Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold232
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: 1304497
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.30
Warning! 90120 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:1017553 original size:14 final size:15
Alignment explanation
Indices: 1017504--1017558 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
1017494 AAAAAAAATG
*
1017504 AAAAATGAAAAAAAT
1 AAAAATGAAAAAAGT
* *
1017519 GAAAATGAAAAAATGAA
1 AAAAATGAAAAAA-G-T
1017536 AAAAATG-AAAAAGT
1 AAAAATGAAAAAAGT
1017550 AAAAATGAA
1 AAAAATGAA
1017559 GAAGAGGCTA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
14 7 0.22
15 14 0.44
16 5 0.16
17 6 0.19
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.13
Consensus pattern (15 bp):
AAAAATGAAAAAAGT
Found at i:1048909 original size:129 final size:129
Alignment explanation
Indices: 1048679--1049120 Score: 760
Period size: 129 Copynumber: 3.4 Consensus size: 129
1048669 ACAGTGAAAT
* *
1048679 CACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAA
1 CACAAGTCCTATATCCCTGGTAAGTAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAA
* * *
1048744 GCAGTAGCGGAGCAGATCAAAGACAGCGAATCTTATCTTCAAGTGTAACGAAGCAGATTTAAGC
66 GCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGC
* *
1048808 CACAAGTCCTATATCCCTGGTAAGAAGTGGAATATGTTGGGAAATTACAGATCTTGTCTCCCTAA
1 CACAAGTCCTATATCCCTGGTAAGTAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAA
1048873 GCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGC
66 GCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGC
*
1048937 CACAAGTCCTATATCCCTGGTCAA-TAGTAGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTA
1 CACAAGTCCTATATCCCTGGT-AAGTAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTA
*
1049001 AGCAGTAGCGGAGCAGATCGAAGACGACGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGC
65 AGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGC
* * *
1049066 CACAAGTCCTATATCCCTGGTTAGTAGTGGAATAGGTTGGGAAATTGCAGGTCTT
1 CACAAGTCCTATATCCCTGGTAAGTAGTGGAATAGGTTGGGAAATTACAGATCTT
1049121 ATCCCCCTGA
Statistics
Matches: 297, Mismatches: 14, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
128 1 0.00
129 294 0.99
130 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.25
Consensus pattern (129 bp):
CACAAGTCCTATATCCCTGGTAAGTAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAA
GCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGC
Found at i:1049429 original size:218 final size:217
Alignment explanation
Indices: 1049112--1049529 Score: 710
Period size: 218 Copynumber: 1.9 Consensus size: 217
1049102 TTGGGAAATT
*
1049112 GCAGGTCTTATCCCCCTGAAGTTGCAGTGGGACAGATCGAAGTAGTAAATCTTATCTCCTTGAGG
1 GCAGGTCTTATCCCCCTGAAGTTGCAGTGGGACAGATCGAAGTAGAAAATCTTATCTCCTTGAGG
*
1049177 TTGTAGTGGAGCAAATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTAGCGGAGCGGGTTAAAG
66 TTGTAGTGGAGCAAATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTAGCGGAACGGGTTAAAG
* * * * *
1049242 TAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCATTAGGTCTTATCTCCCTGAGGT
131 TAATAGATCTTATCTCTCTAAAGTTACAGTAGAGTGGATCGCATCAGGTCTTATCCCCCTGAAGT
1049307 TGCAGCGGAGCAGACTGAGTAA
196 TGCAGCGGAGCAGACTGAGTAA
* *
1049329 GCAGGTCTTATCCCCCTGAAGTTTCAGTGGGACAGATCGAAGATGGAAAATCTTATCTCCTTGAG
1 GCAGGTCTTATCCCCCTGAAGTTGCAGTGGGACAGATCGAAG-TAGAAAATCTTATCTCCTTGAG
* * *
1049394 GTTGTAGTGGAGCAGATTGAGGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGAACGGGTTAAA
65 GTTGTAGTGGAGCAAATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTAGCGGAACGGGTTAAA
*
1049459 GTAATAGATCTTATCTCTCTAAAGTTACAGTAGAGTGGATTGCATCAGGTCTTATCCCCCTGAAG
130 GTAATAGATCTTATCTCTCTAAAGTTACAGTAGAGTGGATCGCATCAGGTCTTATCCCCCTGAAG
1049524 TTGCAG
195 TTGCAG
1049530 TGGGATAGAT
Statistics
Matches: 187, Mismatches: 13, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
217 41 0.22
218 146 0.78
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (217 bp):
GCAGGTCTTATCCCCCTGAAGTTGCAGTGGGACAGATCGAAGTAGAAAATCTTATCTCCTTGAGG
TTGTAGTGGAGCAAATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTAGCGGAACGGGTTAAAG
TAATAGATCTTATCTCTCTAAAGTTACAGTAGAGTGGATCGCATCAGGTCTTATCCCCCTGAAGT
TGCAGCGGAGCAGACTGAGTAA
Found at i:1049558 original size:218 final size:217
Alignment explanation
Indices: 1049117--1049576 Score: 692
Period size: 218 Copynumber: 2.1 Consensus size: 217
1049107 AAATTGCAGG
*
1049117 TCTTATCCCCCTGAAGTTGCAGTGGGACAGATCGAAGTAGTAAATCTTATCTCCTTGAGGTTGTA
1 TCTTATCCCCCTGAAGTTGCAGTGGGACAGATCGAAGTAGAAAATCTTATCTCCTTGAGGTTGTA
*
1049182 GTGGAGCAAATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTAGCGGAGCGGGTTAAAGTAATA
66 GTGGAGCAAATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTAGCGGAACGGGTTAAAGTAATA
* * * * *
1049247 GATCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCATTAGGTCTTATCTCCCTGAGGTTGCAG
131 GATCTTATCTCTCTAAAGTTACAGTAGAGTGGATCGCATCAGGTCTTATCCCCCTGAAGTTGCAG
**
1049312 CGGAGCAGACTGAGTAAGCAGG
196 CGGAGCAGACTGAGTAAGCAAA
* *
1049334 TCTTATCCCCCTGAAGTTTCAGTGGGACAGATCGAAGATGGAAAATCTTATCTCCTTGAGGTTGT
1 TCTTATCCCCCTGAAGTTGCAGTGGGACAGATCGAAG-TAGAAAATCTTATCTCCTTGAGGTTGT
* * *
1049399 AGTGGAGCAGATTGAGGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGAACGGGTTAAAGTAAT
65 AGTGGAGCAAATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTAGCGGAACGGGTTAAAGTAAT
*
1049464 AGATCTTATCTCTCTAAAGTTACAGTAGAGTGGATTGCATCAGGTCTTATCCCCCTGAAGTTGCA
130 AGATCTTATCTCTCTAAAGTTACAGTAGAGTGGATCGCATCAGGTCTTATCCCCCTGAAGTTGCA
* *
1049529 GTGG-GATAGA-TCGAAG-AAGCAAA
195 GCGGAG-CAGACT-G-AGTAAGCAAA
* *
1049552 TCTTATCTCCCTGAGGTTGCAGTGG
1 TCTTATCCCCCTGAAGTTGCAGTGG
1049577 AGCAGACTGA
Statistics
Matches: 219, Mismatches: 20, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
217 38 0.17
218 179 0.82
219 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (217 bp):
TCTTATCCCCCTGAAGTTGCAGTGGGACAGATCGAAGTAGAAAATCTTATCTCCTTGAGGTTGTA
GTGGAGCAAATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTAGCGGAACGGGTTAAAGTAATA
GATCTTATCTCTCTAAAGTTACAGTAGAGTGGATCGCATCAGGTCTTATCCCCCTGAAGTTGCAG
CGGAGCAGACTGAGTAAGCAAA
Found at i:1049735 original size:44 final size:44
Alignment explanation
Indices: 1049117--1049967 Score: 390
Period size: 44 Copynumber: 19.5 Consensus size: 44
1049107 AAATTGCAGG
* * * *
1049117 TCTTATCCCCCTGAAGTTGCAGTGG-GACAGATCGAAGTAGTAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAG-CAGATTGAAGTAATAGA
* * * * **
1049161 TCTTATCTCCTTGAGGTTGTAGTGGAGCAAATTGAAGCCGATA-A
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-TAATAGA
* * * * * *
1049205 TCCTATCTCCCTGAAGTTGTAGCGGAGCGGGTTAAAGTAATAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAATAGA
* * ** * * *
1049249 TCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCA-T--TAGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAATAGA
* * * * *
1049290 TCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTG-AGTAAGCAGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAA-TAGA
* * *
1049334 TCTTATCCCCCTGAAGTTTCAGTGG-GACAGATCGAAGATGGAA-A-A
1 TCTTATCTCCCTGAAGTTGCAGTGGAG-CAGATTGAAG-T--AATAGA
* * * * **
1049379 TCTTATCTCCTTGAGGTTGTAGTGGAGCAGATTGAGGCCGATA-A
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-TAATAGA
* * * * * *
1049423 TCCTATCTCCCTGAAGTTGTAGTGGAACGGGTTAAAGTAATAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAATAGA
* * * * ** * * *
1049467 TCTTATCTCTCTAAAGTTACAGTAGAGTGGATTGCA-T--CAGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAATAGA
* * * * *
1049508 TCTTATCCCCCTGAAGTTGCAGTGG-GATAGATCGAAG-AAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAG-CAGATTGAAGTAA-TAGA
* * *
1049552 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTG-AGTAA-ACAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAATA-GA
* ** ** * *
1049595 GTCTTATCCCCCTGAAGTCACAGTAGG-GCAGACCGAAG-AAGCAAA
1 -TCTTATCTCCCTGAAGTTGCAGT-GGAGCAGATTGAAGTAA-TAGA
* * * **
1049640 CCTTATCTCCCTGAGGTTGCAGGGGAGCAGATTGAAGCCGATA-A
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-TAATAGA
* * * *
1049684 TCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAATAGA
* * ** * * * *
1049728 TCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCA-T--CAGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAATAGA
* * * *
1049769 TCTTATCTCCTTGAGGTTGCAGTGGAGCAGACTG-AGTAA-ACAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAATA-GA
* ** ** * *
1049812 GTCTTATCCCCCTGAAGTCACAGTAGG-GCAGACCGAAG-AAGCAAA
1 -TCTTATCTCCCTGAAGTTGCAGT-GGAGCAGATTGAAGTAA-TAGA
* **
1049857 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGATA-A
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-TAATAGA
* * * * *
1049901 TCCTATCTCCTTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAATAGA
*
1049945 TCTTATCTCTCTGAAGTTGCAGT
1 TCTTATCTCCCTGAAGTTGCAGT
1049968 AGAGTGGATC
Statistics
Matches: 598, Mismatches: 164, Indels: 90
0.70 0.19 0.11
Matches are distributed among these distances:
40 3 0.01
41 87 0.15
42 2 0.00
43 25 0.04
44 424 0.71
45 48 0.08
46 7 0.01
48 2 0.00
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAATAGA
Found at i:1049755 original size:261 final size:262
Alignment explanation
Indices: 1049290--1049793 Score: 796
Period size: 261 Copynumber: 1.9 Consensus size: 262
1049280 TCGCATTAGG
* * **
1049290 TCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGTAAGCAGGTCTTATCCCCCTGAAGTTTCA
1 TCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGTAAACAAGTCTTATCCCCCTGAAGTCACA
* * * * * * *
1049355 GTGGGACAGATCGAAGATGGAAAATCTTATCTCCTTGAGGTTGTAGTGGAGCAGATTGAGGCCGA
66 GTGGGACAGACCGAAGATAGAAAACCTTATCTCCCTGAGGTTGCAGGGGAGCAGATTGAAGCCGA
*
1049420 TAATCCTATCTCCCTGAAGTTGTAGTGGAACGGGTTAAAGTAATAGATCTTATCTCTCTAAAGTT
131 TAATCCTATCTCCCTGAAGTTGTAGTGGAACGGATTAAAGTAATAGATCTTATCTCTCTAAAGTT
*
1049485 ACAGTAGAGTGGATTGCATCAGGTCTTATCCCCCTGAAGTTGCAGTGGGATAGATCGAAGAAGCA
196 ACAGTAGAGTGGATCGCATCAGGTCTTATCCCCCTGAAGTTGCAGTGGGATAGATCGAAGAAGCA
1049550 AA
261 AA
*
1049552 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTGAGTAAACAAGTCTTATCCCCCTGAAGTCACA
1 TCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGTAAACAAGTCTTATCCCCCTGAAGTCACA
*
1049617 GTAGGG-CAGACCGAAGA-AGCAAACCTTATCTCCCTGAGGTTGCAGGGGAGCAGATTGAAGCCG
66 GT-GGGACAGACCGAAGATAGAAAACCTTATCTCCCTGAGGTTGCAGGGGAGCAGATTGAAGCCG
* *
1049680 ATAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGT
130 ATAATCCTATCTCCCTGAAGTTGTAGTGGAACGGATTAAAGTAATAGATCTTATCTCTCTAAAGT
* * * *
1049745 TGCAGTAGAGTGGATCGCATCAGGTCTTATCTCCTTGAGGTTGCAGTGG
195 TACAGTAGAGTGGATCGCATCAGGTCTTATCCCCCTGAAGTTGCAGTGG
1049794 AGCAGACTGA
Statistics
Matches: 220, Mismatches: 21, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
261 145 0.66
262 72 0.33
263 3 0.01
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (262 bp):
TCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGTAAACAAGTCTTATCCCCCTGAAGTCACA
GTGGGACAGACCGAAGATAGAAAACCTTATCTCCCTGAGGTTGCAGGGGAGCAGATTGAAGCCGA
TAATCCTATCTCCCTGAAGTTGTAGTGGAACGGATTAAAGTAATAGATCTTATCTCTCTAAAGTT
ACAGTAGAGTGGATCGCATCAGGTCTTATCCCCCTGAAGTTGCAGTGGGATAGATCGAAGAAGCA
AA
Found at i:1049795 original size:217 final size:217
Alignment explanation
Indices: 1049552--1050046 Score: 909
Period size: 217 Copynumber: 2.3 Consensus size: 217
1049542 AAGAAGCAAA
1049552 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTGAGTAAACAAGTCTTATCCCCCTGAAGTCACA
1 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTGAGTAAACAAGTCTTATCCCCCTGAAGTCACA
1049617 GTAGGGCAGACCGAAGAAGCAAACCTTATCTCCCTGAGGTTGCAGGGGAGCAGATTGAAGCCGAT
66 GTAGGGCAGACCGAAGAAGCAAACCTTATCTCCCTGAGGTTGCAGGGGAGCAGATTGAAGCCGAT
1049682 AATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTG
131 AATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTG
1049747 CAGTAGAGTGGATCGCATCAGG
196 CAGTAGAGTGGATCGCATCAGG
*
1049769 TCTTATCTCCTTGAGGTTGCAGTGGAGCAGACTGAGTAAACAAGTCTTATCCCCCTGAAGTCACA
1 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTGAGTAAACAAGTCTTATCCCCCTGAAGTCACA
* *
1049834 GTAGGGCAGACCGAAGAAGCAAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGAT
66 GTAGGGCAGACCGAAGAAGCAAACCTTATCTCCCTGAGGTTGCAGGGGAGCAGATTGAAGCCGAT
*
1049899 AATCCTATCTCCTTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTG
131 AATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTG
1049964 CAGTAGAGTGGATCGCATCAGG
196 CAGTAGAGTGGATCGCATCAGG
* * * * *
1049986 TCTTGTCTCCCTGAGGTTGCAATGCAGCAGACTAAGAAAACAAGTCTTATCCCCCTGAAGT
1 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTGAGTAAACAAGTCTTATCCCCCTGAAGT
1050047 TTGATGTGAC
Statistics
Matches: 268, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
217 268 1.00
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (217 bp):
TCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTGAGTAAACAAGTCTTATCCCCCTGAAGTCACA
GTAGGGCAGACCGAAGAAGCAAACCTTATCTCCCTGAGGTTGCAGGGGAGCAGATTGAAGCCGAT
AATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTG
CAGTAGAGTGGATCGCATCAGG
Found at i:1049863 original size:261 final size:262
Alignment explanation
Indices: 1049290--1049870 Score: 717
Period size: 261 Copynumber: 2.2 Consensus size: 262
1049280 TCGCATTAGG
* * ** * * * ** **
1049290 TCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGTAAGCAGGTCTTATCCCCCTGAAGTTTCA
1 TCTTATCCCCCTGAAGTCACAGTGGAGCAGACCGAGTAAACAAATCTTATCCCCCTGAAGTCACA
* * * * * * *
1049355 GTGGGACAGATCGAAGATGGAAAATCTTATCTCCTTGAGGTTGTAGTGGAGCAGATTGAGGCCGA
66 GTGGGACAGACCGAAGATAGAAAACCTTATCTCCCTGAGGTTGCAGGGGAGCAGATTGAAGCCGA
*
1049420 TAATCCTATCTCCCTGAAGTTGTAGTGGAACGGGTTAAAGTAATAGATCTTATCTCTCTAAAGTT
131 TAATCCTATCTCCCTGAAGTTGTAGTGGAACGGATTAAAGTAATAGATCTTATCTCTCTAAAGTT
* * *
1049485 ACAGTAGAGTGGATTGCATCAGGTCTTATCCCCCTGAAGTTGCAGTGGGATAGATCGAAGAAGCA
196 ACAGTAGAGTGGATCGCATCAGGTCTTATCCCCCTGAAGTTGCAGTGGGACAGATCGAAGAAACA
1049550 AA
261 AA
* * ** * *
1049552 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTGAGTAAACAAGTCTTATCCCCCTGAAGTCACA
1 TCTTATCCCCCTGAAGTCACAGTGGAGCAGACCGAGTAAACAAATCTTATCCCCCTGAAGTCACA
*
1049617 GTAGGG-CAGACCGAAGA-AGCAAACCTTATCTCCCTGAGGTTGCAGGGGAGCAGATTGAAGCCG
66 GT-GGGACAGACCGAAGATAGAAAACCTTATCTCCCTGAGGTTGCAGGGGAGCAGATTGAAGCCG
* *
1049680 ATAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGT
130 ATAATCCTATCTCCCTGAAGTTGTAGTGGAACGGATTAAAGTAATAGATCTTATCTCTCTAAAGT
* * * *
1049745 TGCAGTAGAGTGGATCGCATCAGGTCTTATCTCCTTGAGGTTGCAGT-GGAGCAGA-CTG-AGTA
195 TACAGTAGAGTGGATCGCATCAGGTCTTATCCCCCTGAAGTTGCAGTGGGA-CAGATC-GAAG-A
*
1049807 AACAAG
257 AACAAA
* *
1049813 TCTTATCCCCCTGAAGTCACAGTAGG-GCAGACCGAAG-AAGCAAATCTTATCTCCCTGA
1 TCTTATCCCCCTGAAGTCACAGT-GGAGCAGACCG-AGTAAACAAATCTTATCCCCCTGA
1049871 GGTTGCAGTG
Statistics
Matches: 281, Mismatches: 32, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
260 6 0.02
261 196 0.70
262 76 0.27
263 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (262 bp):
TCTTATCCCCCTGAAGTCACAGTGGAGCAGACCGAGTAAACAAATCTTATCCCCCTGAAGTCACA
GTGGGACAGACCGAAGATAGAAAACCTTATCTCCCTGAGGTTGCAGGGGAGCAGATTGAAGCCGA
TAATCCTATCTCCCTGAAGTTGTAGTGGAACGGATTAAAGTAATAGATCTTATCTCTCTAAAGTT
ACAGTAGAGTGGATCGCATCAGGTCTTATCCCCCTGAAGTTGCAGTGGGACAGATCGAAGAAACA
AA
Found at i:1063073 original size:21 final size:21
Alignment explanation
Indices: 1063047--1063093 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1063037 ACTCTAAATT
1063047 GTGTGTCAGATAATTCTTTTC
1 GTGTGTCAGATAATTCTTTTC
*
1063068 GTGTGTCGGATAATTCTTTTC
1 GTGTGTCAGATAATTCTTTTC
1063089 GTGTG
1 GTGTG
1063094 GTTTCAACTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.47
Consensus pattern (21 bp):
GTGTGTCAGATAATTCTTTTC
Found at i:1065489 original size:18 final size:19
Alignment explanation
Indices: 1065463--1065499 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1065453 AATTTTGGAA
*
1065463 TGGATAGAAGAGA-GAAAG
1 TGGAAAGAAGAGAGGAAAG
1065481 TGGAAAGAAGAGAGGAAAG
1 TGGAAAGAAGAGAGGAAAG
1065500 ATGTGAATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.41, T:0.08
Consensus pattern (19 bp):
TGGAAAGAAGAGAGGAAAG
Found at i:1068956 original size:22 final size:22
Alignment explanation
Indices: 1068929--1068971 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1068919 ATTAGATAGT
1068929 TAAATTAAAATTTACGAGAAAC
1 TAAATTAAAATTTACGAGAAAC
*
1068951 TAAATTAAAATTTAGGAGAAA
1 TAAATTAAAATTTACGAGAAA
1068972 AATTGGTCTT
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:0.56, C:0.05, G:0.12, T:0.28
Consensus pattern (22 bp):
TAAATTAAAATTTACGAGAAAC
Found at i:1073179 original size:50 final size:51
Alignment explanation
Indices: 1072993--1073183 Score: 158
Period size: 50 Copynumber: 3.8 Consensus size: 51
1072983 GATAATAACA
* * * **
1072993 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA--TGTTTTCT-GTAC
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCG-AC
* * * * * ** * *
1073042 TGCCAATGTCATATCCCAAATATTGTCTTACATTGGAGTTCTCATATC-AG
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGAC
* * * **
1073092 TGCCCATTCTATGTCCCAAACATGGTCTTACGGGGGACCTCTCATCTCGA-
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGAC
*
1073142 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCT
1073184 TTACCCAAAT
Statistics
Matches: 107, Mismatches: 31, Indels: 7
0.74 0.21 0.05
Matches are distributed among these distances:
49 30 0.28
50 72 0.67
51 5 0.05
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.30
Consensus pattern (51 bp):
TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGAC
Found at i:1073551 original size:30 final size:30
Alignment explanation
Indices: 1073516--1073573 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1073506 TTCTTGACTC
*
1073516 AATTTTGGCAAAATTACAGTTTTGCCCCTA
1 AATTTTGGCAAAATTACACTTTTGCCCCTA
* * *
1073546 AATTTTTGCATATTTACACTTTTGCCCC
1 AATTTTGGCAAAATTACACTTTTGCCCC
1073574 AAAGCTCGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.41
Consensus pattern (30 bp):
AATTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:1080642 original size:50 final size:50
Alignment explanation
Indices: 1080518--1080703 Score: 198
Period size: 50 Copynumber: 3.7 Consensus size: 50
1080508 GATAATAACA
* * * *
1080518 TGCCAAAGCCATGTCCCAGACATGGTCTTATATGGGATGTTTTC-TGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATAT-CGG
* * *
1080567 TGCCAATGCCATATCCCAGATATGGTCTTACATTGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
* * ** ** *
1080617 TGCCCATGCTATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
*
1080667 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1080704 CCTCTTTACC
Statistics
Matches: 112, Mismatches: 22, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
48 6 0.05
49 34 0.30
50 72 0.64
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
Found at i:1093487 original size:7 final size:7
Alignment explanation
Indices: 1093456--1093520 Score: 51
Period size: 7 Copynumber: 9.1 Consensus size: 7
1093446 ACCAATTAAT
1093456 CTAAACCC
1 CTAAA-CC
1093464 CT-AACC
1 CTAAACC
*
1093470 CTAATCTC
1 CTAAAC-C
1093478 CTAAACC
1 CTAAACC
*
1093485 CTAAATC
1 CTAAACC
* *
1093492 ATAAAAC
1 CTAAACC
*
1093499 ATAAACC
1 CTAAACC
*
1093506 CTAACCC
1 CTAAACC
1093513 CTAAACC
1 CTAAACC
1093520 C
1 C
1093521 ATGACCCCTA
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
6 4 0.09
7 34 0.74
8 8 0.17
ACGTcount: A:0.42, C:0.40, G:0.00, T:0.18
Consensus pattern (7 bp):
CTAAACC
Found at i:1093933 original size:14 final size:14
Alignment explanation
Indices: 1093916--1093960 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
1093906 TCTTAACCTC
1093916 TAACCCCTAACCCT
1 TAACCCCTAACCCT
*
1093930 TAACCCCTAAACCT
1 TAACCCCTAACCCT
*
1093944 TAAATCCC-AACCCT
1 T-AACCCCTAACCCT
1093958 TAA
1 TAA
1093961 ACCATAATCC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 2 0.07
14 20 0.74
15 5 0.19
ACGTcount: A:0.36, C:0.42, G:0.00, T:0.22
Consensus pattern (14 bp):
TAACCCCTAACCCT
Found at i:1093955 original size:21 final size:21
Alignment explanation
Indices: 1093931--1094011 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
1093921 CCTAACCCTT
*
1093931 AACCCCTAAACCTTAAATCCC
1 AACCCTTAAACCTTAAATCCC
*
1093952 AACCCTTAAACCAT-AATCCC
1 AACCCTTAAACCTTAAATCCC
* * * *
1093972 TAATCCATAATCCCTAAAT-CC
1 -AACCCTTAAACCTTAAATCCC
1093993 ATACTCCTTAAACCTTAAA
1 A-AC-CCTTAAACCTTAAA
1094012 ATATGAACTC
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
20 7 0.15
21 25 0.54
22 14 0.30
ACGTcount: A:0.40, C:0.36, G:0.00, T:0.25
Consensus pattern (21 bp):
AACCCTTAAACCTTAAATCCC
Found at i:1094004 original size:15 final size:15
Alignment explanation
Indices: 1093941--1094004 Score: 62
Period size: 14 Copynumber: 4.5 Consensus size: 15
1093931 AACCCCTAAA
* *
1093941 CCTTAAATCC-CAAC
1 CCTTAAATCCATAAT
1093955 CCTTAAA-CCATAAT
1 CCTTAAATCCATAAT
*
1093969 CCCT-AATCCATAAT
1 CCTTAAATCCATAAT
* *
1093983 CCCTAAATCCATACT
1 CCTTAAATCCATAAT
1093998 CCTTAAA
1 CCTTAAA
1094005 CCTTAAAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
13 4 0.10
14 23 0.55
15 15 0.36
ACGTcount: A:0.38, C:0.36, G:0.00, T:0.27
Consensus pattern (15 bp):
CCTTAAATCCATAAT
Found at i:1094172 original size:8 final size:7
Alignment explanation
Indices: 1094147--1094265 Score: 57
Period size: 7 Copynumber: 16.7 Consensus size: 7
1094137 AATAATTAAT
1094147 CTAAACC
1 CTAAACC
1094154 CTAAACC
1 CTAAACC
1094161 CTAAATCC
1 CTAAA-CC
1094169 CT-AACTC
1 CTAAAC-C
* *
1094176 TTAACCC
1 CTAAACC
***
1094183 CTAATGT
1 CTAAACC
1094190 CT-AACC
1 CTAAACC
1094196 CTTAAACC
1 C-TAAACC
1094204 TCTAAACC
1 -CTAAACC
1094212 CTAAACC
1 CTAAACC
*
1094219 TTAAATCC
1 CTAAA-CC
1094227 C--AACC
1 CTAAACC
1094232 CTTAAACC
1 C-TAAACC
* *
1094240 ATAATCC
1 CTAAACC
*
1094247 CTAATCC
1 CTAAACC
* *
1094254 ATAATCC
1 CTAAACC
1094261 CTAAA
1 CTAAA
1094266 TCCATACTCC
Statistics
Matches: 85, Mismatches: 17, Indels: 20
0.70 0.14 0.16
Matches are distributed among these distances:
5 3 0.04
6 5 0.06
7 54 0.64
8 22 0.26
9 1 0.01
ACGTcount: A:0.38, C:0.37, G:0.01, T:0.24
Consensus pattern (7 bp):
CTAAACC
Found at i:1094255 original size:14 final size:14
Alignment explanation
Indices: 1094238--1094279 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
1094228 AACCCTTAAA
1094238 CCATAATCCCTAAT
1 CCATAATCCCTAAT
1094252 CCATAATCCCTAAAT
1 CCATAATCCCT-AAT
*
1094267 CCATACTCCCTAA
1 CCATAATCCCTAA
1094280 ACCTTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.36, C:0.38, G:0.00, T:0.26
Consensus pattern (14 bp):
CCATAATCCCTAAT
Found at i:1094269 original size:15 final size:15
Alignment explanation
Indices: 1094234--1094280 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
1094224 TCCCAACCCT
1094234 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
1094248 T-AATCCATAATCCC
1 TAAATCCATAATCCC
*
1094262 TAAATCCATACTCCC
1 TAAATCCATAATCCC
1094277 TAAA
1 TAAA
1094281 CCTTAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 2 0.07
14 12 0.40
15 16 0.53
ACGTcount: A:0.40, C:0.34, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:1094518 original size:23 final size:25
Alignment explanation
Indices: 1094491--1094545 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
1094481 TAAATGATAG
*
1094491 TATTTTAATT-TTTCCATGTGT-TT
1 TATTTTAATTATTTCCATGTGTCAT
* *
1094514 TATTTCAAATTATTTCTATGTGTCAT
1 TATTT-TAATTATTTCCATGTGTCAT
1094540 TATTTT
1 TATTTT
1094546 GTTCTGAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 5 0.20
24 4 0.16
25 10 0.40
26 6 0.24
ACGTcount: A:0.22, C:0.09, G:0.07, T:0.62
Consensus pattern (25 bp):
TATTTTAATTATTTCCATGTGTCAT
Found at i:1094731 original size:41 final size:40
Alignment explanation
Indices: 1094630--1094864 Score: 238
Period size: 41 Copynumber: 5.8 Consensus size: 40
1094620 TAAAATGTTT
* * * * * *
1094630 TTAGTGGCGCTTTTTCAAAAACGCCACTAAAGCCCCAACA
1 TTAGCGGCGCTTTTTAAAAAACGCCGCTAAAACCCGAGCA
** * * *
1094670 TTAGCGGCGCTTTTCCAAAAATGCTGCTAAAGCCCTGAGCA
1 TTAGCGGCGCTTTTTAAAAAACGCCGCTAAAACCC-GAGCA
* *
1094711 TTAGTGGCGCTTTCTAAAAAACGCCGCTAAAACCCCGAGCA
1 TTAGCGGCGCTTTTTAAAAAACGCCGCTAAAA-CCCGAGCA
* * *
1094752 TTAGTGGTGCTTTCTAAAAAACGCCGCTAAAACCCCGAGCA
1 TTAGCGGCGCTTTTTAAAAAACGCCGCTAAAA-CCCGAGCA
*
1094793 TTAGCGGC-ATTTTTAAAAAAACGCCGCTAAAACACCGAGCA
1 TTAGCGGCGCTTTTT-AAAAAACGCCGCTAAAAC-CCGAGCA
* * *
1094834 TTAGCGGCGCTTTTTTAAAAATGCTGCTAAA
1 TTAGCGGCGCTTTTTAAAAAACGCCGCTAAA
1094865 GCCCCTAGCA
Statistics
Matches: 167, Mismatches: 23, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
40 35 0.21
41 124 0.74
42 8 0.05
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (40 bp):
TTAGCGGCGCTTTTTAAAAAACGCCGCTAAAACCCGAGCA
Found at i:1094812 original size:82 final size:81
Alignment explanation
Indices: 1094646--1094874 Score: 264
Period size: 82 Copynumber: 2.8 Consensus size: 81
1094636 GCGCTTTTTC
* * * * *
1094646 AAAAACGCCACTAAAGCCCC-AACATTAGCGGCGCTTTTCCAAAAATGCTGCTAAAGCCCTGAGC
1 AAAAACGCCGCTAAAACCCCGAGCATTAGCGGCGCTTTT-AAAAAATGCTGCTAAAGCCCCGAGC
* *
1094710 ATTAGTGGCGCTTTCTA
65 ATTAGCGGCGATTTCTA
* * * * *
1094727 AAAAACGCCGCTAAAACCCCGAGCATTAGTGGTGCTTTCTAAAAAACGCCGCTAAAACCCCGAGC
1 AAAAACGCCGCTAAAACCCCGAGCATTAGCGGCGCTTT-TAAAAAATGCTGCTAAAGCCCCGAGC
*
1094792 ATTAGCGGC-ATTTTTAA
65 ATTAGCGGCGATTTCT-A
* * *
1094809 AAAAACGCCGCTAAAACACCGAGCATTAGCGGCGCTTTTTTAAAAATGCTGCTAAAGCCCCTAGC
1 AAAAACGCCGCTAAAACCCCGAGCATTAGCGGCGC-TTTTAAAAAATGCTGCTAAAGCCCCGAGC
1094874 A
65 A
1094875 CAAAAACGCC
Statistics
Matches: 123, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
81 22 0.18
82 97 0.79
83 4 0.03
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (81 bp):
AAAAACGCCGCTAAAACCCCGAGCATTAGCGGCGCTTTTAAAAAATGCTGCTAAAGCCCCGAGCA
TTAGCGGCGATTTCTA
Found at i:1094880 original size:26 final size:26
Alignment explanation
Indices: 1094850--1094900 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
1094840 GCGCTTTTTT
* * * *
1094850 AAAAATGCTGCTAAAGCCCCTAGCAC
1 AAAAACGCCGCTAAAACCCCCAGCAC
1094876 AAAAACGCCGCTAAAACCCCCAGCA
1 AAAAACGCCGCTAAAACCCCCAGCA
1094901 TTAGCGACGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.41, C:0.35, G:0.14, T:0.10
Consensus pattern (26 bp):
AAAAACGCCGCTAAAACCCCCAGCAC
Found at i:1094921 original size:41 final size:41
Alignment explanation
Indices: 1094875--1095061 Score: 203
Period size: 41 Copynumber: 4.6 Consensus size: 41
1094865 GCCCCTAGCA
* *
1094875 CAAAAACGCCGCTAAAACCCCCAGCATTAGCGACGCTTTTT
1 CAAAAACGCCGCTAAAACCCCGAGCATTAGCGGCGCTTTTT
* * * * *
1094916 AAAAAATGCTGCTAAAACACCGAACATTAGCGGCGCTTTTT
1 CAAAAACGCCGCTAAAACCCCGAGCATTAGCGGCGCTTTTT
* * * * *
1094957 CAAAAACACCGTTAAAACCCCAAGCATTAGAGGCGCATTTT
1 CAAAAACGCCGCTAAAACCCCGAGCATTAGCGGCGCTTTTT
* * *
1094998 CAAAAACGCAGCTAAAGCCCCGAGCATTAGCTGCGCTTTTT
1 CAAAAACGCCGCTAAAACCCCGAGCATTAGCGGCGCTTTTT
** * *
1095039 TGAAAACGCCGCCAAAGCCCCGA
1 CAAAAACGCCGCTAAAACCCCGA
1095062 AAGGTAAGAA
Statistics
Matches: 117, Mismatches: 29, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 117 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.19
Consensus pattern (41 bp):
CAAAAACGCCGCTAAAACCCCGAGCATTAGCGGCGCTTTTT
Found at i:1094962 original size:108 final size:108
Alignment explanation
Indices: 1094768--1094962 Score: 313
Period size: 108 Copynumber: 1.8 Consensus size: 108
1094758 GTGCTTTCTA
* *
1094768 AAAAACGCCGCTAAAACCCCGAGCATTAGCGGCATTTTTAAAAAAACGCCGCTAAAACACCGAGC
1 AAAAACGCCGCTAAAACCCCCAGCATTAGCGGCATTTTTAAAAAAACGCCGCTAAAACACCGAAC
*
1094833 ATTAGCGGCGCTTTTTTAAAAATGCTGCTAAAGCCCCTAGCAC
66 ATTAGCGGCGCTTTTTCAAAAATGCTGCTAAAGCCCCTAGCAC
* *
1094876 AAAAACGCCGCTAAAACCCCCAGCATTAGCGACGC-TTTTT-AAAAAATGCTGCTAAAACACCGA
1 AAAAACGCCGCTAAAACCCCCAGCATTAGCG--GCATTTTTAAAAAAACGCCGCTAAAACACCGA
1094939 ACATTAGCGGCGCTTTTTCAAAAA
64 ACATTAGCGGCGCTTTTTCAAAAA
1094963 CACCGTTAAA
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
108 73 0.91
109 5 0.06
110 2 0.03
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.20
Consensus pattern (108 bp):
AAAAACGCCGCTAAAACCCCCAGCATTAGCGGCATTTTTAAAAAAACGCCGCTAAAACACCGAAC
ATTAGCGGCGCTTTTTCAAAAATGCTGCTAAAGCCCCTAGCAC
Found at i:1095003 original size:149 final size:149
Alignment explanation
Indices: 1094727--1095023 Score: 389
Period size: 149 Copynumber: 2.0 Consensus size: 149
1094717 GCGCTTTCTA
* * ** * *
1094727 AAAAACGCCGCTAAAACCCCGAGCATTAGTGGTGCTTTCTAAAAAACGCCGCTAAAACCCCGAGC
1 AAAAACGCCGCTAAAACCCCCAGCATTAGCGACGCTTTCTAAAAAACGCCGCTAAAACACCGAAC
* * * * * *
1094792 ATTAGCGGCATTTTTAAAAAAACGCCGCTAAAACACCGAGCATTAGCGGCGCTTTTTTAAAAATG
66 ATTAGCGGCATTTTTAAAAAAACACCGCTAAAACACCAAGCATTAGAGGCGCATTTTCAAAAACG
* *
1094857 CTGCTAAAGCCCCTAGCAC
131 CAGCTAAAGCCCCGAGCAC
* * *
1094876 AAAAACGCCGCTAAAACCCCCAGCATTAGCGACGCTTTTTAAAAAATGCTGCTAAAACACCGAAC
1 AAAAACGCCGCTAAAACCCCCAGCATTAGCGACGCTTTCTAAAAAACGCCGCTAAAACACCGAAC
* * * *
1094941 ATTAGCGGCGCTTTTT-CAAAAACACCGTTAAAACCCCAAGCATTAGAGGCGCATTTTCAAAAAC
66 ATTAGCGGC-ATTTTTAAAAAAACACCGCTAAAACACCAAGCATTAGAGGCGCATTTTCAAAAAC
1095005 GCAGCTAAAGCCCCGAGCA
130 GCAGCTAAAGCCCCGAGCA
1095024 TTAGCTGCGC
Statistics
Matches: 126, Mismatches: 21, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
149 121 0.96
150 5 0.04
ACGTcount: A:0.36, C:0.28, G:0.17, T:0.19
Consensus pattern (149 bp):
AAAAACGCCGCTAAAACCCCCAGCATTAGCGACGCTTTCTAAAAAACGCCGCTAAAACACCGAAC
ATTAGCGGCATTTTTAAAAAAACACCGCTAAAACACCAAGCATTAGAGGCGCATTTTCAAAAACG
CAGCTAAAGCCCCGAGCAC
Found at i:1095036 original size:190 final size:190
Alignment explanation
Indices: 1094707--1095059 Score: 458
Period size: 190 Copynumber: 1.9 Consensus size: 190
1094697 TAAAGCCCTG
* * * * * *
1094707 AGCATTAGTGGCGCTTTCTAAAAAACGCCGCTAAAACCCCGAGCATTAGTGGTGCTTTCTAAAAA
1 AGCATTAGCGACGCTTTCTAAAAAACGCCGCTAAAACACCGAACATTAGCGGCGCTTTCTAAAAA
* * *
1094772 ACGCCGCTAAAACCCCGAGCATTAGCGGCATTTTTAAAAAAACGCCGCTAAAACACCGAGCATTA
66 ACACCGCTAAAACCCCAAGCATTAGCGGCATTTTTAAAAAAACGCAGCTAAAACACCGAGCATTA
* * *
1094837 GCGGCGCTTTTTTAAAAATGCTGCTAAAGCCCCTAGCACAAAAACGCCGCTAAAACCCCC
131 GCGGCGCTTTTTTAAAAACGCCGCCAAAGCCCCTAGCACAAAAACGCCGCTAAAACCCCC
* * * * *
1094897 AGCATTAGCGACGCTTTTTAAAAAATGCTGCTAAAACACCGAACATTAGCGGCGCTTTTTCAAAA
1 AGCATTAGCGACGCTTTCTAAAAAACGCCGCTAAAACACCGAACATTAGCGGCGCTTTCTAAAAA
* * * * *
1094962 ACACCGTTAAAACCCCAAGCATTAGAGGCGCA-TTTT-CAAAAACGCAGCTAAAGCCCCGAGCAT
66 ACACCGCTAAAACCCCAAGCATTAG-CG-GCATTTTTAAAAAAACGCAGCTAAAACACCGAGCAT
* *
1095025 TAGCTGCGCTTTTTTGAAAACGCCGCCAAAGCCCC
129 TAGCGGCGCTTTTTTAAAAACGCCGCCAAAGCCCC
1095060 GAAAGGTAAG
Statistics
Matches: 137, Mismatches: 24, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
190 129 0.94
191 5 0.04
192 3 0.02
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (190 bp):
AGCATTAGCGACGCTTTCTAAAAAACGCCGCTAAAACACCGAACATTAGCGGCGCTTTCTAAAAA
ACACCGCTAAAACCCCAAGCATTAGCGGCATTTTTAAAAAAACGCAGCTAAAACACCGAGCATTA
GCGGCGCTTTTTTAAAAACGCCGCCAAAGCCCCTAGCACAAAAACGCCGCTAAAACCCCC
Found at i:1095190 original size:40 final size:40
Alignment explanation
Indices: 1095106--1095218 Score: 129
Period size: 40 Copynumber: 2.8 Consensus size: 40
1095096 TTTGTGGCAT
** * * *
1095106 TTTTCTAAAAAACACCGCGAATGCTC-ATTTTTAGCGGCGT
1 TTTTC-AAAAAATGCCGCTAATGCTCGATTTTTAGCGCCGA
* *
1095146 TTTTCAAAAAATGCCGCTAATGCTCGATCTTTAGTGCCGA
1 TTTTCAAAAAATGCCGCTAATGCTCGATTTTTAGCGCCGA
* *
1095186 TTTTCATAAAGTGCCGCTAATGCTCGATTTTTA
1 TTTTCAAAAAATGCCGCTAATGCTCGATTTTTA
1095219 TTGGCATTGT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
39 17 0.27
40 45 0.73
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (40 bp):
TTTTCAAAAAATGCCGCTAATGCTCGATTTTTAGCGCCGA
Found at i:1118401 original size:18 final size:18
Alignment explanation
Indices: 1118378--1118415 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1118368 TCACTGCCTA
1118378 ACGAATATGCCACATTTG
1 ACGAATATGCCACATTTG
1118396 ACGAATATGCCACATTTG
1 ACGAATATGCCACATTTG
1118414 AC
1 AC
1118416 ACCTCAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (18 bp):
ACGAATATGCCACATTTG
Found at i:1119037 original size:3 final size:3
Alignment explanation
Indices: 1119029--1119068 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
1119019 TTGAAAAAGG
* * *
1119029 TTC TTC TTC ATC TTA TTC TTC TTA TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1119069 GTAAATGTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.07, C:0.28, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:1133671 original size:40 final size:40
Alignment explanation
Indices: 1133627--1133816 Score: 200
Period size: 40 Copynumber: 4.8 Consensus size: 40
1133617 AATTATTGAA
* *
1133627 TGAATGCACATATGTGCCCCTGTTTGTACTTCGGTACCCC
1 TGAATGCACATACGTGCCCCTGTTTATACTTCGGTACCCC
*
1133667 TGAATGCACATACGTGCCCCTGTTTATACTGCGGTACCCC
1 TGAATGCACATACGTGCCCCTGTTTATACTTCGGTACCCC
* ** * *
1133707 TTAATGCACATATATGCCCATGTTTATACTTCAGTACCCC
1 TGAATGCACATACGTGCCCCTGTTTATACTTCGGTACCCC
* ** * ** * * *
1133747 TAAAAACACATACGTGTCGTTGTTTGTGCTTCGGTACCCT
1 TGAATGCACATACGTGCCCCTGTTTATACTTCGGTACCCC
* * *
1133787 TGAATGCACTTTCGTGCCCCTATTTATACT
1 TGAATGCACATACGTGCCCCTGTTTATACT
1133817 CTGGTAACTC
Statistics
Matches: 118, Mismatches: 32, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
40 118 1.00
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.34
Consensus pattern (40 bp):
TGAATGCACATACGTGCCCCTGTTTATACTTCGGTACCCC
Found at i:1133686 original size:20 final size:20
Alignment explanation
Indices: 1133627--1133688 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
1133617 AATTATTGAA
*
1133627 TGAATGCACATATGTGCCCC
1 TGAATGCACATACGTGCCCC
** * * *
1133647 TGTTTGTAC-TTCGGTACCCC
1 TGAATGCACATAC-GTGCCCC
1133667 TGAATGCACATACGTGCCCC
1 TGAATGCACATACGTGCCCC
1133687 TG
1 TG
1133689 TTTATACTGC
Statistics
Matches: 29, Mismatches: 11, Indels: 4
0.66 0.25 0.09
Matches are distributed among these distances:
19 1 0.03
20 26 0.90
21 2 0.07
ACGTcount: A:0.19, C:0.31, G:0.21, T:0.29
Consensus pattern (20 bp):
TGAATGCACATACGTGCCCC
Found at i:1140805 original size:40 final size:40
Alignment explanation
Indices: 1140750--1140859 Score: 150
Period size: 40 Copynumber: 2.8 Consensus size: 40
1140740 TTATAGAATG
1140750 AATGCACATATGTGCCCCTATTTGTACTTCAGTACCCCTA
1 AATGCACATATGTGCCCCTATTTGTACTTCAGTACCCCTA
*
1140790 AATGCACATATGTGCCCCTATTTGTA-TTGCGGTACCCCTA
1 AATGCACATATGTGCCCCTATTTGTACTT-CAGTACCCCTA
* * * * *
1140830 GATGCACTTACGTACCCCTATTTATACTTC
1 AATGCACATATGTGCCCCTATTTGTACTTC
1140860 GATAACTTTG
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
39 2 0.03
40 58 0.94
41 2 0.03
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.34
Consensus pattern (40 bp):
AATGCACATATGTGCCCCTATTTGTACTTCAGTACCCCTA
Found at i:1142282 original size:20 final size:22
Alignment explanation
Indices: 1142257--1142297 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1142247 ATTAATGTTA
1142257 ATAAAAT-TAA-TATATATTAT
1 ATAAAATATAAGTATATATTAT
1142277 ATAAAATATAAGTATATATTA
1 ATAAAATATAAGTATATATTA
1142298 GTTGTTATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.37
21 3 0.16
22 9 0.47
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
ATAAAATATAAGTATATATTAT
Found at i:1142397 original size:32 final size:32
Alignment explanation
Indices: 1142356--1142419 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
1142346 TAGCTATTTA
*
1142356 AAAATAATTAGAGAGAT-GAAAGTTTGTTAATT
1 AAAATAATTAGAGAGATAG-AAGTTTGTAAATT
*
1142388 AAAATAATTAGGGAGATAGAAGTTTGTAAATT
1 AAAATAATTAGAGAGATAGAAGTTTGTAAATT
1142420 TTTTGTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 28 0.97
33 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (32 bp):
AAAATAATTAGAGAGATAGAAGTTTGTAAATT
Found at i:1150535 original size:35 final size:34
Alignment explanation
Indices: 1150456--1150570 Score: 101
Period size: 35 Copynumber: 3.3 Consensus size: 34
1150446 TTTTGCTCTG
* *
1150456 CTTAGTTTTATTCCCAAATC-ATA-TCCTCAAATTCC
1 CTTAATTTT-TTCCCAAA-CAATACTCCCCAAA-TCC
* **
1150491 CTTATTTTTTTCCTCTAAA-AATTTTCCCCAAATCC
1 CTTAATTTTTTCC-C-AAACAATACTCCCCAAATCC
1150526 CTTAATTTTTTCCCAAATCAATACTCCCCAAATCC
1 CTTAATTTTTTCCCAAA-CAATACTCCCCAAATCC
1150561 CTTAGATTTT
1 CTTA-ATTTT
1150571 CCCCAACTGT
Statistics
Matches: 67, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
33 3 0.04
34 5 0.07
35 44 0.66
36 15 0.22
ACGTcount: A:0.28, C:0.29, G:0.02, T:0.42
Consensus pattern (34 bp):
CTTAATTTTTTCCCAAACAATACTCCCCAAATCC
Found at i:1150642 original size:25 final size:25
Alignment explanation
Indices: 1150614--1150688 Score: 105
Period size: 25 Copynumber: 3.0 Consensus size: 25
1150604 ACCTCTATTG
* * *
1150614 CATCGCCGTCAACACTCCTCTGCCC
1 CATCACCGTCGACACTCCTCTACCC
**
1150639 CATCACCGTCGACACTCCTCTACTG
1 CATCACCGTCGACACTCCTCTACCC
1150664 CATCACCGTCGACACTCCTCTACCC
1 CATCACCGTCGACACTCCTCTACCC
1150689 TGAAACAGCA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.19, C:0.49, G:0.11, T:0.21
Consensus pattern (25 bp):
CATCACCGTCGACACTCCTCTACCC
Found at i:1150862 original size:19 final size:21
Alignment explanation
Indices: 1150824--1150868 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
1150814 ATACATCTAT
* *
1150824 TTTTTGGGTTATTTTTATT-A
1 TTTTTGGGTTATTATCATTAA
1150844 TTTTTGGGTTA-TATCATTAA
1 TTTTTGGGTTATTATCATTAA
1150864 TTTTT
1 TTTTT
1150869 ATTATGTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.02, G:0.13, T:0.67
Consensus pattern (21 bp):
TTTTTGGGTTATTATCATTAA
Found at i:1170145 original size:11 final size:11
Alignment explanation
Indices: 1170129--1170158 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1170119 CTCGTATCAG
1170129 AAAAAAATAGA
1 AAAAAAATAGA
*
1170140 AAAAAAAGAGA
1 AAAAAAATAGA
1170151 AAAAAAAT
1 AAAAAAAT
1170159 GCATAGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (11 bp):
AAAAAAATAGA
Found at i:1183673 original size:20 final size:20
Alignment explanation
Indices: 1183650--1183710 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
1183640 CAGCTCCGAC
*
1183650 CAGCTTAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
1183670 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
1183691 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
1183711 ATTTTATTGG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 22 0.63
21 13 0.37
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:1183705 original size:11 final size:10
Alignment explanation
Indices: 1183650--1183707 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
1183640 CAGCTCCGAC
*
1183650 CAGCTTAATT
1 CAGCTCAATT
* *
1183660 GAGCTCATTT
1 CAGCTCAATT
1183670 CAGCTCAA-T
1 CAGCTCAATT
1183679 CGAGCTCAATT
1 C-AGCTCAATT
*
1183690 TAGCTACAATT
1 CAGCT-CAATT
1183701 CAGCTCA
1 CAGCTCA
1183708 TTTATTTTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
9 2 0.05
10 26 0.68
11 10 0.26
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:1198957 original size:24 final size:23
Alignment explanation
Indices: 1198930--1198980 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
1198920 TTAAAACTAC
1198930 TTCTA-GAGAAAACTCAAGAGAAAA
1 TTCTAGGAG-AAACTCAA-AGAAAA
* *
1198954 TTCTTGGAGAAACTCAAAGAGAA
1 TTCTAGGAGAAACTCAAAGAAAA
1198977 TTCT
1 TTCT
1198981 CAATCAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 9 0.38
24 12 0.50
25 3 0.12
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.24
Consensus pattern (23 bp):
TTCTAGGAGAAACTCAAAGAAAA
Found at i:1202681 original size:14 final size:14
Alignment explanation
Indices: 1202653--1202691 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 14
1202643 TTTTTTTTCC
1202653 TTTTTTTTCG-A--
1 TTTTTTTTCGAATT
1202664 TTTTTTTT-GAATT
1 TTTTTTTTCGAATT
1202677 TTTTTTTTCGAATT
1 TTTTTTTTCGAATT
1202691 T
1 T
1202692 CTTCTCTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 1 0.04
11 9 0.38
13 8 0.33
14 6 0.25
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (14 bp):
TTTTTTTTCGAATT
Found at i:1207484 original size:18 final size:16
Alignment explanation
Indices: 1207463--1207497 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
1207453 TTATTTCTCT
1207463 TTTTTTTTATAGTTTTCG
1 TTTTTTTTA-A-TTTTCG
1207481 TTTTTTTTAATTTTCG
1 TTTTTTTTAATTTTCG
1207497 T
1 T
1207498 AACTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 1 0.06
18 9 0.53
ACGTcount: A:0.11, C:0.06, G:0.09, T:0.74
Consensus pattern (16 bp):
TTTTTTTTAATTTTCG
Found at i:1209737 original size:21 final size:21
Alignment explanation
Indices: 1209713--1209752 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1209703 TCTCTCTCGC
*
1209713 TTTCTTTTTCGCCTTTTTCAT
1 TTTCATTTTCGCCTTTTTCAT
**
1209734 TTTCATTTTCTTCTTTTTC
1 TTTCATTTTCGCCTTTTTC
1209753 CCTTGTATTT
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:0.05, C:0.23, G:0.03, T:0.70
Consensus pattern (21 bp):
TTTCATTTTCGCCTTTTTCAT
Found at i:1211784 original size:29 final size:27
Alignment explanation
Indices: 1211751--1211805 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 27
1211741 GTGATTAAAT
1211751 AAAATTGACA-CAAGCAGAATTTAAAAGAA
1 AAAATTGACAGCAAG-A-AA-TTAAAAGAA
1211780 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATTGACAGCAAGAAATTAAAAGA
1211806 TAACTCCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 8 0.32
28 2 0.08
29 11 0.44
30 4 0.16
ACGTcount: A:0.60, C:0.09, G:0.15, T:0.16
Consensus pattern (27 bp):
AAAATTGACAGCAAGAAATTAAAAGAA
Found at i:1218564 original size:12 final size:12
Alignment explanation
Indices: 1218547--1218603 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
1218537 GTAAAAAAAC
1218547 AAAAAGAAATTG
1 AAAAAGAAATTG
*
1218559 AAAAAGAAAATG
1 AAAAAGAAATTG
* *
1218571 AACATGAAA--G
1 AAAAAGAAATTG
1218581 AAAATAAGAAATTG
1 -AAA-AAGAAATTG
1218595 AAAAAGAAA
1 AAAAAGAAA
1218604 ATGAGAGTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
10 1 0.03
11 2 0.06
12 29 0.81
13 3 0.08
14 1 0.03
ACGTcount: A:0.70, C:0.02, G:0.16, T:0.12
Consensus pattern (12 bp):
AAAAAGAAATTG
Found at i:1218641 original size:27 final size:26
Alignment explanation
Indices: 1218594--1218650 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
1218584 ATAAGAAATT
* *
1218594 GAAAAAGAAAATGAGAGTGAGAGTGA
1 GAAAAAGAAAAAGAAAGTGAGAGTGA
* *
1218620 GAAAAAGAAAAAAGAAATTGAGATTGA
1 GAAAAAG-AAAAAGAAAGTGAGAGTGA
1218647 -AAAA
1 GAAAA
1218651 GGATGTGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 11 0.42
27 15 0.58
ACGTcount: A:0.61, C:0.00, G:0.26, T:0.12
Consensus pattern (26 bp):
GAAAAAGAAAAAGAAAGTGAGAGTGA
Found at i:1235209 original size:15 final size:15
Alignment explanation
Indices: 1235172--1235222 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
1235162 TCGAGCGAGA
*
1235172 AAAAGAAAAAGAGAG
1 AAAAGAAAAAGAGTG
*
1235187 -AAACAAAAAGAGTG
1 AAAAGAAAAAGAGTG
*
1235201 AAAAGAAAAAGAATG
1 AAAAGAAAAAGAGTG
1235216 AAAAGAA
1 AAAAGAA
1235223 TGATGAAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 12 0.39
15 19 0.61
ACGTcount: A:0.73, C:0.02, G:0.22, T:0.04
Consensus pattern (15 bp):
AAAAGAAAAAGAGTG
Found at i:1235274 original size:7 final size:6
Alignment explanation
Indices: 1235253--1235283 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1235243 CAAGAGTGAT
*
1235253 AAAAGA AAAAGA AAAAGA AAAAGG AAAAGA A
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA A
1235284 TGTGAAATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:1238966 original size:13 final size:12
Alignment explanation
Indices: 1238948--1238982 Score: 61
Period size: 12 Copynumber: 2.8 Consensus size: 12
1238938 ACGAGTTTGT
1238948 AAAAAAAATTCG
1 AAAAAAAATTCG
1238960 AAAAAAAATTCG
1 AAAAAAAATTCG
1238972 ACAAAAAAATT
1 A-AAAAAAATT
1238983 TATTTTGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 13 0.59
13 9 0.41
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.17
Consensus pattern (12 bp):
AAAAAAAATTCG
Found at i:1254810 original size:16 final size:18
Alignment explanation
Indices: 1254777--1254813 Score: 51
Period size: 16 Copynumber: 2.1 Consensus size: 18
1254767 ATCACTCATT
1254777 TCTTTTTCTTTTGAATCAC
1 TCTTTTTCTTTT-AATCAC
1254796 TCTTTTT-TTTT-ATCAC
1 TCTTTTTCTTTTAATCAC
1254812 TC
1 TC
1254814 ATCTTTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.39
18 4 0.22
19 7 0.39
ACGTcount: A:0.14, C:0.22, G:0.03, T:0.62
Consensus pattern (18 bp):
TCTTTTTCTTTTAATCAC
Found at i:1262740 original size:21 final size:21
Alignment explanation
Indices: 1262714--1262755 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 21
1262704 GAAATTCAAA
1262714 AAAAAAATTTTGAAAAAAAATCG
1 AAAAAAA--TTGAAAAAAAATCG
1262737 AAAAAAATTGAAAAAAAAT
1 AAAAAAATTGAAAAAAAAT
1262756 TGTATACGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
23 7 0.37
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.19
Consensus pattern (21 bp):
AAAAAAATTGAAAAAAAATCG
Found at i:1262756 original size:11 final size:11
Alignment explanation
Indices: 1262713--1262757 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
1262703 AGAAATTCAA
1262713 AAAAAAAATTTTG
1 AAAAAAAA--TTG
*
1262726 AAAAAAAATCG
1 AAAAAAAATTG
1262737 -AAAAAAATTG
1 AAAAAAAATTG
1262747 AAAAAAAATTG
1 AAAAAAAATTG
1262758 TATACGGTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 9 0.31
11 12 0.41
13 8 0.28
ACGTcount: A:0.69, C:0.02, G:0.09, T:0.20
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:1264277 original size:144 final size:144
Alignment explanation
Indices: 1264016--1264297 Score: 424
Period size: 144 Copynumber: 2.0 Consensus size: 144
1264006 GCCACCATGG
* * * * *
1264016 CTCGATTTCTCGCCGGCCTTAATCGTGAAATCGCAAATATTGTGGAGCTACACCACTATGTTGAA
1 CTCGATTTCTCACCAGCCTTAACCGAGAAATCGCAAATATTGTGGAGCTACACCACTATGTCGAA
* *
1264081 GTCATTGATATGGTCCATATGGCCATAAAGGTTGAAAAACAATTAAAAAGAAAAGGTACGTCCCG
66 GTCATTGATATGGTCCATATGGCCATAAAGGTCGAAAAACAACTAAAAAGAAAAGGTACGTCCCG
1264146 TTCTTTCCTTAACA
131 TTCTTTCCTTAACA
* * *
1264160 CTCGATTTCTCACCAGCCTTAACCGAGATATTGCAAATATTGTGGAGCTACACCACTATGTCGAG
1 CTCGATTTCTCACCAGCCTTAACCGAGAAATCGCAAATATTGTGGAGCTACACCACTATGTCGAA
*
1264225 GTCATTGATATGGTCCATATGGCCATCAAA-GTCGAAAAGA-AACTAAAGAGAAAAGGTACGTCC
66 GTCATTGATATGGTCCATATGGCCAT-AAAGGTCGAAAA-ACAACTAAAAAGAAAAGGTACGTCC
*
1264288 TGTTCTTTCC
129 CGTTCTTTCC
1264298 CTAATACTTC
Statistics
Matches: 124, Mismatches: 12, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
144 120 0.97
145 4 0.03
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.28
Consensus pattern (144 bp):
CTCGATTTCTCACCAGCCTTAACCGAGAAATCGCAAATATTGTGGAGCTACACCACTATGTCGAA
GTCATTGATATGGTCCATATGGCCATAAAGGTCGAAAAACAACTAAAAAGAAAAGGTACGTCCCG
TTCTTTCCTTAACA
Found at i:1304478 original size:18 final size:18
Alignment explanation
Indices: 1304445--1304491 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
1304435 TTTTTCAACA
* *
1304445 TCTTTTTCTATATCAATT
1 TCTTTTTCAATCTCAATT
1304463 T-TTTTCTCAATCTCAATT
1 TCTTTT-TCAATCTCAATT
1304481 TCTTTTTCAAT
1 TCTTTTTCAAT
1304492 TTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 4 0.16
18 17 0.68
19 4 0.16
ACGTcount: A:0.21, C:0.19, G:0.00, T:0.60
Consensus pattern (18 bp):
TCTTTTTCAATCTCAATT
Done.