Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 89 of 120
Found at i:25655344 original size:41 final size:41
Alignment explanation
Indices: 25655299--25655380 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
25655289 GATGTCGACA
* *
25655299 TTGATTGTGATTTTTGAATTAGGGTT-TATTCGATTTTGATT
1 TTGATTGTGATTTTTGAATTAGAGTTAT-TTCAATTTTGATT
* *
25655340 TTGATTTTGATTTTTGATTTAGAGTTATTTCAATTTTGATT
1 TTGATTGTGATTTTTGAATTAGAGTTATTTCAATTTTGATT
25655381 GGATTCTGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 35 0.97
42 1 0.03
ACGTcount: A:0.21, C:0.02, G:0.18, T:0.59
Consensus pattern (41 bp):
TTGATTGTGATTTTTGAATTAGAGTTATTTCAATTTTGATT
Found at i:25655347 original size:12 final size:13
Alignment explanation
Indices: 25655330--25655359 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
25655320 GGGTTTATTC
25655330 GATTTTGA-TTTT
1 GATTTTGATTTTT
25655342 GATTTTGATTTTT
1 GATTTTGATTTTT
25655355 GATTT
1 GATTT
25655360 AGAGTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.67
Consensus pattern (13 bp):
GATTTTGATTTTT
Found at i:25655356 original size:7 final size:6
Alignment explanation
Indices: 25655330--25655359 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
25655320 GGGTTTATTC
25655330 GATTTT GATTTT GATTTT GATTTTT GATTT
1 GATTTT GATTTT GATTTT GA-TTTT GATTT
25655360 AGAGTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.67
Consensus pattern (6 bp):
GATTTT
Found at i:25664444 original size:16 final size:18
Alignment explanation
Indices: 25664423--25664456 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
25664413 TGACTTCAAA
25664423 ATGA-TTTTA-TAATTTT
1 ATGATTTTTAGTAATTTT
25664439 ATGATTTTTAGTAATTTT
1 ATGATTTTTAGTAATTTT
25664457 TATATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 5 0.31
18 7 0.44
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (18 bp):
ATGATTTTTAGTAATTTT
Found at i:25664469 original size:21 final size:21
Alignment explanation
Indices: 25664443--25664484 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
25664433 AATTTTATGA
* *
25664443 TTTTTAGTAATTTTTATATAT
1 TTTTTAGGAATTTTTAAATAT
*
25664464 TTTTTAGGATTTTTTAAATAT
1 TTTTTAGGAATTTTTAAATAT
25664485 ATGCCAATGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (21 bp):
TTTTTAGGAATTTTTAAATAT
Found at i:25666237 original size:6 final size:6
Alignment explanation
Indices: 25666226--25666254 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
25666216 CATTATAAGT
25666226 GAGAGG GAGAGG GAGAGG GAGAGG GAGAG
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAG
25666255 AGATGAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:25669669 original size:21 final size:21
Alignment explanation
Indices: 25669645--25669690 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
25669635 AGAAAAAAAG
*
25669645 TTTTGTTGCTTTTTGTTGTTAT
1 TTTTGTTG-TATTTGTTGTTAT
* *
25669667 TTTTATTGTATTTGTTGTTGT
1 TTTTGTTGTATTTGTTGTTAT
25669688 TTT
1 TTT
25669691 GTCACTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.07, C:0.02, G:0.17, T:0.74
Consensus pattern (21 bp):
TTTTGTTGTATTTGTTGTTAT
Found at i:25670407 original size:7 final size:6
Alignment explanation
Indices: 25670369--25670414 Score: 67
Period size: 6 Copynumber: 7.5 Consensus size: 6
25670359 CCCTCCGTTC
25670369 CCCTCT -CCTCT CCCTCT CCCTCT CCCTCT CCCTTCT CCCTTCT CCC
1 CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT CCC-TCT CCC-TCT CCC
25670415 ATTTGTTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.13
6 20 0.53
7 13 0.34
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (6 bp):
CCCTCT
Found at i:25676885 original size:18 final size:18
Alignment explanation
Indices: 25676862--25676896 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
25676852 ATGCGAGTTG
*
25676862 ACTCGAATAACTCGATTA
1 ACTCGAACAACTCGATTA
25676880 ACTCGAACAACTCGATT
1 ACTCGAACAACTCGATT
25676897 CGTTTAACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.26
Consensus pattern (18 bp):
ACTCGAACAACTCGATTA
Found at i:25676897 original size:225 final size:223
Alignment explanation
Indices: 25676468--25676916 Score: 765
Period size: 226 Copynumber: 2.0 Consensus size: 223
25676458 GTTTTGGGCG
* * * *
25676468 AAAGTTGGAAGGAGTAAAAATTTGGGGAAAAAGTAAAATATTTGGGGGTTTGAGGTAAAATTGTA
1 AAAGTTGAAAGGAGTAAAAATTTGGGGAAAAAGTAAAATATTTGAGGGTTTGAGGTAAAACTATA
*
25676533 AAATATTATAGTTTGATATTCGATTTATTCGAATTATTTGAGTTATTCGAATTTGAAAACTCAAT
66 AAATATTATAGTTTGATATTCGATTTATTCGAATTATTCGAGTTATTCGAATTTGAAAACTCAAT
* *
25676598 TCGATTCGAACTCGAAATTCAAAAAAAAAAATCGAGTTGACTCGAATAACTTGATTAACTTGAAC
131 TCGATTCGAACTCGAAATTC-AAAAAAAAAATCGAGTTGACTCGAATAACTCGATTAACTCGAAC
25676663 AACTCGATTCGTTTAACTCGAAATTCGAA
195 AACTCGATTCGTTTAACTCGAAATTCGAA
* *
25676692 AAAGTTGAAAGGAGTAAAAGTTTTGGGGGAAAAGTAAAAATATTTGAGGGTTTGAGGTAAAACTA
1 AAAGTTGAAAGGAGTAAAA-ATTTGGGGAAAAAGT-AAAATATTTGAGGGTTTGAGGTAAAACTA
*
25676757 TAAAATATTATAGTTTGATATTCGGTTTATTCGAATTATTCGAGTTATTCGAATTTGAAAACTCA
64 TAAAATATTATAGTTTGATATTCGATTTATTCGAATTATTCGAGTTATTCGAATTTGAAAACTCA
25676822 ATTCGATTCGAACTCGAAATTC-AAAAAAAAATGCGAGTTGACTCGAATAACTCGATTAACTCGA
129 ATTCGATTCGAACTCGAAATTCAAAAAAAAAAT-CGAGTTGACTCGAATAACTCGATTAACTCGA
25676886 ACAACTCGATTCGTTTAACTCGAAATTCGAA
193 ACAACTCGATTCGTTTAACTCGAAATTCGAA
25676917 TTTTTTTCGA
Statistics
Matches: 212, Mismatches: 10, Indels: 5
0.93 0.04 0.02
Matches are distributed among these distances:
224 28 0.13
225 73 0.34
226 111 0.52
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (223 bp):
AAAGTTGAAAGGAGTAAAAATTTGGGGAAAAAGTAAAATATTTGAGGGTTTGAGGTAAAACTATA
AAATATTATAGTTTGATATTCGATTTATTCGAATTATTCGAGTTATTCGAATTTGAAAACTCAAT
TCGATTCGAACTCGAAATTCAAAAAAAAAATCGAGTTGACTCGAATAACTCGATTAACTCGAACA
ACTCGATTCGTTTAACTCGAAATTCGAA
Found at i:25677951 original size:57 final size:57
Alignment explanation
Indices: 25677882--25677998 Score: 225
Period size: 57 Copynumber: 2.1 Consensus size: 57
25677872 ATAACTCTAG
25677882 AAGTATAATTACATGTAAAACGTGCATGACTCCTATATGTAAAATAGTTGTTAGTAT
1 AAGTATAATTACATGTAAAACGTGCATGACTCCTATATGTAAAATAGTTGTTAGTAT
*
25677939 AAGTATAATTACATGTAAAACGTGCATGACTCCTGTATGTAAAATAGTTGTTAGTAT
1 AAGTATAATTACATGTAAAACGTGCATGACTCCTATATGTAAAATAGTTGTTAGTAT
25677996 AAG
1 AAG
25677999 CAATATGATA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.34
Consensus pattern (57 bp):
AAGTATAATTACATGTAAAACGTGCATGACTCCTATATGTAAAATAGTTGTTAGTAT
Found at i:25678354 original size:15 final size:15
Alignment explanation
Indices: 25678334--25678380 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
25678324 TAGGGCATGA
25678334 TATGATATGATTCGT
1 TATGATATGATTCGT
*
25678349 TATGATATGATACGT
1 TATGATATGATTCGT
25678364 TATGATATGATCTCGT
1 TATGATATGAT-TCGT
25678380 T
1 T
25678381 TAAAATTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 25 0.86
16 4 0.14
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.45
Consensus pattern (15 bp):
TATGATATGATTCGT
Found at i:25680164 original size:221 final size:222
Alignment explanation
Indices: 25679781--25680203 Score: 803
Period size: 221 Copynumber: 1.9 Consensus size: 222
25679771 CCTTTCCAAT
25679781 AGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTATGCCACATCAGTATTTTCATTCTT
1 AGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTATGCCACATCAGTATTTTCATTCTT
*
25679846 AATTTCAACATTTTTATCCTGAAAAAAATCAAATTACAATTAAAATCCTGAAATTTAGGATGAAA
66 AATTTCAACATTTTTATCCTGAAAAAAATCAAATTACAATTAAAATCCTGAAATTTAAGATGAAA
* *
25679911 TTGTTGATGTGTCATAAAACTATTGGAAAGGGATAATATCCCTGTTTCATACAATCCTTTCTC-T
131 TTGTTGATATGTCATAAAACCATTGGAAAGGGATAATATCCCTGTTTCATACAATCCTTTCTCTT
25679975 TATTATAGGAAAAGGATTGAATGAAAC
196 TATTATAGGAAAAGGATTGAATGAAAC
25680002 AGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTATGCCACATCAGTATTTTCATTCTT
1 AGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTATGCCACATCAGTATTTTCATTCTT
*
25680067 AATTTCAACATTTTTATCCTGAAAAAAATCAAATTACAATTACAATCCTGAAATTTAAGATGAAA
66 AATTTCAACATTTTTATCCTGAAAAAAATCAAATTACAATTAAAATCCTGAAATTTAAGATGAAA
25680132 TTGTTGATATGTCATAAAACCATTGGAAAGGGATAATATCCCTGTTTCATACAATCCTTTCTCTT
131 TTGTTGATATGTCATAAAACCATTGGAAAGGGATAATATCCCTGTTTCATACAATCCTTTCTCTT
25680197 TATTATA
196 TATTATA
25680204 TGGGCTTAAA
Statistics
Matches: 197, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
221 189 0.96
222 8 0.04
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (222 bp):
AGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTATGCCACATCAGTATTTTCATTCTT
AATTTCAACATTTTTATCCTGAAAAAAATCAAATTACAATTAAAATCCTGAAATTTAAGATGAAA
TTGTTGATATGTCATAAAACCATTGGAAAGGGATAATATCCCTGTTTCATACAATCCTTTCTCTT
TATTATAGGAAAAGGATTGAATGAAAC
Found at i:25685543 original size:22 final size:23
Alignment explanation
Indices: 25685432--25685545 Score: 117
Period size: 23 Copynumber: 4.9 Consensus size: 23
25685422 ACGCTAGCGC
*
25685432 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTAGCACTTCGTGT
25685455 GCTTACTGTTTAGCACTTCGTGT
1 GCTTACTGTTTAGCACTTCGTGT
* *
25685478 GCCTACTGATT-GCACTGT-GTGT
1 GCTTACTGTTTAGCACT-TCGTGT
25685500 GCTTACTGTTTCCCCAGCACTT-GTGT
1 GCTTACTGTTT----AGCACTTCGTGT
* *
25685526 GCTTACTGTTAAGTACTTCG
1 GCTTACTGTTTAGCACTTCG
25685546 GTACTTTCTG
Statistics
Matches: 77, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
22 24 0.31
23 33 0.43
26 15 0.19
27 5 0.06
ACGTcount: A:0.13, C:0.25, G:0.22, T:0.40
Consensus pattern (23 bp):
GCTTACTGTTTAGCACTTCGTGT
Found at i:25686299 original size:20 final size:20
Alignment explanation
Indices: 25686274--25686311 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
25686264 TTTTTGCATA
*
25686274 AACGCCGCAAAAGGTAAAGC
1 AACGCCGCAAAAGCTAAAGC
25686294 AACGCCGCAAAAGCTAAA
1 AACGCCGCAAAAGCTAAA
25686312 CCAATAGCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.26, G:0.21, T:0.05
Consensus pattern (20 bp):
AACGCCGCAAAAGCTAAAGC
Found at i:25686421 original size:41 final size:41
Alignment explanation
Indices: 25686376--25686591 Score: 299
Period size: 41 Copynumber: 5.3 Consensus size: 41
25686366 GCGTATGGAA
* *
25686376 AAACGCCGCTAAAGGTCATAGCATTAGCGGCGCTTTC-CCT
1 AAACGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTTCTCAT
*
25686416 CAAACGCCGCTAAAAGTCAGAGCATTAGCGGCGCTTTCTCAT
1 -AAACGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTTCTCAT
* ** * *
25686458 AAACACCGCTAAAGGTCAGAGCATTAGCGATGCTTTCCCAC
1 AAACGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTTCTCAT
* *
25686499 AAACGTCGCTAAAGGTCAGAGCATTAGCGGTGCTTTCTCAT
1 AAACGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTTCTCAT
* * *
25686540 AAACACCGCTAAAGGTTAGTGCATTAGCGGCGCTTTCTCAT
1 AAACGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTTCTCAT
25686581 AAACGCCGCTA
1 AAACGCCGCTA
25686592 TTCTATTTAA
Statistics
Matches: 154, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
41 152 0.99
42 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (41 bp):
AAACGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTTCTCAT
Found at i:25691362 original size:43 final size:43
Alignment explanation
Indices: 25691296--25691523 Score: 244
Period size: 43 Copynumber: 5.3 Consensus size: 43
25691286 AATTTGTTAA
* * * *
25691296 TTTAGCAGCGTTTGTGGGAAAAGCGTCGCTAAAGACAGTGTTC
1 TTTAGCGGCATTTGTGGGGAAAGCGCCGCTAAAGACAGTGTTC
* *
25691339 TTTAGCGGCATTTGTGGGGAAAGCGCCACTAAAGACCGTGTTC
1 TTTAGCGGCATTTGTGGGGAAAGCGCCGCTAAAGACAGTGTTC
* * * **
25691382 TTTAGCGGCGTTTGTGGGGAAAGCACCGTTAAAGATTGTGTTC
1 TTTAGCGGCATTTGTGGGGAAAGCGCCGCTAAAGACAGTGTTC
** * *
25691425 TTTAGCAACGTTTGTAGGGAAAGCGCCGCTAAAGATCA-TGTTC
1 TTTAGCGGCATTTGTGGGGAAAGCGCCGCTAAAGA-CAGTGTTC
** *
25691468 TTTAGCGGCATTTGTGGAAAAAGCGCTGCTAAAGACCA-TGTTC
1 TTTAGCGGCATTTGTGGGGAAAGCGCCGCTAAAGA-CAGTGTTC
* *
25691511 TATAGCGACATTT
1 TTTAGCGGCATTT
25691524 TTCCACATAA
Statistics
Matches: 155, Mismatches: 29, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
43 155 1.00
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCATTTGTGGGGAAAGCGCCGCTAAAGACAGTGTTC
Found at i:25693168 original size:110 final size:110
Alignment explanation
Indices: 25693035--25693257 Score: 428
Period size: 110 Copynumber: 2.0 Consensus size: 110
25693025 ACTTTACCTT
* *
25693035 ATCTATAATGATTTAAATTTTAATTAATAATTAGATTAGATATATATATATATCGAAGCATAGTG
1 ATCTATAATGATTTAAATTTTAATTAATAATTAGATTAGACATATATATATATAGAAGCATAGTG
25693100 GATAGAGGGAAGGAAATTTTTATTTTTCTTTCTTCCATCTTCTTC
66 GATAGAGGGAAGGAAATTTTTATTTTTCTTTCTTCCATCTTCTTC
25693145 ATCTATAATGATTTAAATTTTAATTAATAATTAGATTAGACATATATATATATAGAAGCATAGTG
1 ATCTATAATGATTTAAATTTTAATTAATAATTAGATTAGACATATATATATATAGAAGCATAGTG
25693210 GATAGAGGGAAGGAAATTTTTATTTTTCTTTCTTCCATCTTCTTC
66 GATAGAGGGAAGGAAATTTTTATTTTTCTTTCTTCCATCTTCTTC
25693255 ATC
1 ATC
25693258 ACCGTCTTTC
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
110 111 1.00
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (110 bp):
ATCTATAATGATTTAAATTTTAATTAATAATTAGATTAGACATATATATATATAGAAGCATAGTG
GATAGAGGGAAGGAAATTTTTATTTTTCTTTCTTCCATCTTCTTC
Found at i:25699478 original size:15 final size:15
Alignment explanation
Indices: 25699444--25699479 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
25699434 AGTCAAAAAT
25699444 AAAATAAATATGAGA
1 AAAATAAATATGAGA
* *
25699459 CAAATAAATATGTGA
1 AAAATAAATATGAGA
25699474 AAAATA
1 AAAATA
25699480 TACTAAATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.64, C:0.03, G:0.11, T:0.22
Consensus pattern (15 bp):
AAAATAAATATGAGA
Found at i:25700265 original size:9 final size:9
Alignment explanation
Indices: 25700213--25700447 Score: 71
Period size: 9 Copynumber: 25.9 Consensus size: 9
25700203 CTTTTGTATG
25700213 ATAATTTTT
1 ATAATTTTT
*
25700222 ATATTTTTT
1 ATAATTTTT
* *
25700231 ACAAATTTT
1 ATAATTTTT
*
25700240 ATATTTCTTT
1 ATAATT-TTT
25700250 A-AATTTTT
1 ATAATTTTT
25700258 ATAATTTTCT
1 ATAATTTT-T
***
25700268 -TACGGCTTT
1 ATA-ATTTTT
***
25700277 A-AAAAATT
1 ATAATTTTT
25700285 ATAATTTTT
1 ATAATTTTT
* *
25700294 TTATTTTTT
1 ATAATTTTT
25700303 ATATATATTTT
1 ATA-AT-TTTT
25700314 ATAATTTTTTT
1 ATAA--TTTTT
*
25700325 ATGATTTTTT
1 AT-AATTTTT
* *
25700335 AAAAATTTT
1 ATAATTTTT
25700344 A-AATTTTT
1 ATAATTTTT
25700352 ATAATTTTTTT
1 ATAA--TTTTT
*
25700363 CCTAATTTTT
1 -ATAATTTTT
*
25700373 AATAAATTTT
1 -ATAATTTTT
25700383 A-AATATTTT
1 ATAAT-TTTT
*
25700392 -T--TTATT
1 ATAATTTTT
*
25700398 ATAATTTAT
1 ATAATTTTT
25700407 -TAATTTTT
1 ATAATTTTT
*
25700415 ATAACTTTTA
1 ATAA-TTTTT
*
25700425 ATTATTTTT
1 ATAATTTTT
25700434 AT--TTTTT
1 ATAATTTTT
25700441 AT-ATTTT
1 ATAATTTT
25700448 GCCACATATC
Statistics
Matches: 164, Mismatches: 39, Indels: 47
0.66 0.16 0.19
Matches are distributed among these distances:
6 3 0.02
7 9 0.05
8 27 0.16
9 68 0.41
10 34 0.21
11 18 0.11
12 5 0.03
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (9 bp):
ATAATTTTT
Found at i:25700352 original size:38 final size:40
Alignment explanation
Indices: 25700307--25700391 Score: 122
Period size: 38 Copynumber: 2.2 Consensus size: 40
25700297 TTTTTTATAT
*
25700307 ATATTTTATAATTTTTTT-ATGATTTTTTAA-AAATTTTAA
1 ATATTTTATAATTTTTTTCAT-AATTTTTAATAAATTTTAA
*
25700346 AT-TTTTATAATTTTTTTCCTAATTTTTAATAAATTTTAA
1 ATATTTTATAATTTTTTTCATAATTTTTAATAAATTTTAA
25700385 ATATTTT
1 ATATTTT
25700392 TTTATTATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
38 23 0.56
39 14 0.34
40 4 0.10
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.62
Consensus pattern (40 bp):
ATATTTTATAATTTTTTTCATAATTTTTAATAAATTTTAA
Found at i:25700360 original size:10 final size:10
Alignment explanation
Indices: 25700283--25700433 Score: 71
Period size: 10 Copynumber: 15.1 Consensus size: 10
25700273 CTTTAAAAAA
25700283 TTATAATTTT
1 TTATAATTTT
25700293 TT-T-ATTTT
1 TTATAATTTT
*
25700301 TTATATATATT
1 TTATA-ATTTT
25700312 TTATAATTTTT
1 TTATAA-TTTT
*
25700323 TTATGATTTT
1 TTATAATTTT
**
25700333 TTA-AAAATT
1 TTATAATTTT
25700342 TTA-AA-TTT
1 TTATAATTTT
25700350 TTATAATTTTT
1 TTATAA-TTTT
*
25700361 TTCCTAATTTT
1 TT-ATAATTTT
*
25700372 TAATAAATTTT
1 TTAT-AATTTT
** *
25700383 AAATATTTTT
1 TTATAATTTT
* **
25700393 TTATTATAAT
1 TTATAATTTT
25700403 TTATTAA-TTT
1 TTA-TAATTTT
*
25700413 TTATAACTTT
1 TTATAATTTT
* *
25700423 TAATTATTTT
1 TTATAATTTT
25700433 T
1 T
25700434 ATTTTTTATA
Statistics
Matches: 106, Mismatches: 24, Indels: 22
0.70 0.16 0.14
Matches are distributed among these distances:
8 12 0.11
9 15 0.14
10 38 0.36
11 38 0.36
12 3 0.03
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.66
Consensus pattern (10 bp):
TTATAATTTT
Found at i:25701184 original size:20 final size:21
Alignment explanation
Indices: 25701159--25701199 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
25701149 CCTATGATCG
**
25701159 ATTAAATCCTTAATTA-CCTA
1 ATTAAATAATTAATTATCCTA
25701179 ATTAAATAATTAATTATCCTA
1 ATTAAATAATTAATTATCCTA
25701200 TATCGAGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTAAATAATTAATTATCCTA
Found at i:25702385 original size:31 final size:31
Alignment explanation
Indices: 25702350--25702408 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
25702340 TTTTTTCAAG
* *
25702350 TTAAGTATTGAATTTGACAATTGTTTTCGTA
1 TTAAGGATTGAACTTGACAATTGTTTTCGTA
* * *
25702381 TTAAGGCTTGAACTTGATAATTTTTTTC
1 TTAAGGATTGAACTTGACAATTGTTTTC
25702409 ACATTGAAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.49
Consensus pattern (31 bp):
TTAAGGATTGAACTTGACAATTGTTTTCGTA
Found at i:25715032 original size:2 final size:2
Alignment explanation
Indices: 25715025--25715080 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
25715015 AGCACCACTC
25715025 TG TG TG TG TG TG TG TG 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 TG TG TG TG TG TG TG TG
25715067 TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG
25715081 GGGGTGACTC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:25717314 original size:15 final size:15
Alignment explanation
Indices: 25717294--25717346 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
25717284 CACGGCCGTT
25717294 GTTGCTGCTGTCGCA
1 GTTGCTGCTGTCGCA
**
25717309 GTTGCTG-TAGTCGTT
1 GTTGCTGCT-GTCGCA
* *
25717324 GTTGCTGTTGTCACA
1 GTTGCTGCTGTCGCA
25717339 GTTGCTGC
1 GTTGCTGC
25717347 AAAATTTGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
14 1 0.03
15 28 0.93
16 1 0.03
ACGTcount: A:0.08, C:0.21, G:0.32, T:0.40
Consensus pattern (15 bp):
GTTGCTGCTGTCGCA
Found at i:25724030 original size:21 final size:21
Alignment explanation
Indices: 25724005--25724046 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
25723995 TGTACAAATT
25724005 CAAGT-TTCTCTAATAAAAACC
1 CAAGTATTCTCT-ATAAAAACC
25724026 CAAGTAATTCTCTATAAAAAC
1 CAAGT-ATTCTCTATAAAAAC
25724047 TTAGGTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 8 0.42
23 6 0.32
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (21 bp):
CAAGTATTCTCTATAAAAACC
Found at i:25724099 original size:21 final size:22
Alignment explanation
Indices: 25724065--25724114 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
25724055 TTCCCTTTTA
* *
25724065 CTAAAAACACTAAAGTTAAT-T
1 CTAAAAAAACTAAAATTAATAT
*
25724086 CTAAAAAAATTAAAATTAATAT
1 CTAAAAAAACTAAAATTAATAT
*
25724108 TTAAAAA
1 CTAAAAA
25724115 GATGAATGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (22 bp):
CTAAAAAAACTAAAATTAATAT
Found at i:25747999 original size:28 final size:27
Alignment explanation
Indices: 25747968--25748267 Score: 150
Period size: 28 Copynumber: 10.5 Consensus size: 27
25747958 TTCGGGGTTA
25747968 AAAATAGG-ATTTTGGAAGGTTCGAGGGT
1 AAAAT-GGAATTTTGGAA-GTTCGAGGGT
**
25747996 AAAATGGTAATTTTGGCAAAATC-AGGGTT
1 AAAATGG-AATTTTGG-AAGTTCGAGGG-T
* *
25748025 AAAAAGGAATTTTGGAAAGTTCGGGGGGT
1 AAAATGGAATTTTGG-AAGTTC-GAGGGT
* * *
25748054 AGAATGGTAATTTTGGTGAA-ATCGAGGTT
1 AAAATGG-AATTTT-G-GAAGTTCGAGGGT
25748083 AAAATGGAATTTTGGAAGGTTCG-GGGT
1 AAAATGGAATTTTGGAA-GTTCGAGGGT
*
25748110 AAAATGGTAATTTTGGTAAAATT--AGGGTT
1 AAAATGG-AATTTTGG--AAGTTCGAGGG-T
* * *
25748139 AAAATTGAATTTTGGAAAGTTTGGGGGT
1 AAAATGGAATTTTGG-AAGTTCGAGGGT
* *
25748167 AGAATGGTAATTTTGGTGAA-ATCG-GGGTT
1 AAAATGG-AATTTT-G-GAAGTTCGAGGG-T
*
25748196 AAAAATGGAATTTTGGAAGGTTTG-GGGT
1 -AAAATGGAATTTTGGAA-GTTCGAGGGT
* *
25748224 TAAATGGTAATTTTGAAGAAGTTCAAGGGT
1 AAAATGG-AATTTTG--GAAGTTCGAGGGT
*
25748254 CAAAATGTAATTTT
1 -AAAATGGAATTTT
25748268 TAGTAAGTTT
Statistics
Matches: 211, Mismatches: 31, Indels: 58
0.70 0.10 0.19
Matches are distributed among these distances:
26 3 0.01
27 27 0.13
28 67 0.32
29 67 0.32
30 37 0.18
31 9 0.04
32 1 0.00
ACGTcount: A:0.34, C:0.03, G:0.31, T:0.33
Consensus pattern (27 bp):
AAAATGGAATTTTGGAAGTTCGAGGGT
Found at i:25748000 original size:58 final size:57
Alignment explanation
Indices: 25747945--25748238 Score: 351
Period size: 58 Copynumber: 5.1 Consensus size: 57
25747935 GCAAAAATGA
* * *
25747945 AATTTCGGGGAAATTCGGGGTTAAAAATAGG-ATTTTGGAAGGTTCGAGGGTAAAATGGT
1 AATTTTGGTGAAA-TCGGGGTT-AAAAT-GGAATTTTGGAAGGTTCGGGGGTAAAATGGT
** * * * *
25748004 AATTTTGGCAAAATCAGGGTTAAAAAGGAATTTTGGAAAGTTCGGGGGGTAGAATGGT
1 AATTTTGGTGAAATCGGGGTTAAAATGGAATTTTGGAAGGTTC-GGGGGTAAAATGGT
*
25748062 AATTTTGGTGAAATCGAGGTTAAAATGGAATTTTGGAAGGTTC-GGGGTAAAATGGT
1 AATTTTGGTGAAATCGGGGTTAAAATGGAATTTTGGAAGGTTCGGGGGTAAAATGGT
* ** * * * *
25748118 AATTTTGGTAAAATTAGGGTTAAAATTGAATTTTGGAAAGTTTGGGGGTAGAATGGT
1 AATTTTGGTGAAATCGGGGTTAAAATGGAATTTTGGAAGGTTCGGGGGTAAAATGGT
* *
25748175 AATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAGGTT-TGGGGTTAAATGGT
1 AATTTTGGTGAAATCGGGGTT-AAAATGGAATTTTGGAAGGTTCGGGGGTAAAATGGT
25748232 AATTTTG
1 AATTTTG
25748239 AAGAAGTTCA
Statistics
Matches: 200, Mismatches: 31, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
56 50 0.25
57 65 0.32
58 75 0.38
59 10 0.05
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.33
Consensus pattern (57 bp):
AATTTTGGTGAAATCGGGGTTAAAATGGAATTTTGGAAGGTTCGGGGGTAAAATGGT
Found at i:25748125 original size:114 final size:114
Alignment explanation
Indices: 25747945--25748238 Score: 448
Period size: 114 Copynumber: 2.6 Consensus size: 114
25747935 GCAAAAATGA
* *
25747945 AATTTCGGGGAAATTCGGGGTTAAAAATAGG-ATTTTGGAAGGTTCGAGGGTAAAATGGTAATTT
1 AATTTTGGTGAAA-TCGGGGTTAAAAAT-GGAATTTTGGAAGGTTCG-GGGTAAAATGGTAATTT
25748009 TGGCAAAATCAGGGTTAAAAAGGAATTTTGGAAAGTTCGGGGGGTAGAATGGT
63 TGGCAAAATCAGGGTTAAAAAGGAATTTTGGAAAGTT-GGGGGGTAGAATGGT
*
25748062 AATTTTGGTGAAATCGAGGTT-AAAATGGAATTTTGGAAGGTTCGGGGTAAAATGGTAATTTTGG
1 AATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAGGTTCGGGGTAAAATGGTAATTTTGG
* * ** *
25748126 TAAAATTAGGGTTAAAATTGAATTTTGGAAAGTTTGGGGGTAGAATGGT
66 CAAAATCAGGGTTAAAAAGGAATTTTGGAAAGTTGGGGGGTAGAATGGT
* *
25748175 AATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAGGTTTGGGGTTAAATGGTAATTTTG
1 AATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAGGTTCGGGGTAAAATGGTAATTTTG
25748239 AAGAAGTTCA
Statistics
Matches: 164, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
113 34 0.21
114 92 0.56
115 20 0.12
116 7 0.04
117 11 0.07
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.33
Consensus pattern (114 bp):
AATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAGGTTCGGGGTAAAATGGTAATTTTGG
CAAAATCAGGGTTAAAAAGGAATTTTGGAAAGTTGGGGGGTAGAATGGT
Found at i:25748182 original size:57 final size:57
Alignment explanation
Indices: 25747962--25748238 Score: 328
Period size: 57 Copynumber: 4.8 Consensus size: 57
25747952 GGGAAATTCG
* * * *
25747962 GGGTTAAAAATAGG-ATTTTGGAAGGTTCGAGGGTAAAATGGTAATTTTGGCAAAATCA
1 GGGTT-AAAAT-GGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTGGTAAAATCA
* * * *
25748020 GGGTTAAAAAGGAATTTTGGAAAGTTCGGGGGGTAGAATGGTAATTTTGGTGAAATC-
1 GGGTTAAAATGGAATTTTGGAAAGTT-TGGGGGTAAAATGGTAATTTTGGTAAAATCA
* * *
25748077 GAGGTTAAAATGGAATTTTGG-AAGGTTCGGGGTAAAATGGTAATTTTGGTAAAATTA
1 G-GGTTAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTGGTAAAATCA
* * * *
25748134 GGGTTAAAATTGAATTTTGGAAAGTTTGGGGGTAGAATGGTAATTTTGGTGAAATCG
1 GGGTTAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTGGTAAAATCA
* *
25748191 GGGTTAAAAATGGAATTTTGGAAGGTTT-GGGGTTAAATGGTAATTTTG
1 GGGTT-AAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTG
25748239 AAGAAGTTCA
Statistics
Matches: 188, Mismatches: 25, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
56 45 0.24
57 75 0.40
58 68 0.36
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.33
Consensus pattern (57 bp):
GGGTTAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTGGTAAAATCA
Found at i:25748264 original size:30 final size:30
Alignment explanation
Indices: 25748225--25748297 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
25748215 GTTTGGGGTT
25748225 AAATGGTAATTTTGAAG-AAGTTCAAGGGTCA
1 AAAT-GTAATTTT-AAGTAAGTTCAAGGGTCA
* **
25748256 AAATGTAATTTTTAGTAAGTTTTAGGGTCA
1 AAATGTAATTTTAAGTAAGTTCAAGGGTCA
*
25748286 AAATATAATTTT
1 AAATGTAATTTT
25748298 TGGATAGGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 2 0.05
30 31 0.84
31 4 0.11
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.38
Consensus pattern (30 bp):
AAATGTAATTTTAAGTAAGTTCAAGGGTCA
Found at i:25750075 original size:17 final size:17
Alignment explanation
Indices: 25750053--25750128 Score: 73
Period size: 17 Copynumber: 4.5 Consensus size: 17
25750043 AATTTAATTT
*
25750053 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
* **
25750070 TAAATTTAAATTTTATG
1 TAAATTTAAATTTAAAA
* *
25750087 CAAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAA
*
25750104 TAAATCT-AATTTAAAA
1 TAAATTTAAATTTAAAA
25750120 CTAAATTTA
1 -TAAATTTA
25750129 TCTCATTGGG
Statistics
Matches: 44, Mismatches: 13, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
16 8 0.18
17 36 0.82
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:25750126 original size:34 final size:35
Alignment explanation
Indices: 25750053--25750128 Score: 84
Period size: 34 Copynumber: 2.2 Consensus size: 35
25750043 AATTTAATTT
* * * * **
25750053 TAAATTTAAATTTATAATAAATTTAAATTTTATGC
1 TAAATTTAAATTCAAAATAAATCTAAATTTAAAAC
25750088 -AAATTTAAATTCAAAATAAATCT-AATTTAAAAC
1 TAAATTTAAATTCAAAATAAATCTAAATTTAAAAC
25750121 TAAATTTA
1 TAAATTTA
25750129 TCTCATTGGG
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
33 7 0.21
34 27 0.79
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.42
Consensus pattern (35 bp):
TAAATTTAAATTCAAAATAAATCTAAATTTAAAAC
Found at i:25750752 original size:25 final size:26
Alignment explanation
Indices: 25750716--25750769 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
25750706 ATGGTCACGG
*
25750716 TTTATTTATCTTTG-TGATAAATGAC
1 TTTATTTATCTTTGATAATAAATGAC
*
25750741 TTTA-TTACTCTTTGATAATAATTGAC
1 TTTATTTA-TCTTTGATAATAAATGAC
25750767 TTT
1 TTT
25750770 TCATGAAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 3 0.12
25 10 0.40
26 12 0.48
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.54
Consensus pattern (26 bp):
TTTATTTATCTTTGATAATAAATGAC
Found at i:25754182 original size:14 final size:15
Alignment explanation
Indices: 25754160--25754193 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
25754150 ATATGAAAAG
*
25754160 ATAAAAATATT-ATT
1 ATAATAATATTGATT
25754174 ATAATAATATTGATT
1 ATAATAATATTGATT
25754189 ATAAT
1 ATAAT
25754194 TTAAAAGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (15 bp):
ATAATAATATTGATT
Found at i:25754614 original size:15 final size:19
Alignment explanation
Indices: 25754568--25754608 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
25754558 ATTTTTTAAT
25754568 TTTTTAAATATTTATATATA
1 TTTTT-AATATTTATATATA
25754588 TTTTTAATATTTA-ATA-A
1 TTTTTAATATTTATATATA
25754605 TTTT
1 TTTT
25754609 ATATTTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.24
18 3 0.14
19 8 0.38
20 5 0.24
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTTAATATTTATATATA
Found at i:25759344 original size:2 final size:2
Alignment explanation
Indices: 25759339--25759367 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
25759329 TATGAGCATG
25759339 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25759368 ACACAGATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25759547 original size:1 final size:1
Alignment explanation
Indices: 25759541--25759565 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
25759531 AATGTGGGTT
25759541 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
25759566 AGGATGAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:25759873 original size:21 final size:21
Alignment explanation
Indices: 25759835--25759874 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
25759825 GAAGGAATTA
**
25759835 ATTTAATTTCTTTAAATTATT
1 ATTTAATTAATTTAAATTATT
*
25759856 ATTTAATTAATTTTAATTA
1 ATTTAATTAATTTAAATTA
25759875 AATAATTAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTAATTAATTTAAATTATT
Found at i:25759888 original size:19 final size:19
Alignment explanation
Indices: 25759859--25759903 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
25759849 AATTATTATT
25759859 TAATT-AATTTTAATTAAA
1 TAATTAAATTTTAATTAAA
25759877 TAATTAAATTTTAATTAAA
1 TAATTAAATTTTAATTAAA
25759896 TAATTAAA
1 TAATTAAA
25759904 GTTAAAAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TAATTAAATTTTAATTAAA
Found at i:25768471 original size:3 final size:3
Alignment explanation
Indices: 25768465--25768502 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
25768455 ATAGAGGAGG
25768465 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGCC AGC AGC A
1 AGC AGC AGC AGC AGC AGC AGC AGC AGC AG-C AGC AGC A
25768503 CACAATGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.34, C:0.34, G:0.32, T:0.00
Consensus pattern (3 bp):
AGC
Found at i:25773842 original size:25 final size:25
Alignment explanation
Indices: 25773814--25773877 Score: 110
Period size: 25 Copynumber: 2.6 Consensus size: 25
25773804 TGGTAACACT
*
25773814 ATCTATGCATGTAGCACCATTTAGG
1 ATCTATGCATGCAGCACCATTTAGG
*
25773839 ATCTATGCATGCAGCACTATTTAGG
1 ATCTATGCATGCAGCACCATTTAGG
25773864 ATCTATGCATGCAG
1 ATCTATGCATGCAG
25773878 TCACGTATAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (25 bp):
ATCTATGCATGCAGCACCATTTAGG
Found at i:25779264 original size:25 final size:24
Alignment explanation
Indices: 25779218--25779264 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
25779208 ATCTCTAATC
* *
25779218 AATTTAAATGATTAAGACATAAAT
1 AATTTAAATAATTAAGAAATAAAT
*
25779242 AATTTAATATAATTAATAAATAA
1 AATTTAA-ATAATTAAGAAATAA
25779265 TAAGTACAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 7 0.37
25 12 0.63
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.36
Consensus pattern (24 bp):
AATTTAAATAATTAAGAAATAAAT
Found at i:25779266 original size:24 final size:23
Alignment explanation
Indices: 25779213--25779267 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
25779203 ATTTTATCTC
* *
25779213 TAATCAATTTAAATGATTAAGACA
1 TAAT-AATTTAAATAATTAAGAAA
*
25779237 TAAATAATTTAATATAATTAATAAA
1 T-AATAATTTAA-ATAATTAAGAAA
25779262 TAATAA
1 TAATAA
25779268 GTACAAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (23 bp):
TAATAATTTAAATAATTAAGAAA
Found at i:25788569 original size:30 final size:30
Alignment explanation
Indices: 25788534--25788613 Score: 81
Period size: 30 Copynumber: 2.6 Consensus size: 30
25788524 CTTTAAAATC
** * *
25788534 GGGTCAAATTTGAATTTTTAGAAAGTTT-A
1 GGGTCAAATTAAAATTTTTAAAAAATTTGA
*
25788563 GAGGTCAAATCAAAATTTTTAAAAAATTTGA
1 G-GGTCAAATTAAAATTTTTAAAAAATTTGA
*
25788594 GGGTCAAATTCAAATATTTT
1 GGGTCAAATTAAAAT-TTTT
25788614 GGTTGTTAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
29 1 0.02
30 34 0.83
31 6 0.15
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.38
Consensus pattern (30 bp):
GGGTCAAATTAAAATTTTTAAAAAATTTGA
Found at i:25788664 original size:30 final size:30
Alignment explanation
Indices: 25788628--25788752 Score: 94
Period size: 30 Copynumber: 4.2 Consensus size: 30
25788618 GTTAAATTTG
25788628 AATTTTTAGAAAATTT-AGAGATCAAAACAT
1 AATTTTTAGAAAATTTGAG-GATCAAAACAT
* * *
25788658 AATTTTTGGAAAATTTGAGGGTCATAACAT
1 AATTTTTAGAAAATTTGAGGATCAAAACAT
* * * * * * *
25788688 AATATTTGGACAGTTTAAGGGTTAAAACAT
1 AATTTTTAGAAAATTTGAGGATCAAAACAT
* * *
25788718 AATTTATA-AATAGTTTGGGGATCAAAA-AT
1 AATTTTTAGAA-AATTTGAGGATCAAAACAT
25788747 AATTTT
1 AATTTT
25788753 AAAATAAAGC
Statistics
Matches: 75, Mismatches: 18, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
29 8 0.11
30 65 0.87
31 2 0.03
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.36
Consensus pattern (30 bp):
AATTTTTAGAAAATTTGAGGATCAAAACAT
Found at i:25788692 original size:82 final size:81
Alignment explanation
Indices: 25788539--25788694 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
25788529 AAATCGGGTC
* * *
25788539 AAATTTGAATTTTTAGAAAGTTTAGAGGTCAAATCAAAATTTTTAAAAAATTTGAGGGTCAAATT
1 AAATTTGAATTTTTAGAAAATTTAGAGATCAAAACAAAATTTTTAAAAAATTTGAGGGTCAAA-T
25788604 CAAATATTTTGGTTGTT
65 CAAATATTTTGGTTGTT
* **
25788621 AAATTTGAATTTTTAGAAAATTTAGAGATCAAAACATAATTTTTGGAAAATTTGAGGGTCATAA-
1 AAATTTGAATTTTTAGAAAATTTAGAGATCAAAACAAAATTTTTAAAAAATTTGAGGGTCA-AAT
25788685 CATAATATTT
65 CA-AATATTT
25788695 GGACAGTTTA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
81 2 0.03
82 62 0.94
83 2 0.03
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (81 bp):
AAATTTGAATTTTTAGAAAATTTAGAGATCAAAACAAAATTTTTAAAAAATTTGAGGGTCAAATC
AAATATTTTGGTTGTT
Found at i:25790252 original size:21 final size:21
Alignment explanation
Indices: 25790214--25790253 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
25790204 TGGCAACCAT
**
25790214 CAAACCAAAAATTGAAAAGAG
1 CAAACCAAAAATAAAAAAGAG
*
25790235 CAAATCAAAAATAAAAAAG
1 CAAACCAAAAATAAAAAAG
25790254 CCTCTATAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.68, C:0.12, G:0.10, T:0.10
Consensus pattern (21 bp):
CAAACCAAAAATAAAAAAGAG
Found at i:25827848 original size:17 final size:17
Alignment explanation
Indices: 25827823--25827856 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
25827813 CTTAATCAAG
* *
25827823 TTATTTTTTTGTAATTT
1 TTATGTTTTTGAAATTT
25827840 TTATGTTTTTGAAATTT
1 TTATGTTTTTGAAATTT
25827857 CGATATCTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.71
Consensus pattern (17 bp):
TTATGTTTTTGAAATTT
Found at i:25829899 original size:3 final size:3
Alignment explanation
Indices: 25829855--25829889 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
25829845 GATGATGATG
25829855 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
25829890 GTGATAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:25837328 original size:52 final size:51
Alignment explanation
Indices: 25837253--25837439 Score: 216
Period size: 52 Copynumber: 3.6 Consensus size: 51
25837243 GAAGAGGTTC
*
25837253 GATGATTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAACGGTCT
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAA-GGTCT
* * * * *
25837305 AATGACTAAGTGTTATCGTGAGTATATGGATCCTTTACGGATTAAGAGGTCC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAA-AGGTCT
* *
25837357 GATGACTCTGTGTCATCGTGAGTATACGAATCTCTTGT--GGATTATAAGGTCT
1 GATGACTATGTGTCATCGTGAGTATATGAATC-CTT-TACGGATTA-AAGGTCT
* **
25837409 GGTGGTTATGTGTCATCGTGAGTATATGAAT
1 GATGACTATGTGTCATCGTGAGTATATGAAT
25837440 TCAATGAAAT
Statistics
Matches: 113, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
52 107 0.95
53 5 0.04
54 1 0.01
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.36
Consensus pattern (51 bp):
GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAAGGTCT
Found at i:25837427 original size:104 final size:103
Alignment explanation
Indices: 25837244--25837436 Score: 246
Period size: 104 Copynumber: 1.9 Consensus size: 103
25837234 GCCATAAACG
* * *
25837244 AAGAGGTTCGATGATTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAACGGTCTAATG
1 AAGAGGTCCGATGACTATGTGTCATCGTGAGTATACGAATCCTTTA-GGATTAAACGGTCTAATG
*
25837309 ACTAAGTGTTATCGTGAGTATATGGATCCTTTACGGATT
65 ACTAAGTGTCATCGTGAGTATATGGATCCTTTACGGATT
* **
25837348 AAGAGGTCCGATGACTCTGTGTCATCGTGAGTATACGAATCTCTTGT-GGATTATAA-GGTCTGG
1 AAGAGGTCCGATGACTATGTGTCATCGTGAGTATACGAATC-CTT-TAGGATTA-AACGGTCTAA
** *
25837411 TGGTTATGTGTCATCGTGAGTATATG
63 TGACTAAGTGTCATCGTGAGTATATG
25837437 AATTCAATGA
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
104 70 0.92
105 5 0.07
106 1 0.01
ACGTcount: A:0.25, C:0.13, G:0.26, T:0.35
Consensus pattern (103 bp):
AAGAGGTCCGATGACTATGTGTCATCGTGAGTATACGAATCCTTTAGGATTAAACGGTCTAATGA
CTAAGTGTCATCGTGAGTATATGGATCCTTTACGGATT
Found at i:25838624 original size:29 final size:29
Alignment explanation
Indices: 25838592--25838889 Score: 126
Period size: 29 Copynumber: 10.2 Consensus size: 29
25838582 TAAAAATGAG
25838592 ATTTTGGAAGGTTCGAGGGT-AAAATGGTA
1 ATTTTGGAA-GTTCGAGGGTAAAAATGGTA
**
25838621 ATTTTGGTAAAATCGA-GGTCAAAAAATGG-A
1 ATTTTGG-AAGTTCGAGGGT--AAAAATGGTA
* *
25838651 ATTTTGGAAGATTTGGGGGT-AAAATGGTA
1 ATTTTGGAAG-TTCGAGGGTAAAAATGGTA
** * * * * *
25838680 ATTTTGGTGAA-ACCAAAGTTAAAAACGG-G
1 ATTTT-G-GAAGTTCGAGGGTAAAAATGGTA
* *
25838709 ATTTTAGAAAGTTCGAGGGT-AAAACGGTA
1 ATTTT-GGAAGTTCGAGGGTAAAAATGGTA
* *
25838738 ATTTTTGGTGAA-ATCGAGGTTAAAAATGG-A
1 A-TTTT-G-GAAGTTCGAGGGTAAAAATGGTA
*
25838768 ATTTTAGAAAGTTC-AGGGGT-AAAATGGTA
1 ATTTT-GGAAGTTCGA-GGGTAAAAATGGTA
*
25838797 ATTTTTGGTGAAATT-G-GGGTTAAAAATGG-A
1 A-TTTT-G-GAAGTTCGAGGG-TAAAAATGGTA
*
25838827 ATTTTGGAAAGTTCGAGGAT-AAAATGGTA
1 ATTTTGG-AAGTTCGAGGGTAAAAATGGTA
*
25838856 ATTTTTGGAAGTTTCG-GGGTCAAAAT-GTA
1 A-TTTTGGAAG-TTCGAGGGTAAAAATGGTA
25838885 ATTTT
1 ATTTT
25838890 CTAAAGTTTT
Statistics
Matches: 201, Mismatches: 38, Indels: 61
0.67 0.13 0.20
Matches are distributed among these distances:
27 1 0.00
28 45 0.22
29 65 0.32
30 58 0.29
31 32 0.16
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.32
Consensus pattern (29 bp):
ATTTTGGAAGTTCGAGGGTAAAAATGGTA
Found at i:25838732 original size:117 final size:117
Alignment explanation
Indices: 25838580--25838860 Score: 368
Period size: 117 Copynumber: 2.4 Consensus size: 117
25838570 AAAATTTGGG
* *
25838580 GTTAAAAATGAGATTTTGGAAGGTTCGAGGGTAAAATGGTAATTTTGGTAAAATCGAGGTCAAAA
1 GTTAAAAATGGGATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTGGTAAAATCGAGGT-AAAA
* **
25838645 AATGGAATTTT-GGAAGATTTGGGGGTAAAATGGTAA-TTTTGGTGAAACCAAA
65 AATGGAATTTTAGAAAG-TTCAGGGGTAAAATGGTAATTTTTGGTGAAACCAAA
* * * * *
25838697 GTTAAAAACGGGATTTTAGAAAGTTCGAGGGTAAAACGGTAATTTTTGGTGAAATCGAGGTTAAA
1 GTTAAAAATGGGATTTTGGAAAGTTCGAGGGTAAAATGGTAA-TTTTGGTAAAATCGAGGTAAAA
*****
25838762 AATGGAATTTTAGAAAGTTCAGGGGTAAAATGGTAATTTTTGGTGAAATTGGG
65 AATGGAATTTTAGAAAGTTCAGGGGTAAAATGGTAATTTTTGGTGAAACCAAA
* *
25838815 GTTAAAAATGGAATTTTGGAAAGTTCGAGGATAAAATGGTAATTTT
1 GTTAAAAATGGGATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTT
25838861 TGGAAGTTTC
Statistics
Matches: 141, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
117 72 0.51
118 69 0.49
ACGTcount: A:0.37, C:0.04, G:0.28, T:0.31
Consensus pattern (117 bp):
GTTAAAAATGGGATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTGGTAAAATCGAGGTAAAAA
ATGGAATTTTAGAAAGTTCAGGGGTAAAATGGTAATTTTTGGTGAAACCAAA
Found at i:25838861 original size:59 final size:59
Alignment explanation
Indices: 25838579--25838863 Score: 355
Period size: 59 Copynumber: 4.8 Consensus size: 59
25838569 GAAAATTTGG
* *
25838579 GGTTAAAAAT-GAGATTTTGGAAGGTTCGAGGGTAAAATGGTAA-TTTTGGTAAAATCGA
1 GGTTAAAAATGGA-ATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATCGA
* * * * *
25838637 GGTCAAAAAATGGAATTTTGG-AAGATTTGGGGGTAAAATGGTAA-TTTTGGTGAAACCAA
1 GGT-TAAAAATGGAATTTTGGAAAG-TTCGAGGGTAAAATGGTAATTTTTGGTGAAATCGA
* * * * *
25838696 AGTTAAAAACGGGATTTTAGAAAGTTCGAGGGTAAAACGGTAATTTTTGGTGAAATCGA
1 GGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATCGA
* * *
25838755 GGTTAAAAATGGAATTTTAGAAAGTTC-AGGGGTAAAATGGTAATTTTTGGTGAAATTGG
1 GGTTAAAAATGGAATTTTGGAAAGTTCGA-GGGTAAAATGGTAATTTTTGGTGAAATCGA
*
25838814 GGTTAAAAATGGAATTTTGGAAAGTTCGAGGATAAAATGGTAATTTTTGG
1 GGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGG
25838864 AAGTTTCGGG
Statistics
Matches: 195, Mismatches: 25, Indels: 13
0.84 0.11 0.06
Matches are distributed among these distances:
58 35 0.18
59 157 0.81
60 3 0.02
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.31
Consensus pattern (59 bp):
GGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATCGA
Found at i:25838864 original size:30 final size:31
Alignment explanation
Indices: 25838593--25838889 Score: 137
Period size: 30 Copynumber: 10.1 Consensus size: 31
25838583 AAAAATGAGA
*
25838593 TTTTGGAAGGTTCGAGGGT-AAAATGGTAA-
1 TTTTGGAAAGTTCGAGGGTAAAAATGGTAAT
*
25838622 TTTTGGTAAA-ATCGA-GGTCAAAAAATGG-AA-
1 TTTTGG-AAAGTTCGAGGGT--AAAAATGGTAAT
* *
25838652 TTTTGG-AAGATTTGGGGGT-AAAATGGTAAT
1 TTTTGGAAAG-TTCGAGGGTAAAAATGGTAAT
* * * * * * *
25838682 TTTGGTGAAA--CCAAAGTTAAAAACGG-GA-
1 TTTTG-GAAAGTTCGAGGGTAAAAATGGTAAT
* *
25838710 TTTTAGAAAGTTCGAGGGT-AAAACGGTAAT
1 TTTTGGAAAGTTCGAGGGTAAAAATGGTAAT
*
25838740 TTTTGGTGAAA--TCGAGGTTAAAAATGG-AA-
1 TTTT-G-GAAAGTTCGAGGGTAAAAATGGTAAT
*
25838769 TTTTAGAAAGTTC-AGGGGT-AAAATGGTAAT
1 TTTTGGAAAGTTCGA-GGGTAAAAATGGTAAT
25838799 TTTTGGTGAAA-TT-G-GGGTTAAAAATGG-AA-
1 TTTT-G-GAAAGTTCGAGGG-TAAAAATGGTAAT
*
25838828 TTTTGGAAAGTTCGAGGAT-AAAATGGTAAT
1 TTTTGGAAAGTTCGAGGGTAAAAATGGTAAT
*
25838858 TTTTGG-AAGTTTCG-GGGTCAAAAT-GTAAT
1 TTTTGGAAAG-TTCGAGGGTAAAAATGGTAAT
25838887 TTT
1 TTT
25838890 CTAAAGTTTT
Statistics
Matches: 203, Mismatches: 29, Indels: 72
0.67 0.10 0.24
Matches are distributed among these distances:
27 12 0.06
28 40 0.20
29 56 0.28
30 59 0.29
31 26 0.13
32 10 0.05
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.32
Consensus pattern (31 bp):
TTTTGGAAAGTTCGAGGGTAAAAATGGTAAT
Found at i:25838896 original size:29 final size:29
Alignment explanation
Indices: 25838760--25838919 Score: 111
Period size: 29 Copynumber: 5.5 Consensus size: 29
25838750 ATCGAGGTTA
* *
25838760 AAAATGGAATTTTAGAAAG-TTCAGGGGT-
1 AAAATGTAATTTTTGAAAGTTTC-GGGGTC
*
25838788 AAAATGGTAATTTTTGGTGAAA--TT-GGGGTTA
1 AAAAT-GTAA-TTTT--TGAAAGTTTCGGGG-TC
* * *
25838819 AAAATGGAATTTTGGAAAG-TTCGAGGAT-
1 AAAATGTAATTTTTGAAAGTTTCG-GGGTC
*
25838847 AAAATGGTAATTTTTGGAAGTTTCGGGGTC
1 AAAAT-GTAATTTTTGAAAGTTTCGGGGTC
*
25838877 AAAATGTAATTTTCT-AAAGTTTTGGGGTC
1 AAAATGTAATTTT-TGAAAGTTTCGGGGTC
25838906 AAAATGTAATTTTT
1 AAAATGTAATTTTT
25838920 AGACTGTTTT
Statistics
Matches: 108, Mismatches: 11, Indels: 26
0.74 0.08 0.18
Matches are distributed among these distances:
27 4 0.04
28 13 0.12
29 60 0.56
30 20 0.19
31 7 0.06
32 4 0.04
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (29 bp):
AAAATGTAATTTTTGAAAGTTTCGGGGTC
Found at i:25838915 original size:117 final size:113
Alignment explanation
Indices: 25838554--25838918 Score: 344
Period size: 117 Copynumber: 3.1 Consensus size: 113
25838544 CTCGGGGGCA
* *
25838554 AAAAT-GTAA-TTTGGGGAAAATTTGGGGTTAAAAAT-GAGATTTTGGAAGGTTCGAGGGTAAAA
1 AAAATGGTAATTTTGGTG-AAA-TTGGGGTTAAAAATGGA-ATTTTGGAAAGTTCGAGGGTAAAA
* * *
25838616 TGGTAA-TTTTGGTAAAATCGAGGTCAAAAAATGGAATTTTGGAAGATTTGGGGGT
63 TGGTAATTTTTGG--AAATCGGGGTC--AAAATGGAATTTTGAAAG-TTTAGGGGT
***** * * * *
25838671 AAAATGGTAATTTTGGTGAAACCAAAGTTAAAAACGGGATTTTAGAAAGTTCGAGGGTAAAACGG
1 AAAATGGTAATTTTGGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGG
* * *
25838736 TAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAAGTTCAGGGGT
66 TAATTTTT-G-GAAATCG-GGGTCAAAATGGAATTTT-GAAAGTTTAGGGGT
*
25838788 AAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGATAAAATG
1 AAAATGGTAA-TTTTGGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATG
* * * *
25838853 GTAATTTTTGGAAGTTTCGGGGTCAAAATGTAATTTTCTAAAGTTTTGGGGT
65 GTAATTTTTGGAA--ATCGGGGTCAAAATGGAATTTT-GAAAGTTTAGGGGT
25838905 CAAAAT-GTAATTTT
1 -AAAATGGTAATTTT
25838919 TAGACTGTTT
Statistics
Matches: 201, Mismatches: 35, Indels: 25
0.77 0.13 0.10
Matches are distributed among these distances:
116 7 0.03
117 101 0.50
118 83 0.41
119 9 0.04
120 1 0.00
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (113 bp):
AAAATGGTAATTTTGGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGG
TAATTTTTGGAAATCGGGGTCAAAATGGAATTTTGAAAGTTTAGGGGT
Found at i:25838931 original size:30 final size:29
Alignment explanation
Indices: 25838847--25838932 Score: 111
Period size: 29 Copynumber: 2.9 Consensus size: 29
25838837 GTTCGAGGAT
* *
25838847 AAAATGGTAATTTTTGGAAGTTTCGGGGTC
1 AAAAT-GTAATTTTTAGAAGTTTTGGGGTC
25838877 AAAATGTAATTTTCTA-AAGTTTTGGGGTC
1 AAAATGTAATTTT-TAGAAGTTTTGGGGTC
*
25838906 AAAATGTAATTTTTAGACTGTTTTGGG
1 AAAATGTAATTTTTAGA-AGTTTTGGG
25838933 ACCTATAAGC
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
28 2 0.04
29 34 0.68
30 14 0.28
ACGTcount: A:0.29, C:0.06, G:0.24, T:0.41
Consensus pattern (29 bp):
AAAATGTAATTTTTAGAAGTTTTGGGGTC
Found at i:25840949 original size:11 final size:11
Alignment explanation
Indices: 25840933--25841008 Score: 64
Period size: 11 Copynumber: 6.8 Consensus size: 11
25840923 TTATAATAAT
25840933 ATTAAATTTAA
1 ATTAAATTTAA
*
25840944 ATTAAATTCAAA
1 ATTAAATT-TAA
* *
25840956 ATTAAACTAAA
1 ATTAAATTTAA
*
25840967 ATTGAATTTAA
1 ATTAAATTTAA
*
25840978 AATAAATTTAAA
1 ATTAAATTT-AA
*
25840990 ATTAAA-ATAA
1 ATTAAATTTAA
*
25841000 ATTTAATTT
1 ATTAAATTT
25841009 TAAAATGGTT
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
10 7 0.14
11 28 0.55
12 16 0.31
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:25840968 original size:23 final size:23
Alignment explanation
Indices: 25840933--25840995 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
25840923 TTATAATAAT
*
25840933 ATTAAATTTAAATTAAATTCAAA
1 ATTAAATTAAAATTAAATTCAAA
* * *
25840956 ATTAAACTAAAATTGAATTTAAA
1 ATTAAATTAAAATTAAATTCAAA
25840979 A-TAAATTTAAAATTAAA
1 ATTAAA-TTAAAATTAAA
25840996 ATAAATTTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 4 0.12
23 29 0.88
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.37
Consensus pattern (23 bp):
ATTAAATTAAAATTAAATTCAAA
Found at i:25840984 original size:34 final size:33
Alignment explanation
Indices: 25840927--25841014 Score: 104
Period size: 34 Copynumber: 2.6 Consensus size: 33
25840917 TTCTTTTTAT
* *
25840927 AATAATATTAAATTTAAATTAAATTCAAAATTAA
1 AATAA-ATTGAATTTAAAATAAATTCAAAATTAA
* *
25840961 ACTAAAATTGAATTTAAAATAAATTTAAAATTAA
1 AAT-AAATTGAATTTAAAATAAATTCAAAATTAA
*
25840995 AATAAATTTAATTTTAAAAT
1 AATAAATTGAA-TTTAAAAT
25841015 GGTTTGGGCC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
33 7 0.15
34 37 0.80
35 2 0.04
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (33 bp):
AATAAATTGAATTTAAAATAAATTCAAAATTAA
Found at i:25841011 original size:17 final size:17
Alignment explanation
Indices: 25840934--25841014 Score: 90
Period size: 17 Copynumber: 4.8 Consensus size: 17
25840924 TATAATAATA
*
25840934 TTAAATTTAAATTAAAT
1 TTAAATTTAAAATAAAT
* * * *
25840951 TCAAAATTAAACTAAAA
1 TTAAATTTAAAATAAAT
*
25840968 TTGAATTTAAAATAAAT
1 TTAAATTTAAAATAAAT
*
25840985 TTAAAATTAAAATAAAT
1 TTAAATTTAAAATAAAT
*
25841002 TTAATTTTAAAAT
1 TTAAATTTAAAAT
25841015 GGTTTGGGCC
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 51 1.00
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:25841640 original size:21 final size:24
Alignment explanation
Indices: 25841599--25841649 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 24
25841589 TGAATTGTGA
*
25841599 GTATCGGTAGTTATATGCATAGAT
1 GTATCGGTAGTTATATGCATACAT
*
25841623 GTATCGGTAG-T-T-TGCATACTT
1 GTATCGGTAGTTATATGCATACAT
25841644 GTATCG
1 GTATCG
25841650 ATAGAAGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 13 0.52
22 1 0.04
23 1 0.04
24 10 0.40
ACGTcount: A:0.24, C:0.12, G:0.25, T:0.39
Consensus pattern (24 bp):
GTATCGGTAGTTATATGCATACAT
Found at i:25843257 original size:30 final size:32
Alignment explanation
Indices: 25843223--25843283 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 32
25843213 TATGTATTTA
25843223 AAATTTAAT-TTTTCTACTTTTA-A-TTTAAAG
1 AAATTTAATCTTTT-TACTTTTAGAGTTTAAAG
*
25843253 AAATTTTATCTTTTTACTTTTAGAGTTTAAA
1 AAATTTAATCTTTTTACTTTTAGAGTTTAAA
25843284 AATACAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 16 0.59
31 5 0.19
32 6 0.22
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (32 bp):
AAATTTAATCTTTTTACTTTTAGAGTTTAAAG
Found at i:25847840 original size:18 final size:18
Alignment explanation
Indices: 25847800--25847854 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
25847790 AAAATTCTTT
*
25847800 GTTTTGGCGAGATC-TGTG
1 GTTTTGGCGA-CTCTTGTG
25847818 G-TTTGGCGACTCTTGTG
1 GTTTTGGCGACTCTTGTG
*
25847835 GTTTTGTG-GACTCTTTTG
1 GTTTTG-GCGACTCTTGTG
25847853 GT
1 GT
25847855 AAGTATGTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 2 0.06
17 13 0.41
18 16 0.50
19 1 0.03
ACGTcount: A:0.07, C:0.13, G:0.35, T:0.45
Consensus pattern (18 bp):
GTTTTGGCGACTCTTGTG
Found at i:25850449 original size:24 final size:24
Alignment explanation
Indices: 25850385--25850458 Score: 94
Period size: 24 Copynumber: 3.1 Consensus size: 24
25850375 ATGTTTCTTA
*
25850385 TATTTATGTTGACGAGCGTAAACG
1 TATTTATGTTGACGAGTGTAAACG
* * **
25850409 TATTCATGCTGGTGAGTGTAAACG
1 TATTTATGTTGACGAGTGTAAACG
*
25850433 TATTTATGTTGACGAGTATAAACG
1 TATTTATGTTGACGAGTGTAAACG
25850457 TA
1 TA
25850459 ATGAACTTGC
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (24 bp):
TATTTATGTTGACGAGTGTAAACG
Found at i:25851461 original size:21 final size:21
Alignment explanation
Indices: 25851435--25851477 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
25851425 CGGTAAAAGC
25851435 CTTGATAGTATCAGTAGAAGT
1 CTTGATAGTATCAGTAGAAGT
25851456 CTTGATAGTATCAGTAGAAGT
1 CTTGATAGTATCAGTAGAAGT
25851477 C
1 C
25851478 ATCCAGATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.33
Consensus pattern (21 bp):
CTTGATAGTATCAGTAGAAGT
Found at i:25854049 original size:24 final size:24
Alignment explanation
Indices: 25853988--25854050 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
25853978 TAGATTAATA
* *
25853988 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* *
25854012 AGAGTTTAATTGAAACAAATAAGC
1 AGAGTTTAACTGAAACAAATAAAC
25854036 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
25854051 GATTTTTTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.49, C:0.11, G:0.16, T:0.24
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:25856015 original size:24 final size:24
Alignment explanation
Indices: 25855954--25856016 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
25855944 TAGACTAATA
* * *
25855954 AGAGTTTGACTCAAACAGATAAAT
1 AGAGTTTAACTGAAACAAATAAAT
* *
25855978 AGAGTTTAATTGAAATAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAT
25856002 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
25856017 GATTATTTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.49, C:0.06, G:0.16, T:0.29
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAT
Found at i:25864368 original size:24 final size:24
Alignment explanation
Indices: 25864335--25864381 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
25864325 AAAAATAATC
* *
25864335 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
25864359 TTTCAATTAAACTCTATTTATTT
1 TTTCAATTAAACTCTATTTATTT
25864382 ATTTGAGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.13, G:0.06, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTATTTG
Found at i:25864394 original size:24 final size:24
Alignment explanation
Indices: 25864343--25864397 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
25864333 TCTTTCAGTT
* * *
25864343 AAACTCTGTTTATTTGTTTCAATT
1 AAACTCTATTTATTTATTTCAATC
* *
25864367 AAACTCTATTTATTTATTTGAGTC
1 AAACTCTATTTATTTATTTCAATC
25864391 AAACTCT
1 AAACTCT
25864398 TATTACTCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.29, C:0.15, G:0.07, T:0.49
Consensus pattern (24 bp):
AAACTCTATTTATTTATTTCAATC
Found at i:25867443 original size:24 final size:23
Alignment explanation
Indices: 25867393--25867446 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
25867383 TCTTTCAGTT
* * *
25867393 AAACTCTGTTTATTGTTTTAATT
1 AAACTCTATTTATTGTTTGAATC
*
25867416 AAACTCTATTTATTTGTTTGAGTC
1 AAACTCTATTTA-TTGTTTGAATC
25867440 AAACTCT
1 AAACTCT
25867447 TATTACTCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.50
Consensus pattern (23 bp):
AAACTCTATTTATTGTTTGAATC
Found at i:25870912 original size:5 final size:5
Alignment explanation
Indices: 25870902--25870936 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
25870892 ACTGAAAAAC
25870902 AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT
25870937 TTCACATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:25887384 original size:23 final size:24
Alignment explanation
Indices: 25887336--25887396 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 24
25887326 TCAGTCATTT
25887336 GAAAAAGGAAAATGAGAAAAAGAAA
1 GAAAAA-GAAAATGAGAAAAAGAAA
25887361 GAAAAAGAAAA-GAG-AAAAGAAAA
1 GAAAAAGAAAATGAGAAAAAG-AAA
25887384 GAAGAAA-AAAATG
1 GAA-AAAGAAAATG
25887397 TTTGTTATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
22 5 0.15
23 13 0.39
24 9 0.27
25 6 0.18
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (24 bp):
GAAAAAGAAAATGAGAAAAAGAAA
Found at i:25887389 original size:30 final size:29
Alignment explanation
Indices: 25887338--25887394 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 29
25887328 AGTCATTTGA
25887338 AAAAGGAAAATGAGAAAAAGAAAGAAAAAG
1 AAAAGGAAAATGAGAAAAAGAAA-AAAAAG
25887368 AAAAGAGAAAA-GA-AAAGAAGAAAAAAA
1 AAAAG-GAAAATGAGAAA-AAGAAAAAAA
25887395 TGTTTGTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
29 7 0.28
30 13 0.52
31 5 0.20
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (29 bp):
AAAAGGAAAATGAGAAAAAGAAAAAAAAG
Found at i:25894422 original size:222 final size:222
Alignment explanation
Indices: 25894036--25894479 Score: 852
Period size: 222 Copynumber: 2.0 Consensus size: 222
25894026 AACATATTTA
25894036 AATGCAGGCTTGAGCTAGAATTTTGAGGTGTATCATTATTACAATGTGAGACTTAATCTTCAATA
1 AATGCAGGCTTGAGCTAGAATTTTGAGGTGTATCATTATTACAATGTGAGACTTAATCTTCAATA
25894101 AAATTATCCAAAATTGAAAAACATGATCTTCAGTAGATTATATACTTTTGAGTTTATATGTCCAA
66 AAATTATCCAAAATTGAAAAACATGATCTTCAGTAGATTATATACTTTTGAGTTTATATGTCCAA
*
25894166 GCACATAGTTTTATGCAGAGTTCAAAGCACTTATCACTCTCTCTGCTTCTTCACGAATAGACCAA
131 GCACATAGTTTTATGCAGAGTTCAAAGCACTTATCACTCTCTCTGCTTCTTCACGAATAGACAAA
25894231 AGGTTTGTCTTTATCTCGATAGAAAGC
196 AGGTTTGTCTTTATCTCGATAGAAAGC
*
25894258 AATGCAGGCTTGAGCTAGAATTTTGAGGTGTATCATTATTGCAATGTGAGACTTAATCTTCAATA
1 AATGCAGGCTTGAGCTAGAATTTTGAGGTGTATCATTATTACAATGTGAGACTTAATCTTCAATA
*
25894323 AAATTATCCAAAATTGAAAAACTTGATCTTCAGTAGATTATATACTTTTGAGTTTATATGTCCAA
66 AAATTATCCAAAATTGAAAAACATGATCTTCAGTAGATTATATACTTTTGAGTTTATATGTCCAA
*
25894388 GCACATAGTTTTATTCAGAGTTCAAAGCACTTATCACTCTCTCTGCTTCTTCACGAATAGACAAA
131 GCACATAGTTTTATGCAGAGTTCAAAGCACTTATCACTCTCTCTGCTTCTTCACGAATAGACAAA
25894453 AGGTTTGTCTTTATCTCGATAGAAAGC
196 AGGTTTGTCTTTATCTCGATAGAAAGC
25894480 CTGTTCTCAA
Statistics
Matches: 218, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
222 218 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (222 bp):
AATGCAGGCTTGAGCTAGAATTTTGAGGTGTATCATTATTACAATGTGAGACTTAATCTTCAATA
AAATTATCCAAAATTGAAAAACATGATCTTCAGTAGATTATATACTTTTGAGTTTATATGTCCAA
GCACATAGTTTTATGCAGAGTTCAAAGCACTTATCACTCTCTCTGCTTCTTCACGAATAGACAAA
AGGTTTGTCTTTATCTCGATAGAAAGC
Found at i:25897578 original size:23 final size:21
Alignment explanation
Indices: 25897536--25897595 Score: 61
Period size: 23 Copynumber: 2.8 Consensus size: 21
25897526 GAATTGAATA
25897536 AAAATAAGAGATTAGAAAAACAC
1 AAAATAA-AGA-TAGAAAAACAC
*
25897559 AAAATAAAGATAGACTAAAACAT
1 AAAATAAAGATAGA--AAAACAC
25897582 AAAA-AAAG-TAGAAA
1 AAAATAAAGATAGAAA
25897596 TACATGAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 2 0.06
21 8 0.24
22 7 0.21
23 17 0.50
ACGTcount: A:0.68, C:0.07, G:0.12, T:0.13
Consensus pattern (21 bp):
AAAATAAAGATAGAAAAACAC
Found at i:25900866 original size:5 final size:5
Alignment explanation
Indices: 25900856--25900883 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
25900846 CTCGAAATTT
25900856 TTCGA TTCGA TTCGA TTCGA TTCGA TTC
1 TTCGA TTCGA TTCGA TTCGA TTCGA TTC
25900884 AATCAAATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.43
Consensus pattern (5 bp):
TTCGA
Found at i:25900977 original size:43 final size:43
Alignment explanation
Indices: 25900907--25900990 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 43
25900897 CTCCTAGTTA
* *
25900907 AATGTATGGTTCTATTGCGACGGTTGTATAGGTAAACGCCGCT
1 AATGTATGGTTCTATTGCGACGATTGTATAGGCAAACGCCGCT
* ** *
25900950 AATGTATGGTTCTATTGTGGTGATTGTATATGCAAACGCCG
1 AATGTATGGTTCTATTGCGACGATTGTATAGGCAAACGCCG
25900991 TTATATGATA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.35
Consensus pattern (43 bp):
AATGTATGGTTCTATTGCGACGATTGTATAGGCAAACGCCGCT
Found at i:25902237 original size:29 final size:28
Alignment explanation
Indices: 25902196--25902250 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
25902186 ATAGTGCAAA
*
25902196 AAACTAAATTAAAATTAAATAACAAAATT
1 AAACTAAATT-AAATAAAATAACAAAATT
*
25902225 AAACTAAATTAAATAAAATTACAAAA
1 AAACTAAATTAAATAAAATAACAAAA
25902251 GAAAAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.25
Consensus pattern (28 bp):
AAACTAAATTAAATAAAATAACAAAATT
Found at i:25915795 original size:25 final size:26
Alignment explanation
Indices: 25915767--25915838 Score: 65
Period size: 27 Copynumber: 2.7 Consensus size: 26
25915757 AATTTGAATT
* * *
25915767 TAAAATTTTAATTT-TATATAATAAA
1 TAAAAATTTAATTTGAATATAACAAA
*
25915792 TAAAAAATTTGATTTGAATATAACAAA
1 T-AAAAATTTAATTTGAATATAACAAA
*
25915819 TAAAAGAATTTGATTTGAAT
1 T-AAA-AATTTAATTTGAAT
25915839 TTGTGCCCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
25 1 0.03
26 11 0.28
27 14 0.35
28 14 0.35
ACGTcount: A:0.51, C:0.01, G:0.07, T:0.40
Consensus pattern (26 bp):
TAAAAATTTAATTTGAATATAACAAA
Found at i:25915812 original size:27 final size:28
Alignment explanation
Indices: 25915782--25915838 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 28
25915772 TTTTAATTTT
*
25915782 ATATAATAAATAAAA-AATTTGATTTGA
1 ATATAACAAATAAAAGAATTTGATTTGA
25915809 ATATAACAAATAAAAGAATTTGATTTGA
1 ATATAACAAATAAAAGAATTTGATTTGA
25915837 AT
1 AT
25915839 TTGTGCCCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 14 0.50
28 14 0.50
ACGTcount: A:0.54, C:0.02, G:0.09, T:0.35
Consensus pattern (28 bp):
ATATAACAAATAAAAGAATTTGATTTGA
Found at i:25917286 original size:15 final size:15
Alignment explanation
Indices: 25917275--25917303 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
25917265 TTTAATTCTC
25917275 AAATAAAAAATTTAA
1 AAATAAAAAATTTAA
25917290 AAATAAAAAATTTA
1 AAATAAAAAATTTA
25917304 TAGATCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AAATAAAAAATTTAA
Found at i:25919871 original size:3 final size:3
Alignment explanation
Indices: 25919863--25919892 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
25919853 CCATCTTTTG
25919863 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
25919893 AAAACCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:25920881 original size:38 final size:39
Alignment explanation
Indices: 25920837--25920919 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 39
25920827 GCTTTTTAAC
* *
25920837 AAAATTT-GCTTAGAACATTAGTTAG-AGTTCTAACAGTT
1 AAAATTTAG-TTAGAACAATAGTTAGAAGTTCTAACACTT
* *
25920875 AAAATTTAGTTAGAGCAATAGTTAGAATTTCTAACACTT
1 AAAATTTAGTTAGAACAATAGTTAGAAGTTCTAACACTT
25920914 AAAATT
1 AAAATT
25920920 GAAATTTTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
38 21 0.54
39 18 0.46
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (39 bp):
AAAATTTAGTTAGAACAATAGTTAGAAGTTCTAACACTT
Found at i:25923055 original size:39 final size:39
Alignment explanation
Indices: 25922910--25923050 Score: 167
Period size: 39 Copynumber: 3.6 Consensus size: 39
25922900 CTGAATCGGT
* *
25922910 AGTGACACTGTAAACATTGCAATGCTACATTGAACTGGC
1 AGTGACACTGTAAACACTGCAATGCTACACTGAACTGGC
* * * * *
25922949 AGTAACACTATAAACACTACAATGCTACACTGAAATAGC
1 AGTGACACTGTAAACACTGCAATGCTACACTGAACTGGC
** *
25922988 AGTGACACTGTAAACACTGCAATTTTATACTGAACTGGC
1 AGTGACACTGTAAACACTGCAATGCTACACTGAACTGGC
*
25923027 AGTGACACTGTGAACA-TCGCAATG
1 AGTGACACTGTAAACACT-GCAATG
25923051 TTATAATGAA
Statistics
Matches: 84, Mismatches: 17, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
38 1 0.01
39 83 0.99
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (39 bp):
AGTGACACTGTAAACACTGCAATGCTACACTGAACTGGC
Found at i:25923070 original size:39 final size:39
Alignment explanation
Indices: 25922910--25923071 Score: 137
Period size: 39 Copynumber: 4.2 Consensus size: 39
25922900 CTGAATCGGT
* * * * *
25922910 AGTGACACTGTAAACATTGCAATGCTACATTGAACTGGC
1 AGTGACACTGTAAACACTGCAATGTTATAATGAACTGGA
* * * * * * * * *
25922949 AGTAACACTATAAACACTACAATGCTACACTGAAATAGC
1 AGTGACACTGTAAACACTGCAATGTTATAATGAACTGGA
* * *
25922988 AGTGACACTGTAAACACTGCAATTTTATACTGAACTGGC
1 AGTGACACTGTAAACACTGCAATGTTATAATGAACTGGA
* *
25923027 AGTGACACTGTGAACA-TCGCAATGTTATAATGAAGTGGA
1 AGTGACACTGTAAACACT-GCAATGTTATAATGAACTGGA
25923066 AGTGAC
1 AGTGAC
25923072 GCGGTAAAAT
Statistics
Matches: 102, Mismatches: 20, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
38 1 0.01
39 101 0.99
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (39 bp):
AGTGACACTGTAAACACTGCAATGTTATAATGAACTGGA
Found at i:25928093 original size:21 final size:21
Alignment explanation
Indices: 25928046--25928101 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
25928036 GTTGGAAAGA
*
25928046 TTCTACCGATATAAGTATGAC
1 TTCTACCGATACAAGTATGAC
* *
25928067 TACTACCGATACAA-TCATTAC
1 TTCTACCGATACAAGT-ATGAC
25928088 TTCTACCGATACAA
1 TTCTACCGATACAA
25928102 CAAACTCCAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 1 0.03
21 29 0.97
ACGTcount: A:0.36, C:0.25, G:0.09, T:0.30
Consensus pattern (21 bp):
TTCTACCGATACAAGTATGAC
Found at i:25930620 original size:13 final size:14
Alignment explanation
Indices: 25930591--25930628 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
25930581 ATTTTATTTC
25930591 TTTTAAACCATAAA
1 TTTTAAACCATAAA
*
25930605 TTTTAAACTA-AAA
1 TTTTAAACCATAAA
*
25930618 TTTGAAACCAT
1 TTTTAAACCAT
25930629 TCAACTCACC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (14 bp):
TTTTAAACCATAAA
Found at i:25931804 original size:71 final size:71
Alignment explanation
Indices: 25931688--25931878 Score: 314
Period size: 71 Copynumber: 2.7 Consensus size: 71
25931678 TCACATATAG
*
25931688 TGACTCATGATGCTGTAGAGAATCCGCAACAAATGCAGGATCTCAGCCATCGAACCAGTTTCACT
1 TGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAGGATCTCAGCCATCGAACCAGTTTCACT
25931753 TTTCAA
66 TTTCAA
*
25931759 TGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAGGATCTCAGCCATCGGACCAGTTTCACT
1 TGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAGGATCTCAGCCATCGAACCAGTTTCACT
*
25931824 TTTCAG
66 TTTCAA
* * *
25931830 TGACTCACGATGC--TATAGAATCCACAACAAGTGCAGGATCTCAGCCATC
1 TGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAGGATCTCAGCCATC
25931879 AGACCGTTTT
Statistics
Matches: 114, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
69 33 0.29
71 81 0.71
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (71 bp):
TGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAGGATCTCAGCCATCGAACCAGTTTCACT
TTTCAA
Found at i:25932349 original size:15 final size:16
Alignment explanation
Indices: 25932329--25932366 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
25932319 TTTCATCTCA
25932329 AGTCCTTGAA-AATTT
1 AGTCCTTGAACAATTT
* *
25932344 AGTCCTTTAACATTTT
1 AGTCCTTGAACAATTT
25932360 AGTCCTT
1 AGTCCTT
25932367 TAATATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.26, C:0.18, G:0.11, T:0.45
Consensus pattern (16 bp):
AGTCCTTGAACAATTT
Found at i:25934459 original size:24 final size:24
Alignment explanation
Indices: 25934428--25934574 Score: 186
Period size: 24 Copynumber: 6.1 Consensus size: 24
25934418 TGTTTTTATC
**
25934428 TAAAGTGGCTGATGAGCATAAACG
1 TAAAGTGGCTGACAAGCATAAACG
*
25934452 TATAGTGGCTGACAAGCATAAACG
1 TAAAGTGGCTGACAAGCATAAACG
* * *
25934476 TAAAGTGGTTGACAAACATAGACG
1 TAAAGTGGCTGACAAGCATAAACG
*
25934500 TAAAGTGGCTGACGAGCATAAACG
1 TAAAGTGGCTGACAAGCATAAACG
*
25934524 TAAAGTGGCTGGCAAGCATAAACG
1 TAAAGTGGCTGACAAGCATAAACG
* * * *
25934548 TATAGTGGTTGACGAGAATAAACG
1 TAAAGTGGCTGACAAGCATAAACG
25934572 TAA
1 TAA
25934575 TTGAAACTTG
Statistics
Matches: 104, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 104 1.00
ACGTcount: A:0.39, C:0.14, G:0.27, T:0.20
Consensus pattern (24 bp):
TAAAGTGGCTGACAAGCATAAACG
Found at i:25934573 original size:72 final size:72
Alignment explanation
Indices: 25934428--25934574 Score: 224
Period size: 72 Copynumber: 2.0 Consensus size: 72
25934418 TGTTTTTATC
* *
25934428 TAAAGTGGCTGATGAGCATAAACGTATAGTGGCTGACAAGCATAAACGTAAAGTGGTTGACAAAC
1 TAAAGTGGCTGACGAGCATAAACGTAAAGTGGCTGACAAGCATAAACGTAAAGTGGTTGACAAAC
*
25934493 ATAGACG
66 ATAAACG
* * *
25934500 TAAAGTGGCTGACGAGCATAAACGTAAAGTGGCTGGCAAGCATAAACGTATAGTGGTTGACGAGA
1 TAAAGTGGCTGACGAGCATAAACGTAAAGTGGCTGACAAGCATAAACGTAAAGTGGTTGAC-AAA
25934565 -ATAAACG
65 CATAAACG
25934572 TAA
1 TAA
25934575 TTGAAACTTG
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
72 66 0.97
73 2 0.03
ACGTcount: A:0.39, C:0.14, G:0.27, T:0.20
Consensus pattern (72 bp):
TAAAGTGGCTGACGAGCATAAACGTAAAGTGGCTGACAAGCATAAACGTAAAGTGGTTGACAAAC
ATAAACG
Found at i:25939068 original size:19 final size:19
Alignment explanation
Indices: 25939046--25939084 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
25939036 TTTTAAGATC
*
25939046 TATTTTAAGTATTTAATGT
1 TATTTTAAGAATTTAATGT
*
25939065 TATTTTAAGAATTTTATGT
1 TATTTTAAGAATTTAATGT
25939084 T
1 T
25939085 TCTTAGTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (19 bp):
TATTTTAAGAATTTAATGT
Found at i:25940325 original size:2 final size:2
Alignment explanation
Indices: 25940318--25940361 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
25940308 TATGTATTTA
25940318 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25940360 AT
1 AT
25940362 TTAAAAGTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25948289 original size:2 final size:2
Alignment explanation
Indices: 25948284--25948313 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
25948274 AAAAATTGTA
25948284 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
25948314 GGTTTGGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:25949835 original size:29 final size:29
Alignment explanation
Indices: 25949746--25949861 Score: 87
Period size: 29 Copynumber: 4.0 Consensus size: 29
25949736 AAATTTGGGT
**
25949746 CCTTAAAAGTTAAAAAATATTTTTGGGCC
1 CCTTAAAAGTTAAAAAATATTTTTGAACC
* * * *
25949775 CCTCAAAAGTT-GATACT-TTTTT-ATA-C
1 CCTTAAAAGTTAAAAAATATTTTTGA-ACC
**
25949801 TTTTAAAAGTTAAAAAATATTTTTGAACC
1 CCTTAAAAGTTAAAAAATATTTTTGAACC
* *
25949830 CCTTAAAAATTGAAAAATAATATTTTGAACC
1 CCTTAAAAGTTAAAAAAT-AT-TTTTGAACC
25949861 C
1 C
25949862 TTTTCAACTT
Statistics
Matches: 64, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
26 9 0.14
27 8 0.12
28 9 0.14
29 26 0.41
30 2 0.03
31 10 0.16
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.37
Consensus pattern (29 bp):
CCTTAAAAGTTAAAAAATATTTTTGAACC
Found at i:25955790 original size:21 final size:22
Alignment explanation
Indices: 25955766--25955806 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
25955756 ATTAAATTTT
*
25955766 TAAA-TCTGACAAATAAAAAAC
1 TAAATTCTGAAAAATAAAAAAC
*
25955787 TAAATTCTTAAAAATAAAAA
1 TAAATTCTGAAAAATAAAAA
25955807 TATAAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.63, C:0.10, G:0.02, T:0.24
Consensus pattern (22 bp):
TAAATTCTGAAAAATAAAAAAC
Found at i:25960546 original size:29 final size:29
Alignment explanation
Indices: 25960514--25960581 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
25960504 TAACATTAAT
*
25960514 TTATATTTATATATTA-AATAAATAAATAA
1 TTATATTTATATAATATAA-AAATAAATAA
* *
25960543 TTATTTTTATCTAATATAAAAATAAATAA
1 TTATATTTATATAATATAAAAATAAATAA
*
25960572 ATATATTTAT
1 TTATATTTAT
25960582 TTTTTTAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 31 0.94
30 2 0.06
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (29 bp):
TTATATTTATATAATATAAAAATAAATAA
Found at i:25968550 original size:23 final size:24
Alignment explanation
Indices: 25968524--25968581 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 24
25968514 TATTAATAAA
*
25968524 TAAACGAGCTTATAAACAA-TTTT
1 TAAACGAGCTTATAAACAAGCTTT
* *
25968547 TAAATGAGCTTATAAATAAGCTTT
1 TAAACGAGCTTATAAACAAGCTTT
25968571 TAAACGAGCTT
1 TAAACGAGCTT
25968582 GTTCGTGAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 17 0.57
24 13 0.43
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (24 bp):
TAAACGAGCTTATAAACAAGCTTT
Found at i:25971526 original size:32 final size:29
Alignment explanation
Indices: 25971480--25971566 Score: 99
Period size: 28 Copynumber: 3.0 Consensus size: 29
25971470 AACTAATATT
* *
25971480 AAAA-AAATTAATTATGAAAAATAATATTA
1 AAAACAAATTAATTAT-AAAAATAAGAGTA
*
25971509 AAAACATTAATTAATTATAAAAAT-AGAGTG
1 AAAACA--AATTAATTATAAAAATAAGAGTA
25971539 AAAACAAATTAATTATAAAAATAA-AGTA
1 AAAACAAATTAATTATAAAAATAAGAGTA
25971567 TTCGTTTCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
28 19 0.38
29 5 0.10
30 10 0.20
31 6 0.12
32 10 0.20
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (29 bp):
AAAACAAATTAATTATAAAAATAAGAGTA
Found at i:25974993 original size:92 final size:92
Alignment explanation
Indices: 25974836--25975017 Score: 364
Period size: 92 Copynumber: 2.0 Consensus size: 92
25974826 TACTTAAAGA
25974836 CGCTTGAGGGTCTCTCATATGGTCCACTGCATCAGAAAAAGATTATTGAAATTAGGCTTTGCATT
1 CGCTTGAGGGTCTCTCATATGGTCCACTGCATCAGAAAAAGATTATTGAAATTAGGCTTTGCATT
25974901 AATTGATGATATTAATAGTCAGACCCT
66 AATTGATGATATTAATAGTCAGACCCT
25974928 CGCTTGAGGGTCTCTCATATGGTCCACTGCATCAGAAAAAGATTATTGAAATTAGGCTTTGCATT
1 CGCTTGAGGGTCTCTCATATGGTCCACTGCATCAGAAAAAGATTATTGAAATTAGGCTTTGCATT
25974993 AATTGATGATATTAATAGTCAGACC
66 AATTGATGATATTAATAGTCAGACC
25975018 GTCTCGTTTT
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 90 1.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (92 bp):
CGCTTGAGGGTCTCTCATATGGTCCACTGCATCAGAAAAAGATTATTGAAATTAGGCTTTGCATT
AATTGATGATATTAATAGTCAGACCCT
Found at i:25990680 original size:3 final size:3
Alignment explanation
Indices: 25990655--25990719 Score: 78
Period size: 3 Copynumber: 21.3 Consensus size: 3
25990645 TTAAGGTTTA
* * *
25990655 AAG AGAG AAA AAG AAG AAA AAG AAG AAG AAG AGG AA- AAG AAG AAG
1 AAG A-AG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
25990700 AAG AAG AAG AAG AGAG AAG A
1 AAG AAG AAG AAG A-AG AAG A
25990720 TAAAAAATGG
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.04
3 45 0.85
4 6 0.11
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:25990692 original size:26 final size:26
Alignment explanation
Indices: 25990658--25990714 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
25990648 AGGTTTAAAG
25990658 AGAGAAAAAGAAGAAAAAGAAGAAGA
1 AGAGAAAAAGAAGAAAAAGAAGAAGA
* *
25990684 AGAGGAAAAGAAGAAGAAGAAGAAGA
1 AGAGAAAAAGAAGAAAAAGAAGAAGA
25990710 AGAGA
1 AGAGA
25990715 GAAGATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (26 bp):
AGAGAAAAAGAAGAAAAAGAAGAAGA
Found at i:25990699 original size:20 final size:20
Alignment explanation
Indices: 25990655--25990719 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
25990645 TTAAGGTTTA
*
25990655 AAGAGAGAAAAAGAAG-AAA-
1 AAGA-AGAAGAAGAAGAAAAG
*
25990674 AAGAAGAAGAAGAGGAAAAG
1 AAGAAGAAGAAGAAGAAAAG
*
25990694 AAGAAGAAGAAGAAGAAGAG
1 AAGAAGAAGAAGAAGAAAAG
25990714 -AGAAGA
1 AAGAAGA
25990720 TAAAAAATGG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
18 9 0.22
19 13 0.32
20 18 0.45
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (20 bp):
AAGAAGAAGAAGAAGAAAAG
Found at i:25996663 original size:14 final size:14
Alignment explanation
Indices: 25996644--25996675 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
25996634 TTTATTCATC
25996644 TCTTTCTTCTTCTT
1 TCTTTCTTCTTCTT
25996658 TCTTTCTTCTTCTT
1 TCTTTCTTCTTCTT
25996672 TCTT
1 TCTT
25996676 CCTCTCTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (14 bp):
TCTTTCTTCTTCTT
Found at i:25997713 original size:23 final size:23
Alignment explanation
Indices: 25997686--25997767 Score: 103
Period size: 23 Copynumber: 3.5 Consensus size: 23
25997676 GTTCACAAAC
* *
25997686 AAGCTCGTTTATGGTTCGTTTA-
1 AAGCTCGTTTATAGCTCGTTTAT
25997708 ATAGCTCGTTTAATAGCTCGTTTAT
1 A-AGCTCGTTT-ATAGCTCGTTTAT
* *
25997733 AAGCTCGTTTAAAGCCCGTTTAT
1 AAGCTCGTTTATAGCTCGTTTAT
25997756 AAGCTCGTTTAT
1 AAGCTCGTTTAT
25997768 TAGACCCATC
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
22 1 0.02
23 31 0.60
24 19 0.37
25 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.41
Consensus pattern (23 bp):
AAGCTCGTTTATAGCTCGTTTAT
Found at i:25997731 original size:35 final size:35
Alignment explanation
Indices: 25997686--25997767 Score: 105
Period size: 35 Copynumber: 2.3 Consensus size: 35
25997676 GTTCACAAAC
* * *
25997686 AAGCTCGTTTAT-GGTTCGTTTAATAGCTCGTTTA-
1 AAGCTCGTTTATAAGCTCGTTTAA-AGCCCGTTTAT
25997720 ATAGCTCGTTTATAAGCTCGTTTAAAGCCCGTTTAT
1 A-AGCTCGTTTATAAGCTCGTTTAAAGCCCGTTTAT
25997756 AAGCTCGTTTAT
1 AAGCTCGTTTAT
25997768 TAGACCCATC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
34 1 0.02
35 31 0.74
36 10 0.24
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.41
Consensus pattern (35 bp):
AAGCTCGTTTATAAGCTCGTTTAAAGCCCGTTTAT
Found at i:25997767 original size:12 final size:12
Alignment explanation
Indices: 25997686--25997767 Score: 91
Period size: 12 Copynumber: 7.0 Consensus size: 12
25997676 GTTCACAAAC
25997686 AAGCTCGTTTAT
1 AAGCTCGTTTAT
* *
25997698 -GGTTCGTTTA-
1 AAGCTCGTTTAT
25997708 ATAGCTCGTTTA-
1 A-AGCTCGTTTAT
25997720 ATAGCTCGTTTAT
1 A-AGCTCGTTTAT
25997733 AAGCTCGTTTA-
1 AAGCTCGTTTAT
*
25997744 AAGCCCGTTTAT
1 AAGCTCGTTTAT
25997756 AAGCTCGTTTAT
1 AAGCTCGTTTAT
25997768 TAGACCCATC
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
11 18 0.30
12 41 0.68
13 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.41
Consensus pattern (12 bp):
AAGCTCGTTTAT
Found at i:25998731 original size:26 final size:26
Alignment explanation
Indices: 25998695--25998745 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
25998685 TGCCATAATT
25998695 TCTAGCCATTATTGATATTGAAAACC
1 TCTAGCCATTATTGATATTGAAAACC
25998721 TCTAGCCATTATTGATATTGAAAAC
1 TCTAGCCATTATTGATATTGAAAAC
25998746 AATTTCACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (26 bp):
TCTAGCCATTATTGATATTGAAAACC
Found at i:25999473 original size:32 final size:33
Alignment explanation
Indices: 25999411--25999476 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
25999401 GACAGAACCC
*
25999411 CAAGTTTTTGGGACTCCTGGTTTTTTAAACTCT
1 CAAGCTTTTGGGACTCCTGGTTTTTTAAACTCT
25999444 CAAGCTTTTGGGACTCCTGG-TTTTTAAACTCT
1 CAAGCTTTTGGGACTCCTGGTTTTTTAAACTCT
25999476 C
1 C
25999477 TCTCTCTCTC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.42
Consensus pattern (33 bp):
CAAGCTTTTGGGACTCCTGGTTTTTTAAACTCT
Found at i:25999479 original size:2 final size:2
Alignment explanation
Indices: 25999472--25999506 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
25999462 GGTTTTTAAA
25999472 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
25999507 ATGTCTCCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:26002357 original size:23 final size:23
Alignment explanation
Indices: 26002327--26002381 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
26002317 ATAGTTAACA
26002327 TAAACGAACATGTTCGCGAACGT
1 TAAACGAACATGTTCGCGAACGT
26002350 TAAACGAACATGTTCGCGAACGT
1 TAAACGAACATGTTCGCGAACGT
26002373 TAAACGAAC
1 TAAACGAAC
26002382 GTTAAACGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (23 bp):
TAAACGAACATGTTCGCGAACGT
Found at i:26002382 original size:11 final size:11
Alignment explanation
Indices: 26002343--26002391 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
26002333 AACATGTTCG
26002343 CGAACGTTAAA
1 CGAACGTTAAA
**
26002354 CGAACATGTT-CG
1 CGAAC--GTTAAA
26002366 CGAACGTTAAA
1 CGAACGTTAAA
26002377 CGAACGTTAAA
1 CGAACGTTAAA
26002388 CGAA
1 CGAA
26002392 AATGTTCATG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
10 3 0.10
11 20 0.65
12 5 0.16
13 3 0.10
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.18
Consensus pattern (11 bp):
CGAACGTTAAA
Found at i:26002411 original size:24 final size:23
Alignment explanation
Indices: 26002376--26002504 Score: 125
Period size: 24 Copynumber: 5.5 Consensus size: 23
26002366 CGAACGTTAA
*
26002376 ACGAACGTTAAACGAAAATGTTC
1 ACGAACATTAAACGAAAATGTTC
* * *
26002399 ATGAACATATAAACGAATATGTTG
1 ACGAACAT-TAAACGAAAATGTTC
* * **
26002423 ACGAACGTTAAAC-AAACATATAA
1 ACGAACATTAAACGAAA-ATGTTC
*
26002446 ACGAACGTTAAACGAAAATGTTC
1 ACGAACATTAAACGAAAATGTTC
*
26002469 ACGAACATATAAACGAACATGTTC
1 ACGAACAT-TAAACGAAAATGTTC
*
26002493 ACGAACGTTAAA
1 ACGAACATTAAA
26002505 GGAACGATCA
Statistics
Matches: 86, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
22 2 0.02
23 41 0.48
24 43 0.50
ACGTcount: A:0.47, C:0.16, G:0.15, T:0.22
Consensus pattern (23 bp):
ACGAACATTAAACGAAAATGTTC
Found at i:26002428 original size:58 final size:58
Alignment explanation
Indices: 26002327--26002510 Score: 174
Period size: 70 Copynumber: 3.0 Consensus size: 58
26002317 ATAGTTAACA
* * *
26002327 TAAACGAACATGTTCGCGAACGT-TAAACGAACATGTTCG-CGAACGTTAAACGAACGT
1 TAAACGAAAATGTTCACGAACATATAAACGAACATGTT-GACGAACGTTAAACGAACGT
* *
26002384 TAAACGAAAATGTTCATGAACATATAAACGAATATGTTGACGAACGTTAAACAAACATATAAACG
1 TAAACGAAAATGTTCACGAACATATAAACGAACATGTTGACGAACG-----------T-TAAACG
26002449 AACGT
54 AACGT
* *
26002454 TAAACGAAAATGTTCACGAACATATAAACGAACATGTTCACGAACGTTAAAGGAACG
1 TAAACGAAAATGTTCACGAACATATAAACGAACATGTTGACGAACGTTAAACGAACG
26002511 ATCACGAACA
Statistics
Matches: 104, Mismatches: 9, Indels: 27
0.74 0.06 0.19
Matches are distributed among these distances:
57 20 0.19
58 28 0.27
59 1 0.01
69 1 0.01
70 54 0.52
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.21
Consensus pattern (58 bp):
TAAACGAAAATGTTCACGAACATATAAACGAACATGTTGACGAACGTTAAACGAACGT
Found at i:26002454 original size:70 final size:70
Alignment explanation
Indices: 26002373--26002504 Score: 237
Period size: 70 Copynumber: 1.9 Consensus size: 70
26002363 TCGCGAACGT
* * *
26002373 TAAACGAACGTTAAACGAAAATGTTCATGAACATATAAACGAATATGTTGACGAACGTTAAACAA
1 TAAACGAACGTTAAACGAAAATGTTCACGAACATATAAACGAACATGTTCACGAACGTTAAACAA
26002438 ACATA
66 ACATA
26002443 TAAACGAACGTTAAACGAAAATGTTCACGAACATATAAACGAACATGTTCACGAACGTTAAA
1 TAAACGAACGTTAAACGAAAATGTTCACGAACATATAAACGAACATGTTCACGAACGTTAAA
26002505 GGAACGATCA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 59 1.00
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.22
Consensus pattern (70 bp):
TAAACGAACGTTAAACGAAAATGTTCACGAACATATAAACGAACATGTTCACGAACGTTAAACAA
ACATA
Done.