTCCCCAAAATA
1 AGTAGATGTATTCCCATATCTGAATGTCGCAGCATTTTGTCTAGCATTCTGAGTTCCCCAAAATA
* * * *
28581257 GTTGGTTGCGTGCAAAGTTGTTGTAAGAGTTACCTTAAGAATTGTTGTGGATGTACTAATATAAT
66 GTTGGTTGCGTGCAAAGTTGTTGTAAGAGTTACCATAAGAATTGTTGCGGATGTAATAATATAAC
*
28581322 AGGCATTCTTTGCATATTGTGGTCAATCTTCATAGCTATGGTTGTCACTACAAATCTCACAACAA
131 AGGCATTCTCTGCATATTGTGGTCAATCTTCATAGCTATGGTTGTCACTACAAATCTCACAACAA
*
28581387 AAAGTAGGAACATCAACTTGTTAAGCGACTTGTATAGGTGCAACGCCACTAGTCTATTGCATATT
196 AAAGTAGGAACATCAACTTGTTGAGCGACTTGTATAGGTGCAACGCCACTAGTCTATTGCATATT
*
28581452 TTTAATCATGTTTGTGTGAGAAGAAACTTGAGCACTTAGTGCAGTTATTGCATCCAATTCAATAA
261 TTTAATCATGTTTGTGTGAGAAGAAACTTGAGCACTTAGTGCGGTTATTGCATCCAATTCAATAA
* * * *
28581517 CTCCGGGAGTAGTTTTTTCTTGTGCAGCTCTAGAGATAAGGTATTGATAATCATTCTGAGCAATT
326 CTCCTGGAGTAGTTTTTGCTTGTGCAGCTATGGAGATAAGGTATTGATAATCATTCTGAGCAATT
* * *
28581582 CTCTCAAGACTTCTCACAGCATCATCATAAGTACAA-TCTAACAGAGGTCCATTGGCTGATGCGT
391 CTCTCAAGAATTCTCACAGCATCATTATAAGTACAATTC-AACAGAGGTCCATTGGCTGATGCAT
* * *
28581646 CGACAAGTTTCCTTGTATATGAATTCAGCCCGTTATAGAAATCTCAATTTGTATTTCTGGTTGAA
455 CGACAAGTTTCCTTGTATATGAATTCAGCCCATTATAAAAATCTCAATTTGTGTTTCTGGTTGAA
* ** *
28581711 TGTCGTGCATGGGACAAAGCCAAAGTAAAGATTTATAATGTTCCCACATGGTTTGAAGATTTTCA
520 TGTCGTGCATGGGACAAAGTCAAAGTAAAGATTTATAATGTTCCCATGTGGTGTGAAGATTTTCA
* * * * * * *
28581776 TAATCCAACTGATGGTAAGCAATAATATCATTTTCAAGATGAA-CATTCGTTGTTGGTGGGTTAA
585 TCATCCAGCTGATGGTAAGTAGTAATATCATTTTGAAGA-CAAGCATTCATTGTTGGTGGGTTAA
** *
28581840 ATTGCAAAACAAACTGTGTTACTAGTGCATCCCAAGAAGTAATTGATCCGGTAGATAGCCCAAAA
649 ATCACAAAACAAACTGTGTTACTAGTGCATCCCAAGAAGTAATTGATCCGGTAGGTAGCCCAAAA
*
28581905 AACCAAGTACGGGCTCTTCCCTATAAGGAATAAGGAAATAATTACATCTTCAAGGCATCATCAGG
714 AACCAAGTACGGGCTCTTCCCTATAAGGAATAAGGAAATAATTGCATCTTCAAGGCATCATCAGG
*
28581970 ATATCATAAGGAATAAGGATATATCGATCCCACAGGGATGGTTGCCTTTTTTCTATTAGTGTCGA
779 ATATCATAAGGAATAAGGATATATCGATCCCACAGGGATGGTTGTCTTTTTTCTATTAGTGTCGA
* * * *
28582035 TGCGATAACTAGATAGGAACAAGATAAATTGTGACGATAGTTGTTAGAGCAACAACTTGAAAACA
844 TGCAATAACTAGATAGAAACAAGATAAATTGTGAGGATAGTTGTCAGAGCAACAACTTGAAAACA
28582100 ATAAAATAAAATATGATAATTGCCCTG
909 ATAAAATAAAATATGATAATTGCCCTG
* * * *
28582127 AGTAGATGTATTCCCATATCTAAACGTCGCAGTATTTTGTCTAGCATTCTGAGTTCCCCAAAACA
1 AGTAGATGTATTCCCATATCTGAATGTCGCAGCATTTTGTCTAGCATTCTGAGTTCCCCAAAATA
* * * *
28582192 GTTGGTTGCGTGTAAAGTTGTTGTAAGAGTTACCATAGGAATTGTTTCAGATGTAATAATATAAC
66 GTTGGTTGCGTGCAAAGTTGTTGTAAGAGTTACCATAAGAATTGTTGCGGATGTAATAATATAAC
* *** *
28582257 AGACATTCTCTATTTATTGTGGTCAATCTTCATAGCTATGGTTATCACTACAAATCTCACAA-AA
131 AGGCATTCTCTGCATATTGTGGTCAATCTTCATAGCTATGGTTGTCACTACAAATCTCACAACAA
* *
28582321 AAAGTAGGAAAATCAACTTGTTGAGCAACTTGTATAGGTGCAACGCCACTAGTCTATTGCATATT
196 AAAGTAGGAACATCAACTTGTTGAGCGACTTGTATAGGTGCAACGCCACTAGTCTATTGCATATT
28582386 TTTAA
261 TTTAA
28582391 CCAATGGGAT
Statistics
Matches: 1967, Mismatches: 154, Indels: 18
0.92 0.07 0.01
Matches are distributed among these distances:
929 209 0.11
931 1 0.00
933 4 0.00
934 938 0.48
935 813 0.41
936 2 0.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (935 bp):
AGTAGATGTATTCCCATATCTGAATGTCGCAGCATTTTGTCTAGCATTCTGAGTTCCCCAAAATA
GTTGGTTGCGTGCAAAGTTGTTGTAAGAGTTACCATAAGAATTGTTGCGGATGTAATAATATAAC
AGGCATTCTCTGCATATTGTGGTCAATCTTCATAGCTATGGTTGTCACTACAAATCTCACAACAA
AAAGTAGGAACATCAACTTGTTGAGCGACTTGTATAGGTGCAACGCCACTAGTCTATTGCATATT
TTTAATCATGTTTGTGTGAGAAGAAACTTGAGCACTTAGTGCGGTTATTGCATCCAATTCAATAA
CTCCTGGAGTAGTTTTTGCTTGTGCAGCTATGGAGATAAGGTATTGATAATCATTCTGAGCAATT
CTCTCAAGAATTCTCACAGCATCATTATAAGTACAATTCAACAGAGGTCCATTGGCTGATGCATC
GACAAGTTTCCTTGTATATGAATTCAGCCCATTATAAAAATCTCAATTTGTGTTTCTGGTTGAAT
GTCGTGCATGGGACAAAGTCAAAGTAAAGATTTATAATGTTCCCATGTGGTGTGAAGATTTTCAT
CATCCAGCTGATGGTAAGTAGTAATATCATTTTGAAGACAAGCATTCATTGTTGGTGGGTTAAAT
CACAAAACAAACTGTGTTACTAGTGCATCCCAAGAAGTAATTGATCCGGTAGGTAGCCCAAAAAA
CCAAGTACGGGCTCTTCCCTATAAGGAATAAGGAAATAATTGCATCTTCAAGGCATCATCAGGAT
ATCATAAGGAATAAGGATATATCGATCCCACAGGGATGGTTGTCTTTTTTCTATTAGTGTCGATG
CAATAACTAGATAGAAACAAGATAAATTGTGAGGATAGTTGTCAGAGCAACAACTTGAAAACAAT
AAAATAAAATATGATAATTGCCCTG
Found at i:28587643 original size:24 final size:24
Alignment explanation
Indices: 28587610--28587708 Score: 101
Period size: 24 Copynumber: 4.2 Consensus size: 24
28587600 TAAACACGTG
* *
28587610 ATTCTGTAAGTTCCTTTGTGGCAT
1 ATTCTATAAGTGCCTTTGTGGCAT
* *
28587634 ATTCTATAAGTTCCTTTGTGGCGT
1 ATTCTATAAGTGCCTTTGTGGCAT
* * * *
28587658 ATT-TATAAGTGCCATTGTAGAAA
1 ATTCTATAAGTGCCTTTGTGGCAT
* *
28587681 ATTCTGTAAGTGCCTTTGTGGCGT
1 ATTCTATAAGTGCCTTTGTGGCAT
28587705 ATTC
1 ATTC
28587709 GAGGTTGCCT
Statistics
Matches: 60, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
23 17 0.28
24 43 0.72
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.42
Consensus pattern (24 bp):
ATTCTATAAGTGCCTTTGTGGCAT
Found at i:28588938 original size:153 final size:153
Alignment explanation
Indices: 28588651--28588960 Score: 530
Period size: 153 Copynumber: 2.0 Consensus size: 153
28588641 ATTTGATTCT
* *
28588651 TGTTCCCTATCTCTTTATTTTTTGCTGTTGTTATGCTAAACATATCTATCAATATTTATGTTGTT
1 TGTTCCCTATCTCTTTAATTTTTGCTATTGTTATGCTAAACATATCTATCAATATTTATGTTGTT
* ** *
28588716 GGAATGGTTAATTTAATCAATTTATCTTGAATTTAATTCGTGTTATGTTGATTGCATTTTGTTTT
66 GGAATGGTTAATTTAATCAATTTAGCTTGAATTTAATTCGTGTTATGTTGATTGCATTTCATTTG
28588781 TTAAAATCATTAAAATTGTGTTA
131 TTAAAATCATTAAAATTGTGTTA
* *
28588804 TGTTCCCTATCTCTTTAATTTTTGTTATTGTTCTGCTAAACATATCTATCAATATTTATGTTGTT
1 TGTTCCCTATCTCTTTAATTTTTGCTATTGTTATGCTAAACATATCTATCAATATTTATGTTGTT
*
28588869 GGAATGGTTAATTTAATCAATTTAGCTTGAATTTAATTTGTGTTATGTTGATTGCATTTCATTTG
66 GGAATGGTTAATTTAATCAATTTAGCTTGAATTTAATTCGTGTTATGTTGATTGCATTTCATTTG
*
28588934 TTAAAATTATTAAAATTGTGTTA
131 TTAAAATCATTAAAATTGTGTTA
28588957 TGTT
1 TGTT
28588961 GTTATAGGCC
Statistics
Matches: 147, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
153 147 1.00
ACGTcount: A:0.26, C:0.09, G:0.13, T:0.52
Consensus pattern (153 bp):
TGTTCCCTATCTCTTTAATTTTTGCTATTGTTATGCTAAACATATCTATCAATATTTATGTTGTT
GGAATGGTTAATTTAATCAATTTAGCTTGAATTTAATTCGTGTTATGTTGATTGCATTTCATTTG
TTAAAATCATTAAAATTGTGTTA
Found at i:28595237 original size:12 final size:13
Alignment explanation
Indices: 28595212--28595241 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
28595202 AGGGCTATAA
28595212 TTATTGCATTTAT
1 TTATTGCATTTAT
28595225 TTATTGC-TTTAT
1 TTATTGCATTTAT
28595237 TTATT
1 TTATT
28595242 CATGTATAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (13 bp):
TTATTGCATTTAT
Found at i:28608858 original size:23 final size:19
Alignment explanation
Indices: 28608824--28608867 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 19
28608814 AACCAACAAA
28608824 AATATCAATTATAATTACTTC
1 AATATCAATTAT-A-TACTTC
28608845 AATATACATATTATATACTTC
1 AATAT-CA-ATTATATACTTC
28608866 AA
1 AA
28608868 ATGGCATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 13 0.62
22 3 0.14
23 5 0.24
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (19 bp):
AATATCAATTATATACTTC
Found at i:28612669 original size:6 final size:6
Alignment explanation
Indices: 28612654--28612691 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
28612644 TTACCATCTC
28612654 TTTC-T TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT
28612692 GCCACAAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTCTT
Found at i:28617928 original size:26 final size:26
Alignment explanation
Indices: 28617891--28618048 Score: 217
Period size: 26 Copynumber: 6.1 Consensus size: 26
28617881 GTAATAGGCC
* * *
28617891 TAAATTATCGAAACACCCTCTATGGG
1 TAAATTACCGAAATACCCTCGATGGG
28617917 TAAATTACCGAAATACCCTCGATGGG
1 TAAATTACCGAAATACCCTCGATGGG
* * *
28617943 TAAATTACTGAAATACCCCCAATGGG
1 TAAATTACCGAAATACCCTCGATGGG
*
28617969 TAAATTATCGAAATACCCTCGATGGG
1 TAAATTACCGAAATACCCTCGATGGG
*
28617995 TAAATTACCGAAATACCCTTGATGGG
1 TAAATTACCGAAATACCCTCGATGGG
* * *
28618021 TAAATTATCGAAATACCCCCGAAGGG
1 TAAATTACCGAAATACCCTCGATGGG
28618047 TA
1 TA
28618049 GAATGACTGT
Statistics
Matches: 116, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 116 1.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.25
Consensus pattern (26 bp):
TAAATTACCGAAATACCCTCGATGGG
Found at i:28617972 original size:52 final size:52
Alignment explanation
Indices: 28617912--28618066 Score: 211
Period size: 52 Copynumber: 3.0 Consensus size: 52
28617902 AACACCCTCT
*
28617912 ATGGGTAAATTACCGAAATACCCTCGATGGGTAAATTACTGAAATACCCCCA
1 ATGGGTAAATTATCGAAATACCCTCGATGGGTAAATTACTGAAATACCCCCA
* ***
28617964 ATGGGTAAATTATCGAAATACCCTCGATGGGTAAATTACCGAAATACCCTTG
1 ATGGGTAAATTATCGAAATACCCTCGATGGGTAAATTACTGAAATACCCCCA
* * * **
28618016 ATGGGTAAATTATCGAAATACCCCCGAAGGGTAGAATGACTGTTATACCCC
1 ATGGGTAAATTATCGAAATACCCTCGATGGGTA-AATTACTGAAATACCCC
28618067 TAGGAGATAA
Statistics
Matches: 90, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
52 78 0.87
53 12 0.13
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (52 bp):
ATGGGTAAATTATCGAAATACCCTCGATGGGTAAATTACTGAAATACCCCCA
Found at i:28618020 original size:78 final size:78
Alignment explanation
Indices: 28617891--28618048 Score: 257
Period size: 78 Copynumber: 2.0 Consensus size: 78
28617881 GTAATAGGCC
*
28617891 TAAATTATCGAAACACCCTCTATGGGTAAATTACCGAAATACCCTCGATGGGTAAATTA-CTGAA
1 TAAATTATCGAAACACCCTCGATGGGTAAATTACCGAAATACCCTCGATGGGTAAATTATC-GAA
28617955 ATACCCCC-AATGGG
65 ATACCCCCGAA-GGG
* *
28617969 TAAATTATCGAAATACCCTCGATGGGTAAATTACCGAAATACCCTTGATGGGTAAATTATCGAAA
1 TAAATTATCGAAACACCCTCGATGGGTAAATTACCGAAATACCCTCGATGGGTAAATTATCGAAA
28618034 TACCCCCGAAGGG
66 TACCCCCGAAGGG
28618047 TA
1 TA
28618049 GAATGACTGT
Statistics
Matches: 75, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
78 72 0.96
79 3 0.04
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.25
Consensus pattern (78 bp):
TAAATTATCGAAACACCCTCGATGGGTAAATTACCGAAATACCCTCGATGGGTAAATTATCGAAA
TACCCCCGAAGGG
Found at i:28618301 original size:26 final size:26
Alignment explanation
Indices: 28618272--28618321 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
28618262 ACATATACTG
* *
28618272 TACTGGCAGCTCTGCTGCGATATTAT
1 TACTGGCAGCTATGCTGCAATATTAT
28618298 TACTGGCAGCTATGCTGCAATATT
1 TACTGGCAGCTATGCTGCAATATT
28618322 GGTGTGTGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (26 bp):
TACTGGCAGCTATGCTGCAATATTAT
Found at i:28619647 original size:15 final size:14
Alignment explanation
Indices: 28619622--28619669 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
28619612 AATTTGAGAG
*
28619622 AAGAAAAAAAGAAA
1 AAGAGAAAAAGAAA
*
28619636 TGAGAGAAAAAGAAA
1 -AAGAGAAAAAGAAA
28619651 AAGAGATAAAAGAAA
1 AAGAGA-AAAAGAAA
28619666 AAGA
1 AAGA
28619670 AATTGAGAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 5 0.17
15 24 0.83
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (14 bp):
AAGAGAAAAAGAAA
Found at i:28619653 original size:21 final size:21
Alignment explanation
Indices: 28619616--28619671 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
28619606 TGAATGAATT
*
28619616 TGAGAGAAGAA-AAAAAGAAA
1 TGAGAGAAAAAGAAAAAGAAA
*
28619636 TGAGAGAAAAAGAAAAAGAGA
1 TGAGAGAAAAAGAAAAAGAAA
* *
28619657 TAAAAGAAAAAGAAA
1 TGAGAGAAAAAGAAA
28619672 TTGAGAGTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 10 0.32
21 21 0.68
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.05
Consensus pattern (21 bp):
TGAGAGAAAAAGAAAAAGAAA
Found at i:28621796 original size:20 final size:20
Alignment explanation
Indices: 28621753--28621800 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
28621743 TTTAGCTTGG
* ** *
28621753 TTCAGCTCACTTAATTTTAT
1 TTCAGCTCACATAAGCTTAA
28621773 TTCAGCTCACATAAGCTTAA
1 TTCAGCTCACATAAGCTTAA
28621793 TTCAGCTC
1 TTCAGCTC
28621801 GTTTGAGCTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.25, G:0.08, T:0.40
Consensus pattern (20 bp):
TTCAGCTCACATAAGCTTAA
Found at i:28625571 original size:15 final size:15
Alignment explanation
Indices: 28625548--28625604 Score: 75
Period size: 15 Copynumber: 3.9 Consensus size: 15
28625538 TGCATAATAA
28625548 AATAAAATAAAAATCT
1 AATAAAATAAAAAT-T
28625564 AA-AAAAT-AAAA-T
1 AATAAAATAAAAATT
28625576 AATAACAATAAAAATT
1 AATAA-AATAAAAATT
28625592 AATAAAATAAAAA
1 AATAAAATAAAAA
28625605 ACTAAATGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.08
13 2 0.05
14 7 0.19
15 17 0.46
16 8 0.22
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.21
Consensus pattern (15 bp):
AATAAAATAAAAATT
Found at i:28625588 original size:20 final size:20
Alignment explanation
Indices: 28625546--28625604 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 20
28625536 AGTGCATAAT
*
28625546 AAAATAAAATAAAAATCTAA
1 AAAATAAAATAAAAATCAAA
28625566 AAAATAAAATAATAACAAT-AAA
1 AAAATAAAAT-A-AA-AATCAAA
28625588 AATTAATAAAATAAAAA
1 AA--AATAAAATAAAAA
28625605 ACTAAATGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
20 10 0.30
21 3 0.09
22 8 0.24
23 4 0.12
24 8 0.24
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.20
Consensus pattern (20 bp):
AAAATAAAATAAAAATCAAA
Found at i:28625598 original size:29 final size:28
Alignment explanation
Indices: 28625548--28625603 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
28625538 TGCATAATAA
28625548 AATAAAATAAAAATCTAAAAAATAAAAT
1 AATAAAATAAAAATCTAAAAAATAAAAT
28625576 AATAACAATAAAAAT-TAATAAAATAAAA
1 AATAA-AATAAAAATCTAA-AAAATAAAA
28625604 AACTAAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.21
Consensus pattern (28 bp):
AATAAAATAAAAATCTAAAAAATAAAAT
Found at i:28626114 original size:9 final size:9
Alignment explanation
Indices: 28626100--28626130 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
28626090 GTTAAACGAA
28626100 TCGAGTTAT
1 TCGAGTTAT
*
28626109 TCGAGTTAA
1 TCGAGTTAT
28626118 TCGAGTTAT
1 TCGAGTTAT
28626127 TCGA
1 TCGA
28626131 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:28626457 original size:30 final size:31
Alignment explanation
Indices: 28626423--28626482 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
28626413 AAACCTTTTA
*
28626423 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
28626453 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
28626483 TCCCACCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:28649759 original size:23 final size:23
Alignment explanation
Indices: 28649711--28649764 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
28649701 AGATTTATCA
*
28649711 ATTTAAG--TTTTAAAATCAATG
1 ATTTAAGCATTTTAAAATCAAAG
28649732 ATTTAAGCATTTTAAAATCCAAAG
1 ATTTAAGCATTTTAAAAT-CAAAG
*
28649756 -TTTATGCAT
1 ATTTAAGCAT
28649765 GTCTTTGGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 7 0.25
23 17 0.61
24 4 0.14
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (23 bp):
ATTTAAGCATTTTAAAATCAAAG
Found at i:28656921 original size:33 final size:33
Alignment explanation
Indices: 28656879--28656945 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
28656869 TCAAAACTTA
28656879 TAGCAAAAGTATCAATCAAACAGAATCTAGGAT
1 TAGCAAAAGTATCAATCAAACAGAATCTAGGAT
28656912 TAGCAAAAGTATCAATCAAACAGAATCTAGGAT
1 TAGCAAAAGTATCAATCAAACAGAATCTAGGAT
28656945 T
1 T
28656946 TAAAAGTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (33 bp):
TAGCAAAAGTATCAATCAAACAGAATCTAGGAT
Found at i:28660783 original size:20 final size:19
Alignment explanation
Indices: 28660758--28660798 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
28660748 ATATATAATA
28660758 TATATTATATAATATATTTT
1 TATATTA-ATAATATATTTT
* *
28660778 TATATTAGTAATGTATTTT
1 TATATTAATAATATATTTT
28660797 TA
1 TA
28660799 AACTATTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TATATTAATAATATATTTT
Found at i:28660951 original size:40 final size:40
Alignment explanation
Indices: 28660880--28660968 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 40
28660870 AAATATATAA
* * * *
28660880 ATTTCGATTAATTCGGTTATCAAACTAAATTAACTGAAAT
1 ATTTCGATTAATTCAGTTAACAAACCAAATTAACCGAAAT
** *
28660920 ATTTCGATTAATTCAGTTAACGGACCGAATTAACCGAAAT
1 ATTTCGATTAATTCAGTTAACAAACCAAATTAACCGAAAT
28660960 ATTTCGATT
1 ATTTCGATT
28660969 CAACTAATGT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (40 bp):
ATTTCGATTAATTCAGTTAACAAACCAAATTAACCGAAAT
Found at i:28670350 original size:7 final size:7
Alignment explanation
Indices: 28670338--28670366 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
28670328 GAAAAGGGTG
28670338 TTTTCCA
1 TTTTCCA
28670345 TTTTCCA
1 TTTTCCA
28670352 TTTTCCA
1 TTTTCCA
28670359 TTTTCCA
1 TTTTCCA
28670366 T
1 T
28670367 GAATTGGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.28, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTTCCA
Found at i:28671398 original size:29 final size:28
Alignment explanation
Indices: 28671365--28671425 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
28671355 AAGCCGTTTT
28671365 TTTTTTCAAAATTTACCAAAATGGGCCGA
1 TTTTTTCAAAATTTACCAAAATGGGCC-A
* ** **
28671394 TTTTTTGATTATTTACCGGAATGGGCCA
1 TTTTTTCAAAATTTACCAAAATGGGCCA
28671422 TTTT
1 TTTT
28671426 CCGAGAAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.43
Consensus pattern (28 bp):
TTTTTTCAAAATTTACCAAAATGGGCCA
Found at i:28671934 original size:123 final size:124
Alignment explanation
Indices: 28671625--28671973 Score: 601
Period size: 124 Copynumber: 2.8 Consensus size: 124
28671615 TTATTTCAAG
*
28671625 TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTATG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGTG
*
28671690 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
66 AAATTGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
*
28671749 TTGACGTTTCTGAGAAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGTG
*
28671814 AAATTGCGCCCTCGTGGACGCGATTTTGCGACAGTAGGTCATGTAAGAAATAATTTTTT
66 AAATTGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
* * * *
28671873 TT-TCGTTTCTGAGCAAATAGTATAAAATCACTTCTACCAGGATGCTATTTGAAAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* *
28671937 AAATTGTGCCCTCGTGGATGCGATTTTGCTACAGTAG
66 AAATTGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
28671974 CAAGTTTGGG
Statistics
Matches: 213, Mismatches: 12, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
123 91 0.43
124 122 0.57
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.32
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGTG
AAATTGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
Found at i:28674603 original size:40 final size:40
Alignment explanation
Indices: 28674559--28674637 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
28674549 GACTGTGGGA
*
28674559 AGTTTGATACACTTCGTTATCCATGCGCTCATGTTATTGC
1 AGTTTGATACACTTCGCTATCCATGCGCTCATGTTATTGC
*
28674599 AGTTTGATGCACTTCGCTATCCATGCGCTCATGTTATTG
1 AGTTTGATACACTTCGCTATCCATGCGCTCATGTTATTG
28674638 TAAGTTTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (40 bp):
AGTTTGATACACTTCGCTATCCATGCGCTCATGTTATTGC
Found at i:28674714 original size:25 final size:26
Alignment explanation
Indices: 28674661--28674724 Score: 94
Period size: 25 Copynumber: 2.5 Consensus size: 26
28674651 AAATTAGGGT
28674661 TTTTATTACATCAAATAGAACTTCAA
1 TTTTATTACATCAAATAGAACTTCAA
* * *
28674687 TTTTATTATATTAAATA-AACTTCTA
1 TTTTATTACATCAAATAGAACTTCAA
28674712 TTTTATTACATCA
1 TTTTATTACATCA
28674725 GATAATAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
25 18 0.55
26 15 0.45
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.47
Consensus pattern (26 bp):
TTTTATTACATCAAATAGAACTTCAA
Found at i:28675821 original size:7 final size:7
Alignment explanation
Indices: 28675811--28675835 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28675801 TTATATACAT
28675811 AATACTA
1 AATACTA
28675818 AATACTA
1 AATACTA
28675825 AATACTA
1 AATACTA
28675832 AATA
1 AATA
28675836 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:28676947 original size:11 final size:10
Alignment explanation
Indices: 28676917--28676982 Score: 60
Period size: 10 Copynumber: 6.5 Consensus size: 10
28676907 GCCATTGATG
*
28676917 AAAATATAAA
1 AAAATTTAAA
28676927 AAAATTTAAA
1 AAAATTTAAA
* *
28676937 ATTATTTTAAA
1 A-AAATTTAAA
*
28676948 AAAATATAAA
1 AAAATTTAAA
28676958 AAAATTTAAA
1 AAAATTTAAA
** *
28676968 ATTATTTTAA
1 AAAATTTAAA
28676978 AAAAT
1 AAAAT
28676983 GAAATTGAGG
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
10 35 0.81
11 8 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:28676952 original size:31 final size:31
Alignment explanation
Indices: 28676917--28676981 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
28676907 GCCATTGATG
28676917 AAAATATAAAAAAATTTAAAATTATTTTAAA
1 AAAATATAAAAAAATTTAAAATTATTTTAAA
28676948 AAAATATAAAAAAATTTAAAATTATTTTAAA
1 AAAATATAAAAAAATTTAAAATTATTTTAAA
28676979 AAA
1 AAA
28676982 TGAAATTGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (31 bp):
AAAATATAAAAAAATTTAAAATTATTTTAAA
Found at i:28676964 original size:21 final size:20
Alignment explanation
Indices: 28676917--28676968 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
28676907 GCCATTGATG
* *
28676917 AAAATATAAAAAAATTTAAA
1 AAAATTTAAAAAAATATAAA
* *
28676937 ATTATTTTAAAAAAATATAAA
1 A-AAATTTAAAAAAATATAAA
28676958 AAAATTTAAAA
1 AAAATTTAAAA
28676969 TTATTTTAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAATTTAAAAAAATATAAA
Found at i:28677048 original size:51 final size:51
Alignment explanation
Indices: 28676983--28677095 Score: 190
Period size: 51 Copynumber: 2.2 Consensus size: 51
28676973 TTTAAAAAAT
*
28676983 GAAATTGAGGGGAAATTGAAATTAAATATGGATTTAAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTAAGAGAATTTTGGAAG
* *
28677034 GAAATTGAGAGGAAATTGAAATTAAATATGGGTTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTAAGAGAATTTTGGAAG
*
28677085 GAAATTAAGAG
1 GAAATTGAGAG
28677096 AATTTTGGAA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.43, C:0.00, G:0.28, T:0.28
Consensus pattern (51 bp):
GAAATTGAGAGGAAATTGAAATTAAATATGGATTTAAGAGAATTTTGGAAG
Found at i:28677095 original size:22 final size:22
Alignment explanation
Indices: 28677070--28677112 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
28677060 TATGGGTTTG
*
28677070 AGAGAATTTTGGAAGGAAATTA
1 AGAGAATTTTGGAAGAAAATTA
28677092 AGAGAATTTTGGAAGAAAATT
1 AGAGAATTTTGGAAGAAAATT
28677113 GAGAAGATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.26, T:0.28
Consensus pattern (22 bp):
AGAGAATTTTGGAAGAAAATTA
Found at i:28678837 original size:27 final size:27
Alignment explanation
Indices: 28678777--28678864 Score: 115
Period size: 27 Copynumber: 3.3 Consensus size: 27
28678767 TTAGTCTTGC
28678777 GCCGCCAATCTCTTTGGCACCTTTGGT
1 GCCGCCAATCTCTTTGGCACCTTTGGT
*
28678804 -CAGGCCAATCTCTTTGGCACCTTTGGT
1 GC-CGCCAATCTCTTTGGCACCTTTGGT
* ** *
28678831 GCCGCCAATCACTTAAGCACTTTTGGT
1 GCCGCCAATCTCTTTGGCACCTTTGGT
28678858 GCCGCCA
1 GCCGCCA
28678865 CAGGTTTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
26 1 0.02
27 51 0.96
28 1 0.02
ACGTcount: A:0.16, C:0.33, G:0.22, T:0.30
Consensus pattern (27 bp):
GCCGCCAATCTCTTTGGCACCTTTGGT
Found at i:28678956 original size:28 final size:28
Alignment explanation
Indices: 28678900--28678965 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
28678890 TTTTTTTGGT
***
28678900 ATATTTTGGTAAATAAAAAAAATTTATA
1 ATATTTTGGTAAATAAAAAAAAGGGATA
28678928 ATATTTTGGTAAATAAAAAAAAGGGATA
1 ATATTTTGGTAAATAAAAAAAAGGGATA
*
28678956 ACATTTTGGT
1 ATATTTTGGT
28678966 TATTTTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.36
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGGGATA
Found at i:28679730 original size:19 final size:19
Alignment explanation
Indices: 28679706--28679745 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
28679696 TCTATTTATA
28679706 AACATAAGAAGTATAAATG
1 AACATAAGAAGTATAAATG
28679725 AACATAAGAAGTATAAATG
1 AACATAAGAAGTATAAATG
28679744 AA
1 AA
28679746 GTAGAGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.60, C:0.05, G:0.15, T:0.20
Consensus pattern (19 bp):
AACATAAGAAGTATAAATG
Found at i:28679974 original size:22 final size:22
Alignment explanation
Indices: 28679946--28679989 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
28679936 TACTCCCCCT
28679946 CATGAGAACATCACATAATATA
1 CATGAGAACATCACATAATATA
28679968 CATGAGAACATCACATAATATA
1 CATGAGAACATCACATAATATA
28679990 TCATATTCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.18, G:0.09, T:0.23
Consensus pattern (22 bp):
CATGAGAACATCACATAATATA
Found at i:28682748 original size:14 final size:15
Alignment explanation
Indices: 28682714--28682758 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
28682704 ATTAGTCTCC
28682714 AATTATAATAAATAT
1 AATTATAATAAATAT
28682729 AA-TATAATAAATA-
1 AATTATAATAAATAT
*
28682742 AATTATAGTAAAATAT
1 AATTATAAT-AAATAT
28682758 A
1 A
28682759 CCTGAGATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 2 0.08
14 16 0.62
15 7 0.27
16 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (15 bp):
AATTATAATAAATAT
Found at i:28688669 original size:9 final size:9
Alignment explanation
Indices: 28688655--28688686 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
28688645 GATCAAGTAA
28688655 AATAAAATT
1 AATAAAATT
28688664 AATAAAATT
1 AATAAAATT
28688673 AATTAAAATT
1 AA-TAAAATT
28688683 AATA
1 AATA
28688687 TTCAAGTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
AATAAAATT
Found at i:28688681 original size:10 final size:10
Alignment explanation
Indices: 28688657--28688685 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
28688647 TCAAGTAAAA
28688657 TAAAATTAA-
1 TAAAATTAAT
28688666 TAAAATTAAT
1 TAAAATTAAT
28688676 TAAAATTAAT
1 TAAAATTAAT
28688686 ATTCAAGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TAAAATTAAT
Found at i:28689120 original size:16 final size:17
Alignment explanation
Indices: 28689057--28689203 Score: 55
Period size: 17 Copynumber: 8.9 Consensus size: 17
28689047 TCTAAAAATA
* *
28689057 ATATTATTTTAATA-CT
1 ATATTAATTTAATATTT
*
28689073 AAATTAAATTTAATATTT
1 ATATT-AATTTAATATTT
* *
28689091 ATATTGA--TAGTATTT
1 ATATTAATTTAATATTT
*
28689106 -TATTAATTTAATATTAAA
1 ATATTAATTTAATATT--T
*
28689124 ATATTAAATTAAT-TTT
1 ATATTAATTTAATATTT
*
28689140 ATA--AGATTTAATATTG
1 ATATTA-ATTTAATATTT
*
28689156 A-ATTTAATCTAATATTT
1 ATA-TTAATTTAATATTT
* * *
28689173 ATCTTGA--TAAGTA-TA
1 ATATTAATTTAA-TATTT
28689188 ATATTAATTTAATATT
1 ATATTAATTTAATATT
28689204 AAAGTGTTTA
Statistics
Matches: 94, Mismatches: 20, Indels: 33
0.64 0.14 0.22
Matches are distributed among these distances:
14 6 0.06
15 23 0.24
16 20 0.21
17 26 0.28
18 8 0.09
19 11 0.12
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (17 bp):
ATATTAATTTAATATTT
Found at i:28707739 original size:11 final size:11
Alignment explanation
Indices: 28707716--28707751 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
28707706 GATTTACAAC
28707716 TAAATCTGAGCT
1 TAAATC-GAGCT
28707728 TAAATCGAGCT
1 TAAATCGAGCT
*
28707739 TAAATCAAGCT
1 TAAATCGAGCT
28707750 TA
1 TA
28707752 CATAAGCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 17 0.74
12 6 0.26
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.31
Consensus pattern (11 bp):
TAAATCGAGCT
Found at i:28708621 original size:13 final size:13
Alignment explanation
Indices: 28708603--28708627 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28708593 TGGATTAGAT
28708603 TTGATTATGTAAG
1 TTGATTATGTAAG
28708616 TTGATTATGTAA
1 TTGATTATGTAA
28708628 TCTTGTAAAT
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:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (13 bp):
TTGATTATGTAAG
Found at i:28710336 original size:13 final size:13
Alignment explanation
Indices: 28710318--28710392 Score: 54
Period size: 13 Copynumber: 5.9 Consensus size: 13
28710308 TTCTAGTTAA
28710318 TATATATATATAT
1 TATATATATATAT
*
28710331 TATATATATGTA-
1 TATATATATATAT
28710343 -AGTA-ATGAT-TAT
1 TA-TATAT-ATATAT
*
28710355 TAT-TA-ATATTT
1 TATATATATATAT
28710366 TATATTATATTATAT
1 TATA-TATA-TATAT
28710381 TATATATATATA
1 TATATATATATA
28710393 ACAAAAGAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 20
0.68 0.04 0.28
Matches are distributed among these distances:
10 2 0.04
11 10 0.20
12 6 0.12
13 18 0.37
14 5 0.10
15 8 0.16
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (13 bp):
TATATATATATAT
Found at i:28711242 original size:13 final size:13
Alignment explanation
Indices: 28711224--28711255 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
28711214 TTTCCAGCAA
28711224 TTATGAATTTATT
1 TTATGAATTTATT
28711237 TTATGAATTTATT
1 TTATGAATTTATT
*
28711250 TGATGA
1 TTATGA
28711256 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:28711463 original size:50 final size:50
Alignment explanation
Indices: 28711350--28711591 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
28711340 ATTTGGGTAA
* * *
28711350 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
28711406 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
28711456 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
28711506 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
28711556 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
28711592 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:28711539 original size:100 final size:103
Alignment explanation
Indices: 28711350--28711599 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
28711340 ATTTGGGTAA
28711350 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
28711415 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
28711456 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
28711518 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
28711556 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
28711600 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:28715338 original size:45 final size:45
Alignment explanation
Indices: 28715275--28715488 Score: 239
Period size: 45 Copynumber: 4.8 Consensus size: 45
28715265 GTTAGAAAAT
* * * *
28715275 CAACACCGGTACATAGTACCTATTGTATGTATATGGCATGATAGT
1 CAACACCGGTACATAGTACCTGTTGTATGTATATAGCATGAAAGC
* * * *
28715320 CAACACCGGTACATAGTACCTATTGTATTTGTATGGCATGAAAGC
1 CAACACCGGTACATAGTACCTGTTGTATGTATATAGCATGAAAGC
* * * *
28715365 CAACACCGGTAAATAGTACTTGCTGTATGTATATAGCATGATAGC
1 CAACACCGGTACATAGTACCTGTTGTATGTATATAGCATGAAAGC
* * * *
28715410 CAACACCGGTACATAATACTTGCTGTATTTATATAGCATGAAAGC
1 CAACACCGGTACATAGTACCTGTTGTATGTATATAGCATGAAAGC
* * ** *
28715455 CGATACTAGTACATACTACCTGTTGTATGTATAT
1 CAACACCGGTACATAGTACCTGTTGTATGTATAT
28715489 CCTAATTGTT
Statistics
Matches: 145, Mismatches: 24, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 145 1.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (45 bp):
CAACACCGGTACATAGTACCTGTTGTATGTATATAGCATGAAAGC
Found at i:28715482 original size:90 final size:90
Alignment explanation
Indices: 28715275--28715488 Score: 266
Period size: 90 Copynumber: 2.4 Consensus size: 90
28715265 GTTAGAAAAT
* * * * *
28715275 CAACACCGGTACATAGTACCTATTGTATGTATATGGCATGATAGTCAACACCGGTACATAGTACC
1 CAACACCAGTACATAGTACCTGTTGTATGTATATAGCATGATAGCCAACACCGGTACATAATACC
* * *
28715340 TATTGTATTTGTATGGCATGAAAGC
66 TACTGTATTTATATAGCATGAAAGC
* * * * *
28715365 CAACACCGGTAAATAGTACTTGCTGTATGTATATAGCATGATAGCCAACACCGGTACATAATACT
1 CAACACCAGTACATAGTACCTGTTGTATGTATATAGCATGATAGCCAACACCGGTACATAATACC
*
28715430 TGCTGTATTTATATAGCATGAAAGC
66 TACTGTATTTATATAGCATGAAAGC
* * * *
28715455 CGATACTAGTACATACTACCTGTTGTATGTATAT
1 CAACACCAGTACATAGTACCTGTTGTATGTATAT
28715489 CCTAATTGTT
Statistics
Matches: 104, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
90 104 1.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (90 bp):
CAACACCAGTACATAGTACCTGTTGTATGTATATAGCATGATAGCCAACACCGGTACATAATACC
TACTGTATTTATATAGCATGAAAGC
Found at i:28719172 original size:88 final size:87
Alignment explanation
Indices: 28719024--28719194 Score: 272
Period size: 88 Copynumber: 2.0 Consensus size: 87
28719014 CTTCTTTACA
* * *
28719024 AGACTTGTTTACCTATCTAATTTTGTATAGGATCCAATGCTTCATTTATATACATATTTCCATTC
1 AGACTTGTTTACATATCTAATTTCGTATAGGATCCAATGCTTCATTTATATACATATTTCCATTA
*
28719089 CATGTTTATATGAAAGTGCGTG
66 CATGTTGATATGAAAGTGCGTG
*
28719111 AGACTTGTTTACATATCTTAATTTCGTATAGGGTCCAATGCTT-ACTTTATATACATATTTCCAT
1 AGACTTGTTTACATATC-TAATTTCGTATAGGATCCAATGCTTCA-TTTATATACATATTTCCAT
28719175 TACATGTTGATATGAAAGTG
64 TACATGTTGATATGAAAGTG
28719195 TGCGGATAAG
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
87 17 0.22
88 60 0.78
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (87 bp):
AGACTTGTTTACATATCTAATTTCGTATAGGATCCAATGCTTCATTTATATACATATTTCCATTA
CATGTTGATATGAAAGTGCGTG
Found at i:28719597 original size:23 final size:22
Alignment explanation
Indices: 28719571--28719622 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 22
28719561 ATTATATAAT
28719571 TAAATAATTAGGAATTAATTA-AA
1 TAAATAATTA-GAA-TAATTAGAA
28719594 TAAA-ATATTAGAATAATTAGAA
1 TAAATA-ATTAGAATAATTAGAA
*
28719616 TTAATAA
1 TAAATAA
28719623 CTTCAGCTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 6 0.24
22 10 0.40
23 9 0.36
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.35
Consensus pattern (22 bp):
TAAATAATTAGAATAATTAGAA
Found at i:28721397 original size:18 final size:18
Alignment explanation
Indices: 28721369--28721424 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
28721359 TATATTATTA
28721369 TGGCGAACTGTATTAATT
1 TGGCGAACTGTATTAATT
* * *
28721387 TGGTGATCTGTATTAATA
1 TGGCGAACTGTATTAATT
*
28721405 TGGCGAACTATATTAATT
1 TGGCGAACTGTATTAATT
28721423 TG
1 TG
28721425 CCAAATTGTG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (18 bp):
TGGCGAACTGTATTAATT
Found at i:28724374 original size:17 final size:17
Alignment explanation
Indices: 28724291--28724374 Score: 89
Period size: 17 Copynumber: 4.9 Consensus size: 17
28724281 TTATGATGTA
* *
28724291 GTATGAACTATTATTTT
1 GTATGAACTGTTATTTG
*
28724308 GTATGAACTGTTATGTG
1 GTATGAACTGTTATTTG
*
28724325 TTATGAACTGCTTA-TTG
1 GTATGAACTG-TTATTTG
* *
28724342 GAATGAACTGTCATTTG
1 GTATGAACTGTTATTTG
*
28724359 GTATGTACTGTTATTT
1 GTATGAACTGTTATTT
28724375 CATATGAATA
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
16 2 0.04
17 49 0.91
18 3 0.06
ACGTcount: A:0.25, C:0.08, G:0.20, T:0.46
Consensus pattern (17 bp):
GTATGAACTGTTATTTG
Found at i:28724382 original size:34 final size:34
Alignment explanation
Indices: 28724286--28724382 Score: 88
Period size: 34 Copynumber: 2.9 Consensus size: 34
28724276 ATGAGTTATG
* * ** *
28724286 ATGTAGTATGAACTATTATTTTGTATGAACTGTT
1 ATGTGGTATGAACTGTTATTTCATATGAACTGTC
* **
28724320 ATGTGTTATGAACTGCTTATTGGA-ATGAACTGTC
1 ATGTGGTATGAACTG-TTATTTCATATGAACTGTC
* *
28724354 ATTTGGTATGTACTGTTATTTCATATGAA
1 ATGTGGTATGAACTGTTATTTCATATGAA
28724383 TAGATGTTTT
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
33 6 0.12
34 38 0.78
35 5 0.10
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.44
Consensus pattern (34 bp):
ATGTGGTATGAACTGTTATTTCATATGAACTGTC
Found at i:28726641 original size:35 final size:35
Alignment explanation
Indices: 28726594--28726692 Score: 117
Period size: 35 Copynumber: 2.8 Consensus size: 35
28726584 CAGATGTTCA
* * * *
28726594 TAAGAGCCAATCCATCTGAAAGACACCAACGCTCG
1 TAAGAGCTAATCCATCCGAAACACACCAACGCTAG
* *
28726629 TAAGAGCTAATCCCTCCGAAACACACCAATGCTAG
1 TAAGAGCTAATCCATCCGAAACACACCAACGCTAG
* * *
28726664 TAAGAGCTAGTCTAACCGAAACACACCAA
1 TAAGAGCTAATCCATCCGAAACACACCAA
28726693 AACAGAGAGT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 54 1.00
ACGTcount: A:0.39, C:0.30, G:0.15, T:0.15
Consensus pattern (35 bp):
TAAGAGCTAATCCATCCGAAACACACCAACGCTAG
Found at i:28729935 original size:30 final size:29
Alignment explanation
Indices: 28729901--28729958 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
28729891 GTATAAATAC
*
28729901 AAAAATATTTATTAGAAAAATA-AAATATAG
1 AAAAATATTCA-TA-AAAAATATAAATATAG
28729931 AAAAATATTCATAAAAAATATAAATATA
1 AAAAATATTCATAAAAAATATAAATATA
28729959 TATACATATG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 7 0.27
29 9 0.35
30 10 0.38
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (29 bp):
AAAAATATTCATAAAAAATATAAATATAG
Found at i:28729961 original size:23 final size:23
Alignment explanation
Indices: 28729922--28729966 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
28729912 TTAGAAAAAT
*
28729922 AAAATATAGAAAAATATTCATAA
1 AAAATATAGAAAAATATACATAA
*
28729945 AAAATATA-AATATATATACATA
1 AAAATATAGAA-AAATATACATA
28729967 TGTAGATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATATAGAAAAATATACATAA
Found at i:28740068 original size:60 final size:57
Alignment explanation
Indices: 28739997--28740146 Score: 161
Period size: 52 Copynumber: 2.7 Consensus size: 57
28739987 ATTTTATAAT
* * *
28739997 ATTATATATTATGATTT-TTTAATTCATATTTTAATAATAATTAT-TTAAGAATGTTATTAA
1 ATTATATATTAT--TTTATTAAATT-ATA-TTTAATAATAATTATGTTAA-AATATGATTAA
*
28740057 ATTATATATTATTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATGATT-A
1 ATTATATATTATTTTATTAAATTATATTTAATAATAATTATGTTAAAATATGATTAA
*
28740113 A--AT-TATT-TTTTATTAAAATATATTTAATAATAAT
1 ATTATATATTATTTTATTAAATTATATTTAATAATAAT
28740147 CTTATTAAAA
Statistics
Matches: 82, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
52 25 0.30
53 4 0.05
54 2 0.02
56 2 0.02
57 22 0.27
58 9 0.11
59 6 0.07
60 12 0.15
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.53
Consensus pattern (57 bp):
ATTATATATTATTTTATTAAATTATATTTAATAATAATTATGTTAAAATATGATTAA
Found at i:28740151 original size:26 final size:25
Alignment explanation
Indices: 28740069--28740157 Score: 88
Period size: 26 Copynumber: 3.4 Consensus size: 25
28740059 TATATATTAT
* *
28740069 TTTATTAAATTGTATTTAATAATAA
1 TTTATTAAAATATATTTAATAATAA
* * * **
28740094 TTATGTTAAAATATGATTAAATTATTT
1 TT-TATTAAAATAT-ATTTAATAATAA
28740121 TTTATTAAAATATATTTAATAATAA
1 TTTATTAAAATATATTTAATAATAA
28740146 TCTTATTAAAAT
1 T-TTATTAAAAT
28740158 TTAATAACAA
Statistics
Matches: 49, Mismatches: 12, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
25 11 0.22
26 28 0.57
27 10 0.20
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (25 bp):
TTTATTAAAATATATTTAATAATAA
Found at i:28742141 original size:18 final size:19
Alignment explanation
Indices: 28742104--28742144 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
28742094 AATATTATTT
* *
28742104 TAATGTATTATAAATTACA
1 TAATGTATTAAAAATAACA
28742123 TAATGTA-TAAAAATAACA
1 TAATGTATTAAAAATAACA
28742141 TAAT
1 TAAT
28742145 ATAAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (19 bp):
TAATGTATTAAAAATAACA
Found at i:28742227 original size:15 final size:15
Alignment explanation
Indices: 28742209--28742238 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28742199 ATGTTCAAGC
28742209 CCATTTCAAACCTAA
1 CCATTTCAAACCTAA
*
28742224 CCATTTCGAACCTAA
1 CCATTTCAAACCTAA
28742239 TATTTTTGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.33, G:0.03, T:0.27
Consensus pattern (15 bp):
CCATTTCAAACCTAA
Found at i:28742555 original size:69 final size:70
Alignment explanation
Indices: 28742441--28742585 Score: 204
Period size: 69 Copynumber: 2.1 Consensus size: 70
28742431 TCACGTAAGT
* *
28742441 TTTTAGAGCTCTCAAGGTTGAAATAGGTTAAAGCATACTAGAAGTTCTAGTACCATTTCAAAAAG
1 TTTTAGAGCTCTCAAGGTAGAAATAGGTTAAAGCATACTACAAGTTCTAGTACCATTTCAAAAAG
28742506 -CTCA
66 TCTCA
* ** *
28742510 TTTTAGA-CTCCTCAAGGTAGAAATTGGTTAAAGTTTACTACAAGTTTTAGTACCATTTCAAAAA
1 TTTTAGAGCT-CTCAAGGTAGAAATAGGTTAAAGCATACTACAAGTTCTAGTACCATTTCAAAAA
*
28742574 GTTTCA
65 GTCTCA
28742580 TTTTAG
1 TTTTAG
28742586 TCACTGCACA
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
68 2 0.03
69 56 0.84
70 9 0.13
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (70 bp):
TTTTAGAGCTCTCAAGGTAGAAATAGGTTAAAGCATACTACAAGTTCTAGTACCATTTCAAAAAG
TCTCA
Found at i:28744814 original size:10 final size:11
Alignment explanation
Indices: 28744799--28744827 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
28744789 TGATAATAGA
28744799 AAAAGAAAA-G
1 AAAAGAAAAGG
28744809 AAAAGAAAAGG
1 AAAAGAAAAGG
28744820 AAAAGAAA
1 AAAAGAAA
28744828 CGTTAGTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAGG
Found at i:28744817 original size:16 final size:16
Alignment explanation
Indices: 28744796--28744827 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28744786 AAATGATAAT
28744796 AGAAAAAGAAAAGAAA
1 AGAAAAAGAAAAGAAA
*
28744812 AGAAAAGGAAAAGAAA
1 AGAAAAAGAAAAGAAA
28744828 CGTTAGTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (16 bp):
AGAAAAAGAAAAGAAA
Found at i:28751319 original size:70 final size:70
Alignment explanation
Indices: 28751206--28751345 Score: 271
Period size: 70 Copynumber: 2.0 Consensus size: 70
28751196 TTAAAATAAA
28751206 CTTTAACAAAAGCCAACATTAAATCCAAAAGCACCAGATACTAAATGCCAAAATATCATTAGATG
1 CTTTAACAAAAGCCAACATTAAATCCAAAAGCACCAGATACTAAATGCCAAAATATCATTAGATG
28751271 TGATG
66 TGATG
*
28751276 CTTTAACAAAAGCCAACATTAAATCCAAAAGCACCTGATACTAAATGCCAAAATATCATTAGATG
1 CTTTAACAAAAGCCAACATTAAATCCAAAAGCACCAGATACTAAATGCCAAAATATCATTAGATG
28751341 TGATG
66 TGATG
28751346 GCATTGAATA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.24
Consensus pattern (70 bp):
CTTTAACAAAAGCCAACATTAAATCCAAAAGCACCAGATACTAAATGCCAAAATATCATTAGATG
TGATG
Found at i:28756267 original size:2 final size:2
Alignment explanation
Indices: 28756262--28756296 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
28756252 AAAATTTTAA
*
28756262 AG AG AG AG AG AG AG AG GG 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 AG AG A
28756297 AATTAAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28759079 original size:130 final size:130
Alignment explanation
Indices: 28758846--28759079 Score: 441
Period size: 130 Copynumber: 1.8 Consensus size: 130
28758836 AGGGTATTTA
*
28758846 TTTATAACATTGATATGAAACGAAATTGTATGATAACTTATTTTAGCTTGTCTTGGCTTGGAATA
1 TTTATAACATTGATATGAAACAAAATTGTATGATAACTTATTTTAGCTTGTCTTGGCTTGGAATA
* *
28758911 TGTTGAAATTGAAATCAAATCGTCTGTCAAGGGAAATTTTCATATACTACCTTGAACTTATTTTC
66 TGTTGAAACTGAAATCAAATCGTCTGTCAAGAGAAATTTTCATATACTACCTTGAACTTATTTTC
28758976 TTTATAACATTGATATGAAACAAAATTGTATGATAACTTATTTTAGCTTGTCTTGGCTTGGAATA
1 TTTATAACATTGATATGAAACAAAATTGTATGATAACTTATTTTAGCTTGTCTTGGCTTGGAATA
28759041 TGTTGAAACTGAAATCAAATCGTCTGTCAAGAGAAATTT
66 TGTTGAAACTGAAATCAAATCGTCTGTCAAGAGAAATTT
28759080 AACTTATATC
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
130 101 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.39
Consensus pattern (130 bp):
TTTATAACATTGATATGAAACAAAATTGTATGATAACTTATTTTAGCTTGTCTTGGCTTGGAATA
TGTTGAAACTGAAATCAAATCGTCTGTCAAGAGAAATTTTCATATACTACCTTGAACTTATTTTC
Found at i:28760158 original size:25 final size:25
Alignment explanation
Indices: 28760130--28760188 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
28760120 GAAGCTCTAT
28760130 TTGCAATTCAAGAGGTATTTTATAG
1 TTGCAATTCAAGAGGTATTTTATAG
*
28760155 TTGCAATTCAAGAGGTTTTTTATAG
1 TTGCAATTCAAGAGGTATTTTATAG
28760180 TTGCAATTC
1 TTGCAATTC
28760189 CAGTAAATTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (25 bp):
TTGCAATTCAAGAGGTATTTTATAG
Found at i:28760432 original size:32 final size:32
Alignment explanation
Indices: 28760391--28760453 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
28760381 GCTTGCACTA
28760391 GTGTATATTCATATACAACGCATTAATTAAAT
1 GTGTATATTCATATACAACGCATTAATTAAAT
28760423 GTGTATATTCATATACAACGCATTAATTAAA
1 GTGTATATTCATATACAACGCATTAATTAAA
28760454 AATATTTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.37
Consensus pattern (32 bp):
GTGTATATTCATATACAACGCATTAATTAAAT
Found at i:28760736 original size:64 final size:64
Alignment explanation
Indices: 28760570--28760746 Score: 275
Period size: 66 Copynumber: 2.7 Consensus size: 64
28760560 AAATAAAATA
*
28760570 AAAATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACAAATATTTATAACATAT
1 AAAATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACAAATATTGAT-A-ATAT
*
28760635 T
64 G
* * *
28760636 AAAATTGGATCATTAGATATAATCAAGTAAATAACTTGATTAGAAAACAATTATTGGAT-ATATG
1 AAAATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACAAATATT-GATAATATG
28760700 AAAATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAA
1 AAAATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAA
28760747 AATATTCATT
Statistics
Matches: 103, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
64 49 0.48
66 52 0.50
67 2 0.02
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.31
Consensus pattern (64 bp):
AAAATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACAAATATTGATAATATG
Found at i:28762554 original size:49 final size:49
Alignment explanation
Indices: 28762497--28762600 Score: 147
Period size: 49 Copynumber: 2.1 Consensus size: 49
28762487 TTATGTGTTA
* * * *
28762497 TAATTTTATACAGTGTTGA-GTTTGTGATTCATGATATTGAACTCAATTT
1 TAATTTTATAAAGTGTTCACCTTT-TGATTCATGATATTAAACTCAATTT
*
28762546 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
28762595 TAATTT
1 TAATTT
28762601 GTTTTTTTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
49 46 0.94
50 3 0.06
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.49
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
Found at i:28764315 original size:39 final size:41
Alignment explanation
Indices: 28764261--28764371 Score: 109
Period size: 44 Copynumber: 2.6 Consensus size: 41
28764251 TTTCCTTATG
* * *
28764261 CTATTACACATCTATTCCATTCAGCCAAACACAAGAA-TA-
1 CTATTACGCCTCTATTCCATTCAGCCAAACAAAAGAATTAC
* *
28764300 CTATTATGCCTCTATTCCATTCTATTCAACCAAACAAAAGAATTAC
1 CTATTACGCCTCTATT-C---C-ATTCAGCCAAACAAAAGAATTAC
28764346 CTATTACGCCTCTATTCCATTACAGC
1 CTATTACGCCTCTATTCCATT-CAGC
28764372 GAACCAAACG
Statistics
Matches: 57, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
39 13 0.23
40 1 0.02
41 3 0.05
42 4 0.07
43 1 0.02
44 17 0.30
45 3 0.05
46 15 0.26
ACGTcount: A:0.35, C:0.29, G:0.05, T:0.31
Consensus pattern (41 bp):
CTATTACGCCTCTATTCCATTCAGCCAAACAAAAGAATTAC
Found at i:28764333 original size:44 final size:46
Alignment explanation
Indices: 28764274--28764366 Score: 136
Period size: 44 Copynumber: 2.1 Consensus size: 46
28764264 TTACACATCT
* * *
28764274 ATTCCATTCAGCCAAACACAAGAA-TA-CTATTATGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
*
28764318 ATTCTATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
28764364 ATT
1 ATT
28764367 ACAGCGAACC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 21 0.49
45 2 0.05
46 20 0.47
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.31
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
Found at i:28767106 original size:49 final size:49
Alignment explanation
Indices: 28767031--28767124 Score: 161
Period size: 49 Copynumber: 1.9 Consensus size: 49
28767021 TGCTATGCAA
* *
28767031 TGCTAAACTTGGTCTTCAACTGTCTACACTCTTATCACTATTTATACAT
1 TGCTAAACTTAGTCTTCAACTATCTACACTCTTATCACTATTTATACAT
*
28767080 TGCTAAACTTAGTCTTCCACTATCTACACTCTTATCACTATTTAT
1 TGCTAAACTTAGTCTTCAACTATCTACACTCTTATCACTATTTAT
28767125 CCCTTCTTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.27, C:0.26, G:0.06, T:0.41
Consensus pattern (49 bp):
TGCTAAACTTAGTCTTCAACTATCTACACTCTTATCACTATTTATACAT
Found at i:28768411 original size:18 final size:19
Alignment explanation
Indices: 28768377--28768419 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
28768367 TCTTAATTCA
*
28768377 TCATTTCATATTTCATTTC
1 TCATCTCATATTTCATTTC
28768396 TCATCTCATA-TTCATTTC
1 TCATCTCATATTTCATTTC
28768414 TCATCT
1 TCATCT
28768420 TTGTCATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.21, C:0.26, G:0.00, T:0.53
Consensus pattern (19 bp):
TCATCTCATATTTCATTTC
Found at i:28775432 original size:11 final size:11
Alignment explanation
Indices: 28775418--28775447 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
28775408 TATTAACCAC
28775418 ACCACCACCGG
1 ACCACCACCGG
28775429 ACCACCACCGG
1 ACCACCACCGG
28775440 ACCACCAC
1 ACCACCAC
28775448 TACACCATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.30, C:0.57, G:0.13, T:0.00
Consensus pattern (11 bp):
ACCACCACCGG
Found at i:28780345 original size:18 final size:19
Alignment explanation
Indices: 28780322--28780367 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
28780312 TTGATAGAAT
*
28780322 AAAAATAAA-TAAAGAAAG
1 AAAAATAAACAAAAGAAAG
*
28780340 AAAAATAAACAAAAGAAAT
1 AAAAATAAACAAAAGAAAG
28780359 AAAAA-AAAC
1 AAAAATAAAC
28780368 CAATTAGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.80, C:0.04, G:0.07, T:0.09
Consensus pattern (19 bp):
AAAAATAAACAAAAGAAAG
Found at i:28783212 original size:24 final size:24
Alignment explanation
Indices: 28783184--28783233 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
28783174 GGGTTAAAGT
*
28783184 GATAGATTTTAAGTTTATAACTGA
1 GATAGATTTTAAGTTTAGAACTGA
*
28783208 GATAGATTTTAAGTTTAGAATTGA
1 GATAGATTTTAAGTTTAGAACTGA
28783232 GA
1 GA
28783234 AAAGGACTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.02, G:0.20, T:0.40
Consensus pattern (24 bp):
GATAGATTTTAAGTTTAGAACTGA
Found at i:28786441 original size:18 final size:18
Alignment explanation
Indices: 28786405--28786440 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
28786395 CCGATACAAC
28786405 ATCAATACCCAACATAAA
1 ATCAATACCCAACATAAA
*
28786423 ATCAATA-CCAACTTAAA
1 ATCAATACCCAACATAAA
28786440 A
1 A
28786441 ACTTTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.56, C:0.25, G:0.00, T:0.19
Consensus pattern (18 bp):
ATCAATACCCAACATAAA
Found at i:28789738 original size:18 final size:18
Alignment explanation
Indices: 28789704--28789763 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
28789694 TCTAGTTTAT
*
28789704 TTTTTATTT-ATTAAATTA
1 TTTTTCTTTAATT-AATTA
28789722 TTTTTCTTTAATTAATT-
1 TTTTTCTTTAATTAATTA
*
28789739 TTTATT-TTTAAATTTATTA
1 TTT-TTCTTT-AATTAATTA
28789758 TTTTTC
1 TTTTTC
28789764 ATTATCTTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
17 6 0.17
18 23 0.66
19 6 0.17
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTTCTTTAATTAATTA
Found at i:28799961 original size:15 final size:16
Alignment explanation
Indices: 28799936--28799965 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28799926 GTATAATATG
28799936 AAATAGAAAAAAATTA
1 AAATAGAAAAAAATTA
28799952 AAAT-GAAAAAAATT
1 AAATAGAAAAAAATT
28799966 CACTATTTAG
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:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (16 bp):
AAATAGAAAAAAATTA
Found at i:28800351 original size:20 final size:20
Alignment explanation
Indices: 28800316--28800361 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
28800306 GTATCAATCC
* *
28800316 GGTATCGATACTTTTCTTAG
1 GGTATCGATACTTTTCCTAA
28800336 GGTATCGATA-TATTTCCTAA
1 GGTATCGATACT-TTTCCTAA
28800356 GGTATC
1 GGTATC
28800362 TATTGAGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (20 bp):
GGTATCGATACTTTTCCTAA
Found at i:28802647 original size:20 final size:21
Alignment explanation
Indices: 28802617--28802667 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
28802607 AATTTAATTT
28802617 AGTTCAGCTCACTCAAGCTCA
1 AGTTCAGCTCACTCAAGCTCA
* *
28802638 AGTT-AGCTCATTCGAGCTCA
1 AGTTCAGCTCACTCAAGCTCA
28802658 A-TTCAGCTCA
1 AGTTCAGCTCA
28802668 ATCTTAACCC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 21 0.78
21 4 0.15
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.27
Consensus pattern (21 bp):
AGTTCAGCTCACTCAAGCTCA
Found at i:28803129 original size:22 final size:21
Alignment explanation
Indices: 28803100--28803147 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
28803090 AAGCATGAAC
*
28803100 TGAA-ATTTTAATGATTTAGTG
1 TGAACATTTTAATGAATT-GTG
* *
28803121 TGAACATTTTTATTAATTGTG
1 TGAACATTTTAATGAATTGTG
28803142 TGAACA
1 TGAACA
28803148 CATAGATGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (21 bp):
TGAACATTTTAATGAATTGTG
Found at i:28806885 original size:20 final size:20
Alignment explanation
Indices: 28806860--28806907 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
28806850 TTAACTTAGT
28806860 TCAGCTCACTCGAGCTCAAG
1 TCAGCTCACTCGAGCTCAAG
* *
28806880 TCAGCTCATTCGAGCTCAAT
1 TCAGCTCACTCGAGCTCAAG
28806900 TCAGCTCA
1 TCAGCTCA
28806908 ATCTTAACCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (20 bp):
TCAGCTCACTCGAGCTCAAG
Found at i:28806905 original size:10 final size:10
Alignment explanation
Indices: 28806859--28806909 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
28806849 TTTAACTTAG
28806859 TTCAGCTC-A
1 TTCAGCTCAA
*
28806868 CTCGAGCTCAA
1 TTC-AGCTCAA
*
28806879 GTCAGCTC-A
1 TTCAGCTCAA
28806888 TTCGAGCTCAA
1 TTC-AGCTCAA
28806899 TTCAGCTCAA
1 TTCAGCTCAA
28806909 T
1 T
28806910 CTTAACCCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
9 5 0.14
10 23 0.66
11 7 0.20
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.27
Consensus pattern (10 bp):
TTCAGCTCAA
Found at i:28807628 original size:22 final size:21
Alignment explanation
Indices: 28807599--28807646 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
28807589 AAGCATGAAC
*
28807599 TGAA-ATTTTAATGATTTAGTG
1 TGAACATTTTAATGAATT-GTG
* *
28807620 TGAACATTTTTATTAATTGTG
1 TGAACATTTTAATGAATTGTG
28807641 TGAACA
1 TGAACA
28807647 CATAGATGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (21 bp):
TGAACATTTTAATGAATTGTG
Found at i:28810505 original size:23 final size:23
Alignment explanation
Indices: 28810479--28810551 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
28810469 GACTTGCTTG
* *
28810479 GTAAAGCCTGTGTGGCATATTCT
1 GTAAAGCCTATGTGGCGTATTCT
*
28810502 GTAAAGCCTTTGTGGCGTATTCT
1 GTAAAGCCTATGTGGCGTATTCT
* * * *
28810525 ATGATGCCTATGTGGCGTGTTCT
1 GTAAAGCCTATGTGGCGTATTCT
28810548 GTAA
1 GTAA
28810552 CGCCCTTGAG
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.19, C:0.16, G:0.27, T:0.37
Consensus pattern (23 bp):
GTAAAGCCTATGTGGCGTATTCT
Found at i:28817612 original size:23 final size:23
Alignment explanation
Indices: 28817586--28817695 Score: 105
Period size: 23 Copynumber: 4.7 Consensus size: 23
28817576 TAATGTTCAA
* *
28817586 GAACATGTTCATTTAAC-TTAATC
1 GAACATGTTCA-TGAACATTAAAC
28817609 GAACATGTTCATGAACATTAAAC
1 GAACATGTTCATGAACATTAAAC
* * * *
28817632 GAATATGTTCACGAACACTAAAT
1 GAACATGTTCATGAACATTAAAC
***
28817655 GAACATGTTCATGAACATATAGTT
1 GAACATGTTCATGAACAT-TAAAC
*
28817679 GAACATGTTCACGAACA
1 GAACATGTTCATGAACA
28817696 ATGTTAATAA
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
22 4 0.05
23 50 0.68
24 19 0.26
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (23 bp):
GAACATGTTCATGAACATTAAAC
Found at i:28818007 original size:22 final size:22
Alignment explanation
Indices: 28817982--28818026 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
28817972 CTGAAAACCT
*
28817982 GAAAATAAAAAATCCTCAAAAC
1 GAAAACAAAAAATCCTCAAAAC
* * *
28818004 GAAAACACAAAATTCTCTAAAC
1 GAAAACAAAAAATCCTCAAAAC
28818026 G
1 G
28818027 TGTTATGAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.58, C:0.20, G:0.07, T:0.16
Consensus pattern (22 bp):
GAAAACAAAAAATCCTCAAAAC
Found at i:28819930 original size:11 final size:11
Alignment explanation
Indices: 28819914--28819959 Score: 76
Period size: 11 Copynumber: 4.2 Consensus size: 11
28819904 TAGTAGCATC
28819914 TTCAAAAAAAA
1 TTCAAAAAAAA
28819925 TTCAAAAAAAA
1 TTCAAAAAAAA
28819936 -TCGAAAAAAAA
1 TTC-AAAAAAAA
28819947 TTCAAAAAAAA
1 TTCAAAAAAAA
28819958 TT
1 TT
28819960 TAGTTTCTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 2 0.06
11 29 0.88
12 2 0.06
ACGTcount: A:0.70, C:0.09, G:0.02, T:0.20
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:28819933 original size:10 final size:10
Alignment explanation
Indices: 28819918--28819956 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
28819908 AGCATCTTCA
28819918 AAAAAAATTC
1 AAAAAAATTC
*
28819928 AAAAAAAATC
1 AAAAAAATTC
28819938 GAAAAAAAATTC
1 --AAAAAAATTC
28819950 AAAAAAA
1 AAAAAAA
28819957 ATTTAGTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 16 0.64
12 9 0.36
ACGTcount: A:0.77, C:0.08, G:0.03, T:0.13
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:28819945 original size:22 final size:22
Alignment explanation
Indices: 28819917--28819958 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
28819907 TAGCATCTTC
28819917 AAAAAAAATTCAAAAAAAATCG
1 AAAAAAAATTCAAAAAAAATCG
28819939 AAAAAAAATTCAAAAAAAAT
1 AAAAAAAATTCAAAAAAAAT
28819959 TTAGTTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.14
Consensus pattern (22 bp):
AAAAAAAATTCAAAAAAAATCG
Found at i:28826091 original size:24 final size:24
Alignment explanation
Indices: 28826064--28826142 Score: 133
Period size: 24 Copynumber: 3.3 Consensus size: 24
28826054 TCATTAATAA
28826064 ATAAACGAGTCAATAAATGAGTTT
1 ATAAACGAGTCAATAAATGAGTTT
28826088 ATAAACGAGTCAATAAATGAGTTT
1 ATAAACGAGTCAATAAATGAGTTT
* *
28826112 ATAAACGAGCCAATAAATGAGCTT
1 ATAAACGAGTCAATAAATGAGTTT
28826136 A-AAACGA
1 ATAAACGA
28826143 ACCGAACACA
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
23 6 0.11
24 47 0.89
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.24
Consensus pattern (24 bp):
ATAAACGAGTCAATAAATGAGTTT
Found at i:28826133 original size:12 final size:12
Alignment explanation
Indices: 28826063--28826128 Score: 69
Period size: 12 Copynumber: 5.5 Consensus size: 12
28826053 ATCATTAATA
28826063 AATAAACGAGTC
1 AATAAACGAGTC
* *
28826075 AATAAATGAGTT
1 AATAAACGAGTC
*
28826087 TATAAACGAGTC
1 AATAAACGAGTC
* *
28826099 AATAAATGAGTT
1 AATAAACGAGTC
* *
28826111 TATAAACGAGCC
1 AATAAACGAGTC
28826123 AATAAA
1 AATAAA
28826129 TGAGCTTAAA
Statistics
Matches: 41, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.50, C:0.11, G:0.15, T:0.24
Consensus pattern (12 bp):
AATAAACGAGTC
Found at i:28827879 original size:2 final size:2
Alignment explanation
Indices: 28827834--28827859 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28827824 TCTCTCTCTA
28827834 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
28827860 CGCGCGCGCG
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:28833793 original size:24 final size:25
Alignment explanation
Indices: 28833761--28833816 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 25
28833751 TAAAGTAAAA
28833761 AAAATAAAA-AATAATCAAAATTTAT
1 AAAATAAAATAATAAT-AAAATTTAT
* *
28833786 AAAA-AAAATATTAATAAAATTTCT
1 AAAATAAAATAATAATAAAATTTAT
28833810 AGAAATA
1 A-AAATA
28833817 TTATAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 13 0.50
25 12 0.46
26 1 0.04
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.29
Consensus pattern (25 bp):
AAAATAAAATAATAATAAAATTTAT
Found at i:28833836 original size:21 final size:22
Alignment explanation
Indices: 28833788--28833836 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
28833778 AAATTTATAA
* *
28833788 AAAAAATATTAATAAAATTTCT
1 AAAAAATATTAATAAAAATTAT
*
28833810 -AGAAATATT-ATAAAAATTAT
1 AAAAAATATTAATAAAAATTAT
28833830 AAAAAAT
1 AAAAAAT
28833837 TTCCAATAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAAAATATTAATAAAAATTAT
Found at i:28838707 original size:70 final size:70
Alignment explanation
Indices: 28838594--28838733 Score: 280
Period size: 70 Copynumber: 2.0 Consensus size: 70
28838584 CATTTGAATA
28838594 ATATTATTTATATTATCTTGAATAATAGATTTACCACTAAGCAATTTGCTTAGCGTATGATTTTG
1 ATATTATTTATATTATCTTGAATAATAGATTTACCACTAAGCAATTTGCTTAGCGTATGATTTTG
28838659 TTTTC
66 TTTTC
28838664 ATATTATTTATATTATCTTGAATAATAGATTTACCACTAAGCAATTTGCTTAGCGTATGATTTTG
1 ATATTATTTATATTATCTTGAATAATAGATTTACCACTAAGCAATTTGCTTAGCGTATGATTTTG
28838729 TTTTC
66 TTTTC
28838734 TTCGTGCATA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.47
Consensus pattern (70 bp):
ATATTATTTATATTATCTTGAATAATAGATTTACCACTAAGCAATTTGCTTAGCGTATGATTTTG
TTTTC
Found at i:28842423 original size:17 final size:17
Alignment explanation
Indices: 28842397--28842429 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28842387 CACTAACATT
*
28842397 AAAATGCAATGACAATA
1 AAAATACAATGACAATA
28842414 AAAATACAATGACAAT
1 AAAATACAATGACAAT
28842430 TTTCACTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.12, G:0.09, T:0.18
Consensus pattern (17 bp):
AAAATACAATGACAATA
Done.