Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008523.1 Hibiscus syriacus cultivar Beakdansim tig00111392_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4657139
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 18
Found at i:2766528 original size:675 final size:674
Alignment explanation
Indices: 2765239--2766587 Score: 2644
Period size: 675 Copynumber: 2.0 Consensus size: 674
2765229 TGTTCTATAA
*
2765239 CTATACCTATATATTAATGGACTGCTCTTAATATAATTCCTCGGTAGTAATATATGTTGAATAAC
1 CTATACCTATATATTAATGGACTGCTCTTAATATAATTCCTCGGTAGTAATATATGTTGAAGAAC
2765304 ACAATTTTCTTACGATGAATAGAGCCGTCAACGATTGATTTTAATGGTTGTTATTAGGATGAATA
66 ACAATTTTCTTACGATGAATAGAGCCGTCAACGATTGATTTTAATGGTTGTTATTAGGATGAATA
2765369 TATAAATTTATATAAAATAAATGTTTGGATCATAAACAAATAAAAATTATTAAAATAATTATAAC
131 TATAAATTTATATAAAATAAATGTTTGGATCATAAACAAATAAAAATTATTAAAATAATTATAAC
2765434 TTTTAATAAATAAAACATAATTTATTTTATTACTATTAAAATTTAAACTAATTAACAATAAAAGA
196 TTTTAATAAATAAAACATAATTTATTTTATTACTATTAAAATTTAAACTAATTAACAATAAAAGA
*
2765499 TTAATTGTAGATATGTTATTGTATTTTTTTATATTTATTTAATAAGGATAATTTAATTAATGATG
261 TTAATTGTAGATATATTATTGTATTTTTTTATATTTATTTAATAAGGATAATTTAATTAATGATG
2765564 TATATCGATATATTGCAATACTAGTGTGTTTCGATGTTGACGTTCATTCTAGAATTTTCTGTTAT
326 TATATCGATATATTGCAATACTAGTGTGTTTCGATGTTGACGTTCATTCTAGAATTTTCTGTTAT
2765629 TTTTATGATAAAAAATAGTTATCTGATAACTGATATATAAAGTATTTTTTAGGGTAAGAAAATGA
391 TTTTATGATAAAAAATAGTTATCTGATAACTGATATATAAAGTATTTTTTAGGGTAAGAAAATGA
2765694 AAACTATGTAACTACTTATCCCTAATTGCTTTCCTCAAGAGGTAGCTTATATAAGCAGGAGGTTC
456 AAACTATGTAACTACTTATCCCTAATTGCTTTCCTCAAGAGGTAGCTTATATAAGCAGGAGGTTC
*
2765759 CTGAATGAATCTGATTTGACTATCTTCAAAGTTAACACGCTTTGCCAATTTATCTGCGATTTTGT
521 CTGAATGAATCTGATTTGACTATCTTCAAAGTTAACAAGCTTTGCCAATTTATCTGCGATTTTGT
2765824 TCCCCTCTCTGCGTATATGTTGCAGTCGGATAGTCCATGCACAGTTTCTCAGTTCCTTTATGTGT
586 TCCCCTCTCTGCGTATATGTTGCAGTCGGATAGTCCATGCACAGTTTCTCAGTTCCTTTATGTGT
2765889 GCTGTTATGATTGGTGCTCCATTT
651 GCTGTTATGATTGGTGCTCCATTT
*
2765913 CTATACCTATATATTAATGGACTGCTCTTAATATAATTCCTTGGTAGTAATATATGTTGAAGAAC
1 CTATACCTATATATTAATGGACTGCTCTTAATATAATTCCTCGGTAGTAATATATGTTGAAGAAC
2765978 ACAATTTTCTTACGATGAATAGAGCCGTCAACGATTGATTTTAATGGTTGTTATTAGGATGAATA
66 ACAATTTTCTTACGATGAATAGAGCCGTCAACGATTGATTTTAATGGTTGTTATTAGGATGAATA
2766043 TATAAATTTATATAAAATAAATGTTTGGATCATAAACAAATAAAAATTATTAAAATAATTATAAC
131 TATAAATTTATATAAAATAAATGTTTGGATCATAAACAAATAAAAATTATTAAAATAATTATAAC
2766108 TTTTAATAAATAAAACATAATTTTATTTTATTACTATTAAAATTTAAACTAATTAACAATAAAAG
196 TTTTAATAAATAAAACATAA-TTTATTTTATTACTATTAAAATTTAAACTAATTAACAATAAAAG
2766173 ATTAATTGTAGATATATTATTGTATTTTTTTATATTTATTTAATAAGGATAATTTAATTAATGAT
260 ATTAATTGTAGATATATTATTGTATTTTTTTATATTTATTTAATAAGGATAATTTAATTAATGAT
2766238 GTATATCGATATATTGCAATACTAGTGTGTTTCGATGTTGACGTTCATTCTAGAATTTTCTGTTA
325 GTATATCGATATATTGCAATACTAGTGTGTTTCGATGTTGACGTTCATTCTAGAATTTTCTGTTA
*
2766303 TTTTTATGATAAAAAATAGTTATCTGATAACTGATATATAAAGTATTTTTTGGGGTAAGAAAATG
390 TTTTTATGATAAAAAATAGTTATCTGATAACTGATATATAAAGTATTTTTTAGGGTAAGAAAATG
2766368 AAAACTATGTAACTACTTATCCCTAATTGCTTTCCTCAAGAGGTAGCTTATATAAGCAGGAGGTT
455 AAAACTATGTAACTACTTATCCCTAATTGCTTTCCTCAAGAGGTAGCTTATATAAGCAGGAGGTT
2766433 CCTGAATGAATCTGATTTGACTATCTTCAAAGTTAACAAGCTTTGCCAATTTATCTGCGATTTTG
520 CCTGAATGAATCTGATTTGACTATCTTCAAAGTTAACAAGCTTTGCCAATTTATCTGCGATTTTG
2766498 TTCCCCTCTCTGCGTATATGTTGCAGTCGGATAGTCCATGCACAGTTTCTCAGTTCCTTTATGTG
585 TTCCCCTCTCTGCGTATATGTTGCAGTCGGATAGTCCATGCACAGTTTCTCAGTTCCTTTATGTG
2766563 TGCTGTTATGATTGGTGCTCCATTT
650 TGCTGTTATGATTGGTGCTCCATTT
2766588 TTGTTCGTGC
Statistics
Matches: 669, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
674 213 0.32
675 456 0.68
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (674 bp):
CTATACCTATATATTAATGGACTGCTCTTAATATAATTCCTCGGTAGTAATATATGTTGAAGAAC
ACAATTTTCTTACGATGAATAGAGCCGTCAACGATTGATTTTAATGGTTGTTATTAGGATGAATA
TATAAATTTATATAAAATAAATGTTTGGATCATAAACAAATAAAAATTATTAAAATAATTATAAC
TTTTAATAAATAAAACATAATTTATTTTATTACTATTAAAATTTAAACTAATTAACAATAAAAGA
TTAATTGTAGATATATTATTGTATTTTTTTATATTTATTTAATAAGGATAATTTAATTAATGATG
TATATCGATATATTGCAATACTAGTGTGTTTCGATGTTGACGTTCATTCTAGAATTTTCTGTTAT
TTTTATGATAAAAAATAGTTATCTGATAACTGATATATAAAGTATTTTTTAGGGTAAGAAAATGA
AAACTATGTAACTACTTATCCCTAATTGCTTTCCTCAAGAGGTAGCTTATATAAGCAGGAGGTTC
CTGAATGAATCTGATTTGACTATCTTCAAAGTTAACAAGCTTTGCCAATTTATCTGCGATTTTGT
TCCCCTCTCTGCGTATATGTTGCAGTCGGATAGTCCATGCACAGTTTCTCAGTTCCTTTATGTGT
GCTGTTATGATTGGTGCTCCATTT
Found at i:2768621 original size:5 final size:5
Alignment explanation
Indices: 2768611--2768641 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
2768601 CCCCAACCTG
2768611 CACAC CACAC CACAC CACAC CACAC CACAC C
1 CACAC CACAC CACAC CACAC CACAC CACAC C
2768642 TGTATGGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.61, G:0.00, T:0.00
Consensus pattern (5 bp):
CACAC
Found at i:2771685 original size:15 final size:15
Alignment explanation
Indices: 2771661--2771691 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2771651 TTAATAATCG
*
2771661 AATTGGATTATTTAA
1 AATTGAATTATTTAA
2771676 AATTGAATTATTTAA
1 AATTGAATTATTTAA
2771691 A
1 A
2771692 TTTAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (15 bp):
AATTGAATTATTTAA
Found at i:2771930 original size:20 final size:20
Alignment explanation
Indices: 2771905--2771943 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2771895 GGTTGGACTT
2771905 AATATTGAAATTAAAATATA
1 AATATTGAAATTAAAATATA
* *
2771925 AATATTGAATTTTAAATAT
1 AATATTGAAATTAAAATAT
2771944 CATGAGTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (20 bp):
AATATTGAAATTAAAATATA
Found at i:2777080 original size:15 final size:15
Alignment explanation
Indices: 2777059--2777096 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2777049 AAAGATGAAG
*
2777059 TAAATAAAATA-AAA
1 TAAATAAAACATAAA
2777073 TAAAATAAAACATAAA
1 T-AAATAAAACATAAA
2777089 TAAATAAA
1 TAAATAAA
2777097 CTCAACACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 16 0.76
16 4 0.19
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (15 bp):
TAAATAAAACATAAA
Found at i:2778736 original size:19 final size:20
Alignment explanation
Indices: 2778714--2778762 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
2778704 ATAAATAACT
2778714 TAATTTTTTATTTAT-AATA
1 TAATTTTTTATTTATAAATA
* * *
2778733 TAATATCTTA-TTATAAATT
1 TAATTTTTTATTTATAAATA
2778752 TAATTTTTTAT
1 TAATTTTTTAT
2778763 GTGAAATAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
TAATTTTTTATTTATAAATA
Found at i:2778799 original size:21 final size:22
Alignment explanation
Indices: 2778775--2778820 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2778765 GAAATAAATT
2778775 AAATAACAAATAA-AAACTATA
1 AAATAACAAATAACAAACTATA
* * *
2778796 AAATAATATATAACAAACTTTA
1 AAATAACAAATAACAAACTATA
2778818 AAA
1 AAA
2778821 ACTAATTGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (22 bp):
AAATAACAAATAACAAACTATA
Found at i:2781356 original size:74 final size:74
Alignment explanation
Indices: 2781254--2781439 Score: 275
Period size: 74 Copynumber: 2.5 Consensus size: 74
2781244 GTTTTTCTAC
* * * *
2781254 TCTGGGTATTGCTTTGTTCGGGTTGAAAGTGCTTAAATTCTTAATTTCTTCCAAGTTTTT-GAAG
1 TCTGGGTATTGCTTGGTTTGAGCTGAAAGTGCTTAAATTCTTAATTTCTTCCAA-TTTTTCGAAG
*
2781318 TTTTATTGTT
65 TGTTATTGTT
*
2781328 TCTGGGTATTGCTTGGTTTGAGCAGAAAGTGCTTAAATTCTTAATTTCTTCCAATTTTTCCGAAG
1 TCTGGGTATTGCTTGGTTTGAGCTGAAAGTGCTTAAATTCTTAATTTCTTCCAATTTTT-CGAAG
*
2781393 TGTTCTTGTT
65 TGTTATTGTT
*
2781403 TCTGGGCATTGCTTGGTTTGAGCTGAAAGTGCTTAAA
1 TCTGGGTATTGCTTGGTTTGAGCTGAAAGTGCTTAAA
2781440 CTTAGTTATC
Statistics
Matches: 101, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
73 5 0.05
74 49 0.49
75 47 0.47
ACGTcount: A:0.20, C:0.13, G:0.22, T:0.45
Consensus pattern (74 bp):
TCTGGGTATTGCTTGGTTTGAGCTGAAAGTGCTTAAATTCTTAATTTCTTCCAATTTTTCGAAGT
GTTATTGTT
Found at i:2781423 original size:75 final size:74
Alignment explanation
Indices: 2781278--2781439 Score: 263
Period size: 75 Copynumber: 2.2 Consensus size: 74
2781268 TGTTCGGGTT
* *
2781278 GAAAGTGCTTAAATTCTTAATTTCTTCCAAGTTTTTGAAGTTTTATTGTTTCTGGGTATTGCTTG
1 GAAAGTGCTTAAATTCTTAATTTCTTCCAAGTTTTTGAAGTGTTATTGTTTCTGGGCATTGCTTG
2781343 GTTTGAGCA
66 GTTTGAGCA
*
2781352 GAAAGTGCTTAAATTCTTAATTTCTTCCAA-TTTTTCCGAAGTGTTCTTGTTTCTGGGCATTGCT
1 GAAAGTGCTTAAATTCTTAATTTCTTCCAAGTTTTT--GAAGTGTTATTGTTTCTGGGCATTGCT
*
2781416 TGGTTTGAGCT
64 TGGTTTGAGCA
2781427 GAAAGTGCTTAAA
1 GAAAGTGCTTAAA
2781440 CTTAGTTATC
Statistics
Matches: 82, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
73 5 0.06
74 30 0.37
75 47 0.57
ACGTcount: A:0.22, C:0.13, G:0.20, T:0.44
Consensus pattern (74 bp):
GAAAGTGCTTAAATTCTTAATTTCTTCCAAGTTTTTGAAGTGTTATTGTTTCTGGGCATTGCTTG
GTTTGAGCA
Found at i:2786465 original size:7 final size:7
Alignment explanation
Indices: 2786453--2786489 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
2786443 GCCTTTCAAA
2786453 TTTACCC
1 TTTACCC
2786460 TTTACCC
1 TTTACCC
2786467 TTTA-CC
1 TTTACCC
2786473 TTTACCC
1 TTTACCC
2786480 TTTACCC
1 TTTACCC
2786487 TTT
1 TTT
2786490 CCACCTTTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.14, C:0.38, G:0.00, T:0.49
Consensus pattern (7 bp):
TTTACCC
Found at i:2786476 original size:13 final size:13
Alignment explanation
Indices: 2786453--2786485 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2786443 GCCTTTCAAA
2786453 TTTACCCTTTACCC
1 TTTA-CCTTTACCC
2786467 TTTACCTTTACCC
1 TTTACCTTTACCC
2786480 TTTACC
1 TTTACC
2786486 CTTTCCACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.15, C:0.39, G:0.00, T:0.45
Consensus pattern (13 bp):
TTTACCTTTACCC
Found at i:2791321 original size:5 final size:5
Alignment explanation
Indices: 2791311--2791343 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
2791301 CAAATTGTTT
2791311 TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTC
1 TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTC
2791344 ATAATGCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (5 bp):
TTCTC
Found at i:2792635 original size:111 final size:111
Alignment explanation
Indices: 2792478--2792699 Score: 318
Period size: 111 Copynumber: 2.0 Consensus size: 111
2792468 GTGAGAGGCG
* * * * * *
2792478 CACTGCAACAGAAATTCACGAAGATCCAGCTTGTTGTGGTGTTTCAACTTCTAGTCCAGTTACAG
1 CACTGCAACAGAAATTCACCAAGATCCAGCTTGTTCTGGTATTTCAACTTATACTCCAGCTACAG
*
2792543 ATGTTTCCCTAGAATCATGCCACAGTTCATTTGCTGCTCCAACTCC
66 ATGTTTCCCCAGAATCATGCCACAGTTCATTTGCTGCTCCAACTCC
* * * * *
2792589 CACTGCAACAGACATTCACCATGATCCTGTTTGTTCTGGTATTTCAACTTATACTCCAGCTGCAG
1 CACTGCAACAGAAATTCACCAAGATCCAGCTTGTTCTGGTATTTCAACTTATACTCCAGCTACAG
**
2792654 ATGTTTCCCCAGAATCATGCCAGGGTTCATTTGCTGCTCCAACTCC
66 ATGTTTCCCCAGAATCATGCCACAGTTCATTTGCTGCTCCAACTCC
2792700 TATAAACCCT
Statistics
Matches: 97, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
111 97 1.00
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.31
Consensus pattern (111 bp):
CACTGCAACAGAAATTCACCAAGATCCAGCTTGTTCTGGTATTTCAACTTATACTCCAGCTACAG
ATGTTTCCCCAGAATCATGCCACAGTTCATTTGCTGCTCCAACTCC
Found at i:2798418 original size:19 final size:21
Alignment explanation
Indices: 2798394--2798432 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2798384 ATTAAAATCT
2798394 AATTTT-T-TAATTTTTATTG
1 AATTTTCTATAATTTTTATTG
*
2798413 AATTTTCTATTATTTTTATT
1 AATTTTCTATAATTTTTATT
2798433 TTGATCACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 1 0.06
21 10 0.59
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (21 bp):
AATTTTCTATAATTTTTATTG
Found at i:2799026 original size:20 final size:21
Alignment explanation
Indices: 2799001--2799041 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2798991 TTTAGCTGGT
2799001 TTTATTA-TTTTTACATAGAG
1 TTTATTATTTTTTACATAGAG
2799021 TTTATTATTTTTTACATAGAG
1 TTTATTATTTTTTACATAGAG
2799042 CTTCCTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.56
Consensus pattern (21 bp):
TTTATTATTTTTTACATAGAG
Found at i:2799801 original size:23 final size:23
Alignment explanation
Indices: 2799771--2799842 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
2799761 GAGTTGGTCG
2799771 TATTTTTAAAAATTTTAAATTTT
1 TATTTTTAAAAATTTTAAATTTT
* * *
2799794 TATTTTTATTAAATATTAAA-TTA
1 TATTTTTA-AAAATTTTAAATTTT
* *
2799817 TATTTCT-GAAATTTTATAATTTT
1 TATTTTTAAAAATTTTA-AATTTT
2799840 TAT
1 TAT
2799843 CTCTAAATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
21 7 0.18
22 2 0.05
23 21 0.54
24 9 0.23
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (23 bp):
TATTTTTAAAAATTTTAAATTTT
Found at i:2799807 original size:24 final size:23
Alignment explanation
Indices: 2799771--2799815 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
2799761 GAGTTGGTCG
*
2799771 TATTTTTAAAAATTTTAAATTTT
1 TATTTTTAAAAATATTAAATTTT
*
2799794 TATTTTTATTAAATATTAAATT
1 TATTTTTA-AAAATATTAAATT
2799816 ATATTTCTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TATTTTTAAAAATATTAAATTTT
Found at i:2805458 original size:60 final size:60
Alignment explanation
Indices: 2805394--2805508 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
2805384 ATATTTTAAT
* * *
2805394 TTCATCC-CTAAACTATGACTCTCATTTTAAATTGA-TCTCCAAACTTTTGAACATTTCAAA
1 TTCATCCTC-AAACTATGACCCTCATTTTAAATT-ATTCCCCAAACTTGTGAACATTTCAAA
* *
2805454 TTCATCCTCAAACTATGACCCTTATTTTAAATTATTCCCCAAACTTGTGTACATT
1 TTCATCCTCAAACTATGACCCTCATTTTAAATTATTCCCCAAACTTGTGAACATT
2805509 CCAATAATAT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 1 0.02
60 46 0.96
61 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.05, T:0.39
Consensus pattern (60 bp):
TTCATCCTCAAACTATGACCCTCATTTTAAATTATTCCCCAAACTTGTGAACATTTCAAA
Found at i:2807248 original size:18 final size:18
Alignment explanation
Indices: 2807227--2807261 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2807217 TGCTGAAATG
2807227 GAAAGTGGAG-GAGAAAGA
1 GAAAG-GGAGAGAGAAAGA
2807245 GAAAGGGAGAGAGAAAG
1 GAAAGGGAGAGAGAAAG
2807262 GTTGTGAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.51, C:0.00, G:0.46, T:0.03
Consensus pattern (18 bp):
GAAAGGGAGAGAGAAAGA
Found at i:2815526 original size:31 final size:31
Alignment explanation
Indices: 2815490--2815551 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
2815480 AGCTTTTCCT
2815490 TAACTCCTAAATGATACATCATGAATATTGA
1 TAACTCCTAAATGATACATCATGAATATTGA
2815521 TAACTCCTAAATGATACATCATGAATATTGA
1 TAACTCCTAAATGATACATCATGAATATTGA
2815552 AAGAAGAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (31 bp):
TAACTCCTAAATGATACATCATGAATATTGA
Found at i:2820387 original size:12 final size:12
Alignment explanation
Indices: 2820370--2820395 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2820360 AATTTGGAAT
2820370 ATATTATTAAAA
1 ATATTATTAAAA
2820382 ATATTATTAAAA
1 ATATTATTAAAA
2820394 AT
1 AT
2820396 CAAATATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATATTATTAAAA
Found at i:2830802 original size:120 final size:120
Alignment explanation
Indices: 2830590--2831771 Score: 1164
Period size: 120 Copynumber: 10.1 Consensus size: 120
2830580 ATCTACAGAA
* * * * * *
2830590 GCTTCAGAAACAGTGGTCTTAGCACTACCATAAGCTACACGATCTCCATTGC-A-----ATCATC
1 GCTTCAGAGACAGTGGCCTTAGCACTATCATTAGCTAAACCATCTCCATTGCAATCGCCATCATC
* * * *
2830649 AGCTACTA-CCATTCCAGAACTCTCATTCTCTTTTAACCTGAAATCGAGAACATTG
66 AGCTAC-AGCCATTTCAGAACCCTCATTCTCTTTTGACCTGGAATCGAGAACATTG
* * * * * * * *
2830704 GCTTCAGAAACAGCGACCCTAGCACTATCATTAGTTAAACCATCTCCATGGCAACCGTCATCATC
1 GCTTCAGAGACAGTGGCCTTAGCACTATCATTAGCTAAACCATCTCCATTGCAATCGCCATCATC
* * * *
2830769 AGCTAC-GATCATTTCAGAACCCCCATTCTCTTTTGACTTGGAATCGATAACATTG
66 AGCTACAG-CCATTTCAGAACCCTCATTCTCTTTTGACCTGGAATCGAGAACATTG
* * * * *
2830824 GCTTCAGAGACAGTGGCCTTAGCACTATCATTACCTAAATCGTCTCCATTGCAGTTGCCATCATC
1 GCTTCAGAGACAGTGGCCTTAGCACTATCATTAGCTAAACCATCTCCATTGCAATCGCCATCATC
* * **
2830889 AGCTACAGCCGTTTCAGAGCCCTCATTCTCTTTCAACCTGGAATCGAGAACATTG
66 AGCTACAGCCATTTCAGAACCCTCATTCTCTTTTGACCTGGAATCGAGAACATTG
*
2830944 GCTTCAGAGACAGTGGCCTTAGCACTATCATTAGCTAAACCATCTCCATTGCAATTGCCATCATC
1 GCTTCAGAGACAGTGGCCTTAGCACTATCATTAGCTAAACCATCTCCATTGCAATCGCCATCATC
* * * ** * *
2831009 AGCTACAACTATTTCAGAACCCTCAGTCTCTTTTGACCTGGAATAAATAGCATTG
66 AGCTACAGCCATTTCAGAACCCTCATTCTCTTTTGACCTGGAATCGAGAACATTG
* * *
2831064 GCTTCAGAGACAGTGGCCTTGGCACTATCATTAGCT-AACACATTTCCATTGCAATCACCATCAT
1 GCTTCAGAGACAGTGGCCTTAGCACTATCATTAGCTAAAC-CATCTCCATTGCAATCGCCATCAT
* *
2831128 CAGCTACAGCCATTTCAG-ATCCTCCATTCTCTTTTAACCTGGAATCGAGAACATTG
65 CAGCTACAGCCATTTCAGAACCCT-CATTCTCTTTTGACCTGGAATCGAGAACATTG
* * *
2831184 GCTTCAGAG--A-----C--AG---TATCATTAGCTAAAGCATTTCCATTGCAATCACCATCATC
1 GCTTCAGAGACAGTGGCCTTAGCACTATCATTAGCTAAACCATCTCCATTGCAATCGCCATCATC
* * * *
2831237 GGCTACAGCCATTTCAG-AGCCTCCATTCTCTTTTGACCTGGAATCAATAACATTG
66 AGCTACAGCCATTTCAGAACCCT-CATTCTCTTTTGACCTGGAATCGAGAACATTG
* * *
2831292 GCTTCAGAGACAGTGGCCTTAGCACTATCATTAGATAAACCTTCTCCACTGCAATCGCCATCATC
1 GCTTCAGAGACAGTGGCCTTAGCACTATCATTAGCTAAACCATCTCCATTGCAATCGCCATCATC
* * *
2831357 AGCTACAGCCATTTCAGAACCATCATTCTCCTTTGACCTGAAATCGAGAACATTG
66 AGCTACAGCCATTTCAGAACCCTCATTCTCTTTTGACCTGGAATCGAGAACATTG
* * * * * ** * * **
2831412 GCTTCAGACACAGTGTCATTGGCACCATCATTAGCTAAACCATCTCTGTTGCGATCACCATCGGC
1 GCTTCAGAGACAGTGGCCTTAGCACTATCATTAGCTAAACCATCTCCATTGCAATCGCCATCATC
** ** * * *
2831477 AATTACAGCCATTTCAGAACCCTTGTTCTCTTTTGATCTGAAATCGAGATCATTG
66 AGCTACAGCCATTTCAGAACCCTCATTCTCTTTTGACCTGGAATCGAGAACATTG
* * * * *
2831532 GCTTCAGAGACACTGGCCTTAGCACTATCATCAGCTAAACCATCTCCATTGCAATCACTAGCATC
1 GCTTCAGAGACAGTGGCCTTAGCACTATCATTAGCTAAACCATCTCCATTGCAATCGCCATCATC
* * * ** * * * * * *
2831597 AACTTCAGCCATTTCAGAGCTGTCGTTCTCTTTTGAACTGAAATCAACATCATTG
66 AGCTACAGCCATTTCAGAACCCTCATTCTCTTTTGACCTGGAATCGAGAACATTG
* * * * * * *
2831652 AC-T----G-CAGCGGCCTTAGCATTATCATTAGCTAGACCATCTCCATTGTAATCACTATCATC
1 GCTTCAGAGACAGTGGCCTTAGCACTATCATTAGCTAAACCATCTCCATTGCAATCGCCATCATC
* * * * * *
2831711 AGCTACAGCAATTTCA-AATTCCTCATTCCCTCTAGACCTGAAATCGAGAACATTG
66 AGCTACAGCCATTTCAGAA-CCCTCATTCTCTTTTGACCTGGAATCGAGAACATTG
2831766 GCTTCA
1 GCTTCA
2831772 ACACTACCAT
Statistics
Matches: 883, Mismatches: 156, Indels: 55
0.81 0.14 0.05
Matches are distributed among these distances:
108 95 0.11
109 2 0.00
110 1 0.00
111 1 0.00
113 2 0.00
114 129 0.15
115 4 0.00
117 2 0.00
118 1 0.00
119 8 0.01
120 634 0.72
121 4 0.00
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (120 bp):
GCTTCAGAGACAGTGGCCTTAGCACTATCATTAGCTAAACCATCTCCATTGCAATCGCCATCATC
AGCTACAGCCATTTCAGAACCCTCATTCTCTTTTGACCTGGAATCGAGAACATTG
Found at i:2831278 original size:108 final size:107
Alignment explanation
Indices: 2831089--2831431 Score: 409
Period size: 108 Copynumber: 3.1 Consensus size: 107
2831079 GCCTTGGCAC
*
2831089 TATCATTAGCTAACACATTTCCATTGCAATCACCATCATCAGCTACAGCCATTTCAGATCCTCCA
1 TATCATTAGCTAA-ACATTTCCATTGCAATCACCATCATCAGCTACAGCCATTTCAGAACCTCCA
*
2831154 TTCTCTTTTAACCTGGAATCGAGAACATTGGCTTCAGAGACAG
65 TTCTCTTTTGACCTGGAATCGAGAACATTGGCTTCAGAGACAG
* *
2831197 TATCATTAGCTAAAGCATTTCCATTGCAATCACCATCATCGGCTACAGCCATTTCAGAGCCTCCA
1 TATCATTAGCTAAA-CATTTCCATTGCAATCACCATCATCAGCTACAGCCATTTCAGAACCTCCA
* *
2831262 TTCTCTTTTGACCTGGAATCAATAACATTGGCTTCAGAGACAGTGGCCTTAG
65 TTCTCTTTTGACCTGGAATCGAGAACATTGGCTTCAGAG--A-----C--AG
* * * *
2831314 CACTATCATTAGATAAACCTTCTCCACTGCAATCGCCATCATCAGCTACAGCCATTTCAGAACCA
1 ---TATCATTAGCTAAACATT-TCCATTGCAATCACCATCATCAGCTACAGCCATTTCAGAACC-
* * *
2831379 T-CATTCTCCTTTGACCTGAAATCGAGAACATTGGCTTCAGACACAG
61 TCCATTCTCTTTTGACCTGGAATCGAGAACATTGGCTTCAGAGACAG
*
2831425 TGTCATT
1 TATCATT
2831432 GGCACCATCA
Statistics
Matches: 203, Mismatches: 17, Indels: 30
0.81 0.07 0.12
Matches are distributed among these distances:
107 1 0.00
108 103 0.51
110 1 0.00
111 2 0.01
113 1 0.00
115 1 0.00
117 2 0.01
118 1 0.00
119 3 0.01
120 87 0.43
121 1 0.00
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (107 bp):
TATCATTAGCTAAACATTTCCATTGCAATCACCATCATCAGCTACAGCCATTTCAGAACCTCCAT
TCTCTTTTGACCTGGAATCGAGAACATTGGCTTCAGAGACAG
Found at i:2831354 original size:348 final size:348
Alignment explanation
Indices: 2830643--2831771 Score: 1085
Period size: 348 Copynumber: 3.2 Consensus size: 348
2830633 CTCCATTGCA
* * * *
2830643 ATCATCAGCTACTACCATTCCAGAACTCTCATTCTCTTTTAACCTGAAATCGAGAACATTGGCTT
1 ATCATCAGCTACAACCATTTCAGAACCCTCATTCTCTTTTGACCTGAAATCGAGAACATTGGCTT
* * * * * * **
2830708 CAGAAACAGCGACCCTAGCACTATCATTAGTTAAACCATCTCCATGGCAACCGTCATCATCAGCT
66 CAGAAACAGTGACCTTGGCACTATCATTAGCTAAACCATCTCCATTGCAATCACCATCATCAGCT
* * *
2830773 AC-GATCATTTCAGAACCCCCATTCTCTTTTGACTTGGAATCGATAACATTGGCTTCAGAGACAG
131 ACAG-CCATTTCAGAA-CCCCATTCTCTTTTGACCTGGAATCGAGAACATTGGCTTCAGAG--A-
* * * ** *
2830837 TGGCCTTAGCACTATCATTACCTAAATCGTCTCCATTGCAGTTGCCATCATCAGCTACAGCCGTT
191 ----C--AG--CTATCATTACCTAAAGCATCTCCATTGCAATCACCATCATCAGCTACAGCCATT
*
2830902 TCAGAGCCCTCATTCTCTTTCAACCTGGAATCGAGAACATTGGCTTCAGAGACAGTGGCCTTAGC
248 TCAGAGCCCTCATTCTCTTTCAACCTGGAATCAAGAACATTGGCTTCAGAGACAGTGGCCTTAGC
* * *
2830967 ACTATCATTAGCTAAACCATCTCCATTGCAATTGCC
313 ACTATCATTAGATAAACCATCTCCACTGCAATCGCC
* * * ** * *
2831003 ATCATCAGCTACAACTATTTCAGAACCCTCAGTCTCTTTTGACCTGGAATAAATAGCATTGGCTT
1 ATCATCAGCTACAACCATTTCAGAACCCTCATTCTCTTTTGACCTGAAATCGAGAACATTGGCTT
* * *
2831068 CAGAGACAGTGGCCTTGGCACTATCATTAGCT-AACACATTTCCATTGCAATCACCATCATCAGC
66 CAGAAACAGTGACCTTGGCACTATCATTAGCTAAAC-CATCTCCATTGCAATCACCATCATCAGC
* *
2831132 TACAGCCATTTCAGATCCTCCATTCTCTTTTAACCTGGAATCGAGAACATTGGCTTCAGAGACAG
130 TACAGCCATTTCAGAACC-CCATTCTCTTTTGACCTGGAATCGAGAACATTGGCTTCAGAGACAG
* * *
2831197 -TATCATTAGCTAAAGCATTTCCATTGCAATCACCATCATCGGCTACAGCCATTTCAGAG-CCTC
194 CTATCATTACCTAAAGCATCTCCATTGCAATCACCATCATCAGCTACAGCCATTTCAGAGCCCT-
** *
2831260 CATTCTCTTTTGACCTGGAATCAATAACATTGGCTTCAGAGACAGTGGCCTTAGCACTATCATTA
258 CATTCTCTTTCAACCTGGAATCAAGAACATTGGCTTCAGAGACAGTGGCCTTAGCACTATCATTA
*
2831325 GATAAACCTTCTCCACTGCAATCGCC
323 GATAAACCATCTCCACTGCAATCGCC
* * *
2831351 ATCATCAGCTACAGCCATTTCAGAACCATCATTCTCCTTTGACCTGAAATCGAGAACATTGGCTT
1 ATCATCAGCTACAACCATTTCAGAACCCTCATTCTCTTTTGACCTGAAATCGAGAACATTGGCTT
* * * * ** * ** **
2831416 CAGACACAGTGTCATTGGCACCATCATTAGCTAAACCATCTCTGTTGCGATCACCATCGGCAATT
66 CAGAAACAGTGACCTTGGCACTATCATTAGCTAAACCATCTCCATTGCAATCACCATCATCAGCT
** * * *
2831481 ACAGCCATTTCAGAACCCTTGTTCTCTTTTGATCTGAAATCGAGATCATTGGCTTCAGAGACACT
131 ACAGCCATTTCAGAACCC-CATTCTCTTTTGACCTGGAATCGAGAACATTGGCTTCAGAGACA--
* * * * * *
2831546 GGCCTTAGCACTATCATCAGCTAAACCATCTCCATTGCAATCACTAGCATCAACTTCAGCCATTT
193 -G-C-TATCA-T-T-A-C--CTAAAGCATCTCCATTGCAATCACCATCATCAGCTACAGCCATTT
** * * * * * * *
2831611 CAGAGCTGTCGTTCTCTTTTGAA-CTGAAATCAACATCATTGAC-T----G-CAGCGGCCTTAGC
249 CAGAGCCCTCATTCTC-TTTCAACCTGGAATCAAGAACATTGGCTTCAGAGACAGTGGCCTTAGC
* * * * * * *
2831669 ATTATCATTAGCTAGACCATCTCCATTGTAATCACT
313 ACTATCATTAGATAAACCATCTCCACTGCAATCGCC
* * * * * *
2831705 ATCATCAGCTACAGCAATTTCA-AATTCCTCATTCCCTCTAGACCTGAAATCGAGAACATTGGCT
1 ATCATCAGCTACAACCATTTCAGAA-CCCTCATTCTCTTTTGACCTGAAATCGAGAACATTGGCT
2831769 TCA
65 TCA
2831772 ACACTACCAT
Statistics
Matches: 641, Mismatches: 107, Indels: 48
0.81 0.13 0.06
Matches are distributed among these distances:
347 4 0.01
348 291 0.45
349 3 0.00
351 3 0.00
353 3 0.00
354 101 0.16
355 2 0.00
356 1 0.00
357 1 0.00
358 1 0.00
359 6 0.01
360 219 0.34
361 6 0.01
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (348 bp):
ATCATCAGCTACAACCATTTCAGAACCCTCATTCTCTTTTGACCTGAAATCGAGAACATTGGCTT
CAGAAACAGTGACCTTGGCACTATCATTAGCTAAACCATCTCCATTGCAATCACCATCATCAGCT
ACAGCCATTTCAGAACCCCATTCTCTTTTGACCTGGAATCGAGAACATTGGCTTCAGAGACAGCT
ATCATTACCTAAAGCATCTCCATTGCAATCACCATCATCAGCTACAGCCATTTCAGAGCCCTCAT
TCTCTTTCAACCTGGAATCAAGAACATTGGCTTCAGAGACAGTGGCCTTAGCACTATCATTAGAT
AAACCATCTCCACTGCAATCGCC
Found at i:2831366 original size:228 final size:228
Alignment explanation
Indices: 2830969--2831726 Score: 700
Period size: 228 Copynumber: 3.2 Consensus size: 228
2830959 GCCTTAGCAC
** *
2830969 TATCATTAGCTAAACCATCTCCATTGCAATTGCCATCATCAGCTACAACTATTTCAGAACCCTCA
1 TATCATTAGCTAAACCATCTCCATTGCAATCACCATCATCAGCTACAACCATTTCAGAACCCTCA
* * *
2831034 GTCTCTTTTGACCTGGAATAAATAGCATTGGCTTCAGAGACAGTGGCCTTGGCACTATCATTAGC
66 GTCTCTTTTGACCTGGAATAAATAACATTGGCTTCAGAGACAGTGGCCTTAGCACTATCATTAGA
* * *
2831099 TAACACATTTCCATTGCAATCACCATCATCAGCTACAGCCATTTCAGATCC-TCCATTCTCTTTT
131 TAACACATTTCCACTGCAATCACCATCATCAGCTACAGCCATTTCAGAACCAT-CATTCTCCTTT
* *
2831163 AACCTGGAATCGAGAACATTGGCTTCAGAGACAG
195 AACCTGAAATCGAGAACATTGGCTTCAGACACAG
* * * * *
2831197 TATCATTAGCTAAAGCATTTCCATTGCAATCACCATCATCGGCTACAGCCATTTCAG-AGCCTCC
1 TATCATTAGCTAAACCATCTCCATTGCAATCACCATCATCAGCTACAACCATTTCAGAACCCT-C
* *
2831261 ATTCTCTTTTGACCTGGAATCAATAACATTGGCTTCAGAGACAGTGGCCTTAGCACTATCATTAG
65 AGTCTCTTTTGACCTGGAATAAATAACATTGGCTTCAGAGACAGTGGCCTTAGCACTATCATTAG
* *
2831326 ATAA-ACCTTCTCCACTGCAATCGCCATCATCAGCTACAGCCATTTCAGAACCATCATTCTCCTT
130 ATAACACATT-TCCACTGCAATCACCATCATCAGCTACAGCCATTTCAGAACCATCATTCTCCTT
*
2831390 TGACCTGAAATCGAGAACATTGGCTTCAGACACAGTG
194 TAACCTGAAATCGAGAACATTGGCTTCAGACACA--G
** * ** ** *
2831427 TCATTGGCACCATCATTAGCTAAACCATCTCTGTTGCGATCACCATCGGCAATTACAGCCATTTC
1 ----T------ATCATTAGCTAAACCATCTCCATTGCAATCACCATCATCAGCTACAACCATTTC
* * * ** * * *
2831492 AGAACCCT-TGTTCTCTTTTGATCTGAAATCGAGATCATTGGCTTCAGAGACACTGGCCTTAGCA
56 AGAACCCTCAG-TCTCTTTTGACCTGGAATAAATAACATTGGCTTCAGAGACAGTGGCCTTAGCA
* * * * * * * * * **
2831556 CTATCATCAGCTAA-ACCATCTCCATTGCAATCACTAGCATCAACTTCAGCCATTTCAGAGCTGT
120 CTATCATTAGATAACA-CATTTCCACTGCAATCACCATCATCAGCTACAGCCATTTCAGAACCAT
* * * * * * * * *
2831620 CGTTCTCTTTTGAA-CTGAAATCAACATCATTGACTGCAGCGGCCTTAGCAT
184 CATTCTCCTTT-AACCTGAAATCGAGAACATTGGCTTCA---GAC--A-CAG
* * * * *
2831671 TATCATTAGCTAGACCATCTCCATTGTAATCACTATCATCAGCTACAGCAATTTCA
1 TATCATTAGCTAAACCATCTCCATTGCAATCACCATCATCAGCTACAACCATTTCA
2831727 AATTCCTCAT
Statistics
Matches: 431, Mismatches: 74, Indels: 44
0.79 0.13 0.08
Matches are distributed among these distances:
227 8 0.02
228 194 0.45
229 1 0.00
230 1 0.00
234 45 0.10
240 170 0.39
241 7 0.02
243 2 0.00
245 1 0.00
246 2 0.00
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (228 bp):
TATCATTAGCTAAACCATCTCCATTGCAATCACCATCATCAGCTACAACCATTTCAGAACCCTCA
GTCTCTTTTGACCTGGAATAAATAACATTGGCTTCAGAGACAGTGGCCTTAGCACTATCATTAGA
TAACACATTTCCACTGCAATCACCATCATCAGCTACAGCCATTTCAGAACCATCATTCTCCTTTA
ACCTGAAATCGAGAACATTGGCTTCAGACACAG
Found at i:2831608 original size:468 final size:473
Alignment explanation
Indices: 2830590--2831716 Score: 1250
Period size: 468 Copynumber: 2.4 Consensus size: 473
2830580 ATCTACAGAA
* * * * *
2830590 GCTTCAGAAACAGTGGTCTTAGCACTACCATAAGCTACACGATCTCCATTGCAATCA-TCAGC-T
1 GCTTCAGAGACAGTGGCCTTAGCACTATCATAAGCTAAACCATCTCCATTGCAATCACT-AGCAT
*
2830653 --AC-T-A-CCATTCCAGAACTCTCATTCTCTTTTAACCTGAAATCGAGAACATTGGCTTCAGAA
65 CAACTTCAGCCATTTCAGAACTCTCATTCTCTTTTAACCTGAAATCGAGAACATTGGCTTCAG--
* ** *
2830713 ACAGCGACCCTAGCACTATCATTAGTTAAACCATCTCCATGGCAACCGTCATCATCAGCTACGAT
128 A-A-CGA-CCTAG--CTATCATTAGCTAAACCATCTCCATGGCAACCACCATCATCAGCTACGAC
* *
2830778 CATTTCAGAACCCCCATTCTCTTTTGACTTGGAATCGATAACATTGGCTTCAGAGACAGTGGCCT
188 CATTTCAGAACCCCCATTCTCTTTTGACCTGGAATCAATAACATTGGCTTCAGAGACAGTGGCCT
* * * * * * *
2830843 TAGCACTATCATTACCTAAATCGTCTCCATTGCAGTTGCCATCATCAGCTACAGCCGTTTCAGAG
253 TAGCACTATCATTACATAAACCGTCTCCACTGCAATCGCCATCATCAGCTACAGCCATTTCAGAA
* * * * *
2830908 CCCTCATTCTCTTTCAACCTGGAATCGAGAACATTGGCTTCAGAGACAGTGGCCTTAGCACTATC
318 CCATCATTCTCTTTCAACCTGAAATCGAGAACATTGGCTTCAGACACAGTGGCATTAGCACCATC
** * * *
2830973 ATTAGCTAAACCATCTCCATTGCAATTGCCATCATCAGCTACAACTATTTCAGAACCCTCAGTCT
383 ATTAGCTAAACCATCTCCATTGCAATCACCATCAGCAACTACAACCATTTCAGAACCCTCAGTCT
* *
2831038 CTTTTGACCTGGAATAAATAGCATTG
448 CTTTTGACCTGAAATAAAGAGCATTG
* * * * *
2831064 GCTTCAGAGACAGTGGCCTTGGCACTATCATTAGCT-AACACATTTCCATTGCAATCACCATCAT
1 GCTTCAGAGACAGTGGCCTTAGCACTATCATAAGCTAAAC-CATCTCCATTGCAATCACTAGCAT
* * * *
2831128 CAGCTACAGCCATTTCAGATC-CTCCATTCTCTTTTAACCTGGAATCGAGAACATTGGCTTCAG-
65 CAACTTCAGCCATTTCAGAACTCT-CATTCTCTTTTAACCTGAAATCGAGAACATTGGCTTCAGA
* * * * *
2831191 A-GA-C-AG-TATCATTAGCTAAAGCATTTCCATTGCAATCACCATCATCGGCTAC-AGCCATTT
129 ACGACCTAGCTATCATTAGCTAAACCATCTCCATGGCAACCACCATCATCAGCTACGA-CCATTT
* *
2831251 CAGAGCCTCCATTCTCTTTTGACCTGGAATCAATAACATTGGCTTCAGAGACAGTGGCCTTAGCA
193 CAGAACCCCCATTCTCTTTTGACCTGGAATCAATAACATTGGCTTCAGAGACAGTGGCCTTAGCA
* *
2831316 CTATCATTAGATAAACCTTCTCCACTGCAATCGCCATCATCAGCTACAGCCATTTCAGAACCATC
258 CTATCATTACATAAACCGTCTCCACTGCAATCGCCATCATCAGCTACAGCCATTTCAGAACCATC
* * *
2831381 ATTCTCCTTT-GACCTGAAATCGAGAACATTGGCTTCAGACACAGTGTCATTGGCACCATCATTA
323 ATTCT-CTTTCAACCTGAAATCGAGAACATTGGCTTCAGACACAGTGGCATTAGCACCATCATTA
** * * * * *
2831445 GCTAAACCATCTCTGTTGCGATCACCATCGGCAATTACAGCCATTTCAGAACCCT-TGTTCTCTT
387 GCTAAACCATCTCCATTGCAATCACCATCAGCAACTACAACCATTTCAGAACCCTCAG-TCTCTT
* ** *
2831509 TTGATCTGAAATCGAGATCATTG
451 TTGACCTGAAATAAAGAGCATTG
* *
2831532 GCTTCAGAGACACTGGCCTTAGCACTATCATCAGCTAAACCATCTCCATTGCAATCACTAGCATC
1 GCTTCAGAGACAGTGGCCTTAGCACTATCATAAGCTAAACCATCTCCATTGCAATCACTAGCATC
* * * * * * * *
2831597 AACTTCAGCCATTTCAGAGCTGTCGTTCTCTTTTGAA-CTGAAATCAACATCATTGACTGCAG--
66 AACTTCAGCCATTTCAGAACTCTCATTCTCTTTT-AACCTGAAATCGAGAACATTGGCTTCAGAA
* * * * * *
2831659 CGGCCTTAGCATTATCATTAGCTAGACCATCTCCATTGTAATCACTATCATCAGCTAC
130 CGACC-TAGC--TATCATTAGCTAAACCATCTCCATGGCAACCACCATCATCAGCTAC
2831717 AGCAATTTCA
Statistics
Matches: 544, Mismatches: 87, Indels: 44
0.81 0.13 0.07
Matches are distributed among these distances:
467 2 0.00
468 380 0.70
469 11 0.02
471 4 0.01
472 1 0.00
473 2 0.00
474 90 0.17
475 1 0.00
476 1 0.00
477 1 0.00
479 3 0.01
480 48 0.09
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (473 bp):
GCTTCAGAGACAGTGGCCTTAGCACTATCATAAGCTAAACCATCTCCATTGCAATCACTAGCATC
AACTTCAGCCATTTCAGAACTCTCATTCTCTTTTAACCTGAAATCGAGAACATTGGCTTCAGAAC
GACCTAGCTATCATTAGCTAAACCATCTCCATGGCAACCACCATCATCAGCTACGACCATTTCAG
AACCCCCATTCTCTTTTGACCTGGAATCAATAACATTGGCTTCAGAGACAGTGGCCTTAGCACTA
TCATTACATAAACCGTCTCCACTGCAATCGCCATCATCAGCTACAGCCATTTCAGAACCATCATT
CTCTTTCAACCTGAAATCGAGAACATTGGCTTCAGACACAGTGGCATTAGCACCATCATTAGCTA
AACCATCTCCATTGCAATCACCATCAGCAACTACAACCATTTCAGAACCCTCAGTCTCTTTTGAC
CTGAAATAAAGAGCATTG
Found at i:2831752 original size:114 final size:114
Alignment explanation
Indices: 2831546--2831755 Score: 260
Period size: 114 Copynumber: 1.8 Consensus size: 114
2831536 CAGAGACACT
* *
2831546 GGCCTTAGCACTATCATCAGCTAAACCATCTCCATTGCAATCACTAGCATCAACTTCAGCCATTT
1 GGCCTTAGCACTATCATCAGCTAAACCATCTCCATTGCAATCACTAGCATCAACTACAGCAATTT
* * * * * *
2831611 CAGAGCTGTCGTTCTCTTTTGAACTGAAATCAACATCATTGACTGCAGC
66 CAAAGCTCTCATTCCCTCTAGAACTGAAATCAACATCATTGACTGCAGC
* * * * * *
2831660 GGCCTTAGCATTATCATTAGCTAGACCATCTCCATTGTAATCACTATCATCAGCTACAGCAATTT
1 GGCCTTAGCACTATCATCAGCTAAACCATCTCCATTGCAATCACTAGCATCAACTACAGCAATTT
* *
2831725 CAAA-TTCCTCATTCCCTCTAGACCTGAAATC
66 CAAAGCT-CTCATTCCCTCTAGAACTGAAATC
2831756 GAGAACATTG
Statistics
Matches: 79, Mismatches: 16, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
113 1 0.01
114 78 0.99
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.30
Consensus pattern (114 bp):
GGCCTTAGCACTATCATCAGCTAAACCATCTCCATTGCAATCACTAGCATCAACTACAGCAATTT
CAAAGCTCTCATTCCCTCTAGAACTGAAATCAACATCATTGACTGCAGC
Found at i:2838366 original size:18 final size:18
Alignment explanation
Indices: 2838343--2838379 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2838333 TTATTTTACA
2838343 TTTAATTAAAATTAAAAT
1 TTTAATTAAAATTAAAAT
* *
2838361 TTTAATTAATATTTAAAT
1 TTTAATTAAAATTAAAAT
2838379 T
1 T
2838380 GTGTAAGCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTAATTAAAATTAAAAT
Found at i:2838908 original size:25 final size:26
Alignment explanation
Indices: 2838862--2838919 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
2838852 TTTTTTAATT
*
2838862 AAAATATATTAAATTATAAGATAGATA
1 AAAATATATTAAA-TATAAGATAAATA
*
2838889 AAAATATATTAAA-ATTAGATAAATA
1 AAAATATATTAAATATAAGATAAATA
*
2838914 ATAATA
1 AAAATA
2838920 CTAAATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 15 0.54
27 13 0.46
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (26 bp):
AAAATATATTAAATATAAGATAAATA
Found at i:2838926 original size:22 final size:21
Alignment explanation
Indices: 2838883--2838924 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
2838873 AATTATAAGA
*
2838883 TAGATAAAAATATATTAAAAT
1 TAGATAAAAATATACTAAAAT
2838904 TAGATAAATAATAATACTAAA
1 TAGATAAA-AAT-ATACTAAA
2838925 TTTTTTGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 3 0.17
23 7 0.39
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (21 bp):
TAGATAAAAATATACTAAAAT
Found at i:2839123 original size:2 final size:2
Alignment explanation
Indices: 2839116--2839158 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2839106 TTCTCTTAAT
2839116 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2839158 T
1 T
2839159 TTTCTACATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2841644 original size:226 final size:225
Alignment explanation
Indices: 2841195--2841646 Score: 755
Period size: 225 Copynumber: 2.0 Consensus size: 225
2841185 TAGTTATCAA
*
2841195 CAACTGGATGAAGAAATAAAGCAACGGGAGACGAGGAGACACAAGAGTTGCAGCTAAAGACTAAA
1 CAACGGGATGAAGAAATAAAGCAACGGGAGACGAGGAGACACAAGAGTTGCAGCTAAAGACTAAA
*
2841260 CCGAACTCACAGCCTTCTTGCTCTCTTCTCGAGGTTTTCTTTCTACTTCTTTCTTCAGAACTTTC
66 CCGAACTCACAGCCTTCTTGCTCTCTTCTCGAGGTTTTCTTTCTACTTCTTTCTTCAAAACTTTC
* * *
2841325 TCCAGGGAAAAAAAAATGTGAGAATTTTTTATCAGAGAATATGGTACCGGGACATGTATATTGAT
131 CCCAGGGAAAAAAAAAGGTGAGAAATTTTTATCA-AGAATATGGTACCGGGACATGTATATTGAT
*
2841390 ATTAGTAGTAATACATATGGGTAACATTAAG
195 ATTAGTAGTAATACATATGGGCAACATTAAG
* * *
2841421 CAACGGGATGAGGAAATAAAGCAAC-GGAGGCGAGGAGACACAAGAGTTGCAGCTAAAGACTAAC
1 CAACGGGATGAAGAAATAAAGCAACGGGAGACGAGGAGACACAAGAGTTGCAGCTAAAGACTAAA
*
2841485 CCGAACTCACAGGCTTCTTGCTCTCTTCTCGAGGTTTTCTTTCTACTTCTTTCTTCAAAACTTTC
66 CCGAACTCACAGCCTTCTTGCTCTCTTCTCGAGGTTTTCTTTCTACTTCTTTCTTCAAAACTTTC
*
2841550 CCCCGGGAAAAGAAAAAGGTGAGACAAATTTTTATC-AGAATATGGTACCGGGACATGTATATTG
131 CCCAGGGAAAA-AAAAAGGTGAG--AAATTTTTATCAAGAATATGGTACCGGGACATGTATATTG
2841614 ATATTAGTAGTAATACATATGGGCAACATTAAG
193 ATATTAGTAGTAATACATATGGGCAACATTAAG
2841647 TCTAGCACAT
Statistics
Matches: 212, Mismatches: 11, Indels: 6
0.93 0.05 0.03
Matches are distributed among these distances:
225 109 0.51
226 93 0.44
228 10 0.05
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (225 bp):
CAACGGGATGAAGAAATAAAGCAACGGGAGACGAGGAGACACAAGAGTTGCAGCTAAAGACTAAA
CCGAACTCACAGCCTTCTTGCTCTCTTCTCGAGGTTTTCTTTCTACTTCTTTCTTCAAAACTTTC
CCCAGGGAAAAAAAAAGGTGAGAAATTTTTATCAAGAATATGGTACCGGGACATGTATATTGATA
TTAGTAGTAATACATATGGGCAACATTAAG
Found at i:2847867 original size:284 final size:284
Alignment explanation
Indices: 2847357--2847926 Score: 1131
Period size: 284 Copynumber: 2.0 Consensus size: 284
2847347 GTCATGGTTC
2847357 TACTAAATGGAAGCTCATGTCTGCATCTTTAATGGCAATTTAAATAAAAATAAAAATTATTGTGT
1 TACTAAATGGAAGCTCATGTCTGCATCTTTAATGGCAATTTAAATAAAAATAAAAATTATTGTGT
2847422 AAAATATACTCGATTGTAAAATTATTTAAATATGATCGAATTCAATTATAAACCTTACATCTAAT
66 AAAATATACTCGATTGTAAAATTATTTAAATATGATCGAATTCAATTATAAACCTTACATCTAAT
2847487 CATTTAGATATTTAAATAAAAAATAATCTTATTTATTTAAATAAATAAAGGCTTAATTATAAAAT
131 CATTTAGATATTTAAATAAAAAATAATCTTATTTATTTAAATAAATAAAGGCTTAATTATAAAAT
2847552 AAGTGATCAAACTATAATGTTTTTCACGAATAGGTGCTTACAGTTTTTTTTAATGATCTTGGTGC
196 AAGTGATCAAACTATAATGTTTTTCACGAATAGGTGCTTACAGTTTTTTTTAATGATCTTGGTGC
2847617 ATAACATTACAGACGTTATCATTT
261 ATAACATTACAGACGTTATCATTT
2847641 TACTAAATGGAAGCTCATGTCTGCATCTTTAATGGCAATTTAAATAAAAATAAAAATTATTGTGT
1 TACTAAATGGAAGCTCATGTCTGCATCTTTAATGGCAATTTAAATAAAAATAAAAATTATTGTGT
2847706 AAAATATACTCGATTGTAAAATTATTTAAATATGATCGAATTCAATTATAAACCTTACATCTAAT
66 AAAATATACTCGATTGTAAAATTATTTAAATATGATCGAATTCAATTATAAACCTTACATCTAAT
*
2847771 CATTTAGATATTTAAATAAAAAATAATCTTATTTATTTAAATAAATTAAGGCTTAATTATAAAAT
131 CATTTAGATATTTAAATAAAAAATAATCTTATTTATTTAAATAAATAAAGGCTTAATTATAAAAT
2847836 AAGTGATCAAACTATAATGTTTTTCACGAATAGGTGCTTACAGTTTTTTTTAATGATCTTGGTGC
196 AAGTGATCAAACTATAATGTTTTTCACGAATAGGTGCTTACAGTTTTTTTTAATGATCTTGGTGC
2847901 ATAACATTACAGACGTTATCATTT
261 ATAACATTACAGACGTTATCATTT
2847925 TA
1 TA
2847927 GGTGTCCGGG
Statistics
Matches: 285, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
284 285 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.39
Consensus pattern (284 bp):
TACTAAATGGAAGCTCATGTCTGCATCTTTAATGGCAATTTAAATAAAAATAAAAATTATTGTGT
AAAATATACTCGATTGTAAAATTATTTAAATATGATCGAATTCAATTATAAACCTTACATCTAAT
CATTTAGATATTTAAATAAAAAATAATCTTATTTATTTAAATAAATAAAGGCTTAATTATAAAAT
AAGTGATCAAACTATAATGTTTTTCACGAATAGGTGCTTACAGTTTTTTTTAATGATCTTGGTGC
ATAACATTACAGACGTTATCATTT
Found at i:2849838 original size:59 final size:59
Alignment explanation
Indices: 2849768--2849882 Score: 142
Period size: 59 Copynumber: 1.9 Consensus size: 59
2849758 AACGATGACT
* * * *
2849768 ATCATTTTAAATTAGTCCTCAAA-CTTTGAGCATTTCAATTTCATCCCCAAACTATGAAC
1 ATCATTCTAAATTAGTCCCCAAATCTTTGAACATTCCAATTTCAT-CCCAAACTATGAAC
* * *
2849827 ATCATTCTAAATTGGTCCCCAAATTTTTTTAACATTCCAATTTCATCCCAAACTAT
1 ATCATTCTAAATTAGTCCCCAAA-TCTTTGAACATTCCAATTTCATCCCAAACTAT
2849883 ATGTATATAC
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
59 20 0.43
60 10 0.21
61 17 0.36
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.37
Consensus pattern (59 bp):
ATCATTCTAAATTAGTCCCCAAATCTTTGAACATTCCAATTTCATCCCAAACTATGAAC
Found at i:2850114 original size:60 final size:60
Alignment explanation
Indices: 2850006--2850188 Score: 226
Period size: 60 Copynumber: 3.1 Consensus size: 60
2849996 TTTGGATGAA
** ** * * *
2850006 TTTGGGGATGAAATTGGAATATTCAAAAGTGGAGGGACCAATTCAGAATAAGAGATATAG
1 TTTGGGGATGAAATTAAAATATTCAAAAGTTTAAGGACCAATTTAGAATGAGAGATATAG
* * *
2850066 TTTGGGGATGAGATTAAAATGTTCAAAAGTTTAAGGACTAATTTAGAATGAGAG-TCATAG
1 TTTGGGGATGAAATTAAAATATTCAAAAGTTTAAGGACCAATTTAGAATGAGAGAT-ATAG
* * *
2850126 TTTGGGGATAAAATTAAAATATTCAAAAGTTTAAAGACCAATTTAAAATGAGA-ATATAG
1 TTTGGGGATGAAATTAAAATATTCAAAAGTTTAAGGACCAATTTAGAATGAGAGATATAG
2850185 TTTG
1 TTTG
2850189 TGGACATATG
Statistics
Matches: 105, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
59 9 0.09
60 96 0.91
ACGTcount: A:0.42, C:0.05, G:0.23, T:0.30
Consensus pattern (60 bp):
TTTGGGGATGAAATTAAAATATTCAAAAGTTTAAGGACCAATTTAGAATGAGAGATATAG
Found at i:2853809 original size:14 final size:14
Alignment explanation
Indices: 2853790--2853817 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2853780 TTCCAGGCAT
2853790 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
2853804 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
2853818 AAGCATCCGA
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:0.21, C:0.43, G:0.29, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:2853832 original size:20 final size:20
Alignment explanation
Indices: 2853804--2853858 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
2853794 GGCCATCCGA
2853804 CCGAGGCCATCCGAAAGCAT
1 CCGAGGCCATCCGAAAGCAT
* *
2853824 CCGATGCCATCCGAGAGCAT
1 CCGAGGCCATCCGAAAGCAT
*
2853844 TCGAGGCCATCCGAA
1 CCGAGGCCATCCGAA
2853859 CGAGCTATGC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.27, C:0.35, G:0.25, T:0.13
Consensus pattern (20 bp):
CCGAGGCCATCCGAAAGCAT
Found at i:2853883 original size:10 final size:10
Alignment explanation
Indices: 2853785--2853924 Score: 64
Period size: 10 Copynumber: 13.0 Consensus size: 10
2853775 CGACCTTCCA
2853785 GGCATCCGAG
1 GGCATCCGAG
*
2853795 GCCATCCGACCG
1 GGCATCCGA--G
*
2853807 AGGCCATCCGAA
1 -GG-CATCCGAG
* *
2853819 AGCATCCGAT
1 GGCATCCGAG
*
2853829 GCCATCCGAG
1 GGCATCCGAG
* *
2853839 AGCATTCGAG
1 GGCATCCGAG
*
2853849 GCCATCCGAACG
1 GGCATCCG-A-G
* *
2853861 AGCTATGCGAG
1 GGC-ATCCGAG
2853872 GGCATCCGAG
1 GGCATCCGAG
*
2853882 GGCAACCGAG
1 GGCATCCGAG
*
2853892 CGAGCTATGCGAG
1 -G-GC-ATCCGAG
*
2853905 GGAATCCGAG
1 GGCATCCGAG
*
2853915 GGCAACCGAG
1 GGCATCCGAG
2853925 CGAGGGTAGG
Statistics
Matches: 94, Mismatches: 26, Indels: 20
0.67 0.19 0.14
Matches are distributed among these distances:
10 63 0.67
11 7 0.07
12 7 0.07
13 10 0.11
14 7 0.07
ACGTcount: A:0.26, C:0.31, G:0.33, T:0.11
Consensus pattern (10 bp):
GGCATCCGAG
Found at i:2853896 original size:33 final size:33
Alignment explanation
Indices: 2853835--2853928 Score: 134
Period size: 33 Copynumber: 2.8 Consensus size: 33
2853825 CGATGCCATC
* * * * *
2853835 CGAGAGCATTCGAGGCCATCCGAACGAGCTATG
1 CGAGGGCATCCGAGGGCAACCGAGCGAGCTATG
2853868 CGAGGGCATCCGAGGGCAACCGAGCGAGCTATG
1 CGAGGGCATCCGAGGGCAACCGAGCGAGCTATG
*
2853901 CGAGGGAATCCGAGGGCAACCGAGCGAG
1 CGAGGGCATCCGAGGGCAACCGAGCGAG
2853929 GGTAGGTCGA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.27, C:0.27, G:0.37, T:0.10
Consensus pattern (33 bp):
CGAGGGCATCCGAGGGCAACCGAGCGAGCTATG
Found at i:2854010 original size:33 final size:33
Alignment explanation
Indices: 2853973--2854045 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
2853963 CGCACGGTCG
* *
2853973 CTCGGATTCCCTCGCATAGCTCGCTCGGTTGCC
1 CTCGGATACCCTCGCATAGCTCGCTCGGATGCC
* *
2854006 CTCGGATACCCTCGCATAGCTCGTTCGGATGGC
1 CTCGGATACCCTCGCATAGCTCGCTCGGATGCC
2854039 CTCGGAT
1 CTCGGAT
2854046 GCTTTCGGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.12, C:0.36, G:0.26, T:0.26
Consensus pattern (33 bp):
CTCGGATACCCTCGCATAGCTCGCTCGGATGCC
Found at i:2854041 original size:23 final size:20
Alignment explanation
Indices: 2854015--2854062 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 20
2854005 CCTCGGATAC
2854015 CCTCGCATAGCTCGTTCGGATGG
1 CCTCGCAT-GCT--TTCGGATGG
*
2854038 CCTCGGATGCTTTCGGATGG
1 CCTCGCATGCTTTCGGATGG
2854058 CCTCG
1 CCTCG
2854063 GTCGGATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 14 0.58
22 3 0.12
23 7 0.29
ACGTcount: A:0.10, C:0.31, G:0.31, T:0.27
Consensus pattern (20 bp):
CCTCGCATGCTTTCGGATGG
Found at i:2864836 original size:16 final size:16
Alignment explanation
Indices: 2864812--2864845 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2864802 TATCGCCGAC
*
2864812 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
2864828 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
2864844 CG
1 CG
2864846 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:2867584 original size:20 final size:20
Alignment explanation
Indices: 2867534--2867586 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
2867524 CGCGTTGCAT
* *
2867534 TTCGCGTTGCCATTTTTCAT
1 TTCGCGTTGCGATTTTTCAG
2867554 TTCGCGTTGCGATTTTTCAG
1 TTCGCGTTGCGATTTTTCAG
2867574 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
2867587 AGTTGAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.45
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTTCAG
Found at i:2867622 original size:41 final size:41
Alignment explanation
Indices: 2867560--2867671 Score: 170
Period size: 41 Copynumber: 2.7 Consensus size: 41
2867550 TCATTTCGCG
* *
2867560 TTGCGATTTTTCAGTTCGCGTTGCGATAGTTGAAAATAGCA
1 TTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATAGCA
* * *
2867601 TTGCAATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCG
1 TTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATAGCA
*
2867642 TTACGATTTTCCATTTCGCGTTGCGATAGT
1 TTGCGATTTTCCATTTCGCGTTGCGATAGT
2867672 GCGAATGCAA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.38
Consensus pattern (41 bp):
TTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATAGCA
Found at i:2867640 original size:21 final size:21
Alignment explanation
Indices: 2867575--2867648 Score: 60
Period size: 21 Copynumber: 3.6 Consensus size: 21
2867565 ATTTTTCAGT
2867575 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * * * ** **
2867596 TAGCATTGCAAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
2867616 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*
2867637 TCGCGTTACGAT
1 TCGCGTTGCGAT
2867649 TTTCCATTTC
Statistics
Matches: 35, Mismatches: 17, Indels: 2
0.65 0.31 0.04
Matches are distributed among these distances:
20 12 0.34
21 23 0.66
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:2869208 original size:4 final size:4
Alignment explanation
Indices: 2869201--2869225 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2869191 TTTCAATACG
2869201 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
2869226 TCATTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:2874330 original size:18 final size:18
Alignment explanation
Indices: 2874309--2874353 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
2874299 GGTTTGGAGC
2874309 TGGAGGTGGA-CTAGGTGG
1 TGGAGGTGGAGC-AGGTGG
*
2874327 TGGAGGCGGAGCAGGTGG
1 TGGAGGTGGAGCAGGTGG
*
2874345 AGGAGGTGG
1 TGGAGGTGG
2874354 GTTTGGTGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.18, C:0.07, G:0.60, T:0.16
Consensus pattern (18 bp):
TGGAGGTGGAGCAGGTGG
Found at i:2874416 original size:30 final size:30
Alignment explanation
Indices: 2874373--2874450 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 30
2874363 TGGTGGTGGT
* * *
2874373 GGTGGAATCGGAGGAGGAGCGGGTGCCGGG
1 GGTGGAATTGGAGGAGGAGCGGGTGCAGGC
* * *
2874403 GGTGGATTTGGAGGTGGAGCTGGTGCAGGC
1 GGTGGAATTGGAGGAGGAGCGGGTGCAGGC
*
2874433 GGTGGAGTTGGAGGAGGA
1 GGTGGAATTGGAGGAGGA
2874451 TTACCTTGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.17, C:0.09, G:0.58, T:0.17
Consensus pattern (30 bp):
GGTGGAATTGGAGGAGGAGCGGGTGCAGGC
Found at i:2898466 original size:27 final size:27
Alignment explanation
Indices: 2898428--2898483 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
2898418 ATGAAGATCT
*
2898428 TGATGCTGTGGACTTT-AAAGTTCAAAG
1 TGATGCTATGGACTTTCAAA-TTCAAAG
*
2898455 TGATGCTATGGAGTTTCAAATTCAAAG
1 TGATGCTATGGACTTTCAAATTCAAAG
2898482 TG
1 TG
2898484 GTGATGGCGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 23 0.88
28 3 0.12
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (27 bp):
TGATGCTATGGACTTTCAAATTCAAAG
Found at i:2898769 original size:2 final size:2
Alignment explanation
Indices: 2898762--2898796 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2898752 AAAAGAGTGT
2898762 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2898797 TGCTTTGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2900403 original size:16 final size:16
Alignment explanation
Indices: 2900382--2900414 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2900372 TAATAAATAA
*
2900382 ACGAACATGAACGAAC
1 ACGAACATAAACGAAC
2900398 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
2900414 A
1 A
2900415 ATTTTTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.24, G:0.15, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:2904038 original size:20 final size:20
Alignment explanation
Indices: 2904015--2904053 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2904005 AAAAAAGACC
*
2904015 GAAAATATCTCAAAAGACAT
1 GAAAACATCTCAAAAGACAT
* *
2904035 GAAAACGTGTCAAAAGACA
1 GAAAACATCTCAAAAGACA
2904054 AAATTATTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (20 bp):
GAAAACATCTCAAAAGACAT
Found at i:2904428 original size:25 final size:26
Alignment explanation
Indices: 2904390--2904441 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
2904380 TCTTAATTCC
*
2904390 TTAAAAAGCGCCTAAAAT-ATCTATTT
1 TTAAAAAACGCCTAAAATCAT-TATTT
2904416 TTAAAAAAC-CCTAAAATCATTATTT
1 TTAAAAAACGCCTAAAATCATTATTT
2904441 T
1 T
2904442 CTATATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.37
Consensus pattern (26 bp):
TTAAAAAACGCCTAAAATCATTATTT
Found at i:2915955 original size:16 final size:16
Alignment explanation
Indices: 2915936--2915984 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
2915926 AATAAAATAA
2915936 TTATAATTAATATATT
1 TTATAATTAATATATT
2915952 TTATAA--AATA-A--
1 TTATAATTAATATATT
2915963 TTATAATTAATATATT
1 TTATAATTAATATATT
2915979 TTATAA
1 TTATAA
2915985 AATAATTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
11 6 0.21
13 5 0.18
14 5 0.18
16 12 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTATAATTAATATATT
Found at i:2915957 original size:27 final size:27
Alignment explanation
Indices: 2915927--2915997 Score: 142
Period size: 27 Copynumber: 2.6 Consensus size: 27
2915917 ACATTATTAA
2915927 ATAAAATAATTATAATTAATATATTTT
1 ATAAAATAATTATAATTAATATATTTT
2915954 ATAAAATAATTATAATTAATATATTTT
1 ATAAAATAATTATAATTAATATATTTT
2915981 ATAAAATAATTATAATT
1 ATAAAATAATTATAATT
2915998 TATTTTAATC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
ATAAAATAATTATAATTAATATATTTT
Found at i:2915964 original size:21 final size:23
Alignment explanation
Indices: 2915938--2916004 Score: 64
Period size: 27 Copynumber: 2.7 Consensus size: 23
2915928 TAAAATAATT
2915938 ATAATTAATATATTTTATAAAATAA
1 ATAATTAATATATTTTAT-AAAT-A
2915963 TTATAATTAATATATTTTATAAAATA
1 --ATAATTAATATATTTTAT-AAATA
* *
2915989 ATTA-TAATTTATTTTA
1 ATAATTAATATATTTTA
2916005 ATCACAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
23 11 0.29
24 3 0.08
26 1 0.03
27 23 0.61
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATAATTAATATATTTTATAAATA
Found at i:2916476 original size:21 final size:18
Alignment explanation
Indices: 2916450--2916499 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 18
2916440 TTTTATTGTC
2916450 TTTTTATTTTCTTATATT
1 TTTTTATTTTCTTATATT
*
2916468 ATATCTTTATTTTCTTTTATT
1 -T-T-TTTATTTTCTTATATT
2916489 TTTTTATTTTC
1 TTTTTATTTTC
2916500 AATCAATCTG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 9 0.32
19 2 0.07
20 2 0.07
21 15 0.54
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTTATTTTCTTATATT
Found at i:2930990 original size:61 final size:61
Alignment explanation
Indices: 2930920--2931042 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
2930910 ATTTAGTTTT
2930920 ACACCAAATAAATCCCAAATTCAACTTTTTACAATTAGATATATATAATTTTATATAGAAA
1 ACACCAAATAAATCCCAAATTCAACTTTTTACAATTAGATATATATAATTTTATATAGAAA
2930981 ACACCAAATAAATCCCAAATTCAACTTTTTACAATTAGATATATATAATTTTATATAGAAA
1 ACACCAAATAAATCCCAAATTCAACTTTTTACAATTAGATATATATAATTTTATATAGAAA
2931042 A
1 A
2931043 AGAACTAAAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.48, C:0.15, G:0.03, T:0.34
Consensus pattern (61 bp):
ACACCAAATAAATCCCAAATTCAACTTTTTACAATTAGATATATATAATTTTATATAGAAA
Found at i:2934807 original size:17 final size:17
Alignment explanation
Indices: 2934785--2934820 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2934775 CATGATACGG
*
2934785 TAATTTATTATTTTATT
1 TAATTTATTATTCTATT
*
2934802 TAATTTATTCTTCTATT
1 TAATTTATTATTCTATT
2934819 TA
1 TA
2934821 TCTTGTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.67
Consensus pattern (17 bp):
TAATTTATTATTCTATT
Found at i:2934951 original size:42 final size:42
Alignment explanation
Indices: 2934892--2935007 Score: 187
Period size: 42 Copynumber: 2.8 Consensus size: 42
2934882 CCCGAATTCT
* *
2934892 CGTGTTTATTTCACGTAATTCGTTTTTCGGAAAATGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCC
2934934 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCC
* * *
2934976 CATGTTTGTTTAACGTAATTGGTTTTCCGGAA
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
2935008 TGTAATTCAT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.46
Consensus pattern (42 bp):
CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCC
Found at i:2935226 original size:20 final size:20
Alignment explanation
Indices: 2935201--2935239 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2935191 ATTTATTTAT
2935201 TAATATTTATAATAATATAA
1 TAATATTTATAATAATATAA
* *
2935221 TAATATTTTTAATATTATA
1 TAATATTTATAATAATATA
2935240 TAAAATAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TAATATTTATAATAATATAA
Found at i:2935286 original size:28 final size:27
Alignment explanation
Indices: 2935207--2935302 Score: 78
Period size: 28 Copynumber: 3.6 Consensus size: 27
2935197 TTATTAATAT
2935207 TTATAATAATAT-AATA--ATATTTT-
1 TTATAATAATATAAATATCATATTTTA
* * *
2935230 TAAT-ATTATATAAAATAATCA-ATTATA
1 TTATAATAATAT-AAAT-ATCATATTTTA
2935257 TTATAATAATATAAGATATCATATTTTA
1 TTATAATAATATAA-ATATCATATTTTA
*
2935285 TTTTAATAATATATAATA
1 TTATAATAATATA-AATA
2935303 AAAATTTTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
22 6 0.11
23 3 0.05
24 3 0.05
25 1 0.02
26 4 0.07
27 10 0.18
28 28 0.50
29 1 0.02
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (27 bp):
TTATAATAATATAAATATCATATTTTA
Found at i:2935320 original size:30 final size:29
Alignment explanation
Indices: 2935253--2935364 Score: 81
Period size: 28 Copynumber: 3.8 Consensus size: 29
2935243 AATAATCAAT
* *
2935253 TATATTATAATAATATA-AGATATCATATTT-
1 TATATT-TAATAATATATA-ATA-AAAATTTA
2935283 TAT-TTTAATAATATATAATAAAAATTTTA
1 TATATTTAATAATATATAATAAAAA-TTTA
**
2935312 TATATTTAATAATGA-ATAAT-ATTATTTA
1 TATATTTAATAAT-ATATAATAAAAATTTA
*
2935340 TATATTTAAATAATATTTTAATAAA
1 TATATTT-AATAATA-TATAATAAA
2935365 GATATTTAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
27 2 0.03
28 28 0.42
29 14 0.21
30 21 0.31
31 2 0.03
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (29 bp):
TATATTTAATAATATATAATAAAAATTTA
Found at i:2935384 original size:23 final size:23
Alignment explanation
Indices: 2935358--2935402 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2935348 AATAATATTT
2935358 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
2935381 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
2935403 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:2935555 original size:22 final size:22
Alignment explanation
Indices: 2935529--2935575 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2935519 AAAAATTATT
2935529 TTAATATTTTAAAAT-AATAATA
1 TTAAT-TTTTAAAATAAATAATA
**
2935551 TTAATTTTTATGATAAATAATA
1 TTAATTTTTAAAATAAATAATA
2935573 TTA
1 TTA
2935576 TTTATTACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TTAATTTTTAAAATAAATAATA
Found at i:2935788 original size:15 final size:15
Alignment explanation
Indices: 2935746--2935788 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
2935736 TTCCAGAAAT
*
2935746 GTAATTCATTTTTCA
1 GTAATTCATTTTCCA
**
2935761 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
2935775 GTAATTCATTTTCC
1 GTAATTCATTTTCC
2935789 GGAAAACTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.44
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:2935847 original size:35 final size:35
Alignment explanation
Indices: 2935808--2935879 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
2935798 ATTATAGTCA
2935808 AACTAAGTAACGAGGTTAAGAGTATTTCTTGATCT
1 AACTAAGTAACGAGGTTAAGAGTATTTCTTGATCT
2935843 AACTAAGTAACGAGGTTAAGAGTATTTCTTGATCT
1 AACTAAGTAACGAGGTTAAGAGTATTTCTTGATCT
2935878 AA
1 AA
2935880 GAACAGACAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.33
Consensus pattern (35 bp):
AACTAAGTAACGAGGTTAAGAGTATTTCTTGATCT
Found at i:2938315 original size:25 final size:25
Alignment explanation
Indices: 2938285--2938332 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2938275 CTCACAAACT
*
2938285 TAAAATTTTCAAGCTCGACTCGAAA
1 TAAAATATTCAAGCTCGACTCGAAA
* *
2938310 TAAAATATTGAAGCTCGTCTCGA
1 TAAAATATTCAAGCTCGACTCGA
2938333 GCTTGAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.29
Consensus pattern (25 bp):
TAAAATATTCAAGCTCGACTCGAAA
Found at i:2948871 original size:21 final size:22
Alignment explanation
Indices: 2948836--2948881 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 22
2948826 TTTTCCCGGA
*
2948836 TTTAAAATATAAATA-TA-AAT
1 TTTAAAAGATAAATATTATAAT
2948856 TTTAAAAGAGTAAATATTATAAT
1 TTTAAAAGA-TAAATATTATAAT
2948879 TTT
1 TTT
2948882 GTTAATACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 8 0.36
21 6 0.27
22 2 0.09
23 6 0.27
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.43
Consensus pattern (22 bp):
TTTAAAAGATAAATATTATAAT
Found at i:2950938 original size:199 final size:199
Alignment explanation
Indices: 2950598--2951005 Score: 782
Period size: 199 Copynumber: 2.1 Consensus size: 199
2950588 TTCATTTACA
2950598 TTATTTGGGAGGAAAGAAACAGAAGACTTCCAAGGAAGAGCTCGAACGATTGAAGAAATGTTAAG
1 TTATTTGGGAGGAAAGAAACAGAAGACTTCCAAGGAAGAGCTCGAACGATTGAAGAAATGTTAAG
*
2950663 CTCCATAAAGGAGATTGTTGGTACTCAACTTAGAAATCGAGATCTTGATAGACTTGATAATGTTA
66 CTCCATAAAGGAGATTGTTGGTACTCAACTTAGAAATCGAGATCTTAATAGACTTGATAATGTTA
2950728 ATATTTTACTTTGTAACAATTTGGGTATAGGCTAACCATTTTTTGTAGTAAATAGCTTGTCTTTG
131 ATATTTTACTTTGTAACAATTTGGGTATAGGCTAACCATTTTTTGTAGTAAATAGCTTGTCTTTG
2950793 TTCC
196 TTCC
*
2950797 TTATTTGGGTGGAAAGAAACAGAAGACTTCCAAGGAAGAGCTCGAACGATTGAAGAAATGTTAAG
1 TTATTTGGGAGGAAAGAAACAGAAGACTTCCAAGGAAGAGCTCGAACGATTGAAGAAATGTTAAG
2950862 CTCCATAAAGGAGATTGTTGGTACTCAACTTAGAAATCGAGATCTTAATAGACTTGATAATGTTA
66 CTCCATAAAGGAGATTGTTGGTACTCAACTTAGAAATCGAGATCTTAATAGACTTGATAATGTTA
2950927 ATATTTTACTTTGTAACAATTTGGGTATAGGCTAACCATTTTTTGTAGTAAATAGCTTGTCTTTG
131 ATATTTTACTTTGTAACAATTTGGGTATAGGCTAACCATTTTTTGTAGTAAATAGCTTGTCTTTG
2950992 TTCC
196 TTCC
2950996 TTGA-TTGGGA
1 TT-ATTTGGGA
2951006 TGTTTTTGTA
Statistics
Matches: 205, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
199 204 1.00
200 1 0.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.34
Consensus pattern (199 bp):
TTATTTGGGAGGAAAGAAACAGAAGACTTCCAAGGAAGAGCTCGAACGATTGAAGAAATGTTAAG
CTCCATAAAGGAGATTGTTGGTACTCAACTTAGAAATCGAGATCTTAATAGACTTGATAATGTTA
ATATTTTACTTTGTAACAATTTGGGTATAGGCTAACCATTTTTTGTAGTAAATAGCTTGTCTTTG
TTCC
Found at i:2952635 original size:72 final size:72
Alignment explanation
Indices: 2952514--2952731 Score: 355
Period size: 72 Copynumber: 3.0 Consensus size: 72
2952504 ATATGCATGG
* * *
2952514 CCACCACGACCATTCCCTCCCCATCCGCCAAGACCGTTCCCTCCCCACCCACCAAGACCGTTCCC
1 CCACCACGACCGTTCCCTCCCCATCCACCAAGACCGTTCCCTCCTCACCCACCAAGACCGTTCCC
2952579 TCCTCAC
66 TCCTCAC
*
2952586 CCACCACGACCGTTCCCTCCCCATCCACCAAGACCGTTCCCTCCTCACCCACCACGACCGTTCCC
1 CCACCACGACCGTTCCCTCCCCATCCACCAAGACCGTTCCCTCCTCACCCACCAAGACCGTTCCC
* *
2952651 TCCTGAT
66 TCCTCAC
* * *
2952658 CCACCACAACCGTTCCCTCCCCATCCACCAAGGCCGTTCCCTCCTCATCCACCAAGACCGTTCCC
1 CCACCACGACCGTTCCCTCCCCATCCACCAAGACCGTTCCCTCCTCACCCACCAAGACCGTTCCC
2952723 TCCTCAC
66 TCCTCAC
2952730 CC
1 CC
2952732 TCCTGGGGTT
Statistics
Matches: 134, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 134 1.00
ACGTcount: A:0.19, C:0.56, G:0.09, T:0.17
Consensus pattern (72 bp):
CCACCACGACCGTTCCCTCCCCATCCACCAAGACCGTTCCCTCCTCACCCACCAAGACCGTTCCC
TCCTCAC
Found at i:2952726 original size:24 final size:24
Alignment explanation
Indices: 2952514--2952728 Score: 288
Period size: 24 Copynumber: 9.0 Consensus size: 24
2952504 ATATGCATGG
* * *
2952514 CCACCACGACCATTCCCTCCCCAT
1 CCACCAAGACCGTTCCCTCCTCAT
* * *
2952538 CCGCCAAGACCGTTCCCTCCCCAC
1 CCACCAAGACCGTTCCCTCCTCAT
*
2952562 CCACCAAGACCGTTCCCTCCTCAC
1 CCACCAAGACCGTTCCCTCCTCAT
* *
2952586 CCACCACGACCGTTCCCTCCCCAT
1 CCACCAAGACCGTTCCCTCCTCAT
*
2952610 CCACCAAGACCGTTCCCTCCTCAC
1 CCACCAAGACCGTTCCCTCCTCAT
* *
2952634 CCACCACGACCGTTCCCTCCTGAT
1 CCACCAAGACCGTTCCCTCCTCAT
*
2952658 CCACCACA-ACCGTTCCCTCCCCAT
1 CCACCA-AGACCGTTCCCTCCTCAT
*
2952682 CCACCAAGGCCGTTCCCTCCTCAT
1 CCACCAAGACCGTTCCCTCCTCAT
2952706 CCACCAAGACCGTTCCCTCCTCA
1 CCACCAAGACCGTTCCCTCCTCA
2952729 CCCTCCTGGG
Statistics
Matches: 168, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
23 1 0.01
24 167 0.99
ACGTcount: A:0.19, C:0.55, G:0.09, T:0.17
Consensus pattern (24 bp):
CCACCAAGACCGTTCCCTCCTCAT
Found at i:2955728 original size:60 final size:60
Alignment explanation
Indices: 2955635--2955755 Score: 188
Period size: 60 Copynumber: 2.0 Consensus size: 60
2955625 ATTAAATATT
* *
2955635 TTCTCATTTCCTACTATTAATCTTAGTCATTCATTTTCACCCATCCAACGGTCCTAAATC
1 TTCTCATTTCCTACTATTAATCTGAGTCATTCATTTTCACCCATCCAACAGTCCTAAATC
* * * *
2955695 TTCTCATTTCCTATTGTTAATCTGAGTCATTCATTTTCACTCATCCAATAGTCCTAAATC
1 TTCTCATTTCCTACTATTAATCTGAGTCATTCATTTTCACCCATCCAACAGTCCTAAATC
2955755 T
1 T
2955756 ATATAAAACT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.25, C:0.27, G:0.06, T:0.42
Consensus pattern (60 bp):
TTCTCATTTCCTACTATTAATCTGAGTCATTCATTTTCACCCATCCAACAGTCCTAAATC
Found at i:2958135 original size:35 final size:35
Alignment explanation
Indices: 2958070--2958186 Score: 164
Period size: 35 Copynumber: 3.3 Consensus size: 35
2958060 ATATAGACGC
* * **
2958070 ACATAAAATTTA-AACGTCTACATTGGATAATCCAA
1 ACATAAAATTTATAA-ATCTAAATTACATAATCCAA
* *
2958105 ACGTAAAATTTATAAATCTAAATTATATAATCCAA
1 ACATAAAATTTATAAATCTAAATTACATAATCCAA
2958140 ACATAAAATTTATAAATCTAAATTACATAATCCAA
1 ACATAAAATTTATAAATCTAAATTACATAATCCAA
2958175 ACATAAAATTTA
1 ACATAAAATTTA
2958187 AAAGATATAT
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
35 72 0.97
36 2 0.03
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.32
Consensus pattern (35 bp):
ACATAAAATTTATAAATCTAAATTACATAATCCAA
Found at i:2958148 original size:21 final size:21
Alignment explanation
Indices: 2958124--2958184 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2958114 TTATAAATCT
2958124 AAATTATATAATCCAAACATA
1 AAATTATATAATCCAAACATA
*
2958145 AAATT-TAT-A---AATC-T-
1 AAATTATATAATCCAAACATA
*
2958159 AAATTACATAATCCAAACATA
1 AAATTATATAATCCAAACATA
2958180 AAATT
1 AAATT
2958185 TAAAAGATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 3 0.10
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.33
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATTATATAATCCAAACATA
Found at i:2962345 original size:23 final size:24
Alignment explanation
Indices: 2962300--2962346 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
2962290 TCATTTTTAT
*
2962300 AGATTATTAGTCGTAAATAATTTG
1 AGATTATTAGTCGCAAATAATTTG
* *
2962324 AGATT-TTAGTCGCACATCATTTG
1 AGATTATTAGTCGCAAATAATTTG
2962347 CGTCCCCGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (24 bp):
AGATTATTAGTCGCAAATAATTTG
Found at i:2962689 original size:2 final size:2
Alignment explanation
Indices: 2962682--2962707 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2962672 TTAAAAGGAT
2962682 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2962708 AACGTGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2962803 original size:8 final size:8
Alignment explanation
Indices: 2962790--2962816 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
2962780 CCATAATAAC
2962790 GACTCATT
1 GACTCATT
2962798 GACTCATT
1 GACTCATT
2962806 GACTCATT
1 GACTCATT
2962814 GAC
1 GAC
2962817 AACTTTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (8 bp):
GACTCATT
Found at i:2964469 original size:22 final size:22
Alignment explanation
Indices: 2964431--2964472 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2964421 TTTATTTTTA
2964431 TTATTTAAATATAAATTAAAGT
1 TTATTTAAATATAAATTAAAGT
*
2964453 TTATATTAATTAT-AATTAAA
1 TTAT-TTAAATATAAATTAAA
2964473 TATTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TTATTTAAATATAAATTAAAGT
Found at i:2964491 original size:18 final size:16
Alignment explanation
Indices: 2964462--2964495 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
2964452 TTTATATTAA
2964462 TTATAATTAAATATTT
1 TTATAATTAAATATTT
2964478 TTATATATTAAAATATTT
1 TTATA-ATT-AAATATTT
2964496 ATTTTATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 3 0.19
18 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATAATTAAATATTT
Found at i:2973308 original size:13 final size:13
Alignment explanation
Indices: 2973290--2973315 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2973280 AATATATGAG
2973290 ATTTTGAATTAAT
1 ATTTTGAATTAAT
2973303 ATTTTGAATTAAT
1 ATTTTGAATTAAT
2973316 TTCTGGTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
ATTTTGAATTAAT
Found at i:2978666 original size:95 final size:96
Alignment explanation
Indices: 2978558--2978749 Score: 332
Period size: 96 Copynumber: 2.0 Consensus size: 96
2978548 TTGTTCTAAG
*
2978558 ATAAAACATTCATGGTCAAAATACTTC-AAAAAAGTAAAACAAGTGATAAAATGACTATTTAATA
1 ATAAAACATTCATGGTCAAAATACTTCAAAAAAAGAAAAACAAGTGATAAAATGACTATTTAATA
*
2978622 AAATATTAGTCGTTAGGTGCCATTTCACCTT
66 AAATATTAGTCGTTAAGTGCCATTTCACCTT
*
2978653 ATAAAACATTCATGGTCAAAATATTTCAAAAAAAGAAAAACAAGTGATAAAATGACTATTTAATA
1 ATAAAACATTCATGGTCAAAATACTTCAAAAAAAGAAAAACAAGTGATAAAATGACTATTTAATA
* *
2978718 AAATGTTAGTCGTTAAGTGTCATTTCACCTT
66 AAATATTAGTCGTTAAGTGCCATTTCACCTT
2978749 A
1 A
2978750 AAATGAAGCA
Statistics
Matches: 91, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
95 26 0.29
96 65 0.71
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.31
Consensus pattern (96 bp):
ATAAAACATTCATGGTCAAAATACTTCAAAAAAAGAAAAACAAGTGATAAAATGACTATTTAATA
AAATATTAGTCGTTAAGTGCCATTTCACCTT
Found at i:2978781 original size:96 final size:93
Alignment explanation
Indices: 2978560--2978787 Score: 278
Period size: 96 Copynumber: 2.4 Consensus size: 93
2978550 GTTCTAAGAT
* *
2978560 AAAACATTCATGGTCAAAATACTTCAAAAAAGTAAAACAAGTGATAAAATGACTATTTAATAAAA
1 AAAACATTCATGATCAAAATAC-T-AAAAAAGAAAAACAAGTGATAAAATGACTATTTAATAAAA
* *
2978625 TATTAGTCGTTAGGTGCCATTTCACCTTAT
64 TATTAGTCGTTAAGTGCCATTTCACCTTAA
* *
2978655 AAAACATTCATGGTCAAAATATTTCAAAAAAAGAAAAACAAGTGATAAAATGACTATTTAATAAA
1 AAAACATTCATGATCAAAATA---CTAAAAAAGAAAAACAAGTGATAAAATGACTATTTAATAAA
* *
2978720 ATGTTAGTCGTTAAGTGTCATTTCACCTTAA
63 ATATTAGTCGTTAAGTGCCATTTCACCTTAA
* *
2978751 AATGAAGCATTGA-GAATCAAAATACTAAAAAACAAAA
1 AA--AA-CATTCATG-ATCAAAATACTAAAAAAGAAAA
2978788 TTGTGCCAAA
Statistics
Matches: 116, Mismatches: 10, Indels: 13
0.83 0.07 0.09
Matches are distributed among these distances:
95 21 0.18
96 78 0.67
98 4 0.03
99 13 0.11
ACGTcount: A:0.48, C:0.12, G:0.11, T:0.28
Consensus pattern (93 bp):
AAAACATTCATGATCAAAATACTAAAAAAGAAAAACAAGTGATAAAATGACTATTTAATAAAATA
TTAGTCGTTAAGTGCCATTTCACCTTAA
Found at i:2978955 original size:17 final size:17
Alignment explanation
Indices: 2978935--2978968 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2978925 TAAAATAAGT
*
2978935 ATTTACTTATTAAATAA
1 ATTTAATTATTAAATAA
2978952 ATTTAATTATTAAATAA
1 ATTTAATTATTAAATAA
2978969 TCTTTTATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTTAATTATTAAATAA
Found at i:2981335 original size:51 final size:51
Alignment explanation
Indices: 2981269--2981368 Score: 164
Period size: 51 Copynumber: 2.0 Consensus size: 51
2981259 CTTTTGCCTT
*
2981269 CTTAAACTCTTTGTTCTTATGCTTAGCATCAAGACATTCTTACACTTTTGC
1 CTTAAACTCTATGTTCTTATGCTTAGCATCAAGACATTCTTACACTTTTGC
* **
2981320 CTTAAACTCTATGTTCTTATGCTTAGCTTCTGGACATTCTTACACTTTT
1 CTTAAACTCTATGTTCTTATGCTTAGCATCAAGACATTCTTACACTTTT
2981369 TGCTTCATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.22, C:0.23, G:0.10, T:0.45
Consensus pattern (51 bp):
CTTAAACTCTATGTTCTTATGCTTAGCATCAAGACATTCTTACACTTTTGC
Found at i:2985210 original size:31 final size:31
Alignment explanation
Indices: 2985173--2985231 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
2985163 AGTTGTATGG
*
2985173 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATTTCAGTATTGCAAAACTAAA
2985204 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAGTATTGCAAAACT
2985232 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTGCAAAACTAAA
Found at i:2989391 original size:73 final size:73
Alignment explanation
Indices: 2989269--2989408 Score: 235
Period size: 73 Copynumber: 1.9 Consensus size: 73
2989259 CATTGTGACT
* * * *
2989269 CAATACCTCTTGATTTCTGTTGCATTTGGGATCTATGAAAGTGATAGTAATCATTTCTCTATGTG
1 CAATACCACTTGATTTCTGTTGCAGTTGGGATCTATGAAAGTGACAGTAATCATTTCTCAATGTG
2989334 TTTTAGAA
66 TTTTAGAA
*
2989342 CAATACCACTTGATTTCTGTTGTAGTTGGGATCTATGAAAGTGACAGTAATCATTTCTCAATGTG
1 CAATACCACTTGATTTCTGTTGCAGTTGGGATCTATGAAAGTGACAGTAATCATTTCTCAATGTG
2989407 TT
66 TT
2989409 GCAGAACTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 62 1.00
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.41
Consensus pattern (73 bp):
CAATACCACTTGATTTCTGTTGCAGTTGGGATCTATGAAAGTGACAGTAATCATTTCTCAATGTG
TTTTAGAA
Found at i:2996435 original size:2 final size:2
Alignment explanation
Indices: 2996423--2996468 Score: 83
Period size: 2 Copynumber: 22.5 Consensus size: 2
2996413 TATTTTATTA
2996423 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2996466 AT A
1 AT A
2996469 ATTTATTTGA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2997775 original size:20 final size:20
Alignment explanation
Indices: 2997750--2997789 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2997740 GAAATCTTTG
2997750 CTGAAAAGAAGATCTGGGTA
1 CTGAAAAGAAGATCTGGGTA
2997770 CTGAAAAGAAGATCTGGGTA
1 CTGAAAAGAAGATCTGGGTA
2997790 TGCTTTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.30, T:0.20
Consensus pattern (20 bp):
CTGAAAAGAAGATCTGGGTA
Found at i:3002178 original size:39 final size:39
Alignment explanation
Indices: 3002134--3002213 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
3002124 TACACTCGTG
*
3002134 TCTTGTTATTAGTGTTATTACCAGATTTCATTTAGTGAA
1 TCTTGTCATTAGTGTTATTACCAGATTTCATTTAGTGAA
3002173 TCTTGTCATTAGTGTTATTACCAGATTTCATTTAGTGAA
1 TCTTGTCATTAGTGTTATTACCAGATTTCATTTAGTGAA
3002212 TC
1 TC
3002214 CAAGAGCGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.47
Consensus pattern (39 bp):
TCTTGTCATTAGTGTTATTACCAGATTTCATTTAGTGAA
Found at i:3002947 original size:2 final size:2
Alignment explanation
Indices: 3002940--3002967 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3002930 CTAGGAATCC
3002940 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3002968 ACTTACTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3014885 original size:3 final size:3
Alignment explanation
Indices: 3014877--3014906 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3014867 TAATTGGGTA
3014877 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3014907 TACAGTGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3016839 original size:29 final size:30
Alignment explanation
Indices: 3016793--3016854 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
3016783 AAAATTTAAC
* * *
3016793 TAGTGACTAAAATGTAAATTTTG-AAAGTT
1 TAGTGACTAAAATATAAATATGGAAAAGTT
* *
3016822 TAGTGGCTAAAGTATAAATATGGAAAAGTT
1 TAGTGACTAAAATATAAATATGGAAAAGTT
3016852 TAG
1 TAG
3016855 GGACCGAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.34
Consensus pattern (30 bp):
TAGTGACTAAAATATAAATATGGAAAAGTT
Found at i:3025510 original size:2 final size:2
Alignment explanation
Indices: 3025503--3025529 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3025493 CATCAACCTT
3025503 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3025530 TAAAAAGTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3051868 original size:14 final size:15
Alignment explanation
Indices: 3051840--3051868 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3051830 CAAAATGAAA
3051840 TGTTAGAAATCAAAC
1 TGTTAGAAATCAAAC
3051855 TGTTAGAAAT-AAAC
1 TGTTAGAAATCAAAC
3051869 ATTAGACACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28
Consensus pattern (15 bp):
TGTTAGAAATCAAAC
Found at i:3054935 original size:59 final size:59
Alignment explanation
Indices: 3054819--3054935 Score: 146
Period size: 59 Copynumber: 2.0 Consensus size: 59
3054809 TCGATTATAA
* * * * * *
3054819 GGTGTTGCTTTATCGAGTCCCTTGACTCTTAAAAGTTACAAAATATTCATTCTACTATC
1 GGTGTTGCTTTATCGAATCCCTCGACTATTAAAAGTTACAAAATAGTCACTCGACTATC
* *
3054878 GGTGTTGCTTTGTCGAAT-CCTCCGACTATTAAAAGTTACAAAATGGTCACTCGACTAT
1 GGTGTTGCTTTATCGAATCCCT-CGACTATTAAAAGTTACAAAATAGTCACTCGACTAT
3054936 TAATATTCTA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
58 3 0.06
59 46 0.94
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (59 bp):
GGTGTTGCTTTATCGAATCCCTCGACTATTAAAAGTTACAAAATAGTCACTCGACTATC
Found at i:3063240 original size:21 final size:23
Alignment explanation
Indices: 3063208--3063258 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
3063198 ACCGAAAACA
*
3063208 TGTCA-AATGACAAA-AAAAA-G
1 TGTCATAAAGACAAATAAAAATG
3063228 TGTCATAAAGACAAATAAAAATG
1 TGTCATAAAGACAAATAAAAATG
*
3063251 TATCATAA
1 TGTCATAA
3063259 TGATAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 5 0.19
21 8 0.31
22 5 0.19
23 8 0.31
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.22
Consensus pattern (23 bp):
TGTCATAAAGACAAATAAAAATG
Found at i:3063256 original size:23 final size:21
Alignment explanation
Indices: 3063216--3063258 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
3063206 CATGTCAAAT
*
3063216 GACAAAAAAAAGTGTCATAAA
1 GACAAAAAAAAGTATCATAAA
3063237 GACAAATAAAAATGTATCATAA
1 GACAAA-AAAAA-GTATCATAA
3063259 TGATAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 5 0.26
23 8 0.42
ACGTcount: A:0.60, C:0.09, G:0.12, T:0.19
Consensus pattern (21 bp):
GACAAAAAAAAGTATCATAAA
Found at i:3071155 original size:12 final size:13
Alignment explanation
Indices: 3071130--3071159 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
3071120 AATTAAACTC
3071130 ATTAAGCAAGAAA
1 ATTAAGCAAGAAA
3071143 ATTAAGC-AGAAA
1 ATTAAGCAAGAAA
3071155 ATTAA
1 ATTAA
3071160 ATTTAGAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (13 bp):
ATTAAGCAAGAAA
Found at i:3076000 original size:4 final size:4
Alignment explanation
Indices: 3075991--3076031 Score: 64
Period size: 4 Copynumber: 10.2 Consensus size: 4
3075981 ATTGAGAGTT
* *
3075991 TCTG TCTG TCTA TCTA TCTG TCTG TCTG TCTG TCTG TCTG T
1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG T
3076032 ATGTATGTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.05, C:0.24, G:0.20, T:0.51
Consensus pattern (4 bp):
TCTG
Found at i:3076036 original size:4 final size:4
Alignment explanation
Indices: 3076029--3076341 Score: 626
Period size: 4 Copynumber: 78.2 Consensus size: 4
3076019 TCTGTCTGTC
3076029 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
3076077 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
3076125 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
3076173 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
3076221 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
3076269 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
3076317 TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA T
3076342 AAGAAGAGAA
Statistics
Matches: 309, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 309 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:3078762 original size:47 final size:47
Alignment explanation
Indices: 3078709--3078856 Score: 114
Period size: 47 Copynumber: 3.2 Consensus size: 47
3078699 TTTAATTGCT
3078709 TTTAATTGGTCGATAGTGACGGTCTTAGTTCAATGCCTCTCCTGTCG
1 TTTAATTGGTCGATAGTGACGGTCTTAGTTCAATGCCTCTCCTGTCG
* * * ** *
3078756 TTTAATT-GTCTGAGATAGTG-CTATGTTTCTAG--C-ATG--TTTAAT-TGCT
1 TTTAATTGGTC---GATAGTGAC--GGTCT-TAGTTCAATGCCTCTCCTGT-CG
*
3078802 TTTAATTGGTCGATAGTGACGGTCATAGTTCAATGCCTCTCCTGTCG
1 TTTAATTGGTCGATAGTGACGGTCTTAGTTCAATGCCTCTCCTGTCG
3078849 TTTAATTG
1 TTTAATTG
3078857 ACCGAGATTG
Statistics
Matches: 73, Mismatches: 13, Indels: 30
0.63 0.11 0.26
Matches are distributed among these distances:
42 3 0.04
43 2 0.03
44 8 0.11
45 5 0.07
46 14 0.19
47 22 0.30
48 5 0.07
49 8 0.11
50 3 0.04
51 3 0.04
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.42
Consensus pattern (47 bp):
TTTAATTGGTCGATAGTGACGGTCTTAGTTCAATGCCTCTCCTGTCG
Found at i:3078834 original size:93 final size:93
Alignment explanation
Indices: 3078675--3078909 Score: 355
Period size: 93 Copynumber: 2.5 Consensus size: 93
3078665 TCCTGTCGTT
* *
3078675 AGATAGTGCTATGTTTCTTGCATGTTTAATTGCTTTTAATTGGTCGATAGTGACGGTCTTAGTTC
1 AGATAGTGCTATGTTTCTAGCATGTTTAATTGCTTTTAATTGGTCGATAGTGACGGTCATAGTTC
* *
3078740 AATGCCTCTCCTGTCGTTTAATTGTCTG
66 AATGCCTCTCCTGTCGTTTAATTGACCG
3078768 AGATAGTGCTATGTTTCTAGCATGTTTAATTGCTTTTAATTGGTCGATAGTGACGGTCATAGTTC
1 AGATAGTGCTATGTTTCTAGCATGTTTAATTGCTTTTAATTGGTCGATAGTGACGGTCATAGTTC
3078833 AATGCCTCTCCTGTCGTTTAATTGACCG
66 AATGCCTCTCCTGTCGTTTAATTGACCG
* * * ** *
3078861 AGATTGTGCTATCTTTCGTGGCA-GTTTAATTAATTTTAATCGGTGCGAT
1 AGATAGTGCTATGTTTC-TAGCATGTTTAATTGCTTTTAATTGGT-CGAT
3078910 TTCAAAGCCT
Statistics
Matches: 130, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
93 122 0.94
94 8 0.06
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.42
Consensus pattern (93 bp):
AGATAGTGCTATGTTTCTAGCATGTTTAATTGCTTTTAATTGGTCGATAGTGACGGTCATAGTTC
AATGCCTCTCCTGTCGTTTAATTGACCG
Found at i:3082864 original size:18 final size:18
Alignment explanation
Indices: 3082842--3082881 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
3082832 ATTTTTAATA
*
3082842 AAAAATATAAAAAAATATT
1 AAAATTATAAAAAAA-ATT
*
3082861 AAAATTATATAAAAAATT
1 AAAATTATAAAAAAAATT
3082879 AAA
1 AAA
3082882 TTTCTTAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAATTATAAAAAAAATT
Found at i:3086601 original size:31 final size:31
Alignment explanation
Indices: 3086544--3086603 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
3086534 GTTATGTTCT
3086544 TGTTTATTTATTTTTAAAAGTATTAATATTC
1 TGTTTATTTATTTTTAAAAGTATTAATATTC
* * *
3086575 TGTTTATATTTTTTTTCAAA-TTTTAATAT
1 TGTTTAT-TTATTTTTAAAAGTATTAATAT
3086604 CATATTCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 15 0.60
32 10 0.40
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (31 bp):
TGTTTATTTATTTTTAAAAGTATTAATATTC
Found at i:3095426 original size:19 final size:18
Alignment explanation
Indices: 3095402--3095439 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3095392 AATGTAATTT
*
3095402 AAAATATTATTTTTTATTA
1 AAAATATTA-ATTTTATTA
3095421 AAAATATTAATTTTATTA
1 AAAATATTAATTTTATTA
3095439 A
1 A
3095440 CTTATTTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AAAATATTAATTTTATTA
Found at i:3095432 original size:32 final size:33
Alignment explanation
Indices: 3095361--3095433 Score: 80
Period size: 32 Copynumber: 2.2 Consensus size: 33
3095351 GTACTTCAGT
*
3095361 TTTAATATATAAATATTAATATTTTTAATAAAA
1 TTTAATTTATAAATATTAATATTTTTAATAAAA
* *
3095394 TGTAATTTA-AAATATT-AT-TTTTTATTAAAAA
1 TTTAATTTATAAATATTAATATTTTTAAT-AAAA
3095425 TATTAATTT
1 T-TTAATTT
3095434 TATTAACTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
30 7 0.21
31 7 0.21
32 13 0.38
33 7 0.21
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (33 bp):
TTTAATTTATAAATATTAATATTTTTAATAAAA
Found at i:3095562 original size:54 final size:54
Alignment explanation
Indices: 3095459--3095568 Score: 139
Period size: 54 Copynumber: 2.0 Consensus size: 54
3095449 GGAAGTATCT
* * * *
3095459 AATATTTTTATAGAAAAAAACAATATTTTAAATAGTAATTTATCGAAAATATTA
1 AATATTTTGATAAAAAAAAACAATATTTTAAATAATAATTTATCAAAAATATTA
* * * * *
3095513 AATATTTTGATAAAAAAAAATAATATTTTAGATAATATTTTGTTAAAAATATTA
1 AATATTTTGATAAAAAAAAACAATATTTTAAATAATAATTTATCAAAAATATTA
3095567 AA
1 AA
3095569 AAATATTAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (54 bp):
AATATTTTGATAAAAAAAAACAATATTTTAAATAATAATTTATCAAAAATATTA
Found at i:3101167 original size:8 final size:8
Alignment explanation
Indices: 3101154--3101203 Score: 100
Period size: 8 Copynumber: 6.2 Consensus size: 8
3101144 TCTACCCATA
3101154 CATACATG
1 CATACATG
3101162 CATACATG
1 CATACATG
3101170 CATACATG
1 CATACATG
3101178 CATACATG
1 CATACATG
3101186 CATACATG
1 CATACATG
3101194 CATACATG
1 CATACATG
3101202 CA
1 CA
3101204 ACTGTTTCAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 42 1.00
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (8 bp):
CATACATG
Found at i:3110035 original size:26 final size:26
Alignment explanation
Indices: 3109978--3110038 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
3109968 CCTAGTATTG
*
3109978 GTTTTGGTGCTTGGTGCTCTGTTCATT
1 GTTTT-GTGCTTGGTGCTCTGTCCATT
* *
3110005 ATTTTGTGCTTGGTGCTCTGTCCCTT
1 GTTTTGTGCTTGGTGCTCTGTCCATT
3110031 GTTTTGTG
1 GTTTTGTG
3110039 TGTCTGCAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 26 0.87
27 4 0.13
ACGTcount: A:0.03, C:0.16, G:0.28, T:0.52
Consensus pattern (26 bp):
GTTTTGTGCTTGGTGCTCTGTCCATT
Found at i:3110604 original size:5 final size:5
Alignment explanation
Indices: 3110588--3110623 Score: 63
Period size: 5 Copynumber: 7.0 Consensus size: 5
3110578 ACTCGGCAAT
3110588 ACTCG AACTCG ACTCG ACTCG ACTCG ACTCG ACTCG
1 ACTCG -ACTCG ACTCG ACTCG ACTCG ACTCG ACTCG
3110624 TTTACACCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.22, C:0.39, G:0.19, T:0.19
Consensus pattern (5 bp):
ACTCG
Found at i:3118254 original size:31 final size:30
Alignment explanation
Indices: 3118219--3118318 Score: 85
Period size: 31 Copynumber: 3.2 Consensus size: 30
3118209 ATTTATATTA
*
3118219 AATTTAAACTAAAAATTTTAAATAAAATACT
1 AATTTAAACT-TAAATTTTAAATAAAATACT
* * * *
3118250 AATTTAATTCTTAAATTTTAGATGAAGTAAC-
1 AATTTAA-ACTTAAATTTTAAATAAAAT-ACT
* * *
3118281 AATTTAAATTTTAAATTTTATATAAAATAAT
1 AATTTAAA-CTTAAATTTTAAATAAAATACT
3118312 AATTTAA
1 AATTTAA
3118319 TTATAAATCC
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
30 1 0.02
31 49 0.91
32 4 0.07
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (30 bp):
AATTTAAACTTAAATTTTAAATAAAATACT
Found at i:3120192 original size:17 final size:17
Alignment explanation
Indices: 3120170--3120205 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3120160 ATTTTGTAGG
* *
3120170 ATTCACATGCATTATAT
1 ATTCACATACAATATAT
3120187 ATTCACATACAATATAT
1 ATTCACATACAATATAT
3120204 AT
1 AT
3120206 ATATATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.39
Consensus pattern (17 bp):
ATTCACATACAATATAT
Found at i:3120352 original size:31 final size:31
Alignment explanation
Indices: 3120317--3120409 Score: 107
Period size: 31 Copynumber: 3.0 Consensus size: 31
3120307 TTTTGATTGG
3120317 ATTTAAAAATTAAATTATTATTTTATATAAA
1 ATTTAAAAATTAAATTATTATTTTATATAAA
** * * *
3120348 ATTTAAATGTT-AATTGTTAGTTTATCTAAA
1 ATTTAAAAATTAAATTATTATTTTATATAAA
* * *
3120378 ATTTAAGAATTAAATTAGTATTTTATTTAAA
1 ATTTAAAAATTAAATTATTATTTTATATAAA
3120409 A
1 A
3120410 ATTTTATTTT
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
30 24 0.49
31 25 0.51
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.48
Consensus pattern (31 bp):
ATTTAAAAATTAAATTATTATTTTATATAAA
Found at i:3120510 original size:22 final size:22
Alignment explanation
Indices: 3120485--3120526 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3120475 TTACATTTCA
*
3120485 ATAATTAAAAT-ATTATAAATAG
1 ATAATAAAAATAATTA-AAATAG
3120507 ATAATAAAAATAATTAAAAT
1 ATAATAAAAATAATTAAAAT
3120527 GTTATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
ATAATAAAAATAATTAAAATAG
Found at i:3121048 original size:22 final size:23
Alignment explanation
Indices: 3121023--3121067 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
3121013 TCAAACGACT
*
3121023 GAAAACGTGCCA-AAAGGCAAAG
1 GAAAACGTGCCATAAAGACAAAG
3121045 GAAAACGTGCCATAAAGACAAAG
1 GAAAACGTGCCATAAAGACAAAG
3121068 TTATTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.51, C:0.18, G:0.24, T:0.07
Consensus pattern (23 bp):
GAAAACGTGCCATAAAGACAAAG
Found at i:3121124 original size:15 final size:17
Alignment explanation
Indices: 3121085--3121128 Score: 67
Period size: 15 Copynumber: 2.8 Consensus size: 17
3121075 AAATTAGAAA
3121085 ACAAGAAAAATAAAGAT
1 ACAAGAAAAATAAAGAT
3121102 ACAA-AAAAATAAA-AT
1 ACAAGAAAAATAAAGAT
3121117 A-AAGAAAAATAA
1 ACAAGAAAAATAA
3121129 TGAATATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 2 0.08
15 11 0.42
16 9 0.35
17 4 0.15
ACGTcount: A:0.77, C:0.05, G:0.07, T:0.11
Consensus pattern (17 bp):
ACAAGAAAAATAAAGAT
Found at i:3121733 original size:20 final size:20
Alignment explanation
Indices: 3121708--3121846 Score: 97
Period size: 20 Copynumber: 6.8 Consensus size: 20
3121698 ATGCGAAACA
*
3121708 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* * *
3121728 AAAATCGCAATGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
3121748 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
3121768 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
*
3121789 AAGAATCGCAATGCGATTCAA-
1 AA-AATCGCAACGCGATT-AAG
* *
3121810 AGAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTAAG
3121830 AAAATCGCAACGCGATT
1 AAAATCGCAACGCGATT
3121847 CCAAGAATCG
Statistics
Matches: 93, Mismatches: 17, Indels: 18
0.73 0.13 0.14
Matches are distributed among these distances:
18 1 0.01
19 1 0.01
20 70 0.75
21 7 0.08
22 14 0.15
ACGTcount: A:0.42, C:0.21, G:0.20, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:3121855 original size:20 final size:20
Alignment explanation
Indices: 3121770--3121859 Score: 110
Period size: 20 Copynumber: 4.4 Consensus size: 20
3121760 GTCAAAAGAA
3121770 AATCGCAACGCGATCTTCCAAG
1 AATCGCAACGCGA--TTCCAAG
* *
3121792 AATCGCAATGCGATTCAAAG
1 AATCGCAACGCGATTCCAAG
* *
3121812 AATCGCAACGCGATT-GAGAA
1 AATCGCAACGCGATTCCA-AG
3121832 AATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCCAAG
3121852 AATCGCAA
1 AATCGCAA
3121860 AACGGCAAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.02
20 45 0.76
21 1 0.02
22 12 0.20
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.17
Consensus pattern (20 bp):
AATCGCAACGCGATTCCAAG
Found at i:3121981 original size:6 final size:6
Alignment explanation
Indices: 3121970--3122038 Score: 138
Period size: 6 Copynumber: 11.5 Consensus size: 6
3121960 GACACGTATT
3121970 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
3122018 ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACC
3122039 CGAGACGAGA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 63 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Done.