Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 20 of 204
Found at i:5772528 original size:25 final size:25
Alignment explanation
Indices: 5772454--5772569 Score: 128
Period size: 25 Copynumber: 4.7 Consensus size: 25
5772444 TCACTTAAAC
* **
5772454 CTTCCCGTTA-TTGGCTCGTATGAG
1 CTTCCCGTTACATGGCTCACATGAG
* **
5772478 CTTCCCGTTA-ATGGCTCTCCGGAG
1 CTTCCCGTTACATGGCTCACATGAG
*
5772502 CTTCCCGTTACATGGCTCACATAAG
1 CTTCCCGTTACATGGCTCACATGAG
*
5772527 CTTCCCATTACATGGCTCACATGAG
1 CTTCCCGTTACATGGCTCACATGAG
* *
5772552 CTTCCTGTTATATGGCTC
1 CTTCCCGTTACATGGCTC
5772570 GAAAGAGGGC
Statistics
Matches: 77, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
24 29 0.38
25 48 0.62
ACGTcount: A:0.17, C:0.30, G:0.20, T:0.33
Consensus pattern (25 bp):
CTTCCCGTTACATGGCTCACATGAG
Found at i:5782381 original size:44 final size:42
Alignment explanation
Indices: 5782239--5782403 Score: 125
Period size: 43 Copynumber: 3.9 Consensus size: 42
5782229 AGATCGTGCA
* * * * * * *
5782239 ATGCCAATGTCCCAGACGTGGTTTTACATGTATTCAAATAACG
1 ATGCCAACGTCCCAGACATGGTCTTACACGAAATCATA-AACG
* * * *
5782282 ACGCC-ACTGTCCCAGATAGGGTCTTACACGAAATCATATACG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGAAATCATAAACG
* * *
5782324 ATGCTAATGTCCCAGACATGGTCTTACACGTAAATCTTAAATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACG-AAATCATAAA-CG
* * * *
5782368 ATGCCAACGTCCCAAACATGATCTTATACGATATCA
1 ATGCCAACGTCCCAGACATGGTCTTACACGAAATCA
5782404 CGTATCGAAA
Statistics
Matches: 93, Mismatches: 25, Indels: 8
0.74 0.20 0.06
Matches are distributed among these distances:
42 27 0.29
43 39 0.42
44 27 0.29
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGAAATCATAAACG
Found at i:5784333 original size:14 final size:14
Alignment explanation
Indices: 5784314--5784340 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5784304 AGTCATTTTT
5784314 TATTTTTATTTTAA
1 TATTTTTATTTTAA
5784328 TATTTTTATTTTA
1 TATTTTTATTTTA
5784341 TTTAATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TATTTTTATTTTAA
Found at i:5784966 original size:115 final size:115
Alignment explanation
Indices: 5784764--5784993 Score: 460
Period size: 115 Copynumber: 2.0 Consensus size: 115
5784754 TCGTTTGGCT
5784764 AACTTTCTAGTGATTCGCAACACATTCAAGATTAATGGCATTACTGATGATGTCATACACTTACG
1 AACTTTCTAGTGATTCGCAACACATTCAAGATTAATGGCATTACTGATGATGTCATACACTTACG
5784829 GTTAGGGGTGTGCAAAATTCGGGTAAAACCGAAAAAATTCGGTTAACCGA
66 GTTAGGGGTGTGCAAAATTCGGGTAAAACCGAAAAAATTCGGTTAACCGA
5784879 AACTTTCTAGTGATTCGCAACACATTCAAGATTAATGGCATTACTGATGATGTCATACACTTACG
1 AACTTTCTAGTGATTCGCAACACATTCAAGATTAATGGCATTACTGATGATGTCATACACTTACG
5784944 GTTAGGGGTGTGCAAAATTCGGGTAAAACCGAAAAAATTCGGTTAACCGA
66 GTTAGGGGTGTGCAAAATTCGGGTAAAACCGAAAAAATTCGGTTAACCGA
5784994 CCGAATTCGG
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
115 115 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (115 bp):
AACTTTCTAGTGATTCGCAACACATTCAAGATTAATGGCATTACTGATGATGTCATACACTTACG
GTTAGGGGTGTGCAAAATTCGGGTAAAACCGAAAAAATTCGGTTAACCGA
Found at i:5785387 original size:9 final size:9
Alignment explanation
Indices: 5785329--5785386 Score: 89
Period size: 9 Copynumber: 6.4 Consensus size: 9
5785319 GTAGTGATTC
*
5785329 AATTTGGTT
1 AATTCGGTT
5785338 AATTCGGTT
1 AATTCGGTT
*
5785347 AATTCGGGT
1 AATTCGGTT
5785356 AATTCGGTT
1 AATTCGGTT
5785365 AATTCGGTT
1 AATTCGGTT
*
5785374 AATTTGGTT
1 AATTCGGTT
5785383 AATT
1 AATT
5785387 TTTAACCAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 45 1.00
ACGTcount: A:0.24, C:0.07, G:0.22, T:0.47
Consensus pattern (9 bp):
AATTCGGTT
Found at i:5794360 original size:21 final size:22
Alignment explanation
Indices: 5794325--5794365 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5794315 ATTTGATTTT
5794325 TTTCTTTTATGTTCT-TTTAAC
1 TTTCTTTTATGTTCTCTTTAAC
* *
5794346 TTTCTTTTTTTTTCTCTTTA
1 TTTCTTTTATGTTCTCTTTA
5794366 TTTTTCGTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.10, C:0.15, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTCTTTTATGTTCTCTTTAAC
Found at i:5801066 original size:21 final size:22
Alignment explanation
Indices: 5801040--5801080 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
5801030 ATTATAAGTG
5801040 AAAAATA-ATCTCA-TTAAAAGA
1 AAAAATAGATC-CATTTAAAAGA
5801061 AAAAATAGATCCATTTAAAA
1 AAAAATAGATCCATTTAAAA
5801081 TATGTATCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.61, C:0.10, G:0.05, T:0.24
Consensus pattern (22 bp):
AAAAATAGATCCATTTAAAAGA
Found at i:5805828 original size:3 final size:3
Alignment explanation
Indices: 5805820--5805853 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
5805810 TAATATCTCC
5805820 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5805854 GTTTTTTTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5810547 original size:6 final size:6
Alignment explanation
Indices: 5810538--5810575 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
5810528 TGAAAATGAT
* *
5810538 AAAAGG AAAAAG AAAAGG AAAA-G AAAAAG AAAAGG AAA
1 AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAA
5810576 GGCCAATGCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (6 bp):
AAAAGG
Found at i:5810565 original size:17 final size:18
Alignment explanation
Indices: 5810538--5810575 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
5810528 TGAAAATGAT
5810538 AAAAGGAAAAAGAAAAGG
1 AAAAGGAAAAAGAAAAGG
5810556 AAAA-GAAAAAGAAAAGG
1 AAAAGGAAAAAGAAAAGG
5810573 AAA
1 AAA
5810576 GGCCAATGCG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (18 bp):
AAAAGGAAAAAGAAAAGG
Found at i:5812888 original size:129 final size:128
Alignment explanation
Indices: 5812658--5812966 Score: 478
Period size: 129 Copynumber: 2.4 Consensus size: 128
5812648 TGAACAGATC
*
5812658 TGGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAACAGATCAAAGACGGTGAATCTTATC
1 TGGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACGGTGAATCTTATC
*
5812723 TTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGTAGTGGAATAGG
66 TTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGG
5812786 TTGGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACGGT-AAGTCTTA
1 -TGGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACGGTGAA-TCTTA
* * *
5812850 TCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCTCTGGTCAGCAGTGGAGTAGG
64 TCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGG
** * * * *
5812915 T-CAAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGAC
1 TGGGAA-ATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGAC
5812967 ACAAGCCTTG
Statistics
Matches: 167, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
127 2 0.01
128 45 0.27
129 120 0.72
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.24
Consensus pattern (128 bp):
TGGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACGGTGAATCTTATC
TTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGG
Found at i:5813137 original size:44 final size:44
Alignment explanation
Indices: 5813065--5813613 Score: 215
Period size: 44 Copynumber: 12.6 Consensus size: 44
5813055 GAAAGCCTTG
* * * * *
5813065 TCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGCCAGTA-ATCTTA
1 TCTCCCTGAAGTTGCAGTAGAGTAGATTGAA-ACAATAGATCTTA
* *
5813109 TCTCCCTGAAGTTGCAGTAGAGTGGATTGAAATAATAGATCTTA
1 TCTCCCTGAAGTTGCAGTAGAGTAGATTGAAACAATAGATCTTA
* * * * *
5813153 TCTCTCTAAAGTTGCAGTAAAGTAGATT---ACATTAGGTCTTA
1 TCTCCCTGAAGTTGCAGTAGAGTAGATTGAAACAATAGATCTTA
* ** * *
5813194 TCTCCCTGAGGTTGCAGCGGAGCAGACTAAGAAAGC-A-AG-TCTTA
1 TCTCCCTGAAGTTGCAGTAGAGTAGA-T-TGAAA-CAATAGATCTTA
* * * * * * ***
5813238 TCCCCCTAAAGTTGCAGTGGGGCAGACTGAAGATGGT-GAGTCTTA
1 TCTCCCTGAAGTTGCAGTAGAGTAGATTGAA-ACAATAGA-TCTTA
* * * *
5813283 TCTCCCTG-AGTTTGCAGTGGAGCAGATTGAAGCCAATA-ATCCTA
1 TCTCCCTGAAG-TTGCAGTAGAGTAGATTGAA-ACAATAGATCTTA
* ** *
5813327 TCTCCCTAAAGTTGCAGCGGAGTAGATTGAAATAATAGATCTTA
1 TCTCCCTGAAGTTGCAGTAGAGTAGATTGAAACAATAGATCTTA
* * * * * *
5813371 TCTCTCTAAAGTTACAGCAGAGTAGA-T--CAC-ATCAGGTCTTA
1 TCTCCCTGAAGTTGCAGTAGAGTAGATTGAAACAAT-AGATCTTA
* ** * *
5813412 TCTCCCTGAGGTTGCAGCGGAGCAGACTGAGAA-AGCA-AG-TCTTA
1 TCTCCCTGAAGTTGCAGTAGAGTAGATTGA-AACA--ATAGATCTTA
* * * * ***
5813456 TCCCCCTGAAGTTGCAGTGGGGTAGAATGAAGATGGT-GAATCTTA
1 TCTCCCTGAAGTTGCAGTAGAGTAGATTGAA-ACAATAG-ATCTTA
* * * **
5813501 TCTCCCTGAGGTTACAGT-GAAGCAGACAGAAGA-AACTAG-TCTTA
1 TCTCCCTGAAGTTGCAGTAG-AGTAGATTGAA-ACAA-TAGATCTTA
* ** *
5813545 TCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATC-ATAGATCTTA
1 TCTCCCTGAAGTTGCAGTAGAGTAGATTGAAA-CAATAGATCTTA
* *
5813589 TCTCTCTGAAGTTGTAGTAGAGTAG
1 TCTCCCTGAAGTTGCAGTAGAGTAG
5813614 GTCGCGTCCA
Statistics
Matches: 381, Mismatches: 88, Indels: 72
0.70 0.16 0.13
Matches are distributed among these distances:
40 2 0.01
41 57 0.15
42 5 0.01
43 16 0.04
44 227 0.60
45 70 0.18
46 2 0.01
47 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (44 bp):
TCTCCCTGAAGTTGCAGTAGAGTAGATTGAAACAATAGATCTTA
Found at i:5813447 original size:218 final size:217
Alignment explanation
Indices: 5813065--5813601 Score: 788
Period size: 218 Copynumber: 2.5 Consensus size: 217
5813055 GAAAGCCTTG
* * *
5813065 TCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGCCAGTAATCTTATCTCCCTGAAGTTGCAGTAGA
1 TCTCCCTG-AGTTGCAGTGGAGCAGATTGAAGCCAATAATCTTATCTCCCTGAAGTTGCAGTGGA
* * * *
5813130 GTGGATTGAAATAATAGATCTTATCTCTCTAAAGTTGCAGTAAAGTAGATTACATTAGGTCTTAT
65 GTGGATTGAAATAATAGATCTTATCTCTCTAAAGTTACAGCAAAGTAGATCACATCAGGTCTTAT
5813195 CTCCCTGAGGTTGCAGCGGAGCAGACTAAGAAAGCAAGTCTTATCCCCCTAAAGTTGCAGTGGGG
130 CTCCCTGAGGTTGCAGCGGAGCAGACTAAGAAAGCAAGTCTTATCCCCCTAAAGTTGCAGTGGGG
* *
5813260 CAGACTGAAGATGGTGAGTCTTA
195 CAGAATGAAGATGGTGAATCTTA
* * *
5813283 TCTCCCTGAGTTTGCAGTGGAGCAGATTGAAGCCAATAATCCTATCTCCCTAAAGTTGCAGCGGA
1 TCTCCCTGAG-TTGCAGTGGAGCAGATTGAAGCCAATAATCTTATCTCCCTGAAGTTGCAGTGGA
* *
5813348 GTAGATTGAAATAATAGATCTTATCTCTCTAAAGTTACAGCAGAGTAGATCACATCAGGTCTTAT
65 GTGGATTGAAATAATAGATCTTATCTCTCTAAAGTTACAGCAAAGTAGATCACATCAGGTCTTAT
* *
5813413 CTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAAGTCTTATCCCCCTGAAGTTGCAGTGGGG
130 CTCCCTGAGGTTGCAGCGGAGCAGACTAAGAAAGCAAGTCTTATCCCCCTAAAGTTGCAGTGGGG
*
5813478 TAGAATGAAGATGGTGAATCTTA
195 CAGAATGAAGATGGTGAATCTTA
* * ** * *
5813501 TCTCCCTGAGGTTACAGTGAAGCAGACAGAAG-AAACTAGTCTTATCTCCCTGAAGTTGCAGTGG
1 TCTCCCTGA-GTTGCAGTGGAGCAGATTGAAGCCAA-TAATCTTATCTCCCTGAAGTTGCAGTGG
* * * *
5813565 AGCGGATTAAAATCATAGATCTTATCTCTCTGAAGTT
64 AGTGGATTGAAATAATAGATCTTATCTCTCTAAAGTT
5813602 GTAGTAGAGT
Statistics
Matches: 285, Mismatches: 31, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
217 4 0.01
218 280 0.98
219 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (217 bp):
TCTCCCTGAGTTGCAGTGGAGCAGATTGAAGCCAATAATCTTATCTCCCTGAAGTTGCAGTGGAG
TGGATTGAAATAATAGATCTTATCTCTCTAAAGTTACAGCAAAGTAGATCACATCAGGTCTTATC
TCCCTGAGGTTGCAGCGGAGCAGACTAAGAAAGCAAGTCTTATCCCCCTAAAGTTGCAGTGGGGC
AGAATGAAGATGGTGAATCTTA
Found at i:5814990 original size:3 final size:3
Alignment explanation
Indices: 5814982--5815024 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
5814972 TAATATCTCC
5814982 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5815025 GTTTTTTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5817747 original size:29 final size:29
Alignment explanation
Indices: 5817681--5817748 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
5817671 AGCTATACCG
*
5817681 CTAGAACTCCAATATTTGCGGATAAACAA
1 CTAGAACTCCAATATTTACGGATAAACAA
* * *
5817710 CCA-AGACTCCCATATTTACGGATAAACCA
1 CTAGA-ACTCCAATATTTACGGATAAACAA
5817739 CTAGAACTCC
1 CTAGAACTCC
5817749 TCTGTCACCA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
28 1 0.03
29 30 0.94
30 1 0.03
ACGTcount: A:0.38, C:0.28, G:0.12, T:0.22
Consensus pattern (29 bp):
CTAGAACTCCAATATTTACGGATAAACAA
Found at i:5823914 original size:41 final size:41
Alignment explanation
Indices: 5823707--5823903 Score: 367
Period size: 41 Copynumber: 4.8 Consensus size: 41
5823697 TTTATCGTTA
* *
5823707 GTGACATAATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
5823748 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
5823789 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
5823830 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
5823871 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
5823904 AAGAGCCGGT
Statistics
Matches: 153, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 153 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:5824178 original size:33 final size:32
Alignment explanation
Indices: 5824118--5824181 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
5824108 ATAGATATGT
5824118 ATATATATATATGTTGCATTCGACATAGGTGG
1 ATATATATATATGTTGCATTCGACATAGGTGG
* *
5824150 ATATATTTATGTGTATGCATTC-AGCATAGGTG
1 ATATATATATATGT-TGCATTCGA-CATAGGTG
5824182 AAAATAAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (32 bp):
ATATATATATATGTTGCATTCGACATAGGTGG
Found at i:5839261 original size:3 final size:3
Alignment explanation
Indices: 5839253--5839278 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5839243 GCCTTTTCTT
5839253 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
5839279 TTAAAAAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5839314 original size:17 final size:18
Alignment explanation
Indices: 5839292--5839325 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5839282 AAAAGGTATG
*
5839292 AAACAA-AGATGAAAAAA
1 AAACAATAGAAGAAAAAA
5839309 AAACAATAGAAGAAAAA
1 AAACAATAGAAGAAAAA
5839326 CTCGAAGTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.76, C:0.06, G:0.12, T:0.06
Consensus pattern (18 bp):
AAACAATAGAAGAAAAAA
Found at i:5848015 original size:147 final size:147
Alignment explanation
Indices: 5847740--5848015 Score: 417
Period size: 147 Copynumber: 1.9 Consensus size: 147
5847730 GAACGAGAAC
* * *
5847740 ATGGTGGAGAAAAGAAAGGAATAGGGGGAATTGCAGTTGGGATTGTAGGGACTTAAGGAATGCTT
1 ATGGTGGAGAAAAGAAAGGAATAGGGGGAATTGCAGTTGGGATTATAGGGACTGAAGGAAAGCTT
* * * ***
5847805 GGTAGAGGGGGCAGTCCTCTTGGCAATGTGGTAGGAAGTGGAGGAAGCGCCCTAGGGTTTGGGAG
66 GGCAGAAGGGGCAGTCCTCTTGGCAATGTGGTAGGAAGTGGAGGAAGCGCCCCAGGCCATGGGAG
5847870 ATTAGGGAAAGATGGCA
131 ATTAGGGAAAGATGGCA
* * * * *
5847887 ATGGTGGAGAAGAGAAAGGAATAGGGGGAATTGTAGTTGGGATTATGGGGACTGAGGGAAAGTTT
1 ATGGTGGAGAAAAGAAAGGAATAGGGGGAATTGCAGTTGGGATTATAGGGACTGAAGGAAAGCTT
*
5847952 GGCAGAAGGGGCAGTCCTGTTGGCAATGTGGTAGGAAGTGGAGGAAGCGCCCCAGGCCATGGGA
66 GGCAGAAGGGGCAGTCCTCTTGGCAATGTGGTAGGAAGTGGAGGAAGCGCCCCAGGCCATGGGA
5848016 ATGATGGTCG
Statistics
Matches: 114, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
147 114 1.00
ACGTcount: A:0.28, C:0.09, G:0.42, T:0.20
Consensus pattern (147 bp):
ATGGTGGAGAAAAGAAAGGAATAGGGGGAATTGCAGTTGGGATTATAGGGACTGAAGGAAAGCTT
GGCAGAAGGGGCAGTCCTCTTGGCAATGTGGTAGGAAGTGGAGGAAGCGCCCCAGGCCATGGGAG
ATTAGGGAAAGATGGCA
Found at i:5854178 original size:20 final size:21
Alignment explanation
Indices: 5854132--5854178 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
5854122 TTGTTGGAAA
5854132 ATAATTATTGAGTGATGAATG
1 ATAATTATTGAGTGATGAATG
*
5854153 AAAATTATTGAGTGAT-AATG
1 ATAATTATTGAGTGATGAATG
5854173 ATAATT
1 ATAATT
5854179 GTATCTCTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.43, C:0.00, G:0.19, T:0.38
Consensus pattern (21 bp):
ATAATTATTGAGTGATGAATG
Found at i:5869179 original size:28 final size:30
Alignment explanation
Indices: 5869113--5869173 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 30
5869103 GCACAAGAAG
*
5869113 ACATACATATTCGAACAACTTGCAAAACAT
1 ACATACATATTCGAACAACTTACAAAACAT
5869143 ATGCATACATATTC-AACCAACTTACAAAACA
1 A--CATACATATTCGAA-CAACTTACAAAACA
5869174 AATACAACAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 1 0.04
31 2 0.07
32 24 0.89
ACGTcount: A:0.48, C:0.25, G:0.05, T:0.23
Consensus pattern (30 bp):
ACATACATATTCGAACAACTTACAAAACAT
Found at i:5870395 original size:40 final size:40
Alignment explanation
Indices: 5870346--5870424 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
5870336 GCGCTTGGAT
*
5870346 AAAAAACGCCGCTAAAAATCGAGCATTAGCGTCGCTTTAC
1 AAAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTAC
*
5870386 AAAAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTA
1 AAAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTA
5870425 AGGAAAGCAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (40 bp):
AAAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTAC
Found at i:5870438 original size:40 final size:40
Alignment explanation
Indices: 5870346--5870444 Score: 128
Period size: 40 Copynumber: 2.5 Consensus size: 40
5870336 GCGCTTGGAT
* *
5870346 AAAAAACGCCGCTAAAAATCGAGCATTAGCGTCGCTTTAC
1 AAAAAACACCGCTAAAAATCGAGCATTAGCGGCGCTTTAC
* *
5870386 AAAAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTA-
1 AAAAAACACCGCTAAAAATCGAGCATTAGCGGCGCTTTAC
* *
5870425 AGGAAAGCACCGCTAAAAAT
1 A-AAAAACACCGCTAAAAAT
5870445 ACCTTAAAGC
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
39 1 0.02
40 51 0.98
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.17
Consensus pattern (40 bp):
AAAAAACACCGCTAAAAATCGAGCATTAGCGGCGCTTTAC
Found at i:5870597 original size:41 final size:41
Alignment explanation
Indices: 5870540--5870618 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
5870530 TGACCTTTCG
5870540 GGGCTTTAGCGGCGTTTTTAGAGAAGCGCCGCTAATGCTCC
1 GGGCTTTAGCGGCGTTTTTAGAGAAGCGCCGCTAATGCTCC
*
5870581 GGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGC
1 GGGCTTTAGCGGCGTTTTTAGAGAAGCGCCGCTAATGC
5870619 CGGTGTTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.16, C:0.23, G:0.34, T:0.27
Consensus pattern (41 bp):
GGGCTTTAGCGGCGTTTTTAGAGAAGCGCCGCTAATGCTCC
Found at i:5870727 original size:41 final size:40
Alignment explanation
Indices: 5870682--5870758 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
5870672 GCGAACACTT
5870682 ATAACATAATTGCGGCATTTTTATAAAAACGCCACTACCAC
1 ATAACAT-ATTGCGGCATTTTTATAAAAACGCCACTACCAC
* * * * *
5870723 ATAACCTTTTGCGGCGTTTTTGTAAAAATGCCACTA
1 ATAACATATTGCGGCATTTTTATAAAAACGCCACTA
5870759 ATAATGTAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
40 25 0.81
41 6 0.19
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.31
Consensus pattern (40 bp):
ATAACATATTGCGGCATTTTTATAAAAACGCCACTACCAC
Found at i:5870883 original size:114 final size:114
Alignment explanation
Indices: 5870633--5870927 Score: 351
Period size: 114 Copynumber: 2.6 Consensus size: 114
5870623 GTTTTAGTAC
* * *
5870633 AAACGCCACTAAAATTGTAGATAAAAATGACAACGTTTAGC-GAACACTTATAACATAATTGCGG
1 AAACGCCACTAAAA-TGTAGATAAAAATGACAACGTTTA-CAAAAGACTAATAACATAATTGCGG
* ** * * * *
5870697 CATTTTTATAAAAACGCCACTACCACATAACCTTTTGCGGCGTTTTTGTAA
64 CAGTTACATAAAAACGCCACTAACACATAACATTTTGCGGCGTTTTGGCAA
* *
5870748 AAATGCCACTAATAATGTAGATAAAAACGACAACGTTTACAAAAGACTAATAACATAATTGCGGC
1 AAACGCCACTAA-AATGTAGATAAAAATGACAACGTTTACAAAAGACTAATAACATAATTGCGGC
* * * *
5870813 -GTTACCTGAAAATGCCACTAACACATATCATTTTGCGGCGTTTTGGCAA
65 AGTTACATAAAAACGCCACTAACACATAACATTTTGCGGCGTTTTGGCAA
** * * *
5870862 AAACGCCACTGAAAACCTAGATAAAAATGACAACGTTTAAAAAAGACAAAAAACATAATTGCGGC
1 AAACGCCACT-AAAATGTAGATAAAAATGACAACGTTTACAAAAGACTAATAACATAATTGCGGC
5870927 A
65 A
5870928 TTTTTTGTAG
Statistics
Matches: 153, Mismatches: 23, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
114 94 0.61
115 57 0.37
116 2 0.01
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (114 bp):
AAACGCCACTAAAATGTAGATAAAAATGACAACGTTTACAAAAGACTAATAACATAATTGCGGCA
GTTACATAAAAACGCCACTAACACATAACATTTTGCGGCGTTTTGGCAA
Found at i:5871336 original size:14 final size:13
Alignment explanation
Indices: 5871250--5871337 Score: 52
Period size: 14 Copynumber: 6.4 Consensus size: 13
5871240 TTTAACCTCT
*
5871250 TAAACCCTAAACAA
1 TAAA-CCTAAACCA
*
5871264 TAAACACTAGACCA
1 TAAAC-CTAAACCA
*
5871278 TAAACCTACACCA
1 TAAACCTAAACCA
* *
5871291 TAAATCGTAAACAA
1 TAAA-CCTAAACCA
*
5871305 TAAACTCTTAA-CA
1 TAAAC-CTAAACCA
*
5871318 CTAAACCATAAACCT
1 -TAAACC-TAAACCA
5871333 TAAAC
1 TAAAC
5871338 TTTATACCCT
Statistics
Matches: 57, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
13 15 0.26
14 41 0.72
15 1 0.02
ACGTcount: A:0.51, C:0.27, G:0.02, T:0.19
Consensus pattern (13 bp):
TAAACCTAAACCA
Found at i:5871415 original size:22 final size:22
Alignment explanation
Indices: 5871390--5871435 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
5871380 CTAAAATTGT
5871390 AAATCATAAAT-TATAAACCCTA
1 AAATCATAAATCT-TAAACCCTA
*
5871412 AAATCATAAATCTTAAACCTTA
1 AAATCATAAATCTTAAACCCTA
5871434 AA
1 AA
5871436 CCCTAAACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.28
Consensus pattern (22 bp):
AAATCATAAATCTTAAACCCTA
Found at i:5871415 original size:29 final size:29
Alignment explanation
Indices: 5871376--5871442 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
5871366 ACCCTAAATT
** *
5871376 AACCCTAAAATTGTAAATCATAAA-TTATA
1 AACCCTAAAATCATAAATCATAAACCT-TA
*
5871405 AACCCTAAAATCATAAATCTTAAACCTTA
1 AACCCTAAAATCATAAATCATAAACCTTA
5871434 AACCCTAAA
1 AACCCTAAA
5871443 CCCTTAACCC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 32 0.97
30 1 0.03
ACGTcount: A:0.51, C:0.21, G:0.01, T:0.27
Consensus pattern (29 bp):
AACCCTAAAATCATAAATCATAAACCTTA
Found at i:5871447 original size:15 final size:15
Alignment explanation
Indices: 5871425--5871507 Score: 57
Period size: 14 Copynumber: 5.5 Consensus size: 15
5871415 TCATAAATCT
5871425 TAAA-CCTTAAACCC
1 TAAACCCTTAAACCC
5871439 TAAACCCTT-AACCC
1 TAAACCCTTAAACCC
**
5871453 TAAACCAATAAACCCC
1 TAAACCCTTAAA-CCC
* *
5871469 ATGAACCCCTAAACCCC
1 -TAAACCCTTAAA-CCC
5871486 T-AA-CCTATAAACCC
1 TAAACCCT-TAAACCC
5871500 TTAAACCC
1 -TAAACCC
5871508 AAAACTCTAA
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
14 21 0.38
15 13 0.24
16 6 0.11
17 15 0.27
ACGTcount: A:0.41, C:0.40, G:0.01, T:0.18
Consensus pattern (15 bp):
TAAACCCTTAAACCC
Found at i:5871483 original size:8 final size:8
Alignment explanation
Indices: 5871432--5871507 Score: 52
Period size: 8 Copynumber: 9.9 Consensus size: 8
5871422 TCTTAAACCT
5871432 TAAA-CCC
1 TAAACCCC
5871439 TAAA-CCC
1 TAAACCCC
*
5871446 TTAA-CCC
1 TAAACCCC
**
5871453 TAAACCAA
1 TAAACCCC
5871461 TAAACCCC
1 TAAACCCC
*
5871469 ATGAACCCC
1 -TAAACCCC
5871478 TAAACCCC
1 TAAACCCC
**
5871486 T-AACCTA
1 TAAACCCC
*
5871493 TAAACCCT
1 TAAACCCC
5871501 TAAACCC
1 TAAACCC
5871508 AAAACTCTAA
Statistics
Matches: 54, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
7 21 0.39
8 26 0.48
9 7 0.13
ACGTcount: A:0.41, C:0.41, G:0.01, T:0.17
Consensus pattern (8 bp):
TAAACCCC
Found at i:5871697 original size:21 final size:22
Alignment explanation
Indices: 5871667--5871721 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
5871657 ATAAATCCTA
*
5871667 AAACCCTAAACTA-TAAA-AATT
1 AAACCTTAAA-TACTAAACAATT
*
5871688 AAACCTTAAATACTAAACACTT
1 AAACCTTAAATACTAAACAATT
*
5871710 AAACCTAAAATA
1 AAACCTTAAATA
5871722 AATTTATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.07
21 13 0.45
22 14 0.48
ACGTcount: A:0.56, C:0.20, G:0.00, T:0.24
Consensus pattern (22 bp):
AAACCTTAAATACTAAACAATT
Found at i:5879261 original size:20 final size:21
Alignment explanation
Indices: 5879224--5879266 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 21
5879214 TATGCAGCAG
5879224 ATAAACCAAAGGGGGTATTTCA
1 ATAAACCAAA-GGGGTATTTCA
5879246 ATAAACCAAA-GGGTATTTCA
1 ATAAACCAAAGGGGTATTTCA
5879266 A
1 A
5879267 GGAGTAGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 11 0.52
22 10 0.48
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.23
Consensus pattern (21 bp):
ATAAACCAAAGGGGTATTTCA
Found at i:5886436 original size:14 final size:14
Alignment explanation
Indices: 5886417--5886447 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5886407 TGATTGCTTT
*
5886417 TAATCTAAATTTAC
1 TAATCTAAATTAAC
5886431 TAATCTAAATTAAC
1 TAATCTAAATTAAC
5886445 TAA
1 TAA
5886448 GAACACAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATCTAAATTAAC
Found at i:5894046 original size:12 final size:11
Alignment explanation
Indices: 5894022--5894065 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
5894012 TAAGTCTAAG
*
5894022 AAAATAACAAT
1 AAAATAAAAAT
*
5894033 AAACATAAACAT
1 AAA-ATAAAAAT
5894045 AAAAATAAAAAT
1 -AAAATAAAAAT
5894057 AAAATAAAA
1 AAAATAAAA
5894066 CAAATGGACT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
11 12 0.43
12 13 0.46
13 3 0.11
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:5894051 original size:18 final size:17
Alignment explanation
Indices: 5894022--5894065 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
5894012 TAAGTCTAAG
* *
5894022 AAAATAACAATAAACAT
1 AAAATAAAAATAAAAAT
5894039 AAACATAAAAATAAAAAT
1 AAA-ATAAAAATAAAAAT
5894057 AAAATAAAA
1 AAAATAAAA
5894066 CAAATGGACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.16
Consensus pattern (17 bp):
AAAATAAAAATAAAAAT
Found at i:5896825 original size:114 final size:115
Alignment explanation
Indices: 5896641--5896852 Score: 284
Period size: 114 Copynumber: 1.9 Consensus size: 115
5896631 GATTTTTGAA
* * *
5896641 AAAACTAAGTCCCAAAATCCACACGGCCAAGGACACGTCCGTGAGTCTAGGCCATGTGGGTCAAA
1 AAAACTAAGTCCCAAAACCCACACGGCAAAGGACACGTCCGTGAGTCTAGGCCATGTAGGTCAAA
* *
5896706 TGGCCATGTCACCAGGCCATGTAATTCACTATCGATTTTTTTAAAATTTT
66 CGGCCATGTCACCAGGCCATGTAACTCACTATCGATTTTTTTAAAATTTT
** * * * *
5896756 AAAACTAAGTCTTAAGACCCACAC-GCAAAGGACACG-CCTGTGTGTCTAGGCCGTGTAGGTCAC
1 AAAACTAAGTCCCAAAACCCACACGGCAAAGGACACGTCC-GTGAGTCTAGGCCATGTAGGTCAA
* *
5896819 ACGGCCATGTCGCCAGGCCGTGTAACTCACTATC
65 ACGGCCATGTCACCAGGCCATGTAACTCACTATC
5896853 CATGTGGGTT
Statistics
Matches: 83, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
113 2 0.02
114 61 0.73
115 20 0.24
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (115 bp):
AAAACTAAGTCCCAAAACCCACACGGCAAAGGACACGTCCGTGAGTCTAGGCCATGTAGGTCAAA
CGGCCATGTCACCAGGCCATGTAACTCACTATCGATTTTTTTAAAATTTT
Found at i:5904471 original size:16 final size:17
Alignment explanation
Indices: 5904439--5904471 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5904429 ATTCACATGA
5904439 ACCAAAATCATTTCAAG
1 ACCAAAATCATTTCAAG
5904456 ACCAAAATCA-TTCAAG
1 ACCAAAATCATTTCAAG
5904472 TATAGCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.48, C:0.24, G:0.06, T:0.21
Consensus pattern (17 bp):
ACCAAAATCATTTCAAG
Found at i:5909552 original size:24 final size:24
Alignment explanation
Indices: 5909524--5909575 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
5909514 TTAGTAAGTC
* *
5909524 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
5909548 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
5909572 AAAT
1 AAAT
5909576 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:5912503 original size:7 final size:7
Alignment explanation
Indices: 5912477--5912540 Score: 51
Period size: 7 Copynumber: 8.9 Consensus size: 7
5912467 TGAGAGCTAA
*
5912477 GAGAGTT
1 GAGAGAT
5912484 GAGAGA-
1 GAGAGAT
5912490 GAG-GAT
1 GAGAGAT
5912496 GAGAGATGT
1 GAGAGA--T
5912505 GAGAGAT
1 GAGAGAT
5912512 GATGAGAT
1 GA-GAGAT
*
5912520 GAGGGAT
1 GAGAGAT
*
5912527 GAGGGAT
1 GAGAGAT
5912534 GATGAGA
1 GA-GAGA
5912541 AATGAGCTCT
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
5 2 0.04
6 6 0.12
7 23 0.48
8 10 0.21
9 7 0.15
ACGTcount: A:0.36, C:0.00, G:0.47, T:0.17
Consensus pattern (7 bp):
GAGAGAT
Found at i:5912507 original size:9 final size:10
Alignment explanation
Indices: 5912477--5912545 Score: 61
Period size: 10 Copynumber: 6.9 Consensus size: 10
5912467 TGAGAGCTAA
*
5912477 GAGAGTTGA-
1 GAGAGATGAT
*
5912486 GAGAGAGGAT
1 GAGAGATGAT
5912496 GAGAGATG-T
1 GAGAGATGAT
5912505 GAGAGATGAT
1 GAGAGATGAT
*
5912515 GAGATGAGGGAT
1 GAGA-GA-TGAT
*
5912527 GAGGGATGAT
1 GAGAGATGAT
*
5912537 GAGAAATGA
1 GAGAGATGA
5912546 GCTCTTATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
9 16 0.33
10 22 0.46
11 4 0.08
12 6 0.12
ACGTcount: A:0.38, C:0.00, G:0.45, T:0.17
Consensus pattern (10 bp):
GAGAGATGAT
Found at i:5912518 original size:17 final size:17
Alignment explanation
Indices: 5912488--5912540 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
5912478 AGAGTTGAGA
5912488 GAGAGGATGAGAGATGT
1 GAGAGGATGAGAGATGT
5912505 GAGA-GATGATGAGA--T
1 GAGAGGATGA-GAGATGT
*
5912520 GAG-GGATGAGGGATGAT
1 GAGAGGATGAGAGATG-T
5912537 GAGA
1 GAGA
5912541 AATGAGCTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 11
0.71 0.02 0.27
Matches are distributed among these distances:
14 3 0.10
15 9 0.31
16 5 0.17
17 12 0.41
ACGTcount: A:0.36, C:0.00, G:0.47, T:0.17
Consensus pattern (17 bp):
GAGAGGATGAGAGATGT
Found at i:5915678 original size:23 final size:22
Alignment explanation
Indices: 5915537--5915678 Score: 72
Period size: 23 Copynumber: 6.0 Consensus size: 22
5915527 TTTTTCTTTT
* * *
5915537 AAAATAATGCCTAATAAATCTGA
1 AAAATAATACATAATAAAT-TTA
*
5915560 AATGATAATACATAATAAATTTA
1 AA-AATAATACATAATAAATTTA
* *
5915583 AAAATAAATATATAATAAATCTA
1 AAAAT-AATACATAATAAATTTA
*
5915606 AGCTAATAATACATAA-AAATTTA
1 A--AAATAATACATAATAAATTTA
*** *
5915629 TGATGTTAATA-ATATATTGTAATTTA
1 --AAAATAATACATA-A-T-AAATTTA
5915655 AAAATAATACATAATGAAATTTA
1 AAAATAATACATAAT-AAATTTA
5915678 A
1 A
5915679 CGCTAATAAA
Statistics
Matches: 91, Mismatches: 17, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
22 5 0.05
23 44 0.48
24 29 0.32
25 7 0.08
26 6 0.07
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.34
Consensus pattern (22 bp):
AAAATAATACATAATAAATTTA
Found at i:5915793 original size:20 final size:20
Alignment explanation
Indices: 5915752--5915800 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
5915742 GTACATATAT
*
5915752 ATATAAAT-AGATAAATAAA
1 ATATAAATAACATAAATAAA
* *
5915771 ATATAAATAACATAATTACA
1 ATATAAATAACATAAATAAA
*
5915791 ATATCAATAA
1 ATATAAATAA
5915801 GGCTAGTGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (20 bp):
ATATAAATAACATAAATAAA
Found at i:5922396 original size:12 final size:11
Alignment explanation
Indices: 5922379--5922440 Score: 63
Period size: 12 Copynumber: 5.5 Consensus size: 11
5922369 AGGCAACCCA
5922379 ATTTTTATTTTT
1 ATTTTTA-TTTT
5922391 ATTTTTATTTT
1 ATTTTTATTTT
* *
5922402 TTTCTTTACTTT
1 ATT-TTTATTTT
*
5922414 ATTTATTACTTT
1 ATTT-TTATTTT
5922426 A-TTTTATTTT
1 ATTTTTATTTT
5922436 ATTTT
1 ATTTT
5922441 ACTTATTTGG
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
10 7 0.16
11 12 0.28
12 24 0.56
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (11 bp):
ATTTTTATTTT
Found at i:5922414 original size:17 final size:17
Alignment explanation
Indices: 5922394--5922435 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
5922384 TATTTTTATT
*
5922394 TTTATTTTTTTCTTTAC
1 TTTATTTTTTACTTTAC
* *
5922411 TTTATTTATTACTTTAT
1 TTTATTTTTTACTTTAC
5922428 TTTATTTT
1 TTTATTTT
5922436 ATTTTACTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTTTTTACTTTAC
Found at i:5922747 original size:9 final size:9
Alignment explanation
Indices: 5922733--5922758 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
5922723 TTTTGGTTAT
5922733 TGTTGCTGG
1 TGTTGCTGG
5922742 TGTTGCTGG
1 TGTTGCTGG
5922751 TGTTGCTG
1 TGTTGCTG
5922759 CTTGAGACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.42, T:0.46
Consensus pattern (9 bp):
TGTTGCTGG
Found at i:5923487 original size:16 final size:15
Alignment explanation
Indices: 5923466--5923495 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
5923456 TAAAGCATAA
5923466 AAAAAGAGAAAAAAAC
1 AAAAAGA-AAAAAAAC
5923482 AAAAAGAAAAAAAA
1 AAAAAGAAAAAAAA
5923496 AATAATTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAAAC
Found at i:5923496 original size:16 final size:16
Alignment explanation
Indices: 5923466--5923496 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5923456 TAAAGCATAA
*
5923466 AAAAAGAGAAAAAAAC
1 AAAAAGAAAAAAAAAC
5923482 AAAAAGAAAAAAAAA
1 AAAAAGAAAAAAAAA
5923497 ATAATTTGGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAAAAAC
Found at i:5925301 original size:14 final size:15
Alignment explanation
Indices: 5925270--5925305 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
5925260 TGTATTGGAC
5925270 TTTTA-ATATATTTA
1 TTTTATATATATTTA
5925284 TTTTATATATATTT-
1 TTTTATATATATTTA
5925298 TTTTATAT
1 TTTTATAT
5925306 TTGGGTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTATATATATTTA
Found at i:5926092 original size:45 final size:44
Alignment explanation
Indices: 5926026--5926149 Score: 142
Period size: 45 Copynumber: 2.8 Consensus size: 44
5926016 GCAACCTGAA
* * * * *
5926026 GGAGATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAG
1 GGAGATAAGATCTGCAATCTTCAACCTACTCCACTACTGCTTAG
*
5926070 GGAGATAAGATCTGTAATTCTTCAACCTACTCCACTACTGCTTAG
1 GGAGATAAGATCTGCAA-TCTTCAACCTACTCCACTACTGCTTAG
* * *
5926115 GGAGATAAG-GCTTACAATCTTCAACCTATTCCACT
1 GGAGATAAGATC-TGCAATCTTCAACCTACTCCACT
5926150 GTTGTCCCGG
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
44 32 0.47
45 36 0.53
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (44 bp):
GGAGATAAGATCTGCAATCTTCAACCTACTCCACTACTGCTTAG
Found at i:5926123 original size:218 final size:218
Alignment explanation
Indices: 5925670--5926107 Score: 555
Period size: 218 Copynumber: 2.0 Consensus size: 218
5925660 TGCGCCGCTG
*
5925670 CAACTTCAGGGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTAT
1 CAACCTCAGGGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTAT
* * *
5925735 TATTTTAATTCGCTCCGCTGCAACCTCAGGGAGATAAGATTAGTGGCTTCAATCTACTCCAGTGT
66 TATTTTAATTCGCTCCGCTGCAACCTCAGGGAGATAAGATTAATGGCTTCAATCTACTCCACTGC
* * *
5925800 AACCTCAGGAAGGTAAAATCAGCCACCTTCAGTCTGCCCCACTGCAACTTCATGGGGATAAGACT
131 AACCTAAGGAAGATAAAATCAGCCACCTTCAGTCTGCCCCACTACAACTTCATGGGGATAAGACT
* ** * *
5925865 TACTTACTCAGTCTGCTCCACTG
196 TAATTACTCAACCTACTCCACTA
* *
5925888 CAACCTCAGGGAGATAAGACTTGATGCGATCCACTCTACTGCAACTTTAGAGAGATAAGATCTAT
1 CAACCTCAGGGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTAT
* * *
5925953 TATTTTAA-TCTGCTCCGCTGCAACTTCAGGGAGATAGGATTAATGGCTTCAATCTGCTCCACTG
66 TATTTTAATTC-GCTCCGCTGCAACCTCAGGGAGATAAGATTAATGGCTTCAATCTACTCCACTG
* ** * * **
5926017 CAACCTGAAGG-AGATAAGATTTGCCATCTTC-GATCTGCTCCACTACTGCTT-A-GGGAGATAA
130 CAACCT-AAGGAAGATAAAATCAGCCACCTTCAG-TCTGCCCCACTACAACTTCATGGG-GATAA
5926078 GATCTGTAATT-CTTCAACCTACTCCACTA
192 GA-CT-TAATTAC-TCAACCTACTCCACTA
5926107 C
1 C
5926108 TGCTTAGGGA
Statistics
Matches: 189, Mismatches: 24, Indels: 13
0.84 0.11 0.06
Matches are distributed among these distances:
216 3 0.02
217 11 0.06
218 155 0.82
219 20 0.11
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (218 bp):
CAACCTCAGGGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTAT
TATTTTAATTCGCTCCGCTGCAACCTCAGGGAGATAAGATTAATGGCTTCAATCTACTCCACTGC
AACCTAAGGAAGATAAAATCAGCCACCTTCAGTCTGCCCCACTACAACTTCATGGGGATAAGACT
TAATTACTCAACCTACTCCACTA
Found at i:5926178 original size:44 final size:44
Alignment explanation
Indices: 5926088--5926343 Score: 291
Period size: 44 Copynumber: 5.8 Consensus size: 44
5926078 GATCTGTAAT
* * *
5926088 TCTTCAACCTACTCCACTACTG-CTTAGGGAGATAAGGCTT-ACAA
1 TCTTCAACCTACTCCACTGCTGTC-CAGGGAGAT-AGGATTCACAA
* * * * *
5926132 TCTTCAACCTATTCCACTGTTGTCCCGGGATATAGGATTCATAA
1 TCTTCAACCTACTCCACTGCTGTCCAGGGAGATAGGATTCACAA
* * *
5926176 TCTTTAAGCTACTCCACTGCTATCCAGGGAGATAGGATTCACAA
1 TCTTCAACCTACTCCACTGCTGTCCAGGGAGATAGGATTCACAA
* *
5926220 TCTTCAACCTACTCTACTGCTGTCCAGGGAGATAGGATTCATAA
1 TCTTCAACCTACTCCACTGCTGTCCAGGGAGATAGGATTCACAA
* * * *
5926264 TCTTTAACCTACTCCATTACTGTGCAGGGAGATAGGATTCACAA
1 TCTTCAACCTACTCCACTGCTGTCCAGGGAGATAGGATTCACAA
* * **
5926308 TCTTCAACCTATTCTACTATTGTCCAGGGAGATAGG
1 TCTTCAACCTACTCCACTGCTGTCCAGGGAGATAGG
5926344 GATGGGGTCA
Statistics
Matches: 177, Mismatches: 33, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
43 5 0.03
44 171 0.97
45 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.30
Consensus pattern (44 bp):
TCTTCAACCTACTCCACTGCTGTCCAGGGAGATAGGATTCACAA
Found at i:5926220 original size:88 final size:88
Alignment explanation
Indices: 5926088--5926343 Score: 345
Period size: 88 Copynumber: 2.9 Consensus size: 88
5926078 GATCTGTAAT
* * * * *
5926088 TCTTCAACCTACTCCACTACT-GCTTAGGGAGATAAGGCTT-ACAATCTTCAACCTATTCCACTG
1 TCTTTAACCTACTCCACTACTATC-CAGGGAGAT-AGGATTCACAATCTTCAACCTATTCTACTG
* *
5926151 TTGTCCCGGGATATAGGATTCATAA
64 TTGTCCAGGGAGATAGGATTCATAA
* * * *
5926176 TCTTTAAGCTACTCCACTGCTATCCAGGGAGATAGGATTCACAATCTTCAACCTACTCTACTGCT
1 TCTTTAACCTACTCCACTACTATCCAGGGAGATAGGATTCACAATCTTCAACCTATTCTACTGTT
5926241 GTCCAGGGAGATAGGATTCATAA
66 GTCCAGGGAGATAGGATTCATAA
* * * *
5926264 TCTTTAACCTACTCCATTACTGTGCAGGGAGATAGGATTCACAATCTTCAACCTATTCTACTATT
1 TCTTTAACCTACTCCACTACTATCCAGGGAGATAGGATTCACAATCTTCAACCTATTCTACTGTT
5926329 GTCCAGGGAGATAGG
66 GTCCAGGGAGATAGG
5926344 GATGGGGTCA
Statistics
Matches: 147, Mismatches: 19, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
87 5 0.03
88 141 0.96
89 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.30
Consensus pattern (88 bp):
TCTTTAACCTACTCCACTACTATCCAGGGAGATAGGATTCACAATCTTCAACCTATTCTACTGTT
GTCCAGGGAGATAGGATTCATAA
Found at i:5928608 original size:33 final size:32
Alignment explanation
Indices: 5928559--5928640 Score: 85
Period size: 33 Copynumber: 2.5 Consensus size: 32
5928549 TTGACCTCTC
* *
5928559 CTTTTTCTTTTCTTTTTCA-TTTCATCATTTCAT
1 CTTTTT-TTTTATTTTT-ATTTTAATCATTTCAT
* * *
5928592 CATTTTTTTTTGTTTTTATTTTAATTATTTTAT
1 C-TTTTTTTTTATTTTTATTTTAATCATTTCAT
5928625 CTTTTTTTTTATTTTT
1 CTTTTTTTTTATTTTT
5928641 TGATTTTGAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
32 15 0.36
33 22 0.52
34 5 0.12
ACGTcount: A:0.13, C:0.11, G:0.01, T:0.74
Consensus pattern (32 bp):
CTTTTTTTTTATTTTTATTTTAATCATTTCAT
Found at i:5928639 original size:26 final size:26
Alignment explanation
Indices: 5928599--5928664 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
5928589 CATCATTTTT
5928599 TTTTGTTTTTATTTTAATT-ATTTT-ATC
1 TTTT-TTTTTATTTT--TTGATTTTGATC
*
5928626 TTTTTTTTTATTTTTTGATTTTGATT
1 TTTTTTTTTATTTTTTGATTTTGATC
5928652 TCTTTTTTTTATT
1 T-TTTTTTTTATT
5928665 GAATCTGAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
24 2 0.06
25 5 0.14
26 13 0.37
27 15 0.43
ACGTcount: A:0.14, C:0.03, G:0.05, T:0.79
Consensus pattern (26 bp):
TTTTTTTTTATTTTTTGATTTTGATC
Found at i:5933672 original size:20 final size:20
Alignment explanation
Indices: 5933631--5933679 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
5933621 ACATATATAC
*
5933631 ATATAAAT-AGATAAATAAA
1 ATATAAATAACATAAATAAA
* *
5933650 ATATAAATAACATAATTACA
1 ATATAAATAACATAAATAAA
*
5933670 ATATCAATAA
1 ATATAAATAA
5933680 GGCTAGTGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (20 bp):
ATATAAATAACATAAATAAA
Found at i:5937167 original size:17 final size:19
Alignment explanation
Indices: 5937140--5937175 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
5937130 AACGCCAATT
5937140 TGGGTCATGTGGG-CCACA
1 TGGGTCATGTGGGTCCACA
5937158 TGGG-CATGTGGGTCCACA
1 TGGGTCATGTGGGTCCACA
5937176 CGAGCGAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.17, C:0.22, G:0.39, T:0.22
Consensus pattern (19 bp):
TGGGTCATGTGGGTCCACA
Found at i:5940032 original size:11 final size:11
Alignment explanation
Indices: 5940018--5940043 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5940008 AAACACAATC
5940018 AAAACAAAAAT
1 AAAACAAAAAT
5940029 AAAACAAAAAT
1 AAAACAAAAAT
5940040 AAAA
1 AAAA
5940044 TAAACTAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.08, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAACAAAAAT
Found at i:5942339 original size:20 final size:20
Alignment explanation
Indices: 5942314--5942351 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5942304 ACCCCCTTTA
5942314 TTAACATAAA-AATTTAAAAT
1 TTAACA-AAATAATTTAAAAT
5942334 TTAACAAAATAATTTAAA
1 TTAACAAAATAATTTAAA
5942352 CTAGAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
TTAACAAAATAATTTAAAAT
Found at i:5954302 original size:15 final size:15
Alignment explanation
Indices: 5954282--5954329 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
5954272 TTTATGGAAA
5954282 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
5954297 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
5954311 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
5954327 ATC
1 ATC
5954330 GAGATATTGG
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
14 4 0.16
15 17 0.68
16 4 0.16
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:5954310 original size:30 final size:31
Alignment explanation
Indices: 5954276--5954339 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 31
5954266 TCCATATTTA
5954276 TGGAAAATCAAAGATATGGGTATC-AAATAT
1 TGGAAAATCAAAGATATGGGTATCGAAATAT
* *
5954306 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAATCAAAGATATGGGTATCGAAATAT
5954337 TGG
1 TGG
5954340 CATAATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 23 0.74
31 8 0.26
ACGTcount: A:0.41, C:0.06, G:0.27, T:0.27
Consensus pattern (31 bp):
TGGAAAATCAAAGATATGGGTATCGAAATAT
Found at i:5958934 original size:15 final size:15
Alignment explanation
Indices: 5958914--5958991 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
5958904 TTTATGGAAA
5958914 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
5958929 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
5958943 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
5958959 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
5958973 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
5958989 ATC
1 ATC
5958992 GAGATATTGG
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 8 0.17
15 31 0.66
16 8 0.17
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:5958942 original size:30 final size:30
Alignment explanation
Indices: 5958908--5959001 Score: 161
Period size: 30 Copynumber: 3.1 Consensus size: 30
5958898 TCCATATTTA
*
5958908 TGGAAAATCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
5958938 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
5958968 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
5958999 TGG
1 TGG
5959002 CATAATAAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
30 53 0.87
31 8 0.13
ACGTcount: A:0.41, C:0.06, G:0.26, T:0.27
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:5963230 original size:15 final size:15
Alignment explanation
Indices: 5963210--5963244 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5963200 ATCAATACGG
5963210 CCCAATTAGCCTAAA
1 CCCAATTAGCCTAAA
* *
5963225 CCCAATTAGCTTTAA
1 CCCAATTAGCCTAAA
5963240 CCCAA
1 CCCAA
5963245 ACTCTAGCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.34, G:0.06, T:0.23
Consensus pattern (15 bp):
CCCAATTAGCCTAAA
Found at i:5964134 original size:14 final size:14
Alignment explanation
Indices: 5964115--5964142 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5964105 CATATTTTGT
5964115 TCTGTTTTCATTTA
1 TCTGTTTTCATTTA
5964129 TCTGTTTTCATTTA
1 TCTGTTTTCATTTA
5964143 GATCCAGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.64
Consensus pattern (14 bp):
TCTGTTTTCATTTA
Found at i:5964754 original size:19 final size:20
Alignment explanation
Indices: 5964719--5964758 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
5964709 ATACATTATT
5964719 TGTTTAAATTATTATCAATA
1 TGTTTAAATTATTATCAATA
*
5964739 TGTTTTAATT-TTATCAATA
1 TGTTTAAATTATTATCAATA
5964758 T
1 T
5964759 TATTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (20 bp):
TGTTTAAATTATTATCAATA
Found at i:5964764 original size:20 final size:20
Alignment explanation
Indices: 5964725--5964766 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5964715 TATTTGTTTA
*
5964725 AATTATTATCAATATGTTTT
1 AATTATTATCAATATATTTT
5964745 AATT-TTATCAATATTATTTT
1 AATTATTATCAATA-TATTTT
5964765 AA
1 AA
5964767 AAATATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (20 bp):
AATTATTATCAATATATTTT
Found at i:5972569 original size:15 final size:15
Alignment explanation
Indices: 5972549--5972590 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
5972539 ATCAATACGG
5972549 CCCAATTAGCCTAAA
1 CCCAATTAGCCTAAA
* *
5972564 CCCAATTAGCTTTAA
1 CCCAATTAGCCTAAA
5972579 CCCAACTTAGCC
1 CCCAA-TTAGCC
5972591 CAAGACTCTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.33, C:0.36, G:0.07, T:0.24
Consensus pattern (15 bp):
CCCAATTAGCCTAAA
Found at i:5984509 original size:9 final size:9
Alignment explanation
Indices: 5984495--5984525 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
5984485 GTTAAACGAA
5984495 TCGAGTTAT
1 TCGAGTTAT
*
5984504 TCGAGTTAA
1 TCGAGTTAT
5984513 TCGAGTTAT
1 TCGAGTTAT
5984522 TCGA
1 TCGA
5984526 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:5984595 original size:9 final size:9
Alignment explanation
Indices: 5984578--5984614 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
5984568 TGATTTTTCG
5984578 AATTCGAAT
1 AATTCGAAT
*
5984587 AACTCGAAT
1 AATTCGAAT
5984596 AATTCGAAT
1 AATTCGAAT
5984605 AATTCGAAT
1 AATTCGAAT
5984614 A
1 A
5984615 TCAAAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:5986166 original size:11 final size:11
Alignment explanation
Indices: 5986137--5986169 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
5986127 TTATTTTAGA
5986137 TTTCGATTTTAT
1 TTTC-ATTTTAT
5986149 TTT-ATTTTAT
1 TTTCATTTTAT
5986159 TTTCATTTTAT
1 TTTCATTTTAT
5986170 CTTCTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 7 0.35
12 3 0.15
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.73
Consensus pattern (11 bp):
TTTCATTTTAT
Found at i:5986909 original size:3 final size:3
Alignment explanation
Indices: 5986901--5986990 Score: 58
Period size: 3 Copynumber: 27.7 Consensus size: 3
5986891 TTTAGTCCCG
* *
5986901 TTA TTA TTA TTA TTTA TTA -AA CTAA TTA GTT- TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA -TTA TTA -TTA TTA TTA TTA TTA TTA
*
5986947 TTA TTA TTGCA TTTA TTA TTA TTA CCTA CCTTA TTA TTA TTA TT
1 TTA TTA TT--A -TTA TTA TTA TTA -TTA --TTA TTA TTA TTA TT
5986991 TACCCATTTA
Statistics
Matches: 73, Mismatches: 4, Indels: 20
0.75 0.04 0.21
Matches are distributed among these distances:
2 3 0.04
3 54 0.74
4 10 0.14
5 4 0.05
6 2 0.03
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:5987001 original size:21 final size:19
Alignment explanation
Indices: 5986941--5987001 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 19
5986931 TTTATTATTA
*
5986941 TTATTATTATTATT-GCAT
1 TTATTATTATTATTACCAT
*
5986959 TTATTATTATTACCTACC--
1 TTATTATTATTA-TTACCAT
5986977 TTATTATTATTATTTACCCAT
1 TTATTATTATTA-TTA-CCAT
5986998 TTAT
1 TTAT
5987002 ACCGTTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
18 26 0.76
19 3 0.09
20 1 0.03
21 4 0.12
ACGTcount: A:0.28, C:0.13, G:0.02, T:0.57
Consensus pattern (19 bp):
TTATTATTATTATTACCAT
Found at i:5987099 original size:18 final size:18
Alignment explanation
Indices: 5987068--5987102 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5987058 ATGTACGTAC
* *
5987068 TTATATTTTTTATATACT
1 TTATACTTTATATATACT
5987086 TTATACTTTATATATAC
1 TTATACTTTATATATAC
5987103 ATATATACAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATACTTTATATATACT
Found at i:5994028 original size:143 final size:143
Alignment explanation
Indices: 5993770--5994468 Score: 1035
Period size: 143 Copynumber: 4.9 Consensus size: 143
5993760 ACCCAAATTG
* *
5993770 AAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAAATTAAAGCTAAAAATTATGGCGGA
1 AAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGA
*
5993835 TCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTAAAGTTGCA
66 TCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCA
* *
5993900 GCGGAGTACACTA
131 GCGGAGCAGACTA
* * * * * * *
5993913 AAGACAACAAATCTTATTTCCCTGGCGTTGTAGTAGAACAAATTAAAGATACAAATTATGGCTGA
1 AAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGA
* * * *
5993978 TCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTGCCTGAGGTTGTA
66 TCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCA
* *
5994043 GCGGAGTAGACTG
131 GCGGAGCAGACTA
* * *
5994056 AAGACAGCGAATCTTATTTCCTTGGCATTGCATTGGAACAGATTAAAGCTACAAATTATGGCGGA
1 AAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGA
* *
5994121 TCTTATCTTCCTGAAGTTGCAGTGGAGTAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCA
66 TCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCA
* *
5994186 ACGGAGCAGACTG
131 GCGGAGCAGACTA
* * *
5994199 AAGACAGCGAATCTTATTTCCCTTGCGTTGCAGT-GAGATAGATTAAAGTTACAAATTATGGCGG
1 AAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGA-ACAGATTAAAGCTACAAATTATGGCGG
* *
5994263 ATCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTACCTGAAGTTGA
65 ATCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGC
*
5994328 AGC-AAGCAGACTA
130 AGCGGAGCAGACTA
** *
5994341 AAGACAGCGAATCTTATTTCCCTAACGTTGCAGTGGAATAGATTAAAGCTACAAATTATGGCGGA
1 AAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGA
* *
5994406 TCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGATGCCACCAATCC-TATCTCCCTGAAGTTG
66 TCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACC-AGCCTTATCTCCCTGAAGTTG
5994469 TAGTGAAGTG
Statistics
Matches: 504, Mismatches: 49, Indels: 7
0.90 0.09 0.01
Matches are distributed among these distances:
142 125 0.25
143 379 0.75
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (143 bp):
AAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGA
TCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCA
GCGGAGCAGACTA
Found at i:5995165 original size:17 final size:17
Alignment explanation
Indices: 5995143--5995191 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 17
5995133 AAAGGTGTCC
5995143 TTTTTTACTTTTCTATT
1 TTTTTTACTTTTCTATT
5995160 TTTTTT-CTTTTTCTCTATT
1 TTTTTTAC--TTT-TCTATT
5995179 TTTTTTATCTTTT
1 TTTTTTA-CTTTT
5995192 TTTCCTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
16 1 0.04
17 6 0.22
18 4 0.15
19 15 0.56
21 1 0.04
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTTTACTTTTCTATT
Found at i:5996100 original size:26 final size:25
Alignment explanation
Indices: 5995990--5996371 Score: 185
Period size: 26 Copynumber: 15.1 Consensus size: 25
5995980 GTTTATTTAT
* *
5995990 TTATTTTAAAATCTTTTCATATATTA
1 TTATTTTAAACTATTTT-ATATATTA
5996016 CTTATTTTAAACTATTTTAT-TATTA
1 -TTATTTTAAACTATTTTATATATTA
* *
5996041 CTTATTTTAAGATTTTTTTCATATATTA
1 -TTATTTTAA-ACTATTTT-ATATATTA
*
5996069 TTATTTTAAACTATTTTATACATTA
1 TTATTTTAAACTATTTTATATATTA
* * **
5996094 TTCATTTTAAATTGTTTTATATGGTA
1 TT-ATTTTAAACTATTTTATATATTA
* *
5996120 TTCATTTCAAACTATTTTAT-TGTATA
1 TT-ATTTTAAACTATTTTATATAT-TA
*
5996146 TTATTTTAAACTATTATATAT-TTAA
1 TTATTTTAAACTATTTTATATATT-A
* *
5996171 TTTATTTTAAATTACTTTATATA-TA
1 -TTATTTTAAACTATTTTATATATTA
** * *
5996196 -T-TTTCGAACTGTTTTATATTTTA
1 TTATTTTAAACTATTTTATATATTA
* * * * **
5996219 TT-TATGATAAGTTTTTTCATATGGT-
1 TTATTTTA-AACTATTTT-ATATATTA
* * *
5996244 TTATTTTGAACCATTTTCTATATTA
1 TTATTTTAAACTATTTTATATATTA
* *
5996269 TTTATTTTAAATTTTTTTCATATATTA
1 -TTATTTTAAACTATTTT-ATATATTA
* *
5996296 TTTGTTTTAAACT-TTTT-TGTATTA
1 -TTATTTTAAACTATTTTATATATTA
* * * * * *
5996320 TTTACTTTAAATTGTTTCATTTATCA
1 -TTATTTTAAACTATTTTATATATTA
*
5996346 TTTATTTTAAAC-CTTTT-TATATTA
1 -TTATTTTAAACTATTTTATATATTA
5996370 TT
1 TT
5996372 TACTTCAAAT
Statistics
Matches: 273, Mismatches: 63, Indels: 42
0.72 0.17 0.11
Matches are distributed among these distances:
22 13 0.05
23 5 0.02
24 29 0.11
25 65 0.24
26 112 0.41
27 44 0.16
28 5 0.02
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (25 bp):
TTATTTTAAACTATTTTATATATTA
Found at i:5996288 original size:51 final size:48
Alignment explanation
Indices: 5996230--5996387 Score: 156
Period size: 50 Copynumber: 3.1 Consensus size: 48
5996220 TTATGATAAG
* * *
5996230 TTTTTTCATATGGTTTATTTTGAACCATTTTCTATATTATTTATTTTAAAT
1 TTTTTTCATAT-ATTTATTTTAAACC-TTTT-TATATTATTTACTTTAAAT
* * *
5996281 TTTTTTCATATATTATTTGTTTTAAACTTTTTTGTATTATTTACTTTAAA-
1 TTTTTTC--ATA-TATTTATTTTAAACCTTTTTATATTATTTACTTTAAAT
* *
5996331 TTGTTTCATTTATCATTTATTTTAAACCTTTTTATATTATTTACTTCAAAT
1 TTTTTTCA--TAT-ATTTATTTTAAACCTTTTTATATTATTTACTTTAAAT
5996382 TTTTTT
1 TTTTTT
5996388 TACTTATTAT
Statistics
Matches: 88, Mismatches: 12, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
48 1 0.01
49 1 0.01
50 40 0.45
51 28 0.32
52 4 0.05
53 13 0.15
54 1 0.01
ACGTcount: A:0.25, C:0.08, G:0.04, T:0.63
Consensus pattern (48 bp):
TTTTTTCATATATTTATTTTAAACCTTTTTATATTATTTACTTTAAAT
Found at i:5996363 original size:50 final size:50
Alignment explanation
Indices: 5996243--5996382 Score: 172
Period size: 50 Copynumber: 2.7 Consensus size: 50
5996233 TTTCATATGG
* * * *
5996243 TTTATTTTGAACCATTTTCTATATTATTTATTTTAAATTTTTTTCATATATTA
1 TTTATTTTAAACC-TTTT-TATATTATTTACTTTAAA-TTGTTTCATATATCA
* * * *
5996296 TTTGTTTTAAACTTTTTTGTATTATTTACTTTAAATTGTTTCATTTATCA
1 TTTATTTTAAACCTTTTTATATTATTTACTTTAAATTGTTTCATATATCA
*
5996346 TTTATTTTAAACCTTTTTATATTATTTACTTCAAATT
1 TTTATTTTAAACCTTTTTATATTATTTACTTTAAATT
5996383 TTTTTTACTT
Statistics
Matches: 75, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
50 45 0.60
51 16 0.21
52 4 0.05
53 10 0.13
ACGTcount: A:0.27, C:0.09, G:0.03, T:0.61
Consensus pattern (50 bp):
TTTATTTTAAACCTTTTTATATTATTTACTTTAAATTGTTTCATATATCA
Found at i:5998337 original size:5 final size:5
Alignment explanation
Indices: 5998322--5998366 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
5998312 CTCTTTTTTT
*
5998322 TTGCA TT-CA TTGCA TT-CA -TGCA TTATCA TTGCA TTGCA TTGCA TT
1 TTGCA TTGCA TTGCA TTGCA TTGCA TT-GCA TTGCA TTGCA TTGCA TT
5998367 ATATGCATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
3 1 0.03
4 8 0.24
5 21 0.62
6 4 0.12
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.44
Consensus pattern (5 bp):
TTGCA
Found at i:5998361 original size:10 final size:9
Alignment explanation
Indices: 5998322--5998375 Score: 58
Period size: 9 Copynumber: 5.8 Consensus size: 9
5998312 CTCTTTTTTT
5998322 TTGCATTCA
1 TTGCATTCA
5998331 TTGCATTCA
1 TTGCATTCA
5998340 -TGCATTATCA
1 TTGCA-T-TCA
5998350 TTGCATTGCA
1 TTGCATT-CA
5998360 TTGCATT-A
1 TTGCATTCA
5998368 TATGCATT
1 T-TGCATT
5998376 AAATCTCACA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
8 6 0.15
9 17 0.43
10 13 0.32
11 4 0.10
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (9 bp):
TTGCATTCA
Found at i:5998373 original size:19 final size:18
Alignment explanation
Indices: 5998322--5998375 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
5998312 CTCTTTTTTT
5998322 TTGCATTCAT-TGCATTCA
1 TTGCATT-ATATGCATTCA
5998340 -TGCATTATCATTGCATTGCA
1 TTGCATTAT-A-TGCATT-CA
5998360 TTGCATTATATGCATT
1 TTGCATTATATGCATT
5998376 AAATCTCACA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
16 2 0.06
17 6 0.19
19 12 0.39
20 3 0.10
21 8 0.26
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (18 bp):
TTGCATTATATGCATTCA
Found at i:5998375 original size:24 final size:19
Alignment explanation
Indices: 5998328--5998368 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
5998318 TTTTTTGCAT
5998328 TCATTGCATTCATGCATTA
1 TCATTGCATTCATGCATTA
5998347 TCATTGCATTGCATTGCATTA
1 TCATTGCATT-CA-TGCATTA
5998368 T
1 T
5998369 ATGCATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 10 0.50
20 2 0.10
21 8 0.40
ACGTcount: A:0.24, C:0.20, G:0.12, T:0.44
Consensus pattern (19 bp):
TCATTGCATTCATGCATTA
Found at i:6001044 original size:6 final size:6
Alignment explanation
Indices: 6001035--6001080 Score: 62
Period size: 6 Copynumber: 8.0 Consensus size: 6
6001025 TTAAAAAATT
6001035 AAAAAG AAAAAG AAAAA- AATAAA- AAAAAG -AAAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AA-AAAG AAAAAG AAAAAG AAAAAG AAAAAG
6001081 GAGAGGCCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.27
6 27 0.73
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:6001063 original size:17 final size:17
Alignment explanation
Indices: 6001035--6001080 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
6001025 TTAAAAAATT
*
6001035 AAAAAGAAAAAGAAAA-
1 AAAAAAAAAAAGAAAAG
6001051 AAATAAAAAAAAGAAAAG
1 AAA-AAAAAAAAGAAAAG
*
6001069 AAAAAGAAAAAG
1 AAAAAAAAAAAG
6001081 GAGAGGCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 3 0.12
17 20 0.77
18 3 0.12
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (17 bp):
AAAAAAAAAAAGAAAAG
Found at i:6002704 original size:46 final size:46
Alignment explanation
Indices: 6002651--6002920 Score: 201
Period size: 36 Copynumber: 6.6 Consensus size: 46
6002641 TTTGAGTACT
*
6002651 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
6002697 TCTGATCAAGTGAAAAAGTGAT-A-----AG---T-GCTACACTTA
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
6002733 TCTAATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
6002779 TCTGATCAAGTGAAAAAGTGATAA---GT-G--TTA--T--ACTTA
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
6002815 TCTGATCAAGTGAAAAAGTGATAA---GT-GC---A---ATACTTA
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
6002851 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* * *
6002896 TTTGATC-AGGGACAAA-TGATAAGTG
1 TCTGATCAAGAGAAAAAGTGATAAGTG
6002921 ATCATACGTA
Statistics
Matches: 190, Mismatches: 12, Indels: 47
0.76 0.05 0.19
Matches are distributed among these distances:
35 1 0.01
36 89 0.47
37 2 0.01
38 1 0.01
39 2 0.01
40 7 0.04
42 4 0.02
43 11 0.06
44 8 0.04
45 14 0.07
46 51 0.27
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (46 bp):
TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:6002728 original size:36 final size:36
Alignment explanation
Indices: 6002687--6002877 Score: 220
Period size: 36 Copynumber: 5.0 Consensus size: 36
6002677 GGTAGCTTTA
6002687 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* * *
6002723 GCTACACTTATCTAATCAAGAGACAAAGTGATAAGTGGTAGCTTT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGAT-A-----AG---T
6002768 AGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 -GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
6002805 GTTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* * *
6002841 GCAATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
6002877 G
1 G
6002878 GTAGCTTAGC
Statistics
Matches: 134, Mismatches: 11, Indels: 20
0.81 0.07 0.12
Matches are distributed among these distances:
36 97 0.72
37 2 0.01
40 2 0.01
42 2 0.01
45 2 0.01
46 29 0.22
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:6002792 original size:82 final size:82
Alignment explanation
Indices: 6002655--6002841 Score: 320
Period size: 82 Copynumber: 2.3 Consensus size: 82
6002645 AGTACTTCTG
*
6002655 ATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATA
1 ATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATA
6002720 AGTGCTACACTTATCTA
66 AGTGCTACACTTATCTA
*
6002737 ATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATA
1 ATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATA
* * *
6002802 AGTGTTATACTTATCTG
66 AGTGCTACACTTATCTA
*
6002819 ATCAAGTGAAAAAGTGATAAGTG
1 ATCAAGAGAAAAAGTGATAAGTG
6002842 CAATACTTAT
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 99 1.00
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.29
Consensus pattern (82 bp):
ATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATA
AGTGCTACACTTATCTA
Found at i:6010473 original size:36 final size:36
Alignment explanation
Indices: 6010427--6010617 Score: 247
Period size: 36 Copynumber: 5.0 Consensus size: 36
6010417 GGTAGCTTTA
6010427 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
* * *
6010463 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAA---GT
6010502 AGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 -GC--TA--T--ACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
6010545 GTTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
6010581 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
6010617 G
1 G
6010618 GTAGCTTAGC
Statistics
Matches: 136, Mismatches: 9, Indels: 20
0.82 0.05 0.12
Matches are distributed among these distances:
36 97 0.71
38 1 0.01
39 2 0.01
40 4 0.03
42 3 0.02
43 2 0.01
46 27 0.20
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (36 bp):
GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:6010528 original size:82 final size:82
Alignment explanation
Indices: 6010391--6010581 Score: 328
Period size: 82 Copynumber: 2.3 Consensus size: 82
6010381 TTTGAGTACT
* *
6010391 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTATACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
6010456 GATAAGTGCTACACTTA
66 GATAAGTGCTACACTTA
*
6010473 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
* *
6010538 GATAAGTGTTATACTTA
66 GATAAGTGCTACACTTA
*
6010555 TCTGATCAAGTGAAAAAGTGATAAGTG
1 TCTGATCAAGAGAAAAAGTGATAAGTG
6010582 CTATACTTAT
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 103 1.00
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (82 bp):
TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGTGCTACACTTA
Found at i:6013755 original size:143 final size:143
Alignment explanation
Indices: 6012544--6013740 Score: 1441
Period size: 143 Copynumber: 8.4 Consensus size: 143
6012534 GATTGAATTC
* * * * *
6012544 ATTATGACGAATCTTATCTTCCTGAAGTTGTAGTGGAGCAGATTAAAGCCACCAGCCTTATCTCC
1 ATTATGGCGGATCTTATCTTCTTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * * ** * * *
6012609 CTAAAGTTGCAGCGTAGCACACAGAAGACAGTGAATCTTATTTCCCTAACGTTGTAGTGAAATAG
66 CTAAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAG
*
6012674 ATTAAACCTACAA
131 ATTAAAGCTACAA
* * * * *
6012687 ATTATGGCAGATCTTATCTT-TCTGAAGTTACAGTGGAGAAGATTGAGGCCACCAACCTTATCTC
1 ATTATGGCGGATCTTATCTTCT-TGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTC
* * * * * * * *
6012751 CCTGAAG-TGCAGCAGAACAGACTGAAGAAAGTGAATCTAATTTCCCTGGCGTTGCAGTAGAATA
65 CCTAAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACA
6012815 GATTAAAGCTACAA
130 GATTAAAGCTACAA
* * * *
6012829 ATTATGGCTGATCTTATCTTCTTGAAGTTGCAATAGAGCAGATTGAAGCCACAAGCCTTATCTCC
1 ATTATGGCGGATCTTATCTTCTTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * * * *
6012894 CTGAAGTTGTAGCGGAACAGATTGAAGACAGCGAATCTTATTTCCTTGGCCTTGCAGTGGAACAG
66 CTAAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAG
* *
6012959 ATGAAAACTACAA
131 ATTAAAGCTACAA
* *
6012972 ATTATGGTGGATCTTATCTT-TCTGAAGTTGCAGTGGCA-CAGATTAAAGCCACCAGCCTTATCT
1 ATTATGGCGGATCTTATCTTCT-TGAAGTTGCAGTGG-AGCAGATTGAAGCCACCAGCCTTATCT
* * * * * * *
6013035 CTCTAAAGTTGTAGCGGAGCAGACTGAAGATAACAAATCTTATTTCACTGGCGTTGTAGTGGAAC
64 CCCTAAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAAC
*
6013100 AGATTAAAGCTAGAA
129 AGATTAAAGCTACAA
* * * *
6013115 ATTATGGTGGATCTTATCTTCCTGAAGTTGCAGTGGAGTAGATTGAAGCCACTAGCCTTATCTCC
1 ATTATGGCGGATCTTATCTTCTTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * * * ** * *
6013180 TTGAAGTTGCAGCGAAGCAGATTGACGACAGAAAATCTTATTTTCCTGGCGTTGTAGTGGAACAG
66 CTAAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAG
*
6013245 ATTAAAGCTAAAA
131 ATTAAAGCTACAA
* * * *
6013258 ATTATGGCTGATCTTATCTTCCTGAAGTTGTAGTGGAGTAGATTGAAGCCACCAGCCTTATCTCC
1 ATTATGGCGGATCTTATCTTCTTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * *
6013323 CTAAAGTTGCAGCGGAGTAGACTAAAGACAGCGAATCTTATTTCCCTGGCGTTGCATTGTAACAG
66 CTAAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAG
6013388 ATTAAAGCTACAA
131 ATTAAAGCTACAA
* * * * *
6013401 ATTATGGTGGATTTTATCTT-TCTAAAGTTGCAGTGAAGCAGATTGAAGCCACCAGCCTTATCTT
1 ATTATGGCGGATCTTATCTTCT-TGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTC
* * * * ** *
6013465 CCTAAAGTTGCAGCGGAACATACTAAAGACAACGAATCTTATTTCCCTGTTGTTTCAGTGGAACA
65 CCTAAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACA
* *
6013530 GATGAAAACTACAA
130 GATTAAAGCTACAA
* * * *
6013544 ATTATGGCAGATCTTATTTTCTTAAAGTTACAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
1 ATTATGGCGGATCTTATCTTCTTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * * *
6013609 CTAAAGTTGCAGCGGAGCAAACTTAAGACAGCGAATCTTATTTCCCTGGTGTCGCAGTGGAACAT
66 CTAAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAG
*
6013674 ATTAAAGCTTCAA
131 ATTAAAGCTACAA
* *
6013687 ATTATGGCGGATCTTATCTTCTTGAAGTTGTAGTGGAGCAGATTGATGCCACCA
1 ATTATGGCGGATCTTATCTTCTTGAAGTTGCAGTGGAGCAGATTGAAGCCACCA
6013741 ATCCTATCTT
Statistics
Matches: 902, Mismatches: 143, Indels: 18
0.85 0.13 0.02
Matches are distributed among these distances:
142 121 0.13
143 779 0.86
144 2 0.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (143 bp):
ATTATGGCGGATCTTATCTTCTTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
CTAAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAG
ATTAAAGCTACAA
Found at i:6014324 original size:18 final size:18
Alignment explanation
Indices: 6014301--6014352 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
6014291 ACACCAGAGT
6014301 AATCAAAAAAAAGAGAAA
1 AATCAAAAAAAAGAGAAA
* **
6014319 AATCAAAGAAAAGTTAAA
1 AATCAAAAAAAAGAGAAA
*
6014337 AATAAAAAGAAAAGAG
1 AATCAAAA-AAAAGAG
6014353 GTTTTGAAAC
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 21 0.81
19 5 0.19
ACGTcount: A:0.73, C:0.04, G:0.13, T:0.10
Consensus pattern (18 bp):
AATCAAAAAAAAGAGAAA
Found at i:6014408 original size:17 final size:17
Alignment explanation
Indices: 6014386--6014424 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
6014376 AAAAGTGTCC
6014386 TTTTTTACTCTTCTATA
1 TTTTTTACTCTTCTATA
* * *
6014403 TTTTTTATTTTTCTCTA
1 TTTTTTACTCTTCTATA
6014420 TTTTT
1 TTTTT
6014425 GTTATCTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTTACTCTTCTATA
Found at i:6014419 original size:19 final size:20
Alignment explanation
Indices: 6014397--6014434 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
6014387 TTTTTACTCT
6014397 TCTATATTTT-TTAT-TTTTC
1 TCTAT-TTTTGTTATCTTTTC
6014416 TCTATTTTTGTTATCTTTT
1 TCTATTTTTGTTATCTTTT
6014435 TTTCCTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.24
19 9 0.53
20 4 0.24
ACGTcount: A:0.13, C:0.11, G:0.03, T:0.74
Consensus pattern (20 bp):
TCTATTTTTGTTATCTTTTC
Found at i:6015214 original size:27 final size:27
Alignment explanation
Indices: 6015183--6015288 Score: 119
Period size: 27 Copynumber: 3.9 Consensus size: 27
6015173 GTTTATTTAT
* *
6015183 TTATTTTAAAATCTTTTACTATATTAC
1 TTATTTTAAACTTTTTTACTATATTAC
6015210 TTATTTTAAACTTTTTTA-T-TATTAC
1 TTATTTTAAACTTTTTTACTATATTAC
* *
6015235 TTATTTTAAGCTTTTTTTCATATATTA-
1 TTATTTTAAACTTTTTTAC-TATATTAC
*
6015262 TTATTTTAAACTATTTTATACTTTATT
1 TTATTTTAAACT-TTTT-TACTATATT
6015289 CATTTTAAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
25 22 0.33
26 1 0.01
27 28 0.42
28 14 0.21
29 2 0.03
ACGTcount: A:0.29, C:0.08, G:0.01, T:0.61
Consensus pattern (27 bp):
TTATTTTAAACTTTTTTACTATATTAC
Found at i:6015262 original size:24 final size:25
Alignment explanation
Indices: 6015167--6015306 Score: 85
Period size: 25 Copynumber: 5.5 Consensus size: 25
6015157 ACCTTTTTGC
* *
6015167 AAACTTGTTTAT--TTATTTATTTT
1 AAACTTTTTTATCATTACTTATTTT
*
6015190 AAAATCTTTTACTAT-ATTACTTATTTT
1 -AAA-CTTTT-TTATCATTACTTATTTT
*
6015217 AAACTTTTTTATTATTACTTATTTT
1 AAACTTTTTTATCATTACTTATTTT
* *
6015242 AAGCTTTTTT-TCATATATTATTATTTT
1 AAACTTTTTTATCAT-TA--CTTATTTT
* *
6015269 AAACTATTTTATACTTTA-TTCATTTT
1 AAACTTTTTTAT-CATTACTT-ATTTT
6015295 AAA-TTGTTTTAT
1 AAACTT-TTTTAT
6015307 ATGGTATTCA
Statistics
Matches: 94, Mismatches: 11, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
24 9 0.10
25 35 0.37
26 20 0.21
27 25 0.27
28 3 0.03
29 2 0.02
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.61
Consensus pattern (25 bp):
AAACTTTTTTATCATTACTTATTTT
Found at i:6015377 original size:23 final size:23
Alignment explanation
Indices: 6015351--6015523 Score: 59
Period size: 23 Copynumber: 7.1 Consensus size: 23
6015341 ATATTAAGCT
6015351 ATTATATATATTATTTATTTTAA
1 ATTATATATATTATTTATTTTAA
*
6015374 ATTACTTTATA-TATTT-TTTTGAA
1 ATTA-TATATATTATTTATTTT-AA
* * **
6015397 CTATTTTATATTTTATTTATGATAA
1 --ATTATATATATTATTTATTTTAA
* * **
6015422 GTT-TTTCATATGGTTTATTTTCAA
1 ATTATAT-ATATTATTTATTTT-AA
* *
6015446 CCATTTTGTATATTATTTATTTTAA
1 --ATTATATATATTATTTATTTTAA
*
6015471 ATTTATTTTATATATTATTCATTTTAA
1 A-TTA---TATATATTATTTATTTTAA
* *
6015498 ACTT-TTTTTATTATTT-TCTTTAA
1 A-TTATATATATTATTTAT-TTTAA
6015521 ATT
1 ATT
6015524 GCTTCATTTA
Statistics
Matches: 110, Mismatches: 24, Indels: 33
0.66 0.14 0.20
Matches are distributed among these distances:
22 9 0.08
23 38 0.35
24 13 0.12
25 12 0.11
26 16 0.15
27 22 0.20
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.62
Consensus pattern (23 bp):
ATTATATATATTATTTATTTTAA
Found at i:6015486 original size:27 final size:26
Alignment explanation
Indices: 6015179--6015578 Score: 190
Period size: 26 Copynumber: 15.8 Consensus size: 26
6015169 ACTTGTTTAT
* *
6015179 TTATTTATTTTAAAATCTTTTACTATA
1 TTATTTATTTTAAATTATTTTA-TATA
*
6015206 TTACTTATTTTAAACTT-TTTTAT-TA
1 TTATTTATTTTAAA-TTATTTTATATA
* * *
6015231 TTACTTATTTTAAGCTTTTTTTCATATA
1 TTATTTATTTTAA-ATTATTTT-ATATA
*
6015259 TTA-TTATTTTAAACTATTTTATACT-
1 TTATTTATTTTAAATTATTTTATA-TA
* * *
6015284 TTATTCATTTTAAATTGTTTTATATG
1 TTATTTATTTTAAATTATTTTATATA
* * * * *
6015310 GTATTCATTTCAAATTGTTTTAT-TG
1 TTATTTATTTTAAATTATTTTATATA
* ** *
6015335 TGTA-TTATATTAAGCTATTATATATA
1 T-TATTTATTTTAAATTATTTTATATA
*
6015361 TTATTTATTTTAAATTA-CTT-TATA
1 TTATTTATTTTAAATTATTTTATATA
* * *
6015385 -TATTT-TTTTGAACTATTTTATATT
1 TTATTTATTTTAAATTATTTTATATA
** * *
6015409 TTATTTATGAT-AAGT-TTTT-CATA
1 TTATTTATTTTAAATTATTTTATATA
** * ** *
6015432 TGGTTTATTTTCAACCATTTTGTATA
1 TTATTTATTTTAAATTATTTTATATA
6015458 TTATTTATTTTAAATTTATTTTATATA
1 TTATTTATTTTAAA-TTATTTTATATA
* *
6015485 TTATTCATTTTAAACT-TTTT-T-TA
1 TTATTTATTTTAAATTATTTTATATA
** * *
6015508 TTATTT-TCTTTAAATTGCTTCATTTA
1 TTATTTAT-TTTAAATTATTTTATATA
* ** *
6015534 TCATTTATTTTAAA-CCTTTT-TAGA
1 TTATTTATTTTAAATTATTTTATATA
* *
6015558 TTATTTACTTTAAATTGTTTT
1 TTATTTATTTTAAATTATTTT
6015579 TTACATATTG
Statistics
Matches: 284, Mismatches: 64, Indels: 52
0.71 0.16 0.13
Matches are distributed among these distances:
22 9 0.03
23 30 0.11
24 30 0.11
25 64 0.23
26 93 0.33
27 52 0.18
28 6 0.02
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.60
Consensus pattern (26 bp):
TTATTTATTTTAAATTATTTTATATA
Found at i:6015489 original size:49 final size:48
Alignment explanation
Indices: 6015355--6015489 Score: 137
Period size: 49 Copynumber: 2.8 Consensus size: 48
6015345 TAAGCTATTA
* * * *
6015355 TATATATTATTTATTTTAAATTACTTTATATATTTTTTTGAACTATTT
1 TATATATTATTTATTTTAAATTATTTTATATATTATTTTCAACCATTT
* ** * * *
6015403 TATATTTTATTTATGATAAGTT-TTTCATATGGTTTATTTTCAACCATTT
1 TATATATTATTTATTTTAAATTATTTTATAT--ATTATTTTCAACCATTT
*
6015452 TGTATATTATTTATTTTAAATTTATTTTATATATTATT
1 TATATATTATTTATTTTAAA-TTATTTTATATATTATT
6015490 CATTTTAAAC
Statistics
Matches: 66, Mismatches: 17, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
47 6 0.09
48 18 0.27
49 33 0.50
50 2 0.03
51 7 0.11
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.61
Consensus pattern (48 bp):
TATATATTATTTATTTTAAATTATTTTATATATTATTTTCAACCATTT
Found at i:6015520 original size:50 final size:51
Alignment explanation
Indices: 6015438--6015587 Score: 135
Period size: 50 Copynumber: 2.9 Consensus size: 51
6015428 CATATGGTTT
*
6015438 ATTTTCAACCATTTTGTATATTATTTAT-TTTAAATTTATTTTATATATTATTC
1 ATTTTAAACC-TTTT-TATATTATTT-TCTTTAAATTTATTTTATATATTATTC
* ** * * * *
6015491 ATTTTAAA-CTTTTTTTATTATTTTCTTTAAA-TTGCTTCATTTATCATTT
1 ATTTTAAACCTTTTTATATTATTTTCTTTAAATTTATTTTATATATTATTC
* * * *
6015540 ATTTTAAACCTTTTTAGATTATTTACTTTAAATTGTTTTTTACATATT
1 ATTTTAAACCTTTTTATATTATTTTCTTTAAATT-TATTTTATATATT
6015588 GATATTAAAA
Statistics
Matches: 76, Mismatches: 17, Indels: 9
0.75 0.17 0.09
Matches are distributed among these distances:
49 21 0.28
50 35 0.46
51 5 0.07
52 8 0.11
53 7 0.09
ACGTcount: A:0.28, C:0.09, G:0.03, T:0.61
Consensus pattern (51 bp):
ATTTTAAACCTTTTTATATTATTTTCTTTAAATTTATTTTATATATTATTC
Found at i:6017948 original size:147 final size:147
Alignment explanation
Indices: 6017674--6017948 Score: 453
Period size: 147 Copynumber: 1.9 Consensus size: 147
6017664 AACGAGAATG
* *
6017674 TGGTGGAAAAAATAAAGGAATAGAGGGAACTGCAGTTGGGATTGTGGGGACTGAGGGAATGCTTG
1 TGGTGGAAAAAAGAAAGAAATAGAGGGAACTGCAGTTGGGATTGTGGGGACTGAGGGAATGCTTG
* * *
6017739 GCAGAGGGGGTAGTCTTCTTGCCAATGTGGTAGGAAGTGGAGGAAGTGCCCCAGGGTTTGGGAGA
66 GCAGAGGGGGCAGTCCTCTTGCCAATGTGGTAGGAAGTGGAGGAAGTGCCCCAGGGTATGGGAGA
6017804 TTAGAGACAGATGGCAA
131 TTAGAGACAGATGGCAA
* *
6017821 TGGTGGAAAAGAGAAAGAAATAGAGGGAATTGCAGTTGGGATTGTGGGGACTGAGGGAATGCTTG
1 TGGTGGAAAAAAGAAAGAAATAGAGGGAACTGCAGTTGGGATTGTGGGGACTGAGGGAATGCTTG
* *
6017886 GTAGAGGGGGCAGTCCTCTTGGCAATGTGGTAGGAAGTGGAGGAAGTGCCCCA-GGTAATGGGA
66 GCAGAGGGGGCAGTCCTCTTGCCAATGTGGTAGGAAGTGGAGGAAGTGCCCCAGGGT-ATGGGA
6017949 ATGATGGTCG
Statistics
Matches: 118, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
146 3 0.03
147 115 0.97
ACGTcount: A:0.28, C:0.10, G:0.41, T:0.21
Consensus pattern (147 bp):
TGGTGGAAAAAAGAAAGAAATAGAGGGAACTGCAGTTGGGATTGTGGGGACTGAGGGAATGCTTG
GCAGAGGGGGCAGTCCTCTTGCCAATGTGGTAGGAAGTGGAGGAAGTGCCCCAGGGTATGGGAGA
TTAGAGACAGATGGCAA
Found at i:6018391 original size:20 final size:20
Alignment explanation
Indices: 6018366--6018407 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
6018356 GGAACTATCA
*
6018366 TAGAATTAGGGGATTACAAC
1 TAGAATTAGGGAATTACAAC
6018386 TAGAATTAGGGAATTACAAC
1 TAGAATTAGGGAATTACAAC
6018406 TA
1 TA
6018408 ATTACAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.26
Consensus pattern (20 bp):
TAGAATTAGGGAATTACAAC
Found at i:6048359 original size:12 final size:12
Alignment explanation
Indices: 6048342--6048401 Score: 54
Period size: 12 Copynumber: 4.9 Consensus size: 12
6048332 ACTTAATCAC
6048342 TTTAATATTAAA
1 TTTAATATTAAA
6048354 TTTAATA-TAATA
1 TTTAATATTAA-A
*
6048366 TTT-ATCTGATAAA
1 TTTAATAT--TAAA
6048379 TATT-ATATTAAA
1 T-TTAATATTAAA
6048391 TTTAATATTAA
1 TTTAATATTAA
6048402 GTCTTATTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
11 7 0.17
12 23 0.57
13 2 0.05
14 8 0.20
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (12 bp):
TTTAATATTAAA
Found at i:6052157 original size:147 final size:146
Alignment explanation
Indices: 6051883--6052146 Score: 411
Period size: 147 Copynumber: 1.8 Consensus size: 146
6051873 AAGGAGAAGG
*
6051883 TGGTGGAGAAAAGAAAGGAATAGAGGGAACTGCAGTTGGGATTGTGGGGACTAAGGGAATGCTTG
1 TGGTGGAGAAAAGAAAGGAATAGAGGGAACTGCAGTTGGGATTGTGGAGACTAAGGGAATGCTTG
* *
6051948 GCAGAGGGGCCAATCCTCTTGGAAATGTGGTAGGAAGTGGAGGAAGCACCCCAGGATTTGGGAGA
66 GCAGAGGGGCCAATCCTATTGGAAATGTGGTAGGAAGTGGAGGAAGCACCCCAGCA-TTGGGAGA
6052013 TTAGGGAAAGATGGCAA
130 TTAGGGAAAGATGGCAA
* * * *
6052030 TGGTGGAGAAGAGAAAGGAATAGGGGGAATTGCAGTTGGGATTGTGGAGACTGAGGGAATGCTTG
1 TGGTGGAGAAAAGAAAGGAATAGAGGGAACTGCAGTTGGGATTGTGGAGACTAAGGGAATGCTTG
** * * *
6052095 GCAGAGGGGGTAGTCCTATTGGCAATGTGGTAGGAAGTGGAGGAAGCGCCCC
66 GCAGAGGGGCCAATCCTATTGGAAATGTGGTAGGAAGTGGAGGAAGCACCCC
6052147 GAGCCATGGG
Statistics
Matches: 106, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
147 106 1.00
ACGTcount: A:0.29, C:0.11, G:0.41, T:0.19
Consensus pattern (146 bp):
TGGTGGAGAAAAGAAAGGAATAGAGGGAACTGCAGTTGGGATTGTGGAGACTAAGGGAATGCTTG
GCAGAGGGGCCAATCCTATTGGAAATGTGGTAGGAAGTGGAGGAAGCACCCCAGCATTGGGAGAT
TAGGGAAAGATGGCAA
Found at i:6062593 original size:24 final size:23
Alignment explanation
Indices: 6062524--6062594 Score: 81
Period size: 22 Copynumber: 3.1 Consensus size: 23
6062514 TGCATATTAC
*
6062524 TACATATAGGGTTCGCATAAATA
1 TACATATAGGGTTCACATAAATA
**
6062547 -ACATATAGGGTTCACATGTATA
1 TACATATAGGGTTCACATAAATA
* *
6062569 TTCATCCTAGGGTTCACATAAATA
1 TACAT-ATAGGGTTCACATAAATA
6062593 TA
1 TA
6062595 TCAAAAGATC
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
22 19 0.50
23 3 0.08
24 16 0.42
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (23 bp):
TACATATAGGGTTCACATAAATA
Found at i:6067236 original size:63 final size:63
Alignment explanation
Indices: 6067160--6067282 Score: 167
Period size: 63 Copynumber: 2.0 Consensus size: 63
6067150 GTGGTAGGCT
* * *
6067160 GTGTAACTTACTGTTTGGGAAA-TAGAGTCACACGAGCCAGAGGCAAGGGCATGTGTCCAAACC
1 GTGTAACTCACTGTTT-GGAAATTAGAGTCACACAAGCCAGAGACAAGGGCATGTGTCCAAACC
* * * *
6067223 GTGTAACTCACTGTTTTGAAATTAGATTCATACAAGCCAGAGACACGGGCATGTGTCCAA
1 GTGTAACTCACTGTTTGGAAATTAGAGTCACACAAGCCAGAGACAAGGGCATGTGTCCAA
6067283 GCAGTGTGAG
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
62 4 0.08
63 48 0.92
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (63 bp):
GTGTAACTCACTGTTTGGAAATTAGAGTCACACAAGCCAGAGACAAGGGCATGTGTCCAAACC
Found at i:6070113 original size:21 final size:21
Alignment explanation
Indices: 6070089--6070128 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
6070079 ATGCTTGAGT
6070089 TATATA-GTTTTGGTCATGATA
1 TATATATGTTTTGG-CATGATA
6070110 TATATATGTTTTGGCATGA
1 TATATATGTTTTGGCATGA
6070129 AGTAATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.28, C:0.05, G:0.20, T:0.47
Consensus pattern (21 bp):
TATATATGTTTTGGCATGATA
Found at i:6071966 original size:12 final size:12
Alignment explanation
Indices: 6071949--6071973 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6071939 ATTTCATTCC
6071949 ACATATATATAT
1 ACATATATATAT
6071961 ACATATATATAT
1 ACATATATATAT
6071973 A
1 A
6071974 AACACATAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
ACATATATATAT
Found at i:6072323 original size:21 final size:21
Alignment explanation
Indices: 6072291--6072380 Score: 65
Period size: 21 Copynumber: 4.1 Consensus size: 21
6072281 ATTTTCACAC
6072291 CAAAATTTGGACAGCATATATA
1 CAAAA-TTGGACAGCATATATA
* *
6072313 CAAAATTGGACTGCATTTATACA
1 CAAAATTGGACAGCA--TATATA
*
6072336 TCAAAAATT-GACAGCATAAATA
1 -C-AAAATTGGACAGCATATATA
* * * *
6072358 TATAATTGGACTGCATTTATA
1 CAAAATTGGACAGCATATATA
6072379 CA
1 CA
6072381 TCAAAAATTG
Statistics
Matches: 52, Mismatches: 11, Indels: 11
0.70 0.15 0.15
Matches are distributed among these distances:
20 5 0.10
21 20 0.38
22 9 0.17
23 5 0.10
24 7 0.13
25 6 0.12
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.30
Consensus pattern (21 bp):
CAAAATTGGACAGCATATATA
Found at i:6072359 original size:47 final size:47
Alignment explanation
Indices: 6072291--6072916 Score: 1003
Period size: 47 Copynumber: 13.4 Consensus size: 47
6072281 ATTTTCACAC
* * *
6072291 CAAAATTTGGACAGCATAT--ATACAAAATTGGACTGCATTTATACAT
1 CAAAAATT-GACAGCATATACATATATAATTGGACTGCATTTATACAT
6072337 CAAAAATTGACAGCATA-A-ATATATAATTGGACTGCATTTATACAT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
* *
6072382 CAAAAATTGACAGCATATACATATATATTTGGACTGCATTTGTACAT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
* *
6072429 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACGT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
6072476 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
* *
6072523 CAAAAATTGACAGCATATACATATATATTTGGACTGCATTTGTACAT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
**
6072570 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATATGT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
* *
6072617 CAAAAATTGACAGCATATACAAATATAATTGGACTGC-CTTATACAT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
6072663 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
* *
6072710 CAAAAATTGACAGCATATACATATATATTTGGACTGCATTTGTACAT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
* *
6072757 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACGT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
* *
6072804 AAAAAATTGACAGCATATACATATATAATTGGACTGC-CTTATACAT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
* *
6072850 AAAAAATTGACAGCATATACATATATAATTGGACTGCATTTGTACAT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
*
6072897 CAAAATTTGACAGCATATAC
1 CAAAAATTGACAGCATATAC
6072917 TTTCATTTAC
Statistics
Matches: 538, Mismatches: 37, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
45 51 0.09
46 94 0.17
47 393 0.73
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (47 bp):
CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
Found at i:6072749 original size:187 final size:187
Alignment explanation
Indices: 6072291--6072916 Score: 1044
Period size: 187 Copynumber: 3.4 Consensus size: 187
6072281 ATTTTCACAC
* * *
6072291 CAAAATTTGGACAGCATAT--ATACAAAATTGGACTGCATTTATACATCAAAAATTGACAGCATA
1 CAAAAATT-GACAGCATATACATATATAATTGGACTGCATTTATACATCAAAAATTGACAGCATA
* * *
6072354 -A-ATATATAATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATATATTTGGACT
65 TACATATATATTTGGACTGCATTTGTACATCAAAAATTGACAGCATATACATATATAATTGGACT
* * * * *
6072417 GCATTTGTACATCAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACGT
130 GCATTTATACGTCAAAAATTGACAGCATATACATATATAATTGGACTGC-CTTATACAT
6072476 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACATCAAAAATTGACAGCATAT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACATCAAAAATTGACAGCATAT
6072541 ACATATATATTTGGACTGCATTTGTACATCAAAAATTGACAGCATATACATATATAATTGGACTG
66 ACATATATATTTGGACTGCATTTGTACATCAAAAATTGACAGCATATACATATATAATTGGACTG
* *
6072606 CATTTATATGTCAAAAATTGACAGCATATACAAATATAATTGGACTGCCTTATACAT
131 CATTTATACGTCAAAAATTGACAGCATATACATATATAATTGGACTGCCTTATACAT
6072663 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACATCAAAAATTGACAGCATAT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACATCAAAAATTGACAGCATAT
*
6072728 ACATATATATTTGGACTGCATTTGTACATCAAAATTTGACAGCATATACATATATAATTGGACTG
66 ACATATATATTTGGACTGCATTTGTACATCAAAAATTGACAGCATATACATATATAATTGGACTG
*
6072793 CATTTATACGTAAAAAATTGACAGCATATACATATATAATTGGACTGCCTTATACAT
131 CATTTATACGTCAAAAATTGACAGCATATACATATATAATTGGACTGCCTTATACAT
* * *
6072850 AAAAAATTGACAGCATATACATATATAATTGGACTGCATTTGTACATCAAAATTTGACAGCATAT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACATCAAAAATTGACAGCATAT
6072915 AC
66 AC
6072917 TTTCATTTAC
Statistics
Matches: 417, Mismatches: 20, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
184 10 0.02
185 7 0.02
186 42 0.10
187 255 0.61
188 103 0.25
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (187 bp):
CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACATCAAAAATTGACAGCATAT
ACATATATATTTGGACTGCATTTGTACATCAAAAATTGACAGCATATACATATATAATTGGACTG
CATTTATACGTCAAAAATTGACAGCATATACATATATAATTGGACTGCCTTATACAT
Found at i:6073196 original size:14 final size:15
Alignment explanation
Indices: 6073172--6073206 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
6073162 TATATACATT
6073172 ACCATATAAATACTA
1 ACCATATAAATACTA
6073187 ACCATA-AAATACTA
1 ACCATATAAATACTA
6073201 ATCCAT
1 A-CCAT
6073207 GATTAAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (15 bp):
ACCATATAAATACTA
Found at i:6073944 original size:43 final size:43
Alignment explanation
Indices: 6073862--6073979 Score: 114
Period size: 43 Copynumber: 2.7 Consensus size: 43
6073852 TGTAATACCA
* *** * * * *
6073862 ACGTCCCAGACGTGGTCTTACATGTAATCACATACCGATG-CT
1 ACGTCCCAGAAGTGGTCTTACACAAAAACACAAATCGATGCCG
6073904 ACTGTCCCAGACAG-GGTCTTACACAAAAACACAAATCGATGCCG
1 AC-GTCCCAGA-AGTGGTCTTACACAAAAACACAAATCGATGCCG
* *
6073948 ACGTCCCAGATGTGGTCTTACACGAAAACACA
1 ACGTCCCAGAAGTGGTCTTACACAAAAACACA
6073980 TATTGGAGTC
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
42 3 0.05
43 55 0.89
44 4 0.06
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.20
Consensus pattern (43 bp):
ACGTCCCAGAAGTGGTCTTACACAAAAACACAAATCGATGCCG
Found at i:6078688 original size:17 final size:17
Alignment explanation
Indices: 6078636--6078688 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 17
6078626 TATGGAAACA
* *
6078636 TAATCTTTGAGGATATG
1 TAATCTTAGAAGATATG
*
6078653 CAATCTTAGATATGATATG
1 TAATCTTAGA-A-GATATG
6078672 TAATCTTAGAAGATATG
1 TAATCTTAGAAGATATG
6078689 ATTTTGTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 14 0.47
18 1 0.03
19 15 0.50
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.38
Consensus pattern (17 bp):
TAATCTTAGAAGATATG
Found at i:6078688 original size:22 final size:23
Alignment explanation
Indices: 6078660--6078704 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
6078650 ATGCAATCTT
6078660 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
*
6078682 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
6078705 GATTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (23 bp):
AGATATGATTATGTAATCTTAGA
Found at i:6078714 original size:22 final size:23
Alignment explanation
Indices: 6078670--6078714 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
6078660 AGATATGATA
*
6078670 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
6078693 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
6078715 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:6078917 original size:19 final size:21
Alignment explanation
Indices: 6078893--6078931 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
6078883 TACTATTTTC
*
6078893 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
6078912 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
6078932 TTAAAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:6113318 original size:42 final size:42
Alignment explanation
Indices: 6113259--6113343 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
6113249 GCCTCCCCCT
6113259 ACGCCCAAATCACAGAGAAAAACATTATCACTTCAGTCGCTA
1 ACGCCCAAATCACAGAGAAAAACATTATCACTTCAGTCGCTA
6113301 ACGCCCAAATCACAGAGAAAAACATTATCACTTCAGTCGCTA
1 ACGCCCAAATCACAGAGAAAAACATTATCACTTCAGTCGCTA
6113343 A
1 A
6113344 GAGATTCATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.41, C:0.28, G:0.12, T:0.19
Consensus pattern (42 bp):
ACGCCCAAATCACAGAGAAAAACATTATCACTTCAGTCGCTA
Done.