Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 178 of 208
Found at i:54397471 original size:3 final size:3
Alignment explanation
Indices: 54397463--54397502 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
54397453 GCGACGGATA
*
54397463 AGG AGG AGG AGG AGG AGG AGG AGG AGG -GAG AGA AGG AGG A
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AG-G AGG AGG AGG A
54397503 ATGGTTTTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 1 0.03
3 31 0.94
4 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:54398418 original size:2 final size:2
Alignment explanation
Indices: 54398397--54398434 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
54398387 ATCCCAGTTT
* *
54398397 TA TA -A TA TA CA TA CA 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 TA TA TA TA TA TA T
54398435 TATTGTGGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:54399337 original size:21 final size:24
Alignment explanation
Indices: 54399296--54399351 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 24
54399286 TTCAATTTTG
*
54399296 TTTATTATT-TTTTATTTTAAA-A
1 TTTATAATTATTTTATTTTAAATA
54399318 TTT-TAATTATTTTA-TTTAAATA
1 TTTATAATTATTTTATTTTAAATA
54399340 TTTAGTAATTAT
1 TTTA-TAATTAT
54399352 GTGTATCTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
21 10 0.34
22 12 0.41
24 7 0.24
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (24 bp):
TTTATAATTATTTTATTTTAAATA
Found at i:54402047 original size:34 final size:36
Alignment explanation
Indices: 54402001--54402075 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
54401991 GTTCTCCATA
**
54402001 CTAAACTACTTTCAATC-T-CGTGATGACATAAACC
1 CTAAACTACTTTCAATCTTGCGTGAACACATAAACC
*
54402035 CTAAACTGCTTTCAATCTTGCGTGAACACATAAACC
1 CTAAACTACTTTCAATCTTGCGTGAACACATAAACC
54402071 CTAAA
1 CTAAA
54402076 AACTAAAAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 16 0.44
35 1 0.03
36 19 0.53
ACGTcount: A:0.36, C:0.27, G:0.09, T:0.28
Consensus pattern (36 bp):
CTAAACTACTTTCAATCTTGCGTGAACACATAAACC
Found at i:54405931 original size:18 final size:18
Alignment explanation
Indices: 54405895--54405938 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
54405885 TTACTTTTTA
54405895 TAAATTTTATAAAAGTTT
1 TAAATTTTATAAAAGTTT
* *
54405913 TCAATTTTAATTAAA-TTT
1 TAAATTTT-ATAAAAGTTT
54405931 TAAATTTT
1 TAAATTTT
54405939 TTAGAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
TAAATTTTATAAAAGTTT
Found at i:54405951 original size:22 final size:22
Alignment explanation
Indices: 54405929--54405970 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
54405919 TTAATTAAAT
54405929 TTTAA-ATTTTTTAGAATTTAA
1 TTTAAGATTTTTTAGAATTTAA
*
54405950 TTTAATGATTTTTTATAATTT
1 TTTAA-GATTTTTTAGAATTT
54405971 TTATTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
23 13 0.72
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (22 bp):
TTTAAGATTTTTTAGAATTTAA
Found at i:54407136 original size:27 final size:28
Alignment explanation
Indices: 54407104--54407166 Score: 110
Period size: 27 Copynumber: 2.3 Consensus size: 28
54407094 TCTGTTTTCC
54407104 AGATTTTATAGTTTCCCCCTATTTT-TT
1 AGATTTTATAGTTTCCCCCTATTTTGTT
*
54407131 AGATTTTATAGTTTTCCCCTATTTTGTT
1 AGATTTTATAGTTTCCCCCTATTTTGTT
54407159 AGATTTTA
1 AGATTTTA
54407167 CAATTTCATC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 24 0.71
28 10 0.29
ACGTcount: A:0.21, C:0.14, G:0.10, T:0.56
Consensus pattern (28 bp):
AGATTTTATAGTTTCCCCCTATTTTGTT
Found at i:54420262 original size:19 final size:18
Alignment explanation
Indices: 54420182--54420262 Score: 65
Period size: 19 Copynumber: 4.2 Consensus size: 18
54420172 TATAAATTCG
*
54420182 TAAAAAATTATTAAAATTT
1 TAAAAAAAT-TTAAAATTT
*
54420201 TAAATAAATTTGAAAATTT
1 TAAAAAAATTT-AAAATTT
*
54420220 TCATTAAAAAA-TTAAACTTAT
1 T-A--AAAAAATTTAAAATT-T
54420241 TAAAAAACATTTAAAATTT
1 TAAAAAA-ATTTAAAATTT
54420260 TAA
1 TAA
54420263 GTCCAAAATG
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
18 7 0.14
19 20 0.40
20 14 0.28
21 4 0.08
22 5 0.10
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.40
Consensus pattern (18 bp):
TAAAAAAATTTAAAATTT
Found at i:54420520 original size:23 final size:23
Alignment explanation
Indices: 54420493--54420556 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
54420483 CTTTTAAATG
* *
54420493 ATTTTTAATAATTTTTATTTTTT
1 ATTTTTAATAATTTTTATTTATA
*
54420516 ATTTTTATTTAA-TTTTATTTATA
1 ATTTTTA-ATAATTTTTATTTATA
*
54420539 AATTTTAATAATGTTTTA
1 ATTTTTAATAAT-TTTTA
54420557 AAAATTTATA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
22 3 0.09
23 22 0.67
24 8 0.24
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
ATTTTTAATAATTTTTATTTATA
Found at i:54422688 original size:42 final size:42
Alignment explanation
Indices: 54422597--54422688 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 42
54422587 CCACACGGCT
* * * ***
54422597 TGGACACATCTCCATGTCCTTGCCCGTGTGGCTCACATGGCC
1 TGGACACACCCCCATGTCCTTGCCCGTGTGACTCACACAACC
**
54422639 TCAACACACCCCCATGTCCTTGCCCGTGTGACTCACACAACC
1 TGGACACACCCCCATGTCCTTGCCCGTGTGACTCACACAACC
54422681 TGGACACA
1 TGGACACA
54422689 TGCTCATGTC
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.21, C:0.39, G:0.18, T:0.22
Consensus pattern (42 bp):
TGGACACACCCCCATGTCCTTGCCCGTGTGACTCACACAACC
Found at i:54422697 original size:42 final size:41
Alignment explanation
Indices: 54422597--54422700 Score: 109
Period size: 42 Copynumber: 2.5 Consensus size: 41
54422587 CCACACGGCT
* ***
54422597 TGGACACATCTCCATGTCCTTGCCCGTGTGGCTCACATGGCC
1 TGGACACATCT-CATGTCCTTGCCCGTGTGACTCACACAACC
** * *
54422639 TCAACACACCCCCATGTCCTTGCCCGTGTGACTCACACAACC
1 TGGACACA-TCTCATGTCCTTGCCCGTGTGACTCACACAACC
54422681 TGGACACATGCTCATGTCCT
1 TGGACACAT-CTCATGTCCT
54422701 CTTCCCGTAT
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
42 47 0.98
43 1 0.02
ACGTcount: A:0.19, C:0.38, G:0.18, T:0.24
Consensus pattern (41 bp):
TGGACACATCTCATGTCCTTGCCCGTGTGACTCACACAACC
Found at i:54424738 original size:23 final size:24
Alignment explanation
Indices: 54424694--54424738 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
54424684 TTTCTCACAT
* **
54424694 TTTCAATTCAATCATTTTTCCACC
1 TTTCAATTCAATAATTAATCCACC
54424718 TTTCAA-TCAATAATTAATCCA
1 TTTCAATTCAATAATTAATCCA
54424739 TAAATTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.42
Consensus pattern (24 bp):
TTTCAATTCAATAATTAATCCACC
Found at i:54424893 original size:3 final size:3
Alignment explanation
Indices: 54424885--54424937 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
54424875 CCACTCATCT
54424885 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
54424933 TAA TA
1 TAA TA
54424938 CTTACCTCAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:54425492 original size:32 final size:32
Alignment explanation
Indices: 54425451--54425518 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
54425441 ACCTATGAAC
54425451 TTAAGAGAAAAGGGCTTAATTGACTTACCAAA
1 TTAAGAGAAAAGGGCTTAATTGACTTACCAAA
54425483 TTAAGAGAAAAGGGCTTAATTGACTTACCAAA
1 TTAAGAGAAAAGGGCTTAATTGACTTACCAAA
54425515 TTAA
1 TTAA
54425519 ACTCCAAGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.26
Consensus pattern (32 bp):
TTAAGAGAAAAGGGCTTAATTGACTTACCAAA
Found at i:54425570 original size:17 final size:17
Alignment explanation
Indices: 54425541--54425574 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
54425531 AAAAACCCTA
54425541 TTTTCTCTTTTTCTTTC
1 TTTTCTCTTTTTCTTTC
54425558 TTTT-TCTTCTTTCTTTC
1 TTTTCTCTT-TTTCTTTC
54425575 CCCTATTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTCTCTTTTTCTTTC
Found at i:54429311 original size:37 final size:37
Alignment explanation
Indices: 54429261--54429393 Score: 178
Period size: 37 Copynumber: 3.6 Consensus size: 37
54429251 CACGCTCGTG
54429261 AGAGCTAATCCACCCGATAACATGCCAGATGCTCATA
1 AGAGCTAATCCACCCGATAACATGCCAGATGCTCATA
* * *
54429298 AGAGCTAATCCACCTGATAACACGCCTGATGCTCATA
1 AGAGCTAATCCACCCGATAACATGCCAGATGCTCATA
*
54429335 AGAGCTAGTCCACCCGATAAC-TCGCCAGATGCTCATA
1 AGAGCTAATCCACCCGATAACAT-GCCAGATGCTCATA
* * * *
54429372 AAAGCTAGTCCAACCGAAAACA
1 AGAGCTAATCCACCCGATAACA
54429394 CACCAAAAGA
Statistics
Matches: 84, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
37 84 1.00
ACGTcount: A:0.35, C:0.30, G:0.17, T:0.18
Consensus pattern (37 bp):
AGAGCTAATCCACCCGATAACATGCCAGATGCTCATA
Found at i:54439882 original size:19 final size:19
Alignment explanation
Indices: 54439849--54439888 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
54439839 AAAATATCAT
*
54439849 ATTAATTTTAATTTATTTG
1 ATTAATTTTAATTTACTTG
54439868 ATTAA-TTTAATTTTACTTG
1 ATTAATTTTAA-TTTACTTG
54439887 AT
1 AT
54439889 CAAAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (19 bp):
ATTAATTTTAATTTACTTG
Found at i:54446006 original size:40 final size:40
Alignment explanation
Indices: 54445951--54446032 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
54445941 TGAATGGTTT
54445951 GAATAAATACTTATTCGATAAGTTTAAGTTTAAGTTATAC
1 GAATAAATACTTATTCGATAAGTTTAAGTTTAAGTTATAC
54445991 GAATAAATACTTATTCGATAAGTTTAAGTTTAAGTTATAC
1 GAATAAATACTTATTCGATAAGTTTAAGTTTAAGTTATAC
54446031 GA
1 GA
54446033 GCTTACTAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.39
Consensus pattern (40 bp):
GAATAAATACTTATTCGATAAGTTTAAGTTTAAGTTATAC
Found at i:54456389 original size:19 final size:20
Alignment explanation
Indices: 54456365--54456402 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
54456355 AGGAAATTTG
54456365 AGGATCAAATT-ATAGAATT
1 AGGATCAAATTGATAGAATT
54456384 AGGATCAAATTGATAGAAT
1 AGGATCAAATTGATAGAAT
54456403 ATGTAAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.47, C:0.05, G:0.18, T:0.29
Consensus pattern (20 bp):
AGGATCAAATTGATAGAATT
Found at i:54456636 original size:19 final size:19
Alignment explanation
Indices: 54456612--54456718 Score: 160
Period size: 19 Copynumber: 5.6 Consensus size: 19
54456602 TTCAGGGATG
*
54456612 TGCAATCTTAGTTATGATA
1 TGCAATCTTAGATATGATA
*
54456631 TGCAATCTTAGATATAATA
1 TGCAATCTTAGATATGATA
**
54456650 TATAATCTTAGATATGATA
1 TGCAATCTTAGATATGATA
54456669 TGCAATCTTAGATATGATA
1 TGCAATCTTAGATATGATA
**
54456688 TATAATCTTAGATATGATA
1 TGCAATCTTAGATATGATA
54456707 TGCAATCTTAGA
1 TGCAATCTTAGA
54456719 AGATATGATT
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 77 1.00
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.39
Consensus pattern (19 bp):
TGCAATCTTAGATATGATA
Found at i:54456658 original size:38 final size:38
Alignment explanation
Indices: 54456615--54456718 Score: 190
Period size: 38 Copynumber: 2.7 Consensus size: 38
54456605 AGGGATGTGC
*
54456615 AATCTTAGTTATGATATGCAATCTTAGATATAATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
*
54456653 AATCTTAGATATGATATGCAATCTTAGATATGATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
54456691 AATCTTAGATATGATATGCAATCTTAGA
1 AATCTTAGATATGATATGCAATCTTAGA
54456719 AGATATGATT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 64 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (38 bp):
AATCTTAGATATGATATGCAATCTTAGATATAATATAT
Found at i:54456744 original size:22 final size:21
Alignment explanation
Indices: 54456624--54456744 Score: 105
Period size: 19 Copynumber: 6.0 Consensus size: 21
54456614 CAATCTTAGT
*
54456624 TATGATATGCAATCTT--AGA
1 TATGATATGTAATCTTAGAGA
* *
54456643 TATAATATATAATCTT--AGA
1 TATGATATGTAATCTTAGAGA
*
54456662 TATGATATGCAATCTT--AGA
1 TATGATATGTAATCTTAGAGA
*
54456681 TATGATATATAATCTT--AGA
1 TATGATATGTAATCTTAGAGA
*
54456700 TATGATATGCAATCTTAGAAGA
1 TATGATATGTAATCTTAG-AGA
*
54456722 TATGATTTTGTAATCTTAGAGA
1 TATGA-TATGTAATCTTAGAGA
54456744 T
1 T
54456745 TTAATTTGTA
Statistics
Matches: 86, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
19 63 0.73
22 12 0.14
23 11 0.13
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (21 bp):
TATGATATGTAATCTTAGAGA
Found at i:54468569 original size:27 final size:29
Alignment explanation
Indices: 54468537--54468600 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
54468527 AATTAAAATT
**
54468537 AATTTATTTAT-TTTTTAAAATATTAA-A
1 AATTTATTTATGTTTACAAAATATTAATA
*
54468564 ATTTTATTTTATGTTTACAAAATATTAATA
1 AATTTA-TTTATGTTTACAAAATATTAATA
54468594 AATTTAT
1 AATTTAT
54468601 AATAATTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
27 5 0.17
28 5 0.17
29 14 0.47
30 6 0.20
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (29 bp):
AATTTATTTATGTTTACAAAATATTAATA
Found at i:54478479 original size:10 final size:10
Alignment explanation
Indices: 54478464--54478488 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
54478454 TCATTTAATT
54478464 AATTTTTTAA
1 AATTTTTTAA
54478474 AATTTTTTAA
1 AATTTTTTAA
54478484 AATTT
1 AATTT
54478489 CAAAAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
AATTTTTTAA
Found at i:54479795 original size:2 final size:2
Alignment explanation
Indices: 54479788--54479837 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
54479778 TTAGGGGTAA
54479788 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54479830 AT AT AT AT
1 AT AT AT AT
54479838 NNNNNNNNNN
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54480388 original size:2 final size:2
Alignment explanation
Indices: 54480381--54480424 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
54480371 NNNNNNNNNN
54480381 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
54480423 TA
1 TA
54480425 CGTTAACCCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54483471 original size:16 final size:16
Alignment explanation
Indices: 54483452--54483483 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
54483442 AATTATTATT
*
54483452 AAATATGATTTAATAA
1 AAATATAATTTAATAA
54483468 AAATATAATTTAATAA
1 AAATATAATTTAATAA
54483484 CATTCTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
AAATATAATTTAATAA
Found at i:54483482 original size:26 final size:26
Alignment explanation
Indices: 54483411--54483482 Score: 67
Period size: 26 Copynumber: 2.8 Consensus size: 26
54483401 ATTTAATAAA
*
54483411 AATAATAA-ATAATTTAATTATATTTT
1 AATAAAAATATAATTTAA-TATATTTT
* * * *
54483437 AATATAATTATTATTAAATATGA-TTT
1 AATAAAAATATAATTTAATAT-ATTTT
54483463 AATAAAAATATAATTTAATA
1 AATAAAAATATAATTTAATA
54483483 ACATTCTTAA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
26 27 0.77
27 8 0.23
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (26 bp):
AATAAAAATATAATTTAATATATTTT
Found at i:54483498 original size:5 final size:5
Alignment explanation
Indices: 54483497--54483525 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
54483487 TCTTAATATA
54483497 ATTAT ATTAT ATTAT ATTAT ATTAT ATTA
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTA
54483526 AAAGATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:54487071 original size:62 final size:60
Alignment explanation
Indices: 54486963--54487083 Score: 138
Period size: 62 Copynumber: 2.0 Consensus size: 60
54486953 TTAGTCAATG
* *
54486963 TATATTTGAGTTTTATAAGTTAAAATAAATTGCATAAATTCTATATATATTTAGCCGAATA
1 TATATTTGAGTTTTATAAGTTAAAATAAATTGAATAAATTCTATATAT-GTTAGCCGAATA
* * * *
54487024 TATATGTTGAGTTTTGTAAGTT-GAATGAAATTTAATGAATTAC-ATATATGTTAGCCGAAT
1 TATAT-TTGAGTTTTATAAGTTAAAAT-AAATTGAATAAATT-CTATATATGTTAGCCGAAT
54487084 GTATGTATTA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
61 18 0.35
62 32 0.63
63 1 0.02
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.42
Consensus pattern (60 bp):
TATATTTGAGTTTTATAAGTTAAAATAAATTGAATAAATTCTATATATGTTAGCCGAATA
Found at i:54498516 original size:35 final size:36
Alignment explanation
Indices: 54498452--54498521 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 36
54498442 CATTGTTCGT
**
54498452 GAACATGTTCAATTATATGTTCATGAACATGTTTGA
1 GAACATGTTCAATTATATGTTCACAAACATGTTTGA
**
54498488 GAACATGTTCGTTTA-ATGTTCACAAACATGTTTG
1 GAACATGTTCAATTATATGTTCACAAACATGTTTG
54498522 TTTAACTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 17 0.57
36 13 0.43
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (36 bp):
GAACATGTTCAATTATATGTTCACAAACATGTTTGA
Found at i:54498570 original size:301 final size:304
Alignment explanation
Indices: 54498017--54498620 Score: 1099
Period size: 301 Copynumber: 2.0 Consensus size: 304
54498007 ATTAATAAAA
*
54498017 ATATTACGGTTTGTATGCTTTTTTATTTATAAAATAATTATTAATATTTATATTTGACTATTTTA
1 ATATTACGGTTTGTATGCTTTTTTATTTATAAAATAATTATTAATATTTATATTTGACTAGTTTA
54498082 TATCTAAAAAATAATATATATATATATATGTTTATTTATTGTTGGTTTGTTTATTATTACATTGT
66 TATCT-AAAAATAATATATATATATATATGTTTATTTATTGTTGGTTTGTTTATTATTACATTGT
54498147 TCGTGAACATGCTCAATTATATGTTCATGAACATGTTTGAGAACATGTTCGTTTAATGTTCACAA
130 TCGTGAACATGCTCAATTATATGTTCATGAACATGTTTGAGAACATGTTCGTTTAATGTTCACAA
* *
54498212 ACATGTTTGTTTAACTTAAGCGAACGAACACGAAAAAAAATTTTGAAATTCTTAACGAACACGAA
195 ACATGTTTGTTTAACTTAAGCGAACGAACACGAAAAAAAATTTTAAAATTCTTAACGAACACAAA
54498277 CAAACTTAAAAATAAACAAACGAACATGAAAAGAGGTCCGTTCGT
260 CAAACTTAAAAATAAACAAACGAACATGAAAAGAGGTCCGTTCGT
* *
54498322 ATATTATGGTTTGTATGCTTTTTTATTTATAATATAATTATTAATATTTATATTTGACTAGTTTA
1 ATATTACGGTTTGTATGCTTTTTTATTTATAAAATAATTATTAATATTTATATTTGACTAGTTTA
54498387 TATCT-AAAA-AATA-ATATATATATATGTTTATTTATTGTTGGTTTGTTTATTATTACATTGTT
66 TATCTAAAAATAATATATATATATATATGTTTATTTATTGTTGGTTTGTTTATTATTACATTGTT
*
54498449 CGTGAACATGTTCAATTATATGTTCATGAACATGTTTGAGAACATGTTCGTTTAATGTTCACAAA
131 CGTGAACATGCTCAATTATATGTTCATGAACATGTTTGAGAACATGTTCGTTTAATGTTCACAAA
*
54498514 CATGTTTGTTTAACTTAAGCGAATGAACAC-AAACAAAAATTTTAAAATTCTTAACGAACACAAA
196 CATGTTTGTTTAACTTAAGCGAACGAACACGAAA-AAAAATTTTAAAATTCTTAACGAACACAAA
54498578 CAAACTTAAAAATAAACAAACGAACATGAAAAGAGGTCCGTTC
260 CAAACTTAAAAATAAACAAACGAACATGAAAAGAGGTCCGTTC
54498621 ATTCAAGCTC
Statistics
Matches: 291, Mismatches: 7, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
300 3 0.01
301 213 0.73
302 4 0.01
303 4 0.01
305 67 0.23
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.40
Consensus pattern (304 bp):
ATATTACGGTTTGTATGCTTTTTTATTTATAAAATAATTATTAATATTTATATTTGACTAGTTTA
TATCTAAAAATAATATATATATATATATGTTTATTTATTGTTGGTTTGTTTATTATTACATTGTT
CGTGAACATGCTCAATTATATGTTCATGAACATGTTTGAGAACATGTTCGTTTAATGTTCACAAA
CATGTTTGTTTAACTTAAGCGAACGAACACGAAAAAAAATTTTAAAATTCTTAACGAACACAAAC
AAACTTAAAAATAAACAAACGAACATGAAAAGAGGTCCGTTCGT
Found at i:54498763 original size:15 final size:16
Alignment explanation
Indices: 54498736--54498765 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
54498726 TTTGCTTGGT
54498736 ATGAAGAATGGAAAAA
1 ATGAAGAATGGAAAAA
54498752 ATGAAG-ATGGAAAA
1 ATGAAGAATGGAAAA
54498766 TTTGTTAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.60, C:0.00, G:0.27, T:0.13
Consensus pattern (16 bp):
ATGAAGAATGGAAAAA
Found at i:54504283 original size:20 final size:20
Alignment explanation
Indices: 54504254--54504293 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
54504244 TTTCTATAAA
54504254 TATTTTAAAATTT-AAAATT
1 TATTTTAAAATTTGAAAATT
54504273 TATTTTCAAAATTTGAAAATT
1 TATTTT-AAAATTTGAAAATT
54504294 ACTTTGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 7 0.37
21 6 0.32
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (20 bp):
TATTTTAAAATTTGAAAATT
Found at i:54505675 original size:22 final size:22
Alignment explanation
Indices: 54505647--54505692 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
54505637 TAATCCTCCT
54505647 TAGTACTTTTACCCCACACATG
1 TAGTACTTTTACCCCACACATG
54505669 TAGTACTTTTACCCCACACATG
1 TAGTACTTTTACCCCACACATG
54505691 TA
1 TA
54505693 AATAGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (22 bp):
TAGTACTTTTACCCCACACATG
Found at i:54508983 original size:30 final size:30
Alignment explanation
Indices: 54508949--54509011 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
54508939 ACTTAACAAG
54508949 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
*
54508979 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
54509009 CAA
1 CAA
54509012 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.16, G:0.03, T:0.24
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:54510783 original size:16 final size:16
Alignment explanation
Indices: 54510752--54510798 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
54510742 ATATGAAGAA
54510752 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
54510768 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
*
54510784 TATTAAATTAAAATT
1 TATT-ATTTAAAATT
54510799 GAAATATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 7 0.26
16 12 0.44
17 2 0.07
18 6 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:54526922 original size:31 final size:29
Alignment explanation
Indices: 54526884--54526959 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
54526874 TAACGGCTCG
* *
54526884 GTGACTAAAATGTTACAACATGATAACATAA
1 GTGACTAAAATGTAAC-ACATCA-AACATAA
**
54526915 GTGACTAAAATGTAACATTTCAAACATAA
1 GTGACTAAAATGTAACACATCAAACATAA
54526944 GTGACTAAAATGTAAC
1 GTGACTAAAATGTAAC
54526960 TTGAGCCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 23 0.56
30 3 0.07
31 15 0.37
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.26
Consensus pattern (29 bp):
GTGACTAAAATGTAACACATCAAACATAA
Found at i:54526977 original size:31 final size:29
Alignment explanation
Indices: 54526908--54526981 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 29
54526898 ACAACATGAT
*
54526908 AACATAAGTGACTAAAATGTAACATTTCA
1 AACATAAGTGACTAAAATGTAACATTCCA
54526937 AACATAAGTGACTAAAATGTAAC-TTGAGCCA
1 AACATAAGTGACTAAAATGTAACATT---CCA
*
54526968 AACAAAAGTGACTA
1 AACATAAGTGACTA
54526982 TTTTGGTAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 2 0.05
29 23 0.57
31 15 0.38
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.23
Consensus pattern (29 bp):
AACATAAGTGACTAAAATGTAACATTCCA
Found at i:54528426 original size:12 final size:12
Alignment explanation
Indices: 54528409--54528440 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
54528399 ACTACAATAT
54528409 TGTCTTCTGGAA
1 TGTCTTCTGGAA
54528421 TGTCTTCTGGAA
1 TGTCTTCTGGAA
*
54528433 TGCCTTCT
1 TGTCTTCT
54528441 TTAACCCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (12 bp):
TGTCTTCTGGAA
Found at i:54538722 original size:73 final size:73
Alignment explanation
Indices: 54538601--54538739 Score: 260
Period size: 73 Copynumber: 1.9 Consensus size: 73
54538591 ATCTATTTGA
*
54538601 TACACAATTGAGATATGATAAAATAATTGCAACAATAGTTATTAAGATTTAAAAAGCTTAAATTT
1 TACACAATTGAGATATAATAAAATAATTGCAACAATAGTTATTAAGATTTAAAAAGCTTAAATTT
54538666 TACTTTTT
66 TACTTTTT
*
54538674 TACACAATTGAGATATAATAAAATAATTGCAACAATAGTTATTGAGATTTAAAAAGCTTAAATTT
1 TACACAATTGAGATATAATAAAATAATTGCAACAATAGTTATTAAGATTTAAAAAGCTTAAATTT
54538739 T
66 T
54538740 TATGAAAGGG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 64 1.00
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (73 bp):
TACACAATTGAGATATAATAAAATAATTGCAACAATAGTTATTAAGATTTAAAAAGCTTAAATTT
TACTTTTT
Found at i:54540830 original size:41 final size:41
Alignment explanation
Indices: 54540768--54540860 Score: 141
Period size: 41 Copynumber: 2.3 Consensus size: 41
54540758 ACACTTCTAG
* *
54540768 TTCAGGTGAAATGTAGAAAAACACTTCCAACTTGAAGCGCT
1 TTCAGGTGAAATATAGAAAAACACTTCCAACTAGAAGCGCT
* **
54540809 TTCAAGTGAAATATAGAAAAACACTTCCTGCTAGAAGCGCT
1 TTCAGGTGAAATATAGAAAAACACTTCCAACTAGAAGCGCT
54540850 TTCAGGTGAAA
1 TTCAGGTGAAA
54540861 AACACTTCCA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (41 bp):
TTCAGGTGAAATATAGAAAAACACTTCCAACTAGAAGCGCT
Found at i:54540866 original size:33 final size:33
Alignment explanation
Indices: 54540824--54540893 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
54540814 GTGAAATATA
*
54540824 GAAAAACACTTCCTGCTAGAAGCGCTTTCAGGT
1 GAAAAACACTTCCAGCTAGAAGCGCTTTCAGGT
*
54540857 GAAAAACACTTCCAGCTGGAAGCGCTTTCAGGT
1 GAAAAACACTTCCAGCTAGAAGCGCTTTCAGGT
54540890 GAAA
1 GAAA
54540894 TGCGGAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.21
Consensus pattern (33 bp):
GAAAAACACTTCCAGCTAGAAGCGCTTTCAGGT
Found at i:54545481 original size:18 final size:18
Alignment explanation
Indices: 54545458--54545497 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
54545448 ACCCAATCTA
**
54545458 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
54545476 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
54545494 AACC
1 AACC
54545498 TAATCATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.40, C:0.45, G:0.03, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:54545635 original size:18 final size:18
Alignment explanation
Indices: 54545608--54545648 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
54545598 GTAGTGATTC
*
54545608 AATTTGGTTAATTCGGGT
1 AATTTAGTTAATTCGGGT
*
54545626 AATTTAGTTAATTCGGTT
1 AATTTAGTTAATTCGGGT
54545644 AATTT
1 AATTT
54545649 TTGAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.27, C:0.05, G:0.20, T:0.49
Consensus pattern (18 bp):
AATTTAGTTAATTCGGGT
Found at i:54545738 original size:12 final size:12
Alignment explanation
Indices: 54545721--54545745 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54545711 TGTTATTTCG
54545721 GGTCGGTTAACC
1 GGTCGGTTAACC
54545733 GGTCGGTTAACC
1 GGTCGGTTAACC
54545745 G
1 G
54545746 AATAAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:54546911 original size:13 final size:13
Alignment explanation
Indices: 54546895--54546920 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54546885 ATGCTCTCAA
54546895 GCATTCCAGTACT
1 GCATTCCAGTACT
54546908 GCATTCCAGTACT
1 GCATTCCAGTACT
54546921 CATCGGCTGT
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:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (13 bp):
GCATTCCAGTACT
Found at i:54549302 original size:21 final size:21
Alignment explanation
Indices: 54549276--54549330 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
54549266 AACAGCGGTG
*
54549276 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGGTACTGTA
*
54549297 GCGGTGAGATTTGGTACTGTA
1 GCGGTGAGATTAGGTACTGTA
54549318 GCGGTGAGATTAG
1 GCGGTGAGATTAG
54549331 AAACAATGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.22, C:0.09, G:0.38, T:0.31
Consensus pattern (21 bp):
GCGGTGAGATTAGGTACTGTA
Found at i:54556974 original size:8 final size:8
Alignment explanation
Indices: 54556961--54557008 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
54556951 TACTCTTCAT
54556961 TTTTTTTC
1 TTTTTTTC
54556969 TTTTTTTC
1 TTTTTTTC
*
54556977 TTTTATTTA
1 TTTT-TTTC
* *
54556986 TTTGTTTG
1 TTTTTTTC
*
54556994 TTTTATTC
1 TTTTTTTC
54557002 TTTTTTT
1 TTTTTTT
54557009 TCCTTTCTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
8 26 0.81
9 6 0.19
ACGTcount: A:0.06, C:0.06, G:0.04, T:0.83
Consensus pattern (8 bp):
TTTTTTTC
Found at i:54558335 original size:15 final size:16
Alignment explanation
Indices: 54558304--54558336 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
54558294 ATATCCTTTT
*
54558304 AAATTTCAAACACATA
1 AAATTTCAAACAAATA
54558320 AAATTTCAAA-AAATA
1 AAATTTCAAACAAATA
54558335 AA
1 AA
54558337 GGCAATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATTTCAAACAAATA
Found at i:54570199 original size:29 final size:29
Alignment explanation
Indices: 54570165--54570226 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
54570155 TCAAATATCA
54570165 ACTTGGTTCAAACCAACAGCTCAGATACC
1 ACTTGGTTCAAACCAACAGCTCAGATACC
* * *
54570194 ACTTGGTTCAAACCTACAGCTCTGATACT
1 ACTTGGTTCAAACCAACAGCTCAGATACC
54570223 ACTT
1 ACTT
54570227 TTCACGGGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (29 bp):
ACTTGGTTCAAACCAACAGCTCAGATACC
Found at i:54577397 original size:22 final size:21
Alignment explanation
Indices: 54577367--54577409 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
54577357 AACCCAAAAT
54577367 AAATATAACACCCATGCCCAATA
1 AAATATAAC-CCCA-GCCCAATA
*
54577390 AAAT-TAACCCTAGCCCAATA
1 AAATATAACCCCAGCCCAATA
54577410 CCTTTCAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 8 0.42
21 3 0.16
22 4 0.21
23 4 0.21
ACGTcount: A:0.47, C:0.30, G:0.05, T:0.19
Consensus pattern (21 bp):
AAATATAACCCCAGCCCAATA
Found at i:54578963 original size:12 final size:13
Alignment explanation
Indices: 54578932--54578964 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
54578922 TTTGCAAATT
54578932 TACTTGTATATTA
1 TACTTGTATATTA
54578945 TACTTGTATA-TA
1 TACTTGTATATTA
*
54578957 TATTTGTA
1 TACTTGTA
54578965 AATGTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (13 bp):
TACTTGTATATTA
Found at i:54581523 original size:12 final size:13
Alignment explanation
Indices: 54581492--54581524 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
54581482 TTTGCAAATT
54581492 TACTTGTATATTA
1 TACTTGTATATTA
54581505 TACTTGTATA-TA
1 TACTTGTATATTA
*
54581517 TATTTGTA
1 TACTTGTA
54581525 AATGTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (13 bp):
TACTTGTATATTA
Found at i:54600298 original size:105 final size:103
Alignment explanation
Indices: 54600014--54600520 Score: 388
Period size: 111 Copynumber: 4.7 Consensus size: 103
54600004 NNNNNNNNNN
* * *
54600014 GCCAATGACAACCCAAAATGTAATTTTTTTTTACATAAAGGTGGTGTCGGCCATTGGCAGGTCAC
1 GCCAATTACAGCCCAAAATGTAATTTTTTTTTACATAAAGGTGGTGTCGGCCATTGGCAGGCCAC
* * * * *
54600079 CACCAATTTTTTTTTAAATTTTTTTGTATACTAGCGTC
66 CACCAATTTTTTTTTTAATTTTTTCGTATATTAGTGCC
* ****** * *
54600117 GCCAATTAAAGCCCAAAATGTAAAACAAAAAAAAATTTACAAAAAGGTGGTGCCGGCCATTGGCA
1 GCCAATTACAGCCCAAAATGT------AATTTTTTTTTACATAAAGGTGGTGTCGGCCATTGGCA
* * *
54600182 GGCCGCTACCAAATTTTTTTTTTAATTTTTTCGTATATTGGTGCC
60 GGCCACCACC-AATTTTTTTTTTAATTTTTTCGTATATTAGTGCC
* *
54600227 AGCCATTTACAGCCCAAAATGTAATTTTTTTTTACATAAAGGTGGTGTCGGCCATTGTCAGGCCA
1 -GCCAATTACAGCCCAAAATGTAATTTTTTTTTACATAAAGGTGGTGTCGGCCATTGGCAGGCCA
54600292 CCACCAATTTTTTTTTTAAATTTTTTCGTATATTAGTGCC
65 CCACCAATTTTTTTTTT-AATTTTTTCGTATATTAGTGCC
* ****** * * *
54600332 GGCCAATGACAGCCCAAAATGTAAAAAGAAAAAAAATTTACATAAAGGTAGTGCCGACCATTGGC
1 -GCCAATTACAGCCCAAAATGT------AATTTTTTTTTACATAAAGGTGGTGTCGGCCATTGGC
* ** * * *
54600397 AAGCCACCACCAAAAAAAGAAATTTTTTTAACATTTTTTCGTATACTGGTGCC
59 AGGCCACCACC------A-ATTTTTTTTTTA-ATTTTTTCGTATATTAGTGCC
* * * *
54600450 GGCCAATTACAGCCCAAAATAT-ATTTTTTTTAACATAAAGGTGATG-CTGGTCATTGGCAGGCC
1 -GCCAATTACAGCCCAAAATGTAATTTTTTTTTACATAAAGGTGGTGTC-GGCCATTGGCAGGCC
54600513 ACCACCAA
64 ACCACCAA
54600521 AAAAAATATT
Statistics
Matches: 313, Mismatches: 67, Indels: 47
0.73 0.16 0.11
Matches are distributed among these distances:
103 18 0.06
104 13 0.04
105 78 0.25
109 37 0.12
110 29 0.09
111 89 0.28
117 2 0.01
118 47 0.15
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (103 bp):
GCCAATTACAGCCCAAAATGTAATTTTTTTTTACATAAAGGTGGTGTCGGCCATTGGCAGGCCAC
CACCAATTTTTTTTTTAATTTTTTCGTATATTAGTGCC
Found at i:54600573 original size:223 final size:216
Alignment explanation
Indices: 54600014--54600579 Score: 561
Period size: 223 Copynumber: 2.6 Consensus size: 216
54600004 NNNNNNNNNN
* * * * * *
54600014 GCCAATGACAACCCAAAATGTAATTTTTTTTTACATAAAGGTGGTGTCGGCCATTGGCAGGTCAC
1 GCCAATTACAGCCCAAAATATAATTTTTTTTAACATAAAGGTGATGTCGGCCATTGGCAGGCCAC
*** * * ** *
54600079 CACC-AATTTTTTTTTAAATTTTTTTGTATACTAGCGTC-GCCAATTAA-AGCCCAAAATGTAAA
66 CACCAAAAAATATTTTAAATTTTTTCGTATACTAGCACCGGCCAA-TAACAACCCAAAATGTAAA
* * * * * ** *
54600141 ACAAAAAAAAATTTACAAAAAGGTGGTGCCGGCCATTGGCAGGCCGCTACCAAATTTTTTTTTTA
130 ACAAAAAAAAATTTACAAAAAGGTAGTGCCGACCATTGGCAAGCCACCACCAAAAATTTTTTTAA
*
54600206 ATTTTTTCGTATATTGGTGCCA
195 ATTTTTTCGTATACTGGTGCCA
* * * * *
54600228 GCCATTTACAGCCCAAAATGTAATTTTTTTTTACATAAAGGTGGTGTCGGCCATTGTCAGGCCAC
1 GCCAATTACAGCCCAAAATATAATTTTTTTTAACATAAAGGTGATGTCGGCCATTGGCAGGCCAC
**** * * ** * *
54600293 CACCAATTTTTTTTTTAAATTTTTTCGTATATTAGTGCCGGCCAATGACAGCCCAAAATGTAAAA
66 CACCAAAAAATATTTTAAATTTTTTCGTATACTAGCACCGGCCAATAACAACCCAAAATGTAAAA
*
54600358 -AGAAAAAAAATTTACATAAAGGTAGTGCCGACCATTGGCAAGCCACCACCAAAAAAAGAAATTT
131 CA-AAAAAAAATTTACAAAAAGGTAGTGCCGACCATTGGCAAGCCACCACC-----AA-AAATTT
*
54600422 TTTTAACATTTTTTCGTATACTGGTGCCG
189 TTTTAA-ATTTTTTCGTATACTGGTGCCA
*
54600451 GCCAATTACAGCCCAAAATAT-ATTTTTTTTAACATAAAGGTGATG-CTGGTCATTGGCAGGCCA
1 GCCAATTACAGCCCAAAATATAATTTTTTTTAACATAAAGGTGATGTC-GGCCATTGGCAGGCCA
* * ***
54600514 CCACCAAAAAAAATATTTT-ATTTTTTTCGTATACTGGCACCGGTTGATAACAACCCAAAATGTA
65 CCACC--AAAAAATATTTTAAATTTTTTCGTATACTAGCACCGGCCAATAACAACCCAAAATGTA
54600578 AA
128 AA
54600580 TTTTTTTTAC
Statistics
Matches: 295, Mismatches: 43, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
214 64 0.22
215 32 0.11
216 63 0.21
221 3 0.01
222 50 0.17
223 76 0.26
224 7 0.02
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (216 bp):
GCCAATTACAGCCCAAAATATAATTTTTTTTAACATAAAGGTGATGTCGGCCATTGGCAGGCCAC
CACCAAAAAATATTTTAAATTTTTTCGTATACTAGCACCGGCCAATAACAACCCAAAATGTAAAA
CAAAAAAAAATTTACAAAAAGGTAGTGCCGACCATTGGCAAGCCACCACCAAAAATTTTTTTAAA
TTTTTTCGTATACTGGTGCCA
Found at i:54600784 original size:104 final size:104
Alignment explanation
Indices: 54600306--54600928 Score: 333
Period size: 104 Copynumber: 5.8 Consensus size: 104
54600296 CAATTTTTTT
* * * * *
54600306 TTTAAATTTTTTCGTATATTAGTGCCGGCCAATGACAGCCCAAAATGTAAAAAGAAAAAAAATTT
1 TTTAAATTTTTTCGTAAACTAGTGCCGGCAAATGACAACCCAAAA--T----ATAAAAAAAATTT
* * * *
54600371 ACATAAAGGTAGTGCC-GACCATTGGCAAGCCACCACCAAAAAAAGAAA
60 ACATAAAGGTGGTGCCGGA-CATTGACAGGCCACCA--TAAAAAA-AAA
* * * * * *****
54600419 TTTTTTTAACATTTTTTCGTATACTGGTGCCGGCCAATTACAGCCCAAAATAT--ATTTTTTTTA
1 ----TTTAA-ATTTTTTCGTAAACTAGTGCCGGCAAATGACAACCCAAAATATAAAAAAAATTT-
* * * * *
54600482 ACATAAAGGTGATGCTGGTCATTGGCAGGCCACCACCAAAAAAAATA
60 ACATAAAGGTGGTGCCGGACATTGACAGGCCACCA-TAAAAAAAA-A
* * * * ** *** * * *****
54600529 TTTTATTTTTTTCGTATACTGGCACCGGTTGATAACAACCCAAAATGTAAATTTTTTTTACATAA
1 TTTAAATTTTTTCGTAAACTAGTGCCGGCAAATGACAACCCAAAATATAAAAAAAATTTACATAA
* * * * *
54600594 AAGTGGTGTC-GACTATTGCCAAGCCACCACAAAAAGAAAA
66 AGGTGGTGCCGGAC-ATTGACAGGCCACCATAAAAA-AAAA
* * * * * *
54600634 TTTTAAAATTTTTCGTATATTAGTGCCGGTC-ATTAACAGCCCAAAATATAAAAAAAATTTACAT
1 -TTTAAATTTTTTCGTAAACTAGTGCCGG-CAAATGACAACCCAAAATATAAAAAAAATTTACAT
* ** *
54600698 AAAGGTGGTGTCGGATTTTGACAGGCTA-CA-AAAAAAACAA
64 AAAGGTGGTGCCGGACATTGACAGGCCACCATAAAAAAA-AA
* * *
54600738 TTTCATATTTTTTCGTAAACTAGTGCCGGCAAATGACAACCTAAAATGTAAAAAAAATTTACATA
1 TTT-AAATTTTTTCGTAAACTAGTGCCGGCAAATGACAACCCAAAATATAAAAAAAATTTACATA
* * **
54600803 AAGGTGGTGCCGGCCATTGGCAGGCCACCATTGAAAAAAA
65 AAGGTGGTGCCGGACATTGACAGGCCACCATAAAAAAAAA
* * * * * *
54600843 TTTAAATTTTTTCGTATACTGGTGCCGGCCAATGACAGCCCAAAATGTAAAAAAAAAAAATTACA
1 TTTAAATTTTTTCGTAAACTAGTGCCGGCAAATGACAACCCAAAA--T-ATAAAAAAAATTTACA
*
54600908 TAAAGGTGGTGCCGGCCATTG
63 TAAAGGTGGTGCCGGACATTG
54600929 GTAGGCTACC
Statistics
Matches: 406, Mismatches: 81, Indels: 48
0.76 0.15 0.09
Matches are distributed among these distances:
103 6 0.01
104 114 0.28
105 52 0.13
106 102 0.25
107 45 0.11
109 2 0.00
110 12 0.03
111 28 0.07
112 2 0.00
116 1 0.00
117 5 0.01
118 37 0.09
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.28
Consensus pattern (104 bp):
TTTAAATTTTTTCGTAAACTAGTGCCGGCAAATGACAACCCAAAATATAAAAAAAATTTACATAA
AGGTGGTGCCGGACATTGACAGGCCACCATAAAAAAAAA
Found at i:54600947 original size:107 final size:105
Alignment explanation
Indices: 54600482--54600947 Score: 375
Period size: 104 Copynumber: 4.4 Consensus size: 105
54600472 ATTTTTTTTA
* * * * * *
54600482 ACATAAAGGTGATGCTGGTCATTGGCAGGCCACCACCAAAAAAAATATTTTATTTTTTTCGTATA
1 ACATAAAGGTGGTGCCGGCCATTGGCAGGCTACCA-CAAAAAAAA-ATTTAAATTTTTTCGTATA
* ** *** * * *****
54600547 CTGGCACCGGTTGATAACAACCCAAAATGT-AAATTTTTTTT
64 CTAGTGCCGGCCAATGACAGCCCAAAATGTAAAAAAAAATTT
* * * * * * * *
54600588 ACATAAAAGTGGTGTCGACTATTGCCAAGCCACCACAAAAAGAAAATTTTAAAATTTTTCGTATA
1 ACATAAAGGTGGTGCCGGCCATTGGCAGGCTACCACAAAAA-AAAA-TTTAAATTTTTTCGTATA
* * * * *
54600653 TTAGTGCCGGTCATTAACAGCCCAAAATAT-AAAAAAAATTT
64 CTAGTGCCGGCCAATGACAGCCCAAAATGTAAAAAAAAATTT
* *** * * *
54600694 ACATAAAGGTGGTGTCGGATTTTGACAGGCTA-CA-AAAAAAACAATTTCATATTTTTTCGTAAA
1 ACATAAAGGTGGTGCCGGCCATTGGCAGGCTACCACAAAAAAA-AATTT-AAATTTTTTCGTATA
* * *
54600757 CTAGTGCCGGCAAATGACAACCTAAAATGT-AAAAAAAATTT
64 CTAGTGCCGGCCAATGACAGCCCAAAATGTAAAAAAAAATTT
* ***
54600798 ACATAAAGGTGGTGCCGGCCATTGGCAGGCCACCATTGAAAAAAATTTAAATTTTTTCGTATACT
1 ACATAAAGGTGGTGCCGGCCATTGGCAGGCTACCACAAAAAAAAATTTAAATTTTTTCGTATACT
* *
54600863 GGTGCCGGCCAATGACAGCCCAAAATGTAAAAAAAAAAAATT
66 AGTGCCGGCCAATGACAGCCCAAAATGT--AAAAAAAAATTT
* *
54600905 ACATAAAGGTGGTGCCGGCCATTGGTAGGCTACCACCAAAAAA
1 ACATAAAGGTGGTGCCGGCCATTGGCAGGCTACCACAAAAAAA
54600948 TTACATAAAG
Statistics
Matches: 287, Mismatches: 64, Indels: 17
0.78 0.17 0.05
Matches are distributed among these distances:
103 5 0.02
104 117 0.41
105 16 0.06
106 101 0.35
107 48 0.17
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (105 bp):
ACATAAAGGTGGTGCCGGCCATTGGCAGGCTACCACAAAAAAAAATTTAAATTTTTTCGTATACT
AGTGCCGGCCAATGACAGCCCAAAATGTAAAAAAAAATTT
Found at i:54600953 original size:152 final size:156
Alignment explanation
Indices: 54600789--54601106 Score: 437
Period size: 153 Copynumber: 2.0 Consensus size: 156
54600779 TAAAATGTAA
*** *
54600789 AAAAAATTTACATAAAGGTGGTGCCGGCCATTGGCAGGCCACCA-TTGAAAAAAATTTAAATTTT
1 AAAAAATTTACATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAAAAAAATTCAAATTTT
*
54600853 TTCGTATACTGGTGCCGGCCAATGACAGCCCAAAATGTAAAAAAAAAAA-A-TTACATAAAGGTG
66 TCCGTATACTGGTGCCGGCCAATGACAGCCCAAAATGTAAAAAAAAAAATATTTACATAAAGGTG
* *
54600916 GTGCCGGCCATTGGTAGGCTACCACC
131 GTGCCGGCCATTGGCACGCTACCACC
* *
54600942 AAAAAA-TTACATAAAGGTGGTGCCGGCCATTGGTAGGCTACCACCAAAAAAAAATTCAAATTTT
1 AAAAAATTTACATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAAAAAAATTCAAATTTT
* * * *
54601006 TCCGTATATTGGTGTCGGTCAATGATAGCCCAAAATGTAAAAAAAAAAATATTTTTTTACATAAA
66 TCCGTATACTGGTGCCGGCCAATGACAGCCCAAAATGTAAAAAAAAAAATA----TTTACATAAA
* *
54601071 GTTGGTGCCTGCCATTGGCACGCTACCACC
127 GGTGGTGCCGGCCATTGGCACGCTACCACC
54601101 AAAAAA
1 AAAAAA
54601107 AAGTTTTTTT
Statistics
Matches: 143, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
152 35 0.24
153 66 0.46
154 1 0.01
159 41 0.29
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (156 bp):
AAAAAATTTACATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAAAAAAATTCAAATTTT
TCCGTATACTGGTGCCGGCCAATGACAGCCCAAAATGTAAAAAAAAAAATATTTACATAAAGGTG
GTGCCGGCCATTGGCACGCTACCACC
Found at i:54600961 original size:45 final size:45
Alignment explanation
Indices: 54600897--54600992 Score: 192
Period size: 45 Copynumber: 2.1 Consensus size: 45
54600887 ATGTAAAAAA
54600897 AAAAAATTACATAAAGGTGGTGCCGGCCATTGGTAGGCTACCACC
1 AAAAAATTACATAAAGGTGGTGCCGGCCATTGGTAGGCTACCACC
54600942 AAAAAATTACATAAAGGTGGTGCCGGCCATTGGTAGGCTACCACC
1 AAAAAATTACATAAAGGTGGTGCCGGCCATTGGTAGGCTACCACC
54600987 AAAAAA
1 AAAAAA
54600993 AAATTCAAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.19
Consensus pattern (45 bp):
AAAAAATTACATAAAGGTGGTGCCGGCCATTGGTAGGCTACCACC
Found at i:54601299 original size:112 final size:112
Alignment explanation
Indices: 54601172--54601386 Score: 263
Period size: 112 Copynumber: 1.9 Consensus size: 112
54601162 GTAAAAAAAA
* *
54601172 TTACATAAAGGTGGTGCC-GTCCATTGAAAGGCCAAAATTAAAAAAAAAATT-AAATTTTTTCGT
1 TTACATAAAGATGGTGCCAG-CCATTGAAAGGCCAAAA-CAAAAAAAAAATTCAAATTTTTTCGT
* * *
54601235 ATACTGGTGCCGGCCAATAACAGCCCAAAATGTAAAAAAATATTTTTTT
64 ATACTGATGCCGGCCAATAACAGACAAAAATGTAAAAAAATATTTTTTT
** * ** * *
54601284 TTACATAAAGATGGTGCCAGCCATTGGTAGGCTACCACCAAAAAAAATTTCAAATTTTTTCGTAT
1 TTACATAAAGATGGTGCCAGCCATTGAAAGGCCAAAACAAAAAAAAAATTCAAATTTTTTCGTAT
* * *
54601349 ACTGATGTCGGCCAATGACATACAAAAATGTAAAAAAA
66 ACTGATGCCGGCCAATAACAGACAAAAATGTAAAAAAA
54601387 AAATTACATA
Statistics
Matches: 86, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
111 10 0.12
112 75 0.87
113 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.28
Consensus pattern (112 bp):
TTACATAAAGATGGTGCCAGCCATTGAAAGGCCAAAACAAAAAAAAAATTCAAATTTTTTCGTAT
ACTGATGCCGGCCAATAACAGACAAAAATGTAAAAAAATATTTTTTT
Found at i:54601485 original size:48 final size:48
Alignment explanation
Indices: 54601380--54601487 Score: 139
Period size: 48 Copynumber: 2.2 Consensus size: 48
54601370 ACAAAAATGT
* * *
54601380 AAAAAAAAAATTACATAAAGATGGTGCTTGCCATTGGCAGGCTAACAC
1 AAAAAAAAATTTACATAAAGATGATGCTGGCCATTGGCAGGCTAACAC
* *
54601428 AAAAAAAAATTTACATAAAGTTGATG-TCGGCCATT-GCTAGGCTACCAC
1 AAAAAAAAATTTACATAAAGATGATGCT-GGCCATTGGC-AGGCTAACAC
54601476 AAAAAAAAATTT
1 AAAAAAAAATTT
54601488 CAGATTTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
47 3 0.06
48 50 0.94
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (48 bp):
AAAAAAAAATTTACATAAAGATGATGCTGGCCATTGGCAGGCTAACAC
Found at i:54601760 original size:5 final size:5
Alignment explanation
Indices: 54601750--54601789 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
54601740 TTCTTCGTGT
* *
54601750 TTTTA TTTTA TTTTA -TTTA TGTTA TCTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
54601790 ATATATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:54607008 original size:74 final size:74
Alignment explanation
Indices: 54606719--54607148 Score: 490
Period size: 74 Copynumber: 5.6 Consensus size: 74
54606709 NNNNNNNNNN
*
54606719 CATGCCGAGGTATTTCGTTTAAATTTCTGTTGTTCAAAAATCAACTCATATTGCGAGAAGTGAGT
1 CATGCCGAGGTATTT--TTT-AATTTCTGTT-TTCAAAAATCAACTCATATTGCGAGAGGTGAGT
* *
54606784 TGAACCTCGGGTC
62 TGAGCCTCGAGTC
* * *
54606797 ACATGCTGAGGTATTTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCTAGAGGTGAGT
1 -CATGCCGAGGTATTTTTTAATTTCTG-TTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGT
*
54606862 TGAGCCTCGGGTC
62 TGAGCCTCGAGTC
54606875 GCATGCCGAGGTATTCTTTTCAATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAG
1 -CATGCCGAGGTATT-TTTT-AATTTCTG--TTTTCAAAAATCAACTCATATTGCGAGAGGTGAG
54606940 TTGAGCCTCGAGT-
61 TTGAGCCTCGAGTC
** *
54606953 CATGTTGAGGTATTTTTTAATTTTTGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
1 CATGCCGAGGTATTTTTTAATTTCTG-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
54607018 GCCTCGAGT-
65 GCCTCGAGTC
* * * *
54607027 CACGTCGATGTATTTTTCAATTTCTGTTTTCTAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
1 CATGCCGAGGTATTTTTTAATTTCTGTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGA
* *
54607092 GCCTCGGGTTG
65 GCCTCGAG-TC
* * *
54607103 CACGCTGAGG--TGTTTTAAGTTTCTGTTTTTTCAAAAATCAACTCAT
1 CATGCCGAGGTATTTTTTAA-TTTCTG--TTTTCAAAAATCAACTCAT
54607149 GGCTCGAGAG
Statistics
Matches: 314, Mismatches: 25, Indels: 27
0.86 0.07 0.07
Matches are distributed among these distances:
73 5 0.02
74 114 0.36
75 14 0.04
76 36 0.11
77 21 0.07
78 53 0.17
79 57 0.18
80 8 0.03
81 6 0.02
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.37
Consensus pattern (74 bp):
CATGCCGAGGTATTTTTTAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
CCTCGAGTC
Found at i:54607096 original size:148 final size:153
Alignment explanation
Indices: 54606722--54607148 Score: 530
Period size: 157 Copynumber: 2.8 Consensus size: 153
54606712 NNNNNNNCAT
* * *
54606722 GCCGAGGTATTTCGTTTAAATTTCTGTTGTTC-AAAAATCAACTCATATTGCGAGAAGTGAGTTG
1 GCCGAGGTA-TTCTTTTCAATTTCTGTT-TTCTAAAAATCAACTCATATTGCGAGAGGTGAGTTG
* * *
54606786 AACCTCGGGTCACATGCTGAGGTATTTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGC
64 AGCCTCGAGT-ACATGCTGAGGTATTTTTCAATTTCTGCTTTTC-AAAAAATCAACTCATATTGC
* * *
54606851 TAGAGGTGAGTTGAGCCTCGGGTCGCAT
127 GAGAGGTGAGTTGAGCCTCGAGTC-CAC
*
54606879 GCCGAGGTATTCTTTTCAATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
1 GCCGAGGTATTCTTTTCAATTTCTGTTTTCT-AAAAATCAACTCATATTGCGAGAGGTGAGTTGA
* * *
54606944 GCCTCGAGT-CATGTTGAGGTATTTTTTAATTTTTGCTTTTC-AAAAATCAACTCATATTGCGAG
65 GCCTCGAGTACATGCTGAGGTATTTTTCAATTTCTGCTTTTCAAAAAATCAACTCATATTGCGAG
54607007 AGGTGAGTTGAGCCTCGAGT-CAC
130 AGGTGAGTTGAGCCTCGAGTCCAC
* *
54607030 GTCGATGTA-T-TTTTCAATTTCTGTTTTCTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
1 GCCGAGGTATTCTTTTCAATTTCTGTTTTCTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
* * * * *
54607093 CCTCGGGTTGCACGCTGAGGT-GTTTT-AAGTTTCTGTTTTTTC-AAAAATCAACTCAT
66 CCTCGAG-TACATGCTGAGGTATTTTTCAA-TTTCTG-CTTTTCAAAAAATCAACTCAT
54607149 GGCTCGAGAG
Statistics
Matches: 242, Mismatches: 22, Indels: 19
0.86 0.08 0.07
Matches are distributed among these distances:
148 42 0.17
149 28 0.12
150 29 0.12
151 9 0.04
153 40 0.17
155 30 0.12
156 16 0.07
157 48 0.20
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.37
Consensus pattern (153 bp):
GCCGAGGTATTCTTTTCAATTTCTGTTTTCTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
CCTCGAGTACATGCTGAGGTATTTTTCAATTTCTGCTTTTCAAAAAATCAACTCATATTGCGAGA
GGTGAGTTGAGCCTCGAGTCCAC
Found at i:54607351 original size:5 final size:5
Alignment explanation
Indices: 54607341--54607381 Score: 57
Period size: 5 Copynumber: 8.2 Consensus size: 5
54607331 TTCTTCGTGT
*
54607341 TTTTA TTTTA TTTTA -TTTA TTTTA TCTTA TTTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA T
54607382 ATATATTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 4 0.12
5 24 0.75
6 4 0.12
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:54607361 original size:14 final size:14
Alignment explanation
Indices: 54607342--54607372 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
54607332 TCTTCGTGTT
*
54607342 TTTATTTTATTTTA
1 TTTATTTTATCTTA
54607356 TTTATTTTATCTTA
1 TTTATTTTATCTTA
54607370 TTT
1 TTT
54607373 TTATTTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTTATCTTA
Found at i:54608561 original size:12 final size:12
Alignment explanation
Indices: 54608545--54608578 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
54608535 GAAAAAAGGG
54608545 GAAGAAAAAGAAA
1 GAAGAAAAA-AAA
54608558 -AAGAAAAAAAA
1 GAAGAAAAAAAA
54608569 GAAGAAAAAA
1 GAAGAAAAAA
54608579 CAAAAAAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 3 0.15
12 17 0.85
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (12 bp):
GAAGAAAAAAAA
Found at i:54608573 original size:18 final size:18
Alignment explanation
Indices: 54608552--54608587 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
54608542 GGGGAAGAAA
54608552 AAGAAAAAGA-AAAAAAAG
1 AAGAAAAA-ACAAAAAAAG
54608570 AAGAAAAAACAAAAAAAG
1 AAGAAAAAACAAAAAAAG
54608588 GCCCGAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.06
18 16 0.94
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (18 bp):
AAGAAAAAACAAAAAAAG
Found at i:54609185 original size:18 final size:18
Alignment explanation
Indices: 54609162--54609310 Score: 124
Period size: 18 Copynumber: 8.3 Consensus size: 18
54609152 TTTTAAAAAT
*
54609162 AATTTCCGTATTTTTAAA
1 AATTTCCGTGTTTTTAAA
*
54609180 AATTTCCGTGTTTTAAAA
1 AATTTCCGTGTTTTTAAA
* * *
54609198 AATCTT-CGTGTCTTCAAG
1 AAT-TTCCGTGTTTTTAAA
* **
54609216 AA-TCCTCGTGTTTCAAAA
1 AATTTC-CGTGTTTTTAAA
* *
54609234 AATTT-CATGTTTTCAAA
1 AATTTCCGTGTTTTTAAA
54609251 AATTTCCGTGTTTTTTAAA
1 AATTTCCGTG-TTTTTAAA
*
54609270 AATTTCCGTGTTTTCAAA
1 AATTTCCGTGTTTTTAAA
* * *
54609288 AATTTTCGTATTTTTAAG
1 AATTTCCGTGTTTTTAAA
54609306 AATTT
1 AATTT
54609311 TCGTATCTCT
Statistics
Matches: 104, Mismatches: 21, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
16 1 0.01
17 14 0.13
18 69 0.66
19 20 0.19
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.46
Consensus pattern (18 bp):
AATTTCCGTGTTTTTAAA
Found at i:54609265 original size:19 final size:18
Alignment explanation
Indices: 54609162--54609292 Score: 126
Period size: 18 Copynumber: 7.3 Consensus size: 18
54609152 TTTTAAAAAT
* *
54609162 AATTTCCGTATTTTTAAA
1 AATTTCCGTGTTTTCAAA
*
54609180 AATTTCCGTGTTTTAAAA
1 AATTTCCGTGTTTTCAAA
* *
54609198 AATCTT-CGTGTCTTCAAG
1 AAT-TTCCGTGTTTTCAAA
*
54609216 AA-TCCTCGTG-TTTCAAAA
1 AATTTC-CGTGTTTTC-AAA
*
54609234 AATTT-CATGTTTTCAAA
1 AATTTCCGTGTTTTCAAA
*
54609251 AATTTCCGTGTTTTTTAAA
1 AATTTCCGTG-TTTTCAAA
54609270 AATTTCCGTGTTTTCAAA
1 AATTTCCGTGTTTTCAAA
54609288 AATTT
1 AATTT
54609293 TCGTATTTTT
Statistics
Matches: 92, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
16 1 0.01
17 14 0.15
18 57 0.62
19 20 0.22
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.45
Consensus pattern (18 bp):
AATTTCCGTGTTTTCAAA
Found at i:54609271 original size:37 final size:38
Alignment explanation
Indices: 54609118--54609302 Score: 145
Period size: 37 Copynumber: 4.9 Consensus size: 38
54609108 AATAATAATG
*
54609118 AAATTTACCGTG-TTTCAAAAAATATATTCGTGTTTTTTAAAA
1 AAATTT-CCGTGTTTTC-AAAAAT-T-TCCGTGTTTTTT-AAA
* *
54609160 ATAATTTCCGTATTTTTAAAAATTTCCGTG--TTTTAAA
1 A-AATTTCCGTGTTTTCAAAAATTTCCGTGTTTTTTAAA
* * * *
54609197 AAATCTT-CGTGTCTTCAAGAA--TCC-TCGTGTTTCAAA
1 AAAT-TTCCGTGTTTTCAAAAATTTCCGT-GTTTTTTAAA
*
54609233 AAATTT-CATGTTTTCAAAAATTTCCGTGTTTTTT-AA
1 AAATTTCCGTGTTTTCAAAAATTTCCGTGTTTTTTAAA
* *
54609269 AAATTTCCGTGTTTTCAAAAATTTTCGTATTTTT
1 AAATTTCCGTGTTTTCAAAAATTTCCGTGTTTTT
54609303 AAGAATTTTC
Statistics
Matches: 117, Mismatches: 16, Indels: 25
0.74 0.10 0.16
Matches are distributed among these distances:
33 1 0.01
34 4 0.03
35 13 0.11
36 31 0.26
37 38 0.32
38 5 0.04
40 5 0.04
41 1 0.01
42 11 0.09
43 8 0.07
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (38 bp):
AAATTTCCGTGTTTTCAAAAATTTCCGTGTTTTTTAAA
Found at i:54609354 original size:90 final size:90
Alignment explanation
Indices: 54609152--54609354 Score: 214
Period size: 90 Copynumber: 2.2 Consensus size: 90
54609142 TATTCGTGTT
* *
54609152 TTTTAAAAATAATTTC-CGTATTTTTAAAAATTTCCGTGTTTTAAAAAATCTTCGTGTCTTCAAG
1 TTTTAAAAAT-TTTTCGCGT-TTTTTAAAAATTTCCGTGTTTTAAAAAATCTTCGTATCTTCAAG
* * *
54609216 AATCCTCGTGTTTCAAAAAATTTCATG
64 AATCCTCGTATCTCAAAAAATTTCATA
* * * * * *
54609243 TTTTCAAAAA-TTTCCGTGTTTTTTAAAAATTTCCGTGTTTTCAAAAATTTTCGTATTTTTAAGA
1 TTTT-AAAAATTTTTCGCGTTTTTTAAAAATTTCCGTGTTTTAAAAAATCTTCGTATCTTCAAGA
** * *
54609307 ATTTTCGTATCTC-TAAAATTCTCGTA
65 ATCCTCGTATCTCAAAAAATT-TCATA
54609333 TTTTAAAAATTTTTCGCGTTTT
1 TTTTAAAAATTTTTCGCGTTTT
54609355 CAAAAAACTA
Statistics
Matches: 91, Mismatches: 17, Indels: 9
0.78 0.15 0.08
Matches are distributed among these distances:
89 11 0.12
90 69 0.76
91 6 0.07
92 5 0.05
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.47
Consensus pattern (90 bp):
TTTTAAAAATTTTTCGCGTTTTTTAAAAATTTCCGTGTTTTAAAAAATCTTCGTATCTTCAAGAA
TCCTCGTATCTCAAAAAATTTCATA
Found at i:54609394 original size:18 final size:18
Alignment explanation
Indices: 54609144--54609396 Score: 115
Period size: 18 Copynumber: 13.9 Consensus size: 18
54609134 AAAAAATATA
*
54609144 TTCGTGTTTTTTAAAAATAAT
1 TTCGTG-TTTTTAAAAAT--C
*
54609165 TTCCGTATTTTTAAAAAT-
1 TT-CGTGTTTTTAAAAATC
*
54609183 TTCCGTGTTTTAAAAAATC
1 TT-CGTGTTTTTAAAAATC
* * *
54609202 TTCGTGTCTTCAAGAATC
1 TTCGTGTTTTTAAAAATC
* **
54609220 CTCGTGTTTCAAAAAAT-
1 TTCGTGTTTTTAAAAATC
* *
54609237 TTCATGTTTTCAAAAAT-
1 TTCGTGTTTTTAAAAATC
54609254 TTCCGTGTTTTTTAAAAAT-
1 TT-CGTG-TTTTTAAAAATC
* *
54609273 TTCCGTGTTTTCAAAAATT
1 TT-CGTGTTTTTAAAAATC
* * *
54609292 TTCGTATTTTTAAGAATT
1 TTCGTGTTTTTAAAAATC
* * * *
54609310 TTCGTATCTCTAAAATTC
1 TTCGTGTTTTTAAAAATC
* *
54609328 -TCGT-ATTTTAAAAATTT
1 TTCGTGTTTTTAAAAA-TC
* * *
54609345 TTCGCGTTTTCAAAAAAC
1 TTCGTGTTTTTAAAAATC
*** *
54609363 TAATTG-TTTCAAAAATC
1 TTCGTGTTTTTAAAAATC
54609380 TTCGTGTTTTTAAAAAT
1 TTCGTGTTTTTAAAAAT
54609397 TCTCGTATTT
Statistics
Matches: 178, Mismatches: 45, Indels: 21
0.73 0.18 0.09
Matches are distributed among these distances:
16 6 0.03
17 33 0.19
18 94 0.53
19 29 0.16
21 13 0.07
22 3 0.02
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.46
Consensus pattern (18 bp):
TTCGTGTTTTTAAAAATC
Found at i:54610134 original size:107 final size:106
Alignment explanation
Indices: 54610023--54610303 Score: 314
Period size: 107 Copynumber: 2.6 Consensus size: 106
54610013 ATATATATAT
* * * * * *
54610023 ATAAAGGTGGTGGCAACTATTGGCAGTCCATCATTAAAAAAAATTTAAAATTTTTTCGTATACTG
1 ATAAAGGTGGTGGCAGCCATTGGCAGGCCACCA-AAAAAAAAATTTCAAATTTTTTCGTATACTG
* * *
54610088 GTGTCGACAAATGATAGCTCAAAATGTAAAAAAAAAAATTAC
65 GGGTCGACAAATGATAACCCAAAATGTAAAAAAAAAAATTAC
* **
54610130 ATAAAGGTGGT-GCAGGCCATTGGCAGGCTACCACCAAAAAAATATTCAAA-TTTTTCTGTATAC
1 ATAAAGGTGGTGGCA-GCCATTGGCAGGCCACCAAAAAAAAAAT-TTCAAATTTTTTC-GTATAC
* * * *
54610193 TGGGGTTGGCCAATGATAACCCAAAATGTAAAAAAAAAAATTAT
63 TGGGGTCGACAAATGATAACCCAAAATGTAAAAAAAAAAATTAC
* * *
54610237 ATAAAGGTGGTGTCGGCCATTGGCAGGCCACCACCAAAAAAAAAATTTCAAATTTTTTCGTTTAC
1 ATAAAGGTGGTGGCAGCCATTGGCAGG---CCACCAAAAAAAAAATTTCAAATTTTTTCGTATAC
54610302 TG
63 TG
54610304 TTACCGGCCA
Statistics
Matches: 145, Mismatches: 21, Indels: 14
0.81 0.12 0.08
Matches are distributed among these distances:
106 17 0.12
107 95 0.66
108 1 0.01
109 13 0.09
110 19 0.13
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (106 bp):
ATAAAGGTGGTGGCAGCCATTGGCAGGCCACCAAAAAAAAAATTTCAAATTTTTTCGTATACTGG
GGTCGACAAATGATAACCCAAAATGTAAAAAAAAAAATTAC
Found at i:54610328 original size:109 final size:107
Alignment explanation
Indices: 54610058--54610335 Score: 355
Period size: 107 Copynumber: 2.6 Consensus size: 107
54610048 GTCCATCATT
* * *
54610058 AAAAAAAATTTAAAATTTTTTCGTATACTGGTGTCGACAAATGATAGCTCAAAATGTAAAAAAAA
1 AAAAAAAATTTCAAATTTTTTCGTATACTGGTGTCGGCCAATGATAGC-CAAAATGTAAAAAAAA
*
54610123 AAATTACATAAAGGTGGTGCAGGCCATTGGCAGGCTACCACCA
65 AAATTACATAAAGGTGGTGCAGGCCATTGGCAGGCCACCACCA
* * * *
54610166 AAAAAATA-TTCAAA-TTTTTCTGTATACTGGGGTTGGCCAATGATAACCCAAAATGTAAAAAAA
1 AAAAAAAATTTCAAATTTTTTC-GTATACTGGTGTCGGCCAATGAT-AGCCAAAATGTAAAAAAA
*
54610229 AAAATTATATAAAGGTGGTGTC-GGCCATTGGCAGGCCACCACCAA
64 AAAATTACATAAAGGTGGTG-CAGGCCATTGGCAGGCCACCACC-A
* * ** *
54610274 AAAAAAAATTTCAAATTTTTTCGTTTACTGTTACCGGCCAATGACAGCCAAAAATGTAAAAA
1 AAAAAAAATTTCAAATTTTTTCGTATACTGGTGTCGGCCAATGATAGCC-AAAATGTAAAAA
54610336 TATATATTTT
Statistics
Matches: 145, Mismatches: 18, Indels: 13
0.82 0.10 0.07
Matches are distributed among these distances:
106 6 0.04
107 78 0.54
108 21 0.14
109 34 0.23
110 6 0.04
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.26
Consensus pattern (107 bp):
AAAAAAAATTTCAAATTTTTTCGTATACTGGTGTCGGCCAATGATAGCCAAAATGTAAAAAAAAA
AATTACATAAAGGTGGTGCAGGCCATTGGCAGGCCACCACCA
Found at i:54610335 original size:107 final size:106
Alignment explanation
Indices: 54610058--54611196 Score: 385
Period size: 110 Copynumber: 10.6 Consensus size: 106
54610048 GTCCATCATT
* * *
54610058 AAAAAAAATTTAAAATTTTTTCGTATACTGGTGTCGACAAATGATAGCTCAAAATGTAAAAAAAA
1 AAAAAAAATTTCAAATTTTTTCGTATACTGGTGTCGGCCAATGATAGC-CAAAATGT-AAAAAAA
*
54610123 AAATTACATAAAGGTGGTGCAGGCCATTGGCAGGCTACCACCA
64 AAATTACATAAAGGTGGTGCAGGCCATTGGCAGGCCACCACCA
* * * *
54610166 AAAAAATA-TTCAAA-TTTTTCTGTATACTGGGGTTGGCCAATGATAACCCAAAATGTAAAAAAA
1 AAAAAAAATTTCAAATTTTTTC-GTATACTGGTGTCGGCCAATGAT-AGCCAAAATGT-AAAAAA
*
54610229 AAAATTATATAAAGGTGGTGTC-GGCCATTGGCAGGCCACCACCAA
63 AAAATTACATAAAGGTGGTG-CAGGCCATTGGCAGGCCACCACC-A
* * ** *
54610274 AAAAAAAATTTCAAATTTTTTCGTTTACTGTTACCGGCCAATGACAGCCAAAAATGTAAAAATAT
1 AAAAAAAATTTCAAATTTTTTCGTATACTGGTGTCGGCCAATGATAGCC-AAAATGTAAAAA-A-
** * * * *
54610339 ATATTTTTTTTCCATAAAGGTGGTGTCA-GCCATTGTCAAGCCACCAACA
63 A-A----AATTACATAAAGGTGGTG-CAGGCCATTGGCAGGCCACCACCA
****** * * * * * * * ***
54610388 AATTTTTTTTTTTAAA-TTTTTCGTATATTGGTGCCGGCAAATAACAGCCCCAAATGT----TTT
1 AA-AAAAAATTTCAAATTTTTTCGTATACTGGTGTCGGCCAATGATAG-CCAAAATGTAAAAAAA
*** * * *
54610448 TTTTTACACAAAGGTAGTGCCGGCCATTGGCAGGCCACCACCAAAAAA
64 AAATTACATAAAGGTGGTGCAGGCCATTGGCAGGCCACCACC-----A
* * * * * **
54610496 AAAAAAAATTTTTTAAATTTTTTCATATACTGGTGCCGGCAAATGACAGCCCAAAATGT--AATT
1 AAAAAAAA--TTTCAAATTTTTTCGTATACTGGTGTCGGCCAATGATAG-CCAAAATGTAAAAAA
**** *
54610559 TTTTTTACATAAAGGTGATGTC-GGCCATTGGCA----A--A--A
63 AAAATTACATAAAGGTGGTG-CAGGCCATTGGCAGGCCACCACCA
* *** ** ** * * * * * * * *
54610595 AAATTATTTTTTCGTATATTGGT-GCT-GAC-GAATGACATGACAA-AAT-G-TAAACT-T----
1 AAA-AAAAATTTCAAAT-TTTTTCG-TATACTG-GTGTC-GGCCAATGATAGCCAAAATGTAAAA
****** *
54610649 TTTTTTTTACATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAA
61 AAAAAATTACATAAAGGTGGTGCAGGCCATTGGCAGGCCACCACC-A
* * * *
54610696 AAGAAGAAAATTTTTTAAAATTTTTTCGTATA-TGGGTGTCGGCTAATGACATCCCAAAATGT-A
1 AA-AA-AAAA---TTTCAAATTTTTTCGTATACT-GGTGTCGGCCAATGATA-GCCAAAATGTAA
* * *
54610759 AAAAAAAATTCCATAAAGGTGGTGCTGGCCATTGGCGGGCCACCACC-
59 AAAAAAAATTACATAAAGGTGGTGCAGGCCATTGGCAGGCCACCACCA
**** ** * * * *
54610806 -AAATTTTTTTTTAATTTTTTCGTATACTGGTGCCAGCAAATGACAGCCAAAAATGTAAAAAAAA
1 AAAAAAAATTTCAAATTTTTTCGTATACTGGTGTCGGCCAATGATAGCC-AAAATGTAAAAAAAA
* * * *
54610870 ATTTACATAAAGGTGGTGCCGGCTATTTGCAGGCCACCACCA
65 AATTACATAAAGGTGGTGCAGGCCATTGGCAGGCCACCACCA
*** * * * * *
54610912 AACAAATTTTTTCTTTTGAATTTTTTCGTATACTGGTGCCAGCAAATGACAGCCCAAAATGT-AA
1 AA-AAAAAATTTC----AAATTTTTTCGTATACTGGTGTCGGCCAATGATAG-CCAAAATGTAAA
*
54610976 AAAAAAATTACATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCA
60 AAAAAAATTACATAAAGGTGGTGCAGGCCATTGGCAGGCCACCACCA
** * * * * *
54611023 AAAATATATTTTTTTAAATTGTTTCTTATACTGGTGTTGGCCAATGACAGCCCAAAATGTAAAAA
1 AAAA-A-A-AATTTCAAATTTTTTCGTATACTGGTGTCGGCCAATGATAG-CCAAAATGTAAAAA
* *
54611088 AAAAATTACATAAAGGTCGTGTC-GGCCATTGGTAGGCCACCA--A
62 AAAAATTACATAAAGGTGGTG-CAGGCCATTGGCAGGCCACCACCA
* * * * * *
54611131 AAAAATAATTTTTTTTAAAATTTTTTCGTATACTAGTGCCGGCTAATGACAGCCCAAAATGTAAA
1 AAAAA-AA----ATTTCAAATTTTTTCGTATACTGGTGTCGGCCAATGATAG-CCAAAATGTAAA
54611196 A
60 A
54611197 TTATTATTTT
Statistics
Matches: 796, Mismatches: 154, Indels: 160
0.72 0.14 0.14
Matches are distributed among these distances:
91 1 0.00
92 32 0.04
94 1 0.00
95 4 0.01
96 1 0.00
97 2 0.00
98 12 0.02
99 11 0.01
100 1 0.00
101 3 0.00
102 3 0.00
103 34 0.04
104 45 0.06
105 54 0.07
106 8 0.01
107 82 0.10
108 49 0.06
109 77 0.10
110 135 0.17
111 51 0.06
112 107 0.13
113 8 0.01
114 34 0.04
115 41 0.05
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (106 bp):
AAAAAAAATTTCAAATTTTTTCGTATACTGGTGTCGGCCAATGATAGCCAAAATGTAAAAAAAAA
ATTACATAAAGGTGGTGCAGGCCATTGGCAGGCCACCACCA
Found at i:54610652 original size:88 final size:89
Alignment explanation
Indices: 54610512--54610683 Score: 213
Period size: 88 Copynumber: 1.9 Consensus size: 89
54610502 AATTTTTTAA
* * *
54610512 ATTTTTTCATATACTGGTGCCGGCAAATGACAGCCCAAAATGT-AATTTTTTTTACATAAAGGTG
1 ATTTTTTCATATACTGGTGCCGACAAATGACAGCACAAAATGTAAACTTTTTTTACATAAAGGTG
*
54610576 ATGTCGGCCATTGGCAAAAAAATT
66 ATGCCGGCCATTGGCAAAAAAATT
* * * *
54610600 ATTTTTTCGTATATTGGTGCTGACGAATGACATG-ACAAAATGTAAACTTTTTTTTTTACATAAA
1 ATTTTTTCATATACTGGTGCCGACAAATGACA-GCACAAAATGTAAAC---TTTTTTTACATAAA
*
54610664 GGTGGTGCCGGCCATTGGCA
62 GGTGATGCCGGCCATTGGCA
54610684 GGCCACCACC
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
88 35 0.50
89 3 0.04
92 32 0.46
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (89 bp):
ATTTTTTCATATACTGGTGCCGACAAATGACAGCACAAAATGTAAACTTTTTTTACATAAAGGTG
ATGCCGGCCATTGGCAAAAAAATT
Found at i:54610804 original size:112 final size:109
Alignment explanation
Indices: 54610655--54611196 Score: 684
Period size: 110 Copynumber: 5.0 Consensus size: 109
54610645 ACTTTTTTTT
** *
54610655 TTACATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAAGAAGAAAATTTTTTAAAATTTT
1 TTACATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACC-AAA-AA-AATTTTTTTTTAAATTTT
* * *
54610720 TTCGTATA-TGGGTGTCGGCTAATGACATCCCAAAATGTAAAAAAAAA
63 TTCGTATACT-GGTGCCGGCAAATGACAGCCCAAAATGTAAAAAAAAA
* * *
54610767 TTCCATAAAGGTGGTGCTGGCCATTGGCGGGCCACCACC----AAATTTTTTTTT-AATTTTTTC
1 TTACATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAAAAATTTTTTTTTAAATTTTTTC
* *
54610827 GTATACTGGTGCCAGCAAATGACAGCCAAAAATGTAAAAAAAAA
66 GTATACTGGTGCCGGCAAATGACAGCCCAAAATGTAAAAAAAAA
* * * *
54610871 TTTACATAAAGGTGGTGCCGGCTATTTGCAGGCCACCACCAAACAAATTTTTTCTTTTGAATTTT
1 -TTACATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAA-AAAATTTTT-TTTTAAATTTT
*
54610936 TTCGTATACTGGTGCCAGCAAATGACAGCCCAAAATGTAAAAAAAAA
63 TTCGTATACTGGTGCCGGCAAATGACAGCCCAAAATGTAAAAAAAAA
* * *
54610983 TTACATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAAATATATTTTTTTAAATTGTTTC
1 TTACATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAAAAATTTTTTTTTAAATTTTTTC
* ** *
54611048 TTATACTGGTGTTGGCCAATGACAGCCCAAAATGTAAAAAAAAAA
66 GTATACTGGTGCCGGCAAATGACAGCCCAAAATGT-AAAAAAAAA
* * * * *
54611093 TTACATAAAGGTCGTGTCGGCCATTGGTAGGCCACCA-AAAAAATAATTTTTTTTAAAATTTTTT
1 TTACATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAAA-AATTTTTTTTTAAATTTTTT
* *
54611157 CGTATACTAGTGCCGGCTAATGACAGCCCAAAATGTAAAA
65 CGTATACTGGTGCCGGCAAATGACAGCCCAAAATGTAAAA
54611197 TTATTATTTT
Statistics
Matches: 376, Mismatches: 43, Indels: 25
0.85 0.10 0.06
Matches are distributed among these distances:
104 46 0.12
105 43 0.11
106 1 0.00
109 51 0.14
110 103 0.27
111 44 0.12
112 88 0.23
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (109 bp):
TTACATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAAAAATTTTTTTTTAAATTTTTTC
GTATACTGGTGCCGGCAAATGACAGCCCAAAATGTAAAAAAAAA
Found at i:54611229 original size:221 final size:215
Alignment explanation
Indices: 54610655--54611196 Score: 723
Period size: 216 Copynumber: 2.5 Consensus size: 215
54610645 ACTTTTTTTT
* **
54610655 TTACATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAAGAAGAAAATTTTTTAAAATTTT
1 TTACATAAAGGTGGTGCCGGCCATTGGCAGGCCACCA-CAAAA-AATAATTTTTTTTAAAATTTT
* * *
54610720 TTCGTATA-TGGGTGTCGGCTAATGACATCCCAAAATGTAAAAAAAAATTCCATAAAGGTGGTGC
64 TTCGTATACT-GGTGCCGGCTAATGACAGCCCAAAATGTAAAAAAAAATTACATAAAGGTGGTGC
* * *
54610784 TGGCCATTGGCGGGCCACCACCAAATTTTTTTTTAATTTTTTCGTATACTGGTGCCAGCAAATGA
128 CGGCCATTGGCAGGCCACCACCAAATTTTTTTTTAATTGTTTCGTATACTGGTGCCAGCAAATGA
*
54610849 CAGCCAAAAATGTAAAAAAAAAT
193 CAGCCAAAAATGTAAAAAAAAAA
* * **
54610872 TTACATAAAGGTGGTGCCGGCTATTTGCAGGCCACCACCAAACAAAT--TTTTTCTTTTGAATTT
1 TTACATAAAGGTGGTGCCGGCCATTGGCAGGCCACCA-CAAA-AAATAATTTTT-TTTAAAATTT
* *
54610935 TTTCGTATACTGGTGCCAGCAAATGACAGCCCAAAATGTAAAAAAAAATTACATAAAGGTGGTGC
63 TTTCGTATACTGGTGCCGGCTAATGACAGCCCAAAATGTAAAAAAAAATTACATAAAGGTGGTGC
* *** *
54611000 CGGCCATTGGCAGGCCACCACCAAAAATATATTTTTTTAAATTGTTTCTTATACTGGTGTTGGCC
128 CGGCCATTGGCAGGCCACCACC--AAAT-T-TTTTTTT-AATTGTTTCGTATACTGGTGCCAGCA
*
54611065 AATGACAGCCCAAAATGTAAAAAAAAAA
188 AATGACAGCCAAAAATGTAAAAAAAAAA
* * *
54611093 TTACATAAAGGTCGTGTCGGCCATTGGTAGGCCACCA-AAAAAATAATTTTTTTTAAAATTTTTT
1 TTACATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACAAAAAATAATTTTTTTTAAAATTTTTT
*
54611157 CGTATACTAGTGCCGGCTAATGACAGCCCAAAATGTAAAA
66 CGTATACTGGTGCCGGCTAATGACAGCCCAAAATGTAAAA
54611197 TTATTATTTT
Statistics
Matches: 283, Mismatches: 32, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
215 3 0.01
216 86 0.30
217 43 0.15
218 9 0.03
219 52 0.18
220 12 0.04
221 78 0.28
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (215 bp):
TTACATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACAAAAAATAATTTTTTTTAAAATTTTTT
CGTATACTGGTGCCGGCTAATGACAGCCCAAAATGTAAAAAAAAATTACATAAAGGTGGTGCCGG
CCATTGGCAGGCCACCACCAAATTTTTTTTTAATTGTTTCGTATACTGGTGCCAGCAAATGACAG
CCAAAAATGTAAAAAAAAAA
Found at i:54613085 original size:13 final size:13
Alignment explanation
Indices: 54613067--54613096 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
54613057 AGCCCAAACT
54613067 CAATTACCCAACC
1 CAATTACCCAACC
54613080 CAATTACCCAACC
1 CAATTACCCAACC
54613093 CAAT
1 CAAT
54613097 AAAACTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:54613254 original size:9 final size:9
Alignment explanation
Indices: 54613242--54613300 Score: 66
Period size: 9 Copynumber: 6.4 Consensus size: 9
54613232 AAAATAAAAA
54613242 AATTCGGGT
1 AATTCGGGT
*
54613251 AATTCGAGT
1 AATTCGGGT
*
54613260 ATTTTTC-GGT
1 A--ATTCGGGT
*
54613270 AATTCGGTT
1 AATTCGGGT
54613279 AATTCGGGT
1 AATTCGGGT
54613288 AATTCGGGT
1 AATTCGGGT
54613297 AATT
1 AATT
54613301 TAGGTAATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
8 3 0.07
9 32 0.78
10 3 0.07
11 3 0.07
ACGTcount: A:0.24, C:0.10, G:0.25, T:0.41
Consensus pattern (9 bp):
AATTCGGGT
Found at i:54613306 original size:18 final size:18
Alignment explanation
Indices: 54613248--54613309 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
54613238 AAAAAATTCG
* * *
54613248 GGTAATTCGAGTATTTTTC
1 GGTAATTCGGGTA-ATTTA
* **
54613267 GGTAATTCGGTTAATTCG
1 GGTAATTCGGGTAATTTA
54613285 GGTAATTCGGGTAATTTA
1 GGTAATTCGGGTAATTTA
54613303 GGTAATT
1 GGTAATT
54613310 TTTAACCAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
18 24 0.69
19 11 0.31
ACGTcount: A:0.24, C:0.08, G:0.26, T:0.42
Consensus pattern (18 bp):
GGTAATTCGGGTAATTTA
Found at i:54615783 original size:20 final size:20
Alignment explanation
Indices: 54615760--54615806 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
54615750 ATTTTTTTAG
*
54615760 TTTTTTATTAACTTTTGTCT
1 TTTTTTATAAACTTTTGTCT
* *
54615780 TTTTCTT-TAAATTTTTTTCT
1 TTTT-TTATAAACTTTTGTCT
54615800 TTTTTTA
1 TTTTTTA
54615807 AGTTTTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 2 0.09
20 18 0.82
21 2 0.09
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (20 bp):
TTTTTTATAAACTTTTGTCT
Found at i:54615895 original size:13 final size:13
Alignment explanation
Indices: 54615863--54615898 Score: 65
Period size: 12 Copynumber: 2.8 Consensus size: 13
54615853 ATTTTAAAAA
54615863 ATTTGAAATGTAT
1 ATTTGAAATGTAT
54615876 A-TTGAAATGTAT
1 ATTTGAAATGTAT
54615888 ATTTGAAATGT
1 ATTTGAAATGT
54615899 TTTATAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.44
Consensus pattern (13 bp):
ATTTGAAATGTAT
Found at i:54615936 original size:23 final size:23
Alignment explanation
Indices: 54615905--54615951 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
54615895 ATGTTTTATA
*
54615905 ATATATTTTTAA-AATATTAAAT
1 ATATATTTTTAATAATATAAAAT
54615927 ATATATTTTTAATAATATAAAAT
1 ATATATTTTTAATAATATAAAAT
54615950 AT
1 AT
54615952 TTAAATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATATATTTTTAATAATATAAAAT
Found at i:54616366 original size:13 final size:13
Alignment explanation
Indices: 54616320--54616367 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
54616310 TAATTAAAAA
*
54616320 TAAAAATATTTGT
1 TAAAAATATTTAT
54616333 TAAAAATAAATTTATT
1 TAAAAAT--ATTTA-T
*
54616349 TAAAAATATATAT
1 TAAAAATATTTAT
54616362 TAAAAA
1 TAAAAA
54616368 GTAAAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 14 0.47
14 4 0.13
15 4 0.13
16 8 0.27
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (13 bp):
TAAAAATATTTAT
Found at i:54616444 original size:7 final size:7
Alignment explanation
Indices: 54616432--54616499 Score: 109
Period size: 7 Copynumber: 9.7 Consensus size: 7
54616422 ATGCCAGTAA
54616432 AAATATT
1 AAATATT
54616439 AAATATT
1 AAATATT
54616446 AAATATT
1 AAATATT
54616453 AAATATT
1 AAATATT
54616460 AAATATT
1 AAATATT
54616467 AAATATT
1 AAATATT
* **
54616474 ATATAAA
1 AAATATT
54616481 AAATATT
1 AAATATT
54616488 AAATATT
1 AAATATT
54616495 AAATA
1 AAATA
54616500 AAAAAATCAA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 55 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATATT
Found at i:54616936 original size:40 final size:41
Alignment explanation
Indices: 54616881--54616965 Score: 129
Period size: 40 Copynumber: 2.1 Consensus size: 41
54616871 GTGTTGGTTA
*
54616881 TAATTTTTTAATTTTAG-GACACATTTATAAATTTATATA-T
1 TAATTTTTTAATTTTAGTG-CACATTCATAAATTTATATACT
*
54616921 TAATTTTTTAATTTTAGTGCACATTCATAAATTTATCTACT
1 TAATTTTTTAATTTTAGTGCACATTCATAAATTTATATACT
54616962 TAAT
1 TAAT
54616966 ATATATTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
40 35 0.85
41 6 0.15
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.52
Consensus pattern (41 bp):
TAATTTTTTAATTTTAGTGCACATTCATAAATTTATATACT
Found at i:54616976 original size:40 final size:40
Alignment explanation
Indices: 54616889--54616976 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 40
54616879 TATAATTTTT
* * *
54616889 TAATTTTAGGACACATTTATAAATTTATATATTAATTTTT
1 TAATTTTAGGACACATTCATAAATTTATATATTAATTATA
*
54616929 TAATTTTAGTG-CACATTCATAAATTTATCTACTTAA-TATA
1 TAATTTTAG-GACACATTCATAAATTTATATA-TTAATTATA
*
54616969 TATTTTTA
1 TAATTTTA
54616977 ATAGATAAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
40 36 0.88
41 5 0.12
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (40 bp):
TAATTTTAGGACACATTCATAAATTTATATATTAATTATA
Found at i:54619421 original size:30 final size:30
Alignment explanation
Indices: 54619387--54619453 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
54619377 ATATCATTCG
* *
54619387 GACATTGCCGATTCAAATTCATATCACCTA
1 GACATAGCCGATTCAAATTCATATCACCCA
* * *
54619417 GACATAGGCGGTTCAAGTTCATATCACCCA
1 GACATAGCCGATTCAAATTCATATCACCCA
54619447 GACATAG
1 GACATAG
54619454 GTTGTTCGAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (30 bp):
GACATAGCCGATTCAAATTCATATCACCCA
Found at i:54619454 original size:30 final size:30
Alignment explanation
Indices: 54619398--54619478 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
54619388 ACATTGCCGA
* *
54619398 TTCAAATTCATATCACCTAGACATAGGCGG
1 TTCAAGTTCATATCACCCAGACATAGGCGG
**
54619428 TTCAAGTTCATATCACCCAGACATAGGTTG
1 TTCAAGTTCATATCACCCAGACATAGGCGG
* * *
54619458 TTCGAGATCATTTCACCCAGA
1 TTCAAGTTCATATCACCCAGA
54619479 GCAACCATCG
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (30 bp):
TTCAAGTTCATATCACCCAGACATAGGCGG
Found at i:54622840 original size:13 final size:13
Alignment explanation
Indices: 54622809--54622847 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
54622799 TTTAAACCTT
54622809 TTTAAAAGATTTT-
1 TTTAAAA-ATTTTA
*
54622822 TATAAAAATTTTA
1 TTTAAAAATTTTA
54622835 TTTAAAAATTTTA
1 TTTAAAAATTTTA
54622848 AATGTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 5 0.22
13 18 0.78
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (13 bp):
TTTAAAAATTTTA
Found at i:54622881 original size:21 final size:21
Alignment explanation
Indices: 54622856--54622915 Score: 56
Period size: 19 Copynumber: 3.0 Consensus size: 21
54622846 TAAATGTTTA
54622856 AATATTATTAAAAATATATTT
1 AATATTATTAAAAATATATTT
*
54622877 AATA-T-TTAGAAATAATATTT
1 AATATTATTAAAAAT-ATATTT
* *
54622897 AAAATTA-AAAAAATA-ATTT
1 AATATTATTAAAAATATATTT
54622916 CAAATATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
19 11 0.34
20 11 0.34
21 10 0.31
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
AATATTATTAAAAATATATTT
Found at i:54622977 original size:21 final size:22
Alignment explanation
Indices: 54622947--54622991 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
54622937 TATAAGAAAT
54622947 AATTTCAAAAATATATATTTAA
1 AATTTCAAAAATATATATTTAA
*
54622969 AATTT-AAAAATATATTTTTAA
1 AATTTCAAAAATATATATTTAA
54622990 AA
1 AA
54622992 ATATATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
AATTTCAAAAATATATATTTAA
Found at i:54622998 original size:14 final size:14
Alignment explanation
Indices: 54622971--54623046 Score: 59
Period size: 14 Copynumber: 5.5 Consensus size: 14
54622961 ATATTTAAAA
54622971 TTTAAAAATATATT
1 TTTAAAAATATATT
54622985 TTTAAAAATATA--
1 TTTAAAAATATATT
* *
54622997 TTTAAAATTTAAAATT
1 TTTAAAA-AT-ATATT
** *
54623013 TAGAAAAAT-TAAT
1 TTTAAAAATATATT
*
54623026 TTAAAAAATATATT
1 TTTAAAAATATATT
54623040 TTTAAAA
1 TTTAAAA
54623047 TTTATAAGAC
Statistics
Matches: 46, Mismatches: 11, Indels: 10
0.69 0.16 0.15
Matches are distributed among these distances:
12 7 0.15
13 10 0.22
14 23 0.50
15 1 0.02
16 5 0.11
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (14 bp):
TTTAAAAATATATT
Found at i:54623027 original size:76 final size:79
Alignment explanation
Indices: 54622928--54623089 Score: 226
Period size: 76 Copynumber: 2.1 Consensus size: 79
54622918 AATATATATT
* * **
54622928 TTTAAAATTTATAAGAAATAATTTCAAAAATATATATTTAAAATTTA-AA-A-ATATATTTTTAA
1 TTTAAAATTTAGAAGAAATAATTTAAAAAATATATATTTAAAATTTATAAGACATA-ATTTGAAA
54622990 AAAT-ATATTTAAAA
65 AAATAATATTTAAAA
*
54623004 TTTAAAATTTAGAA-AAATTAATTTAAAAAATATATTTTTAAAATTTATAAGACATAATTTGAAA
1 TTTAAAATTTAGAAGAAA-TAATTTAAAAAATATATATTTAAAATTTATAAGACATAATTTGAAA
54623068 AAATAATATTTAAAA
65 AAATAATATTTAAAA
54623083 TTTAAAA
1 TTTAAAA
54623090 AATAATTTAA
Statistics
Matches: 76, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
75 3 0.04
76 40 0.53
77 2 0.03
78 11 0.14
79 20 0.26
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (79 bp):
TTTAAAATTTAGAAGAAATAATTTAAAAAATATATATTTAAAATTTATAAGACATAATTTGAAAA
AATAATATTTAAAA
Found at i:54623037 original size:112 final size:110
Alignment explanation
Indices: 54622893--54623123 Score: 324
Period size: 112 Copynumber: 2.1 Consensus size: 110
54622883 TAGAAATAAT
* *
54622893 ATTTAAAATTAAAAAAATAATTTCAAATATATATTTTTAAAATTTATAAGAAATAATTTC-AAAA
1 ATTTAAAATTAAAAAAATAATTTAAAAAATATATTTTTAAAATTTATAAGAAATAATTTCAAAAA
*
54622957 ATATATATTTAAAATTTAAAAATATATTTTTAAAAAT-ATATTT-AAA
66 ATA-ATATTTAAAATTTAAAAA-ATA-ATTTAAAAATAATATTTAAAA
* * *
54623003 ATTTAAAATTTAGAAAAATTAATTTAAAAAATATATTTTTAAAATTTATAAGACATAATTTGAAA
1 ATTTAAAA-TTA-AAAAAATAATTTAAAAAATATATTTTTAAAATTTATAAGAAATAATTTCAAA
*
54623068 AAATAATATTTAAAATTTAAAAAATAATTTAAAATTAATATTTAAAA
64 AAATAATATTTAAAATTTAAAAAATAATTTAAAAATAATATTTAAAA
54623115 ATTTTAAAA
1 A-TTTAAAA
54623124 AATATATATT
Statistics
Matches: 108, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
110 16 0.15
111 12 0.11
112 66 0.61
113 14 0.13
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (110 bp):
ATTTAAAATTAAAAAAATAATTTAAAAAATATATTTTTAAAATTTATAAGAAATAATTTCAAAAA
ATAATATTTAAAATTTAAAAAATAATTTAAAAATAATATTTAAAA
Found at i:54623105 original size:18 final size:21
Alignment explanation
Indices: 54623059--54623103 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
54623049 TATAAGACAT
54623059 AATTTGAAAAAATAATATTTAA
1 AATTT-AAAAAATAATATTTAA
54623081 AATTTAAAAAAT-A-ATTTAA
1 AATTTAAAAAATAATATTTAA
54623100 AATT
1 AATT
54623104 AATATTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.43
20 1 0.04
21 7 0.30
22 5 0.22
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
AATTTAAAAAATAATATTTAA
Found at i:54623106 original size:11 final size:12
Alignment explanation
Indices: 54622969--54623127 Score: 61
Period size: 13 Copynumber: 13.1 Consensus size: 12
54622959 ATATATTTAA
54622969 AATTTAAAAATAT
1 AATTTAAAAA-AT
* *
54622982 ATTTTTAAAAAT
1 AATTTAAAAAAT
54622994 ATATTTAAAATTTAA-
1 A-ATTTAAAA---AAT
54623009 AATTTAGAAAAATT
1 AATTTA-AAAAA-T
54623023 AATTTAAAAAAT
1 AATTTAAAAAAT
**
54623035 ATATTTTTAAAAT
1 A-ATTTAAAAAAT
* *
54623048 --TTATAAGACAT
1 AATT-TAAAAAAT
54623059 AATTTGAAAAAAT
1 AATTT-AAAAAAT
*
54623072 AATATT---TAA-
1 AAT-TTAAAAAAT
54623081 AATTTAAAAAAT
1 AATTTAAAAAAT
54623093 AATTTAAAATTAAT
1 AATTTAAAA--AAT
54623107 -ATTT-AAAAAT
1 AATTTAAAAAAT
54623117 --TTTAAAAAAT
1 AATTTAAAAAAT
54623127 A
1 A
54623128 TATATTATAA
Statistics
Matches: 111, Mismatches: 14, Indels: 44
0.66 0.08 0.26
Matches are distributed among these distances:
8 2 0.02
9 6 0.05
10 13 0.12
11 6 0.05
12 20 0.18
13 42 0.38
14 16 0.14
15 4 0.04
16 2 0.02
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (12 bp):
AATTTAAAAAAT
Found at i:54623233 original size:18 final size:18
Alignment explanation
Indices: 54623207--54623268 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 18
54623197 AGAAAAATGT
*
54623207 AAAACTTAA-AAAAAGAA
1 AAAATTTAAGAAAAAGAA
*
54623224 ATAAATTTAAAGAAAAAGAC
1 A-AAATTT-AAGAAAAAGAA
*
54623244 AAAATTTAATAAAAAAGTAA
1 AAAATTTAA-GAAAAAG-AA
54623264 AAAAT
1 AAAAT
54623269 AAAAAATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
17 1 0.03
18 7 0.19
19 14 0.39
20 14 0.39
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.19
Consensus pattern (18 bp):
AAAATTTAAGAAAAAGAA
Found at i:54623267 original size:20 final size:18
Alignment explanation
Indices: 54623214--54623282 Score: 66
Period size: 20 Copynumber: 3.6 Consensus size: 18
54623204 TGTAAAACTT
54623214 AAAAAAAGAAATAAATTTA
1 AAAAAAAGAAA-AAATTTA
*
54623233 AAGAAAAAGACAAAATTTA
1 AA-AAAAAGAAAAAATTTA
**
54623252 ATAAAAAAGTAAAAAATAAA
1 A-AAAAAAG-AAAAAATTTA
54623272 AAATAAAAGAA
1 AAA-AAAAGAA
54623283 GGGTGTCAGG
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
19 20 0.48
20 22 0.52
ACGTcount: A:0.75, C:0.01, G:0.07, T:0.16
Consensus pattern (18 bp):
AAAAAAAGAAAAAATTTA
Found at i:54624456 original size:43 final size:42
Alignment explanation
Indices: 54624405--54624488 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 42
54624395 CTTGTTTTTT
* *
54624405 TTATTTGTTTTTCATTT-TTTCCTTTTTCTGATTTTTTTATTTG
1 TTATTTGTTTTTC-TTTATTTACTTTTTCAG-TTTTTTTATTTG
54624448 TTATTTGTTTTTCTTTATTTACTTTTTCAGTTTTTTTATTT
1 TTATTTGTTTTTCTTTATTTACTTTTTCAGTTTTTTTATTT
54624489 ATTTGCTTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
42 14 0.37
43 24 0.63
ACGTcount: A:0.11, C:0.08, G:0.06, T:0.75
Consensus pattern (42 bp):
TTATTTGTTTTTCTTTATTTACTTTTTCAGTTTTTTTATTTG
Found at i:54624511 original size:23 final size:21
Alignment explanation
Indices: 54624482--54624556 Score: 75
Period size: 23 Copynumber: 3.6 Consensus size: 21
54624472 TTTCAGTTTT
54624482 TTTATTTATTTGCTTGTCCTTTA
1 TTTATTTATTTGCTT-T-CTTTA
*
54624505 TTTATTTATTTGTTTTTCTTTA
1 TTTATTTATTTG-CTTTCTTTA
* *
54624527 -TT-TTTCTTT-CTTTCTTTC
1 TTTATTTATTTGCTTTCTTTA
54624545 TTTATTTATTTG
1 TTTATTTATTTG
54624557 TTTATTATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
18 7 0.16
19 2 0.05
20 12 0.28
21 2 0.05
22 5 0.12
23 13 0.30
24 2 0.05
ACGTcount: A:0.11, C:0.11, G:0.05, T:0.73
Consensus pattern (21 bp):
TTTATTTATTTGCTTTCTTTA
Found at i:54625845 original size:60 final size:61
Alignment explanation
Indices: 54625756--54625894 Score: 158
Period size: 61 Copynumber: 2.3 Consensus size: 61
54625746 ATTTATCTTT
* * * * *
54625756 AATAAAAAAAAAACAAAGGATAAATAAAT-AAAAAAGCTGAGAAA-GTAAATAAAGAAAAACA
1 AATAAAAAAAGAA-AAAGGACAAACAAATAAAAAAAGATGAAAAAGGTAAA-AAAGAAAAACA
* * *
54625817 AATAAAAAACGAAAAAGGACAAACAAATAAAAAAATATGAAAAAGGTAAAAATGAAAAACA
1 AATAAAAAAAGAAAAAGGACAAACAAATAAAAAAAGATGAAAAAGGTAAAAAAGAAAAACA
*
54625878 AA-AAAAAAGGAAAAAGG
1 AATAAAAAAAGAAAAAGG
54625895 TGTTGGAATA
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
60 27 0.40
61 35 0.52
62 5 0.07
ACGTcount: A:0.73, C:0.05, G:0.13, T:0.09
Consensus pattern (61 bp):
AATAAAAAAAGAAAAAGGACAAACAAATAAAAAAAGATGAAAAAGGTAAAAAAGAAAAACA
Found at i:54625850 original size:36 final size:35
Alignment explanation
Indices: 54625810--54625885 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 35
54625800 GTAAATAAAG
* *
54625810 AAAAACAAATAAAAAACG-AAAAAGGACAAACAAA
1 AAAAAAAAATAAAAAACGTAAAAAGGAAAAACAAA
* * * *
54625844 TAAAAAAATATGAAAAAGGTAAAAATGAAAAACAAA
1 -AAAAAAAAATAAAAAACGTAAAAAGGAAAAACAAA
54625880 AAAAAA
1 AAAAAA
54625886 GGAAAAAGGT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
35 20 0.59
36 14 0.41
ACGTcount: A:0.76, C:0.07, G:0.09, T:0.08
Consensus pattern (35 bp):
AAAAAAAAATAAAAAACGTAAAAAGGAAAAACAAA
Found at i:54626096 original size:17 final size:17
Alignment explanation
Indices: 54626070--54626102 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
54626060 TGATGTGGCA
*
54626070 TATTGGTGGCGCCAAAG
1 TATTGATGGCGCCAAAG
54626087 TATTGATGGCGCCAAA
1 TATTGATGGCGCCAAA
54626103 CATTTTGGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.24
Consensus pattern (17 bp):
TATTGATGGCGCCAAAG
Found at i:54628851 original size:14 final size:15
Alignment explanation
Indices: 54628826--54628855 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
54628816 TTTTTGTACT
54628826 TTTTATATTTTAAAA
1 TTTTATATTTTAAAA
54628841 TTTTA-ATTTTAAAA
1 TTTTATATTTTAAAA
54628855 T
1 T
54628856 AAATAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTATATTTTAAAA
Found at i:54636782 original size:3 final size:3
Alignment explanation
Indices: 54636774--54636836 Score: 63
Period size: 3 Copynumber: 20.7 Consensus size: 3
54636764 GTAAAAGAGA
* * * * * *
54636774 AAT AAT AAT ACT AAT ACT AAT ACT AAT ACT AAT ACT AAT ACT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
54636822 AAT AAAT AAT AAT AA
1 AAT -AAT AAT AAT AA
54636837 ACAACTAATT
Statistics
Matches: 47, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
3 44 0.94
4 3 0.06
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:54636795 original size:18 final size:18
Alignment explanation
Indices: 54636774--54636835 Score: 83
Period size: 18 Copynumber: 3.6 Consensus size: 18
54636764 GTAAAAGAGA
54636774 AATAATAATACTAATACT
1 AATAATAATACTAATACT
*
54636792 AATACTAATACTAATACT
1 AATAATAATACTAATACT
* *
54636810 AATACTAATAATAATA--
1 AATAATAATACTAATACT
54636826 AATAATAATA
1 AATAATAATA
54636836 AACAACTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
16 9 0.22
18 32 0.78
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (18 bp):
AATAATAATACTAATACT
Found at i:54636836 original size:6 final size:6
Alignment explanation
Indices: 54636774--54636825 Score: 86
Period size: 6 Copynumber: 8.7 Consensus size: 6
54636764 GTAAAAGAGA
* *
54636774 AATAAT AATACT AATACT AATACT AATACT AATACT AATACT AATAAT
1 AATACT AATACT AATACT AATACT AATACT AATACT AATACT AATACT
54636822 AATA
1 AATA
54636826 AATAATAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.33
Consensus pattern (6 bp):
AATACT
Found at i:54638627 original size:132 final size:132
Alignment explanation
Indices: 54638486--54638872 Score: 569
Period size: 132 Copynumber: 2.9 Consensus size: 132
54638476 CAGCCTACTT
* * * * * * * * * *
54638486 CACTGCTGCTCAGGGAGACATGGTTTGCAATCTTCAACCTACTTCACTGCTGCTCAGAGAGATAT
1 CACTACTGCTTAGGGAGACAAGATCTACAATCTTCAACCTACTCCACTGTTGCTCAGGGAGATAG
* * * * *
54638551 GACTGGTGGCCTAAATTTGCTTCCCTACTACCTTGAGAAGATAAGATTCGTCGTCTTCGATCTGC
66 GACTGGTGGCTTAAATCTACTTCCCTACTTCCTTGAGAAGATAAGATTCGCCGTCTTCGATCTGC
54638616 TC
131 TC
54638618 CACTACTGCTTAGGGAGACAAGATCTACAATCTTCAACCTACTCCACTGTTGCTCAGGGAGATAG
1 CACTACTGCTTAGGGAGACAAGATCTACAATCTTCAACCTACTCCACTGTTGCTCAGGGAGATAG
* * * * *
54638683 GACTGGTGGCTTAAATCTACTTCCCTACTTCTTTGGGAAGATAAAAGTCGCCGTCTTCGATTTGC
66 GACTGGTGGCTTAAATCTACTTCCCTACTTCCTTGAGAAGATAAGATTCGCCGTCTTCGATCTGC
54638748 TC
131 TC
*
54638750 CACTACTGCTTAGGGAGACAAGATCTACAATTTTCAACCTACTCCACTGTTGCTCAGGGAGATAG
1 CACTACTGCTTAGGGAGACAAGATCTACAATCTTCAACCTACTCCACTGTTGCTCAGGGAGATAG
54638815 GACTGGTGGCTTAAATCTACTTCCCTACTTCCTT-AGGAAGATAAGATTCGCCGTCTTC
66 GACTGGTGGCTTAAATCTACTTCCCTACTTCCTTGA-GAAGATAAGATTCGCCGTCTTC
54638873 TTCAATCCAC
Statistics
Matches: 229, Mismatches: 25, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
132 229 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (132 bp):
CACTACTGCTTAGGGAGACAAGATCTACAATCTTCAACCTACTCCACTGTTGCTCAGGGAGATAG
GACTGGTGGCTTAAATCTACTTCCCTACTTCCTTGAGAAGATAAGATTCGCCGTCTTCGATCTGC
TC
Found at i:54638641 original size:44 final size:44
Alignment explanation
Indices: 54638593--54638773 Score: 100
Period size: 44 Copynumber: 4.1 Consensus size: 44
54638583 TTGAGAAGAT
* *
54638593 AAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGAC
1 AAGATTCGTCGTCTTCAATCTACTCCACTACTGCTTAGGGAGAC
* * ** * *
54638637 AAGA-TC-TACAATCTTCAACCTACTCCACTGTTGCTCAGGGAGAT
1 AAGATTCGT-C-GTCTTCAATCTACTCCACTACTGCTTAGGGAGAC
* * * * * * * *
54638681 AGGACTGGT-GGCTTAAATCTACTTCC-CTACTTCTTTGGGAAGAT
1 AAGATTCGTCGTCTTCAATCTAC-TCCACTACTGCTTAGGG-AGAC
* * * * * *
54638725 AAAAGTCGCCGTCTTCGATTTGCTCCACTACTGCTTAGGGAGAC
1 AAGATTCGTCGTCTTCAATCTACTCCACTACTGCTTAGGGAGAC
54638769 AAGAT
1 AAGAT
54638774 CTACAATTTT
Statistics
Matches: 95, Mismatches: 34, Indels: 16
0.66 0.23 0.11
Matches are distributed among these distances:
42 1 0.01
43 20 0.21
44 53 0.56
45 20 0.21
46 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (44 bp):
AAGATTCGTCGTCTTCAATCTACTCCACTACTGCTTAGGGAGAC
Found at i:54650994 original size:15 final size:14
Alignment explanation
Indices: 54650975--54651032 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 14
54650965 ATGTGATGAA
54650975 AATAATAAATAAAT
1 AATAATAAATAAAT
*
54650989 AAATAA-AAGAGAAAT
1 -AATAATAA-ATAAAT
54651004 AATAAT-AAT-AAT
1 AATAATAAATAAAT
54651016 AATAAT-AAT-AAT
1 AATAATAAATAAAT
54651028 AATAA
1 AATAA
54651033 ACAACTAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
12 20 0.51
13 1 0.03
14 8 0.21
15 10 0.26
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (14 bp):
AATAATAAATAAAT
Found at i:54651009 original size:3 final size:3
Alignment explanation
Indices: 54651001--54651032 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
54650991 ATAAAAGAGA
54651001 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
54651033 ACAACTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:54653222 original size:9 final size:9
Alignment explanation
Indices: 54653204--54653242 Score: 69
Period size: 9 Copynumber: 4.3 Consensus size: 9
54653194 TGAATTTTGC
*
54653204 AATTCGAAT
1 AATTCAAAT
54653213 AATTCAAAT
1 AATTCAAAT
54653222 AATTCAAAT
1 AATTCAAAT
54653231 AATTCAAAT
1 AATTCAAAT
54653240 AAT
1 AAT
54653243 AGATTGGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (9 bp):
AATTCAAAT
Found at i:54657635 original size:19 final size:20
Alignment explanation
Indices: 54657611--54657655 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
54657601 TAAAAATTCC
*
54657611 AAAATTTAT-ATTTTTTTGA
1 AAAATTTATAATTTTTTTAA
*
54657630 AAAATTTTTAATTTTTTTAA
1 AAAATTTATAATTTTTTTAA
54657650 AAAATT
1 AAAATT
54657656 CTAAAGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
AAAATTTATAATTTTTTTAA
Found at i:54667685 original size:43 final size:43
Alignment explanation
Indices: 54667618--54667712 Score: 163
Period size: 43 Copynumber: 2.2 Consensus size: 43
54667608 AGGTTAATAC
*
54667618 GCTACTAGATGGTTGTGAATACACAACATAAATGTAGATGAGA
1 GCTACCAGATGGTTGTGAATACACAACATAAATGTAGATGAGA
* *
54667661 GCTATCAGATGGTTGTGAATACACAAGATAAATGTAGATGAGA
1 GCTACCAGATGGTTGTGAATACACAACATAAATGTAGATGAGA
54667704 GCTACCAGA
1 GCTACCAGA
54667713 AAGTATGTGG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (43 bp):
GCTACCAGATGGTTGTGAATACACAACATAAATGTAGATGAGA
Found at i:54669879 original size:21 final size:21
Alignment explanation
Indices: 54669842--54669894 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 21
54669832 GGAGAAGAGA
*
54669842 AATGG-GTTATGTAATATGTTT
1 AATGGAGTTTTGTAATAT-TTT
54669863 AATGGAGTTTTGT-ATATTTT
1 AATGGAGTTTTGTAATATTTT
*
54669883 -CTGGAGTTTTGT
1 AATGGAGTTTTGT
54669895 TATTAGAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 11 0.38
20 3 0.10
21 9 0.31
22 6 0.21
ACGTcount: A:0.23, C:0.02, G:0.25, T:0.51
Consensus pattern (21 bp):
AATGGAGTTTTGTAATATTTT
Found at i:54674261 original size:13 final size:13
Alignment explanation
Indices: 54674227--54674262 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
54674217 TTTAGCATAA
54674227 CTTTTGAAAAATG
1 CTTTTGAAAAATG
* *
54674240 CTGTGGAAAAATG
1 CTTTTGAAAAATG
54674253 CTTTTGAAAA
1 CTTTTGAAAA
54674263 GTCCGGTTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.33
Consensus pattern (13 bp):
CTTTTGAAAAATG
Done.