Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 25 of 168
Found at i:6504152 original size:16 final size:17
Alignment explanation
Indices: 6504117--6504151 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
6504107 TTTTGTGTAT
6504117 AATTATAATTTCAAAAA
1 AATTATAATTTCAAAAA
*
6504134 AATTATAATTTTAAAAA
1 AATTATAATTTCAAAAA
6504151 A
1 A
6504152 TGAATTGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (17 bp):
AATTATAATTTCAAAAA
Found at i:6505745 original size:16 final size:16
Alignment explanation
Indices: 6505726--6505781 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 16
6505716 TTTAAAGTTA
6505726 TTTATTAAAATAAAAT
1 TTTATTAAAATAAAAT
6505742 TTTAATATAAAAT--AA-
1 TTT-AT-TAAAATAAAAT
6505757 TTTATTAAAATAATAAT
1 TTTATTAAAATAA-AAT
6505774 TTATATTA
1 TT-TATTA
6505782 GTTATATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 6 0.18
14 2 0.06
15 3 0.09
16 7 0.21
17 4 0.12
18 11 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TTTATTAAAATAAAAT
Found at i:6505780 original size:18 final size:17
Alignment explanation
Indices: 6505726--6505781 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 17
6505716 TTTAAAGTTA
6505726 TTTATTAAAATAA-AAT
1 TTTATTAAAATAATAAT
* *
6505742 TTTAATATAA-AATAA-
1 TTTATTAAAATAATAAT
6505757 TTTATTAAAATAATAAT
1 TTTATTAAAATAATAAT
6505774 TTATATTA
1 TT-TATTA
6505782 GTTATATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
15 10 0.31
16 15 0.47
17 2 0.06
18 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTATTAAAATAATAAT
Found at i:6506079 original size:19 final size:19
Alignment explanation
Indices: 6506051--6506090 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
6506041 GTTGTCTTAT
6506051 AAGTTA-TTTTCAGTGAACC
1 AAGTTATTTTTCA-TGAACC
*
6506070 AAGTTGTTTTTCATGAACC
1 AAGTTATTTTTCATGAACC
6506089 AA
1 AA
6506091 ACACAAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (19 bp):
AAGTTATTTTTCATGAACC
Found at i:6507455 original size:2 final size:2
Alignment explanation
Indices: 6507450--6507485 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
6507440 TTAGTGTGTC
*
6507450 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6507486 TGCTGACTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:6507524 original size:15 final size:15
Alignment explanation
Indices: 6507504--6507532 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6507494 TTAAAAGCTG
6507504 TCAAGCTTTTGATTT
1 TCAAGCTTTTGATTT
6507519 TCAAGCTTTTGATT
1 TCAAGCTTTTGATT
6507533 ATGGTGGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.52
Consensus pattern (15 bp):
TCAAGCTTTTGATTT
Found at i:6508069 original size:22 final size:22
Alignment explanation
Indices: 6508044--6508088 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
6508034 TGTCAGAATT
6508044 TCATG-TAATTTTACCGATCTGA
1 TCATGATAATTTTACCGA-CTGA
*
6508066 TCATGATAATTTTGCCGACTGA
1 TCATGATAATTTTACCGACTGA
6508088 T
1 T
6508089 AGTAGTGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.40
Consensus pattern (22 bp):
TCATGATAATTTTACCGACTGA
Found at i:6510407 original size:19 final size:20
Alignment explanation
Indices: 6510360--6510410 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
6510350 TTTTAGATCT
*
6510360 TTTAAAATTTTTATATATTC
1 TTTAAATTTTTTATATATTC
*
6510380 TTTAGATTTTTTA-ATATT-
1 TTTAAATTTTTTATATATTC
6510398 TTTATAATTTTTT
1 TTTA-AATTTTTT
6510411 TAAAAATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 4 0.15
19 12 0.44
20 11 0.41
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTAAATTTTTTATATATTC
Found at i:6510412 original size:29 final size:29
Alignment explanation
Indices: 6510345--6510410 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
6510335 TTCTAAAAAT
6510345 TATTATTTTAGATCTTTTAAAATTTTTATA
1 TATT-TTTTAGATCTTTTAAAATTTTTATA
* * *
6510375 TATTCTTTAGATTTTTTAATATTTTTATA
1 TATTTTTTAGATCTTTTAAAATTTTTATA
6510404 -ATTTTTT
1 TATTTTTT
6510411 TAAAAATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 6 0.19
29 22 0.69
30 4 0.12
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (29 bp):
TATTTTTTAGATCTTTTAAAATTTTTATA
Found at i:6510449 original size:17 final size:18
Alignment explanation
Indices: 6510408--6510461 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 18
6510398 TTTATAATTT
6510408 TTTTAAAAATATAATTTTGTAA
1 TTTTAAAAAT-T-A-TTT-TAA
*
6510430 TTTTATAAA-TATTTTAA
1 TTTTAAAAATTATTTTAA
6510447 TTTTAAAAATTATTT
1 TTTTAAAAATTATTT
6510462 GGAATTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 11 0.38
18 8 0.28
19 1 0.03
20 1 0.03
22 8 0.28
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TTTTAAAAATTATTTTAA
Found at i:6510586 original size:19 final size:18
Alignment explanation
Indices: 6510552--6510600 Score: 71
Period size: 19 Copynumber: 2.7 Consensus size: 18
6510542 ACACCAATCT
*
6510552 GTTATTTGAGTTATTCAA
1 GTTATTTGAATTATTCAA
6510570 GTTATTTGGAATTATTCAA
1 GTTATTT-GAATTATTCAA
*
6510589 GTTATTCGAATT
1 GTTATTTGAATT
6510601 GTAAAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 12 0.43
19 16 0.57
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.49
Consensus pattern (18 bp):
GTTATTTGAATTATTCAA
Found at i:6517541 original size:35 final size:35
Alignment explanation
Indices: 6517502--6517574 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
6517492 TAAATCGAAA
6517502 CATTTGTTATCTAAATTCAAATGAACATGGACAAC
1 CATTTGTTATCTAAATTCAAATGAACATGGACAAC
6517537 CATTTGTTATCTAAATTCAAATGAACATGGACAAC
1 CATTTGTTATCTAAATTCAAATGAACATGGACAAC
6517572 CAT
1 CAT
6517575 GTGTCCCAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.32
Consensus pattern (35 bp):
CATTTGTTATCTAAATTCAAATGAACATGGACAAC
Found at i:6526056 original size:52 final size:51
Alignment explanation
Indices: 6525963--6526062 Score: 123
Period size: 52 Copynumber: 1.9 Consensus size: 51
6525953 ACTTATATAT
6525963 ATATAAAATACATAATGCATTTATGAAAACAAGGAAAATATAAATATACAC
1 ATATAAAATACATAATGCATTTATGAAAACAAGGAAAATATAAATATACAC
* * * *
6526014 ATATAAAATATATTCATGCATTTACT-AAAA-AATGAAATATATAAGTATA
1 ATATAAAATACA-TAATGCATTTA-TGAAAACAAGGAAA-ATATAAATATA
6526063 ATATAAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
51 17 0.40
52 24 0.57
53 1 0.02
ACGTcount: A:0.55, C:0.08, G:0.07, T:0.30
Consensus pattern (51 bp):
ATATAAAATACATAATGCATTTATGAAAACAAGGAAAATATAAATATACAC
Found at i:6526340 original size:3 final size:3
Alignment explanation
Indices: 6526332--6526388 Score: 66
Period size: 3 Copynumber: 19.0 Consensus size: 3
6526322 ATATGTAGGT
6526332 ATA ATA ATA ATA TATA AT- ATA ATA ATAA ATA ATA ATA ATA ATA A-A
1 ATA ATA ATA ATA -ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA
6526377 ATTA ATA A-A ATA
1 A-TA ATA ATA ATA
6526389 GACTAAAAAC
Statistics
Matches: 48, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
2 6 0.12
3 34 0.71
4 8 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:6526355 original size:15 final size:16
Alignment explanation
Indices: 6526332--6526388 Score: 75
Period size: 15 Copynumber: 3.8 Consensus size: 16
6526322 ATATGTAGGT
*
6526332 ATAATAATAATATATA
1 ATAATAATAATAAATA
6526348 AT-ATAATAATAAATA
1 ATAATAATAATAAATA
6526363 ATAATAATAATAAA-A
1 ATAATAATAATAAATA
*
6526378 TTAATAA-AATA
1 ATAATAATAATA
6526389 GACTAAAAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
14 4 0.11
15 21 0.55
16 13 0.34
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAATAATAATAAATA
Found at i:6526630 original size:19 final size:21
Alignment explanation
Indices: 6526592--6526630 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
6526582 CCTTTTTTAA
*
6526592 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
6526613 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
6526631 CAGTAAGCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:6526701 original size:45 final size:46
Alignment explanation
Indices: 6526646--6526733 Score: 144
Period size: 45 Copynumber: 1.9 Consensus size: 46
6526636 AGCCACCTTT
6526646 AAAAAACTGTCAATCGTTCT-CATTTTTTCATTGATT-TTTTTTAAA
1 AAAAAACTGTCAATCGTTCTCCATTTTTT-ATTGATTCTTTTTTAAA
*
6526691 AAAAAACTGTCAATCGTTCTCCCTTTTTTATTGATTCTTTTTT
1 AAAAAACTGTCAATCGTTCTCCATTTTTTATTGATTCTTTTTT
6526734 TTCTACAATG
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
45 27 0.68
46 13 0.32
ACGTcount: A:0.27, C:0.16, G:0.07, T:0.50
Consensus pattern (46 bp):
AAAAAACTGTCAATCGTTCTCCATTTTTTATTGATTCTTTTTTAAA
Found at i:6526872 original size:23 final size:22
Alignment explanation
Indices: 6526829--6526886 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
6526819 AAAGGGTATC
* *
6526829 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
6526850 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
6526873 TACATATCATATCT
1 TACAAATCATATCT
6526887 AAGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:6526889 original size:19 final size:20
Alignment explanation
Indices: 6526842--6526899 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 20
6526832 AAATTAAATC
*
6526842 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTAC-ATATCATA--T
6526865 TCTAAGATTACATATCATA-
1 TCTAAGATTACATATCATAT
*
6526884 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
6526900 CTCGAAGGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.45
22 7 0.21
23 11 0.33
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (20 bp):
TCTAAGATTACATATCATAT
Found at i:6527952 original size:44 final size:44
Alignment explanation
Indices: 6527902--6528216 Score: 177
Period size: 44 Copynumber: 7.2 Consensus size: 44
6527892 CGGTGTAGGA
*
6527902 AGGCAAGATCTGTTATTTTTAACCTGCTCCGCTGCAATCCAGGG
1 AGGCAAGATCTGGTATTTTTAACCTGCTCCGCTGCAATCCAGGG
* * * ** * * * ** * *
6527946 AGGCAAG-GCTGGTGTCTTCGATCTACTTCGCTGTCGGTGCAGGA
1 AGGCAAGATCTGGTATTTTTAACCTGCTCCGCTG-CAATCCAGGG
* * * *
6527990 AGGCAAGATCTGTTATTTTTAACCTGCTCCGCTGTAACCCAAGG
1 AGGCAAGATCTGGTATTTTTAACCTGCTCCGCTGCAATCCAGGG
* * * ** * * ** ** *
6528034 AGGCAAG-GCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGTAGGA
1 AGGCAAGATCTGGTATTTTTAACCTGCTCCGCTG-CAATCCAGGG
* *
6528078 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCAGGG
1 AGGCAAGATCTGGTATTTTTAACCTGCTCCGCTGCAATCCAGGG
* * * * * * ** * *
6528122 AGGCAAG-GCTGGTGTCTTTGATCTGCTTCGCTGTCGGTACAGGA
1 AGGCAAGATCTGGTATTTTTAACCTGCTCCGCTG-CAATCCAGGG
* * * *
6528166 AAGCAAGATCTGTTATTTTTAACTTGCTCCGCTGCAACCCAGGG
1 AGGCAAGATCTGGTATTTTTAACCTGCTCCGCTGCAATCCAGGG
6528210 AGGCAAG
1 AGGCAAG
6528217 GTTGGGTCTT
Statistics
Matches: 179, Mismatches: 86, Indels: 12
0.65 0.31 0.04
Matches are distributed among these distances:
43 54 0.30
44 72 0.40
45 53 0.30
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.28
Consensus pattern (44 bp):
AGGCAAGATCTGGTATTTTTAACCTGCTCCGCTGCAATCCAGGG
Found at i:6527995 original size:88 final size:88
Alignment explanation
Indices: 6527875--6528356 Score: 750
Period size: 88 Copynumber: 5.5 Consensus size: 88
6527865 GTTGGGGTCA
* * * *
6527875 TCGATCTGCTTCACTATCGGTGTAGGAAGGCAAGATCTGTTATTTTTAACCTGCTCCGCTGCAAT
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGTTATTTTTAACCTGCTCCGCTGCAAC
6527940 CCAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* *
6527963 TCGATCTACTTCGCTGTCGGTGCAGGAAGGCAAGATCTGTTATTTTTAACCTGCTCCGCTGTAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGTTATTTTTAACCTGCTCCGCTGCAAC
*
6528028 CCAAGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* *
6528051 TCGATCTGCTTCGCTGTCGGTGTAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGTTATTTTTAACCTGCTCCGCTGCAAC
6528116 CCAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * * *
6528139 TTGATCTGCTTCGCTGTCGGTACAGGAAAGCAAGATCTGTTATTTTTAACTTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGTTATTTTTAACCTGCTCCGCTGCAAC
*
6528204 CCAGGGAGGCAAGGTTGG-GTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * * *
6528226 TCGATCTGCTTCGCTGTCGGTACAGGAAGGCAAGATCTGCTATTTTTAACCTGTTCCGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGTTATTTTTAACCTGCTCCGCTGCAAC
* * *
6528291 CCAGAGAGACAAGGTTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* *
6528314 TCGATCTGCTTTGCTGTCGGTGCAAGAAGGCAAGATCTGTTAT
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGTTAT
6528357 CTTCACTGAT
Statistics
Matches: 362, Mismatches: 31, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
87 79 0.22
88 283 0.78
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.29
Consensus pattern (88 bp):
TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGTTATTTTTAACCTGCTCCGCTGCAAC
CCAGGGAGGCAAGGCTGGTGTCT
Found at i:6528066 original size:43 final size:43
Alignment explanation
Indices: 6528013--6528155 Score: 115
Period size: 43 Copynumber: 3.3 Consensus size: 43
6528003 TATTTTTAAC
*
6528013 CTGCTCCGCTGTAACCCAAGGAGGCAAGGCTGGTGTCTTCGAT
1 CTGCTCCGCTGTAACCCAAGGAGGCAAGGCTGGTGTCTTTGAT
* ****** * * * * * *
6528056 CTGCTTCGCTGTCGGTGTAGGAAGGCAAGATCTGCTATTTTTAAC
1 CTGCTCCGCTGTAACCCAAGG-AGGCAAG-GCTGGTGTCTTTGAT
* *
6528101 CTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTTGAT
1 CTGCTCCGCTGTAACCCAAGGAGGCAAGGCTGGTGTCTTTGAT
*
6528144 CTGCTTCGCTGT
1 CTGCTCCGCTGT
6528156 CGGTACAGGA
Statistics
Matches: 67, Mismatches: 31, Indels: 4
0.66 0.30 0.04
Matches are distributed among these distances:
43 33 0.49
44 14 0.21
45 20 0.30
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.28
Consensus pattern (43 bp):
CTGCTCCGCTGTAACCCAAGGAGGCAAGGCTGGTGTCTTTGAT
Found at i:6534170 original size:56 final size:56
Alignment explanation
Indices: 6534105--6534229 Score: 198
Period size: 56 Copynumber: 2.2 Consensus size: 56
6534095 TATTTAAAAC
*
6534105 TATGTAAAATTATTAAG-CCCAAAAAATTTTGTTAATGGTTAGTAAAATTATCAAAT
1 TATGTAAAATTATTAAGCCCCAAAAAA-TGTGTTAATGGTTAGTAAAATTATCAAAT
**
6534161 TATGTAAAATTATTAAGCCCCAAAAAATGTGTTAATGGTTAGTAGGATTATCAAAT
1 TATGTAAAATTATTAAGCCCCAAAAAATGTGTTAATGGTTAGTAAAATTATCAAAT
*
6534217 TAGGTAAAATTAT
1 TATGTAAAATTAT
6534230 GTTAGGGTTT
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
56 55 0.86
57 9 0.14
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (56 bp):
TATGTAAAATTATTAAGCCCCAAAAAATGTGTTAATGGTTAGTAAAATTATCAAAT
Found at i:6534256 original size:23 final size:23
Alignment explanation
Indices: 6534223--6534285 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
6534213 AAATTAGGTA
*
6534223 AAATTATGTTAGGGTTTTTACA-T
1 AAATTAGGTTAGGGTTTTTA-ATT
*
6534246 AAATTAGGTTAGGGGTTTTAATT
1 AAATTAGGTTAGGGTTTTTAATT
*
6534269 AAAATAGGTTAGGGTTT
1 AAATTAGGTTAGGGTTT
6534286 AGGGTTTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 1 0.03
23 34 0.97
ACGTcount: A:0.32, C:0.02, G:0.24, T:0.43
Consensus pattern (23 bp):
AAATTAGGTTAGGGTTTTTAATT
Found at i:6534290 original size:29 final size:29
Alignment explanation
Indices: 6534252--6534435 Score: 269
Period size: 29 Copynumber: 6.1 Consensus size: 29
6534242 ACATAAATTA
* *
6534252 GGTTAGGGGTTTTAATTAAAATAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
6534281 GGTTTAGGGTTTTTAATTAAATTAGGTTAG
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAG
*
6534311 AGTTAGGGCTTTTAATTAAATTAAATTAGGTTAG
1 GGTTAGGG--TTT--TT-AATTAAATTAGGTTAG
*
6534345 AGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
6534374 GGTTAGGGTTTTTAATTAAATTAGGCTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
6534403 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
6534432 GGTT
1 GGTT
6534436 TTTAAATAAA
Statistics
Matches: 143, Mismatches: 6, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
29 83 0.58
30 28 0.20
31 3 0.02
32 3 0.02
33 2 0.01
34 24 0.17
ACGTcount: A:0.29, C:0.01, G:0.27, T:0.43
Consensus pattern (29 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAG
Found at i:6534369 original size:63 final size:58
Alignment explanation
Indices: 6534249--6534457 Score: 261
Period size: 63 Copynumber: 3.6 Consensus size: 58
6534239 TTTACATAAA
* *
6534249 TTAG-GTTAGGGGTTTTAATTAAAATAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGG
1 TTAGAGTTAGGGTTTTTAATTAAATTAGGTTAGGG-TTAGGGTTTTTAATTAAATTAGG
*
6534307 TTAGAGTTAGGGCTTTTAATTAAATTAAATTAGGTTAGAGTTAGGGTTTTTAATTAAATTAGG
1 TTAGAGTTAGGG--TTT--TT-AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGG
* *
6534370 TTAGGGTTAGGGTTTTTAATTAAATTAGGCTAGGGTTAGGGTTTTTAATT-AA--A--
1 TTAGAGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGG
*
6534423 TTAG-GTTAGGGTTTTTAAATAAATTAGGTTAGGGT
1 TTAGAGTTAGGGTTTTTAATTAAATTAGGTTAGGGT
6534458 ATCAAATAAT
Statistics
Matches: 137, Mismatches: 8, Indels: 18
0.84 0.05 0.11
Matches are distributed among these distances:
52 29 0.21
53 4 0.03
55 1 0.01
57 2 0.01
58 35 0.26
59 9 0.07
61 5 0.04
63 36 0.26
64 16 0.12
ACGTcount: A:0.30, C:0.01, G:0.26, T:0.43
Consensus pattern (58 bp):
TTAGAGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGG
Found at i:6534376 original size:23 final size:24
Alignment explanation
Indices: 6534340--6534457 Score: 105
Period size: 29 Copynumber: 4.5 Consensus size: 24
6534330 ATTAAATTAG
6534340 GTTAGAGTTAGGGTTTTTAATTAAATTA
1 GTTAG-GTTAGGGTTTTTAATT-AA--A
6534368 GGTTAGGGTTAGGGTTTTTAATTAAATTA
1 -GTTA-GGTTAGGGTTTTTAATT-AA--A
*
6534397 GGCTAGGGTTAGGGTTTTTAATTAAA
1 -GTTA-GGTTAGGGTTTTTAATTAAA
*
6534423 -TTAGGTTAGGGTTTTTAAATAAA
1 GTTAGGTTAGGGTTTTTAATTAAA
6534446 -TTAGGTTAGGGT
1 GTTAGGTTAGGGT
6534458 ATCAAATAAT
Statistics
Matches: 85, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
23 31 0.36
24 2 0.02
26 1 0.01
28 2 0.02
29 48 0.56
30 1 0.01
ACGTcount: A:0.29, C:0.01, G:0.27, T:0.43
Consensus pattern (24 bp):
GTTAGGTTAGGGTTTTTAATTAAA
Found at i:6534432 original size:92 final size:92
Alignment explanation
Indices: 6534249--6534425 Score: 293
Period size: 92 Copynumber: 1.9 Consensus size: 92
6534239 TTTACATAAA
*
6534249 TTAGGTTAGGGGTTTTAATTAAAATAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGAGT
1 TTAGGTTAGGGGTTTTAATTAAAATAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGCTAGAGT
6534314 TAGGGCTTTTAATTAAATTAAATTAGG
66 TAGGGCTTTTAATTAAATTAAATTAGG
* * *
6534341 TTAGAGTTAGGGTTTTTAATTAAATTAGGTTAGGG-TTAGGGTTTTTAATTAAATTAGGCTAGGG
1 TTAG-GTTAGGGGTTTTAATTAAAATAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGCTAGAG
*
6534405 TTAGGGTTTTTAATTAAATTA
65 TTAGGGCTTTTAATTAAATTA
6534426 GGTTAGGGTT
Statistics
Matches: 79, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
92 51 0.65
93 28 0.35
ACGTcount: A:0.31, C:0.01, G:0.25, T:0.44
Consensus pattern (92 bp):
TTAGGTTAGGGGTTTTAATTAAAATAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGCTAGAGT
TAGGGCTTTTAATTAAATTAAATTAGG
Found at i:6535633 original size:7 final size:7
Alignment explanation
Indices: 6535623--6535647 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6535613 TTATATACAT
6535623 AATACTA
1 AATACTA
6535630 AATACTA
1 AATACTA
6535637 AATACTA
1 AATACTA
6535644 AATA
1 AATA
6535648 TCAATCCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:6536760 original size:20 final size:20
Alignment explanation
Indices: 6536735--6536776 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
6536725 TGAAAATATT
*
6536735 AAAAAT-TAAAATTATTTTAA
1 AAAAATATAAAAATA-TTTAA
6536755 AAAAATATAAAAATATTTAA
1 AAAAATATAAAAATATTTAA
6536775 AA
1 AA
6536777 TTATCTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAATATAAAAATATTTAA
Found at i:6536778 original size:31 final size:29
Alignment explanation
Indices: 6536727--6536789 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 29
6536717 GCCATTGTTG
* *
6536727 AAAATATTAAAAATTAAAATTATTTTAAA
1 AAAATATAAAAAATTAAAATTATCTTAAA
6536756 AAAATATAAAAATATTTAAAATTATCTTAAA
1 AAAATATAAAAA-A-TTAAAATTATCTTAAA
6536787 AAA
1 AAA
6536790 TGAAATTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 11 0.37
30 1 0.03
31 18 0.60
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (29 bp):
AAAATATAAAAAATTAAAATTATCTTAAA
Found at i:6536811 original size:17 final size:18
Alignment explanation
Indices: 6536785--6536818 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
6536775 AATTATCTTA
6536785 AAAAATGAAATTGAATAG
1 AAAAATGAAATTGAATAG
*
6536803 AAAAA-GAAATTTAATA
1 AAAAATGAAATTGAATA
6536819 TGGATTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.24
Consensus pattern (18 bp):
AAAAATGAAATTGAATAG
Found at i:6536860 original size:22 final size:22
Alignment explanation
Indices: 6536833--6536929 Score: 116
Period size: 22 Copynumber: 4.7 Consensus size: 22
6536823 TTTTAAAGAT
*
6536833 TTTTGGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGAA
*
6536855 TTTTGGAAGGAATTTGAGAG--
1 TTTTGGAAGGAAATTGAGAGAA
**
6536875 -TTT-G-A-GAGTTTGAGAGAA
1 TTTTGGAAGGAAATTGAGAGAA
6536893 TTTTGGAAGGAAATTGAGAGAA
1 TTTTGGAAGGAAATTGAGAGAA
6536915 TTTTGGAAGGAAATT
1 TTTTGGAAGGAAATT
6536930 TAGATAGGAT
Statistics
Matches: 65, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
16 10 0.15
17 1 0.02
18 1 0.02
19 6 0.09
20 1 0.02
21 1 0.02
22 45 0.69
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.32
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGAA
Found at i:6537290 original size:12 final size:13
Alignment explanation
Indices: 6537271--6537307 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
6537261 TTGAATAAAT
6537271 TAAATTTTTAATA
1 TAAATTTTTAATA
*
6537284 T-AATTTTTAAAA
1 TAAATTTTTAATA
6537296 TAAATTTTTAAT
1 TAAATTTTTAAT
6537308 TTTCAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TAAATTTTTAATA
Found at i:6537301 original size:13 final size:13
Alignment explanation
Indices: 6537266--6537306 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
6537256 GTTGGTTGAA
*
6537266 TAAATTAAATTTT
1 TAAAATAAATTTT
*
6537279 TAATAT-AATTTT
1 TAAAATAAATTTT
6537291 TAAAATAAATTTT
1 TAAAATAAATTTT
6537304 TAA
1 TAA
6537307 TTTTCAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TAAAATAAATTTT
Found at i:6537436 original size:17 final size:17
Alignment explanation
Indices: 6537425--6537485 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 17
6537415 AAAAAGTTCT
6537425 ATTTTTTAAAAATTATA
1 ATTTTTTAAAAATTATA
*
6537442 ATTTTTT-AAAATTTTAA
1 ATTTTTTAAAAATTAT-A
*
6537459 GATTTTTTATTGAAATTATA
1 -ATTTTTTA--AAAATTATA
6537479 ATTTTTT
1 ATTTTTT
6537486 TTTTATTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
16 7 0.19
17 8 0.22
18 7 0.19
19 7 0.19
20 1 0.03
21 6 0.17
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
ATTTTTTAAAAATTATA
Found at i:6537437 original size:23 final size:21
Alignment explanation
Indices: 6537393--6537434 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
6537383 TTTTAAATTT
* *
6537393 TAAAGAGTTTTATTTTTTAAA
1 TAAAAAGTTCTATTTTTTAAA
6537414 TAAAAAGTTCTATTTTTTAAA
1 TAAAAAGTTCTATTTTTTAAA
6537435 AATTATAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.50
Consensus pattern (21 bp):
TAAAAAGTTCTATTTTTTAAA
Found at i:6537447 original size:18 final size:17
Alignment explanation
Indices: 6537425--6537486 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 17
6537415 AAAAAGTTCT
*
6537425 ATTTTTTAAAAATTATA
1 ATTTTTTTAAAATTATA
*
6537442 A-TTTTTTAAAATTTTAA
1 ATTTTTTTAAAATTAT-A
*
6537459 GATTTTTTATTGAAATTATA
1 -A-TTTTT-TTAAAATTATA
6537479 ATTTTTTT
1 ATTTTTTT
6537487 TTTATTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
16 12 0.33
17 4 0.11
18 6 0.17
19 1 0.03
20 5 0.14
21 8 0.22
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (17 bp):
ATTTTTTTAAAATTATA
Found at i:6537515 original size:21 final size:21
Alignment explanation
Indices: 6537474--6537515 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6537464 TTTATTGAAA
* *
6537474 TTATAATTTTTTTTTTATTTT
1 TTATAATTTTTATGTTATTTT
*
6537495 TTATAATTTTTATGTTCTTTT
1 TTATAATTTTTATGTTATTTT
6537516 AAAGAGTAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.76
Consensus pattern (21 bp):
TTATAATTTTTATGTTATTTT
Found at i:6539143 original size:2 final size:2
Alignment explanation
Indices: 6539138--6539169 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6539128 TATATTCTTA
6539138 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
6539170 GAGGGTTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6547835 original size:33 final size:33
Alignment explanation
Indices: 6547798--6547864 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
6547788 AAAATGATAG
6547798 CCTCAGAGGTAGTGACGACAAGCTTTTATATAC
1 CCTCAGAGGTAGTGACGACAAGCTTTTATATAC
6547831 CCTCAGAGGTAGTGACGACAAGCTTTTATATAC
1 CCTCAGAGGTAGTGACGACAAGCTTTTATATAC
6547864 C
1 C
6547865 TCTTAGAGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (33 bp):
CCTCAGAGGTAGTGACGACAAGCTTTTATATAC
Found at i:6555615 original size:14 final size:16
Alignment explanation
Indices: 6555585--6555619 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
6555575 GTGAAAAAAA
6555585 ATTAAAATATATATAT
1 ATTAAAATATATATAT
*
6555601 ATTAAAATATTTATAT
1 ATTAAAATATATATAT
6555617 ATT
1 ATT
6555620 TTTAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTAAAATATATATAT
Found at i:6558054 original size:31 final size:31
Alignment explanation
Indices: 6558017--6558079 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
6558007 TTAATAAAGT
6558017 AAGTCTCGTATGAACTTACTTGAAAAAAACA
1 AAGTCTCGTATGAACTTACTTGAAAAAAACA
6558048 AAGTCTCGTATGAACTTACTTGAAAAAAACA
1 AAGTCTCGTATGAACTTACTTGAAAAAAACA
6558079 A
1 A
6558080 CAACTAGCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (31 bp):
AAGTCTCGTATGAACTTACTTGAAAAAAACA
Found at i:6559447 original size:26 final size:25
Alignment explanation
Indices: 6559389--6559447 Score: 59
Period size: 26 Copynumber: 2.2 Consensus size: 25
6559379 GCAAAAATAT
6559389 AAATAATATTAATAAAAAATTACGAA
1 AAAT-ATATTAATAAAAAATTACGAA
6559415 AACATATATTAAATCAATAAAA-TAC-AA
1 AA-ATATATT-AAT-AA-AAAATTACGAA
6559442 AAATAT
1 AAATAT
6559448 TAGTAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
26 11 0.38
27 9 0.31
28 5 0.17
29 4 0.14
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (25 bp):
AAATATATTAATAAAAAATTACGAA
Found at i:6560925 original size:29 final size:30
Alignment explanation
Indices: 6560879--6560936 Score: 75
Period size: 29 Copynumber: 1.9 Consensus size: 30
6560869 TATAAGATTA
*
6560879 TATAAAAGTACATTTTATTA-ATTTATTTT
1 TATAAAAGAACATTTTATTATATTTATTTT
6560908 TATAAAA-AACATTATTATTATTATTTATT
1 TATAAAAGAACATT-TTATTA-TATTTATT
6560937 ACAAAATGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 5 0.20
29 13 0.52
31 7 0.28
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.53
Consensus pattern (30 bp):
TATAAAAGAACATTTTATTATATTTATTTT
Found at i:6560942 original size:28 final size:28
Alignment explanation
Indices: 6560888--6560942 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
6560878 ATATAAAAGT
*
6560888 ACATTTTATTAATTTATTTTTATAAAAA
1 ACATTTTATTAATTTATTTTTACAAAAA
6560916 ACATTATTATT-A-TTATTTATTACAAAA
1 ACATT-TTATTAATTTATTT-TTACAAAA
6560943 TGAAATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 6 0.25
28 13 0.54
29 5 0.21
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (28 bp):
ACATTTTATTAATTTATTTTTACAAAAA
Found at i:6562147 original size:22 final size:23
Alignment explanation
Indices: 6562106--6562148 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
6562096 CGATGATAAT
*
6562106 AAAATTATATTTAAACTTCTTAA
1 AAAATTATAATTAAACTTCTTAA
*
6562129 AAAATTATAATTCAA-TTCTT
1 AAAATTATAATTAAACTTCTT
6562149 CTTAATTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (23 bp):
AAAATTATAATTAAACTTCTTAA
Found at i:6563936 original size:43 final size:43
Alignment explanation
Indices: 6563846--6563937 Score: 116
Period size: 43 Copynumber: 2.1 Consensus size: 43
6563836 TTACAAAAAT
* * * *
6563846 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTATTCAC
1 AAACGCCGCTAAAGATAATATTCTTTAGCGGCGCTTTATTAAA
6563889 AAACGCCGCTGAAAGA-AATATTCTTTAGCGGCGCTTT-TATAAA
1 AAACGCCGCT-AAAGATAATATTCTTTAGCGGCGCTTTAT-TAAA
6563932 AAACGC
1 AAACGC
6563938 TACTATTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
42 1 0.02
43 37 0.86
44 5 0.12
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTAAAGATAATATTCTTTAGCGGCGCTTTATTAAA
Found at i:6564270 original size:21 final size:21
Alignment explanation
Indices: 6564244--6564331 Score: 108
Period size: 21 Copynumber: 4.2 Consensus size: 21
6564234 TTTTGCTCTG
6564244 CTCTGCTT-CTCTCGCTGCAGC
1 CTCTGCTTCCT-TCGCTGCAGC
* *
6564265 CTCTGCTTCCCTCGCTGCAGT
1 CTCTGCTTCCTTCGCTGCAGC
*
6564286 CGCTGCTTCCTTCGCTGCAGC
1 CTCTGCTTCCTTCGCTGCAGC
*
6564307 CGCTGCTTCCTTCGCTGTC-GC
1 CTCTGCTTCCTTCGCTG-CAGC
6564328 CTCT
1 CTCT
6564332 ACTTTAAGTT
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
21 57 0.97
22 2 0.03
ACGTcount: A:0.03, C:0.43, G:0.20, T:0.33
Consensus pattern (21 bp):
CTCTGCTTCCTTCGCTGCAGC
Found at i:6566545 original size:114 final size:113
Alignment explanation
Indices: 6566333--6566734 Score: 409
Period size: 114 Copynumber: 3.5 Consensus size: 113
6566323 AATTATTTTA
* * * *
6566333 CGGCGCTTGTTAAAAAACGCCGCTAAATCCCCCAATGCTCAGTCAAACGACATCGTTGGGCTTAG
1 CGGCGCTTCTCAAAAAACGCCGCTAAATCCCCGAATGCTCAG--AAACGACGTCGTTGGGCTTAG
* * *
6566398 GTTT-TCTGCGGCGCTTTCC-CAAAAATGCTGCTAAAGCCCTGAGCATTAG
64 GTTTCTTTGCGGCGC-TTCCTCAAAAACGCCGCTAAAGCCCTGAGCATTAG
* * * * * * *
6566447 CAGCGCTTCTCCATAAACGCCGCTAAATCCCCGAATACTCAGAGAATGGCGTTGTTGGGCTTAGG
1 CGGCGCTTCTCAAAAAACGCCGCTAAATCCCCGAATGCTCAGA-AACGACGTCGTTGGGCTTAGG
* * * * *
6566512 TTTCTTTGTGGCGCTTCCTCAGAAACGCCGCTAAAGCACTGAACATTGG
65 TTTCTTTGCGGCGCTTCCTCAAAAACGCCGCTAAAGCCCTGAGCATTAG
* * * * *
6566561 CGGCACTAC-CTAAAAAACGCCGCTAAGTCACCGAATGCTCAGAAAACAACGTCGTTGGGCTTAG
1 CGGCGCTTCTC-AAAAAACGCCGCTAAATCCCCGAATGCTCAG-AAACGACGTCGTTGGGCTTAG
* * * *
6566625 GTTTCTTTGCAGCGAATT-CTCAAAAACGCCGCTAAATCCCTGAGCTTTAG
64 GTTTCTTTGCGGCG-CTTCCTCAAAAACGCCGCTAAAGCCCTGAGCATTAG
* * *
6566675 CGGCGCTTCAT-AAAAAACGCTGCTAAATCCCCGAATGCGCGAAAAACGACGTCGTTGGGC
1 CGGCGCTTC-TCAAAAAACGCCGCTAAATCCCCGAATGCTC-AGAAACGACGTCGTTGGGC
6566735 CGAAGTTTTT
Statistics
Matches: 231, Mismatches: 48, Indels: 18
0.78 0.16 0.06
Matches are distributed among these distances:
112 1 0.00
113 25 0.11
114 201 0.87
115 4 0.02
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (113 bp):
CGGCGCTTCTCAAAAAACGCCGCTAAATCCCCGAATGCTCAGAAACGACGTCGTTGGGCTTAGGT
TTCTTTGCGGCGCTTCCTCAAAAACGCCGCTAAAGCCCTGAGCATTAG
Found at i:6576788 original size:20 final size:19
Alignment explanation
Indices: 6576751--6576790 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
6576741 ATCTAAATTA
* *
6576751 TTTTACTATTTTTTATATG
1 TTTTAATATTTTTGATATG
6576770 TTTTAATATTTTTAGATATG
1 TTTTAATATTTTT-GATATG
6576790 T
1 T
6576791 GTATTTGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.25, C:0.03, G:0.07, T:0.65
Consensus pattern (19 bp):
TTTTAATATTTTTGATATG
Found at i:6582489 original size:29 final size:29
Alignment explanation
Indices: 6582457--6582514 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
6582447 TCACTTATAA
6582457 ATTGCCATTAACATTACTTTTGTTTATTT
1 ATTGCCATTAACATTACTTTTGTTTATTT
6582486 ATTGCCATTAACATTACTTTTGTTTATTT
1 ATTGCCATTAACATTACTTTTGTTTATTT
6582515 GAATTTGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.14, G:0.07, T:0.55
Consensus pattern (29 bp):
ATTGCCATTAACATTACTTTTGTTTATTT
Found at i:6585259 original size:141 final size:141
Alignment explanation
Indices: 6585005--6585279 Score: 353
Period size: 141 Copynumber: 2.0 Consensus size: 141
6584995 TCCAGTTAAG
* *
6585005 AGAGTAAGGGTTTTTAGCATTCTAATTAGCATGTTTCTTGAACAACAAACGAGGAGTAGAAGAGA
1 AGAGTAAGGGTTTTTAGCACTCTAATTAGCAAGTTTCTTGAACAACAAACGAGGAGTAGAAGAGA
* * *
6585070 TTATGGAAGGTGAAGCTATGTTGAGTGAGTGATGCTGGTTATTAAATTGTTGAAGCT-TTGATTG
66 GTATAGAAGGTGAAGCTATGTTGAGTAAGTGATGCTGGTTATTAAATTGTTGAAGCTCTTG-TTG
6585134 TTGTTGGTCAAA
130 TTGTTGGTCAAA
* * *
6585146 AGAGTAAGGGGTTTTTGGCACTCTGATT-GACAAGTTTTTTGAACAA-AAA-GAGGGAGTAGAAG
1 AGAGTAA-GGGTTTTTAGCACTCTAATTAG-CAAGTTTCTTGAACAACAAACGA-GGAGTAGAAG
* * * * *
6585208 AGAGTATAGAAGTTGAAGTTGTGTTGAGTAAGTGAT-CTTGGTTGTTGAATTGTTGAAGCTCTTG
63 AGAGTATAGAAGGTGAAGCTATGTTGAGTAAGTGATGC-TGGTTATTAAATTGTTGAAGCTCTTG
6585272 TTGTTGTT
127 TTGTTGTT
6585280 ATTTTCCAAG
Statistics
Matches: 116, Mismatches: 13, Indels: 10
0.83 0.09 0.07
Matches are distributed among these distances:
140 3 0.03
141 79 0.68
142 34 0.29
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.35
Consensus pattern (141 bp):
AGAGTAAGGGTTTTTAGCACTCTAATTAGCAAGTTTCTTGAACAACAAACGAGGAGTAGAAGAGA
GTATAGAAGGTGAAGCTATGTTGAGTAAGTGATGCTGGTTATTAAATTGTTGAAGCTCTTGTTGT
TGTTGGTCAAA
Found at i:6589120 original size:6 final size:7
Alignment explanation
Indices: 6589104--6589129 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
6589094 ATACCAATAG
6589104 TTTTTAT
1 TTTTTAT
6589111 TTTTTAT
1 TTTTTAT
6589118 TTTTTAT
1 TTTTTAT
6589125 TTTTT
1 TTTTT
6589130 CAAGTATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:6591230 original size:18 final size:18
Alignment explanation
Indices: 6591194--6591257 Score: 69
Period size: 18 Copynumber: 3.5 Consensus size: 18
6591184 AAATAATTTT
6591194 AAAATT-ATAAAATTATTAA
1 AAAATTCATAAAA-T-TTAA
6591213 AAAATTCA-AAGAATTTAA
1 AAAATTCATAA-AATTTAA
*
6591231 AAAGTTCATAAAATTTAA
1 AAAATTCATAAAATTTAA
*
6591249 AAAAATCAT
1 AAAATTCAT
6591258 GAAGTACACT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 25 0.64
19 11 0.28
20 3 0.08
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.31
Consensus pattern (18 bp):
AAAATTCATAAAATTTAA
Found at i:6591965 original size:16 final size:15
Alignment explanation
Indices: 6591920--6591967 Score: 50
Period size: 11 Copynumber: 3.4 Consensus size: 15
6591910 AAATCATATT
6591920 TTTTAAATTTAAATA
1 TTTTAAATTTAAATA
*
6591935 TTTTTAA--T-AAT-
1 TTTTAAATTTAAATA
6591946 TTTTAAATTTAAATCA
1 TTTTAAATTTAAAT-A
6591962 TTTTAA
1 TTTTAA
6591968 TAATTGTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 9
0.70 0.05 0.24
Matches are distributed among these distances:
11 6 0.23
12 3 0.12
13 2 0.08
14 3 0.12
15 6 0.23
16 6 0.23
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTTAAATTTAAATA
Found at i:6591980 original size:26 final size:26
Alignment explanation
Indices: 6591919--6591978 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
6591909 AAAATCATAT
6591919 TTTTTAAATTTAAATATTTTTAATAA
1 TTTTTAAATTTAAATATTTTTAATAA
6591945 TTTTTAAATTTAAATCA-TTTTAATAA
1 TTTTTAAATTTAAAT-ATTTTTAATAA
6591971 TTGTTTAA
1 TT-TTTAA
6591979 TTATAGTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
26 26 0.81
27 6 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (26 bp):
TTTTTAAATTTAAATATTTTTAATAA
Found at i:6594422 original size:21 final size:21
Alignment explanation
Indices: 6594398--6594450 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
6594388 TCGAGGATAG
6594398 GCAATCTTAGATATGATATAT
1 GCAATCTTAGATATGATATAT
6594419 GCAATCTTAGATATGATATAT
1 GCAATCTTAGATATGATATAT
*
6594440 ACAATCTTAGA
1 GCAATCTTAGA
6594451 AGATATGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (21 bp):
GCAATCTTAGATATGATATAT
Found at i:6594684 original size:20 final size:17
Alignment explanation
Indices: 6594647--6594691 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
6594637 ACTGTTTTCT
*
6594647 TTTTTTTTCTTTTTCGA
1 TTTTTTTACTTTTTCGA
6594664 TTATTTTTACTTATTTACGA
1 TT-TTTTTACTT-TTT-CGA
6594684 TTTTTTTA
1 TTTTTTTA
6594692 AAAAAAAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 2 0.08
18 8 0.33
19 9 0.38
20 5 0.21
ACGTcount: A:0.16, C:0.09, G:0.04, T:0.71
Consensus pattern (17 bp):
TTTTTTTACTTTTTCGA
Found at i:6594941 original size:21 final size:20
Alignment explanation
Indices: 6594911--6594951 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
6594901 AGTAATTTTG
6594911 TTATTATTATTATAATTATA
1 TTATTATTATTATAATTATA
6594931 TTATATATTATTATAATTATA
1 TTAT-TATTATTATAATTATA
6594952 CCTACATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTATTATTATTATAATTATA
Found at i:6600100 original size:6 final size:6
Alignment explanation
Indices: 6600089--6600117 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
6600079 TGAAAGTGAT
6600089 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
6600118 TGGAGAGGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:6601439 original size:44 final size:44
Alignment explanation
Indices: 6601364--6601586 Score: 150
Period size: 44 Copynumber: 5.1 Consensus size: 44
6601354 CCAAGCCTTG
* * * * **
6601364 TCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGTAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGTAGATCTTA
* * *
6601408 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGAAAATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGTAGATCTTA
* * ** * *
6601452 TCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCAC-CAAG-CCTTG
1 TC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAG--ACGGTAGATCTTA
* * * * * **
6601496 TCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGTAGATCTTA
* *
6601540 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTAAATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGTAGATCTTA
6601584 TCT
1 TCT
6601587 TTCCAAGATA
Statistics
Matches: 132, Mismatches: 37, Indels: 20
0.70 0.20 0.11
Matches are distributed among these distances:
42 5 0.04
43 8 0.06
44 107 0.81
45 8 0.06
46 4 0.03
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.25
Consensus pattern (44 bp):
TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGTAGATCTTA
Found at i:6601589 original size:132 final size:132
Alignment explanation
Indices: 6601352--6601678 Score: 557
Period size: 132 Copynumber: 2.5 Consensus size: 132
6601342 ACCGGTGAAA
*
6601352 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
6601417 GCAGTAGTGGAGCAGATCGAAGACGGAAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGGAAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
6601482 GC
131 GC
6601484 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
*
6601549 GCAGTAGTGGAGCAGATCGAAGACGGTAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGGAAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
6601614 GC
131 GC
* ** * * * *
6601616 CACCAAGCCTTATCTCCCCCAGCAGCAGCAGAGTAGGTTGAAGA-TGACAAATCTTATCTCCCT
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTG-TAGATCTTATCTCCCT
6601679 GAAGTTGCAG
Statistics
Matches: 185, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
131 2 0.01
132 183 0.99
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (132 bp):
CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
GCAGTAGTGGAGCAGATCGAAGACGGAAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
GC
Found at i:6601742 original size:132 final size:132
Alignment explanation
Indices: 6601352--6601717 Score: 434
Period size: 132 Copynumber: 2.8 Consensus size: 132
6601342 ACCGGTGAAA
* ** ** * *
6601352 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTATCTCCCCCAGCAGCAGCAGAGAAGGTTGAAGATTGCAAATCTTATCTCCCTAA
* * * *
6601417 GCAGTAGTGGAGCAGATCGAAGACGGA-AAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTA
66 GCAGCAGTGGAGCAGATCAAAGAC-GATAAATCCTATCTTTCAAAGATAGTGGGAAGCAGATTTA
6601481 AGC
130 AGC
* ** * * *
6601484 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTATCTCCCCCAGCAGCAGCAGAGAAGGTTGAAGATTGCAAATCTTATCTCCCTAA
* * * * *
6601549 GCAGTAGTGGAGCAGATCGAAGACGGTAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGCAGTGGAGCAGATCAAAGACGATAAATCCTATCTTTCAAAGATAGTGGGAAGCAGATTTAA
6601614 GC
131 GC
*
6601616 CACCAAGCCTTATCTCCCCCAGCAGCAGCAGAGTAGGTTGAAGA-TGACAAATCTTATCTCCCTG
1 CACCAAGCCTTATCTCCCCCAGCAGCAGCAGAGAAGGTTGAAGATTG-CAAATCTTATCTCCCT-
** * *
6601680 AAGTTGCAGTGGAG-AGATTAAAGCCGAT-AATCCTATCT
64 AAGCAGCAGTGGAGCAGATCAAAGACGATAAATCCTATCT
6601718 CCTTAAAGTT
Statistics
Matches: 214, Mismatches: 17, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
131 12 0.06
132 191 0.89
133 11 0.05
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (132 bp):
CACCAAGCCTTATCTCCCCCAGCAGCAGCAGAGAAGGTTGAAGATTGCAAATCTTATCTCCCTAA
GCAGCAGTGGAGCAGATCAAAGACGATAAATCCTATCTTTCAAAGATAGTGGGAAGCAGATTTAA
GC
Found at i:6601762 original size:44 final size:43
Alignment explanation
Indices: 6601665--6601748 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
6601655 GAAGATGACA
* *
6601665 AATCTTATCTCCCTGAAGTTGCAGTGGAGAGATTAAAGCCGAT
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGAGATTAAAACCGAT
* *
6601708 AATCCTATCTCCTTAAAGTTGCAGTGGAGCAGATTAAAACC
1 AATCTTATCTCCCTAAAGTTGCAGTGGAG-AGATTAAAACC
6601749 TTGGATCTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 26 0.72
44 10 0.28
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.27
Consensus pattern (43 bp):
AATCTTATCTCCCTAAAGTTGCAGTGGAGAGATTAAAACCGAT
Found at i:6601771 original size:44 final size:43
Alignment explanation
Indices: 6601666--6602078 Score: 199
Period size: 44 Copynumber: 9.6 Consensus size: 43
6601656 AAGATGACAA
* *
6601666 ATCTTATCTCCCTGAAGTTGCAGTGGAG-AGATTAAAGCCGATA-
1 ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACC--TAG
* * *
6601709 ATCCTATCTC-CTTAAAGTTGCAGTGGAGCAGATTAAAACCTTGG
1 ATCTTATCTCTC-TGAAGTTGCAGTGGAGCAGATTAAAACC-TAG
* * *** *
6601753 ATCTTATCTCTCTGAAGTTACAG-AGAGCAGA-TCGCATCTAG
1 ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACCTAG
* * * * *
6601794 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAGCAAGCAAG
1 ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGA-TTA-AAACCTAG
* * ** *
6601838 -TCTTATC-CTCCTGAAGTTGCAGT-GAGGTAGACTGAAGATGGC-AA
1 ATCTTATCTCT-CTGAAGTTGCAGTGGA-GCAGA-TTAA-A-ACCTAG
* * * * * *
6601882 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAGAGCCGACA
1 ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACCTA-G
* * * * * *
6601926 ATCCTATCTCGCTGAAGTTACAGTGGAGCAGATCAAAACATTGG
1 ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAAC-CTAG
* * ****
6601970 ATCTTATCTCTCTGAAGTTGTAG-AGAGCAGATT-GCGTCTAG
1 ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACCTAG
* * *
6602011 -TCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTAAGTAAACAAG
1 ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAA--AACCTAG
6602055 -TCTTATC-CTCCTGAAGTTGCAGTG
1 ATCTTATCTCT-CTGAAGTTGCAGTG
6602079 AGGCAGACTA
Statistics
Matches: 283, Mismatches: 64, Indels: 45
0.72 0.16 0.11
Matches are distributed among these distances:
40 41 0.14
41 19 0.07
42 6 0.02
43 47 0.17
44 139 0.49
45 28 0.10
46 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (43 bp):
ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACCTAG
Found at i:6601902 original size:45 final size:44
Alignment explanation
Indices: 6601663--6602124 Score: 198
Period size: 44 Copynumber: 10.7 Consensus size: 44
6601653 TTGAAGATGA
* *
6601663 CAAATCTTATCTCCCTGAAGTTGCAGTGGAG-AGATTAAAGC-CG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGCAAG
* * * * *
6601706 -ATAATCCTATCTCCTTAAAGTTGCAGTGGAGCAGATTAA--AAC
1 CA-AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAG
** * * * * *
6601748 CTTGGATCTTATCTCTCTGAAGTTACAG-AGAGCAGA-T-CGC-AT
1 C--AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAG
* * *
6601790 CTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAGCAAG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAG
* * *
6601834 CAAGTCTTATC-CTCCTGAAGTTGCAGT-GAGGTAGACTGAAG-ATGG
1 CAAATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGCA-AG
* * *
6601879 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAGAGC-CG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTA-AGCAAG
* * * * * *
6601923 -ACAATCCTATCTCGCTGAAGTTACAGTGGAGCAGATCAAAACATTG
1 CA-AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTAAGCA-AG
* * * * *
6601969 --GATCTTATCTCTCTGAAGTTGTAG-AGAGCAGA-T-TGC--G
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAG
* * * * *
6602006 TCTAGTCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTAAGTAAA
1 -CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAG
* ** *
6602051 CAAGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTAAATAAA
1 CAAATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACTAAGCAAG
* * * *
6602095 CAAATCCTGTCT-CCTTAAGTTGTAGTGGAG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAG
6602125 TGGATTAGAG
Statistics
Matches: 321, Mismatches: 62, Indels: 72
0.71 0.14 0.16
Matches are distributed among these distances:
37 1 0.00
40 42 0.13
41 14 0.04
42 6 0.02
43 65 0.20
44 153 0.48
45 36 0.11
46 4 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (44 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAG
Found at i:6601980 original size:217 final size:217
Alignment explanation
Indices: 6601654--6602134 Score: 711
Period size: 217 Copynumber: 2.2 Consensus size: 217
6601644 CAGAGTAGGT
* *
6601654 TGAAGATGACAAATCTTATCTCCCTGAAGTTGCAGTGGAG-AGATTAAAGCCGATAATCCTATCT
1 TGAAGATGACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAGAGCCGACAATCCTATCT
* * *
6601718 CCTTAAAGTTGCAGTGGAGCAGATTAAAACCTTGGATCTTATCTCTCTGAAGTTACAGAGAGCAG
66 CCTTAAAGTTACAGTGGAGCAGATCAAAACATTGGATCTTATCTCTCTGAAGTTACAGAGAGCAG
* *
6601783 ATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAGCAAGCAAGTCTTATCCTC
131 ATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAACAAGTCTTATCCTC
*
6601848 CTGAAGTTGCAGTGAGGTAGAC
196 CTGAAGTTGCAGTGAGGCAGAC
*
6601870 TGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAGAGCCGACAATCCTATCT
1 TGAAGATGACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAGAGCCGACAATCCTATCT
* **
6601935 CGC-TGAAGTTACAGTGGAGCAGATCAAAACATTGGATCTTATCTCTCTGAAGTTGTAGAGAGCA
66 C-CTTAAAGTTACAGTGGAGCAGATCAAAACATTGGATCTTATCTCTCTGAAGTTACAGAGAGCA
* * * *
6601999 GATTGCGTCTAGTCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTAAGTAAACAAGTCTTATCCT
130 GATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAACAAGTCTTATCCT
6602064 CCTGAAGTTGCAGTGAGGCAGAC
195 CCTGAAGTTGCAGTGAGGCAGAC
* * * * * *
6602087 T-AA-ATAAACAAATCCTGTCT-CCTTAAGTTGTAGTGGAGTGGATTAGAG
1 TGAAGAT-GACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAGAG
6602135 TGATGGATTT
Statistics
Matches: 239, Mismatches: 23, Indels: 7
0.89 0.09 0.03
Matches are distributed among these distances:
215 27 0.11
216 51 0.21
217 160 0.67
218 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.28
Consensus pattern (217 bp):
TGAAGATGACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAGAGCCGACAATCCTATCT
CCTTAAAGTTACAGTGGAGCAGATCAAAACATTGGATCTTATCTCTCTGAAGTTACAGAGAGCAG
ATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAACAAGTCTTATCCTC
CTGAAGTTGCAGTGAGGCAGAC
Found at i:6602085 original size:44 final size:43
Alignment explanation
Indices: 6601792--6602124 Score: 202
Period size: 44 Copynumber: 7.7 Consensus size: 43
6601782 GATCGCATCT
* * *
6601792 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAGCAAGCA
1 AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTAAGTAAACA
* **
6601836 AGTCTTATCCTCCTGAAGTTGCAGT-GAGGTAGACTGAAG-ATGGCA
1 AGTCTTAT-CTCCTGAAGTTGCAGTGGA-GCAGACT-AAGTA-AACA
* * * ***
6601881 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAGAGCCGACA
1 AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTA-AGTAAACA
* * *
6601926 A-TCCTATCTCGCTGAAGTTACAGTGGAGCAGA-TCA--AAACA
1 AGTCTTATCTC-CTGAAGTTGCAGTGGAGCAGACTAAGTAAACA
* * * * ** *
6601966 TTGGATCTTATCTCTCTGAAGTTGTAG-AGAGCAGATTGCGT---CT
1 --AG-TCTTATCTC-CTGAAGTTGCAGTGGAGCAGACTAAGTAAACA
6602009 AGTCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTAAGTAAACA
1 AGTCTTATCTC-CTGAAGTTGCAGTGGAGCAGACTAAGTAAACA
*
6602053 AGTCTTATCCTCCTGAAGTTGCAGT-GAGGCAGACTAAATAAACA
1 AGTCTTAT-CTCCTGAAGTTGCAGTGGA-GCAGACTAAGTAAACA
* * * * *
6602097 AATCCTGTCTCCTTAAGTTGTAGTGGAG
1 AGTCTTATCTCCTGAAGTTGCAGTGGAG
6602125 TGGATTAGAG
Statistics
Matches: 231, Mismatches: 35, Indels: 47
0.74 0.11 0.15
Matches are distributed among these distances:
40 24 0.10
41 11 0.05
42 1 0.00
43 29 0.13
44 121 0.52
45 43 0.19
46 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (43 bp):
AGTCTTATCTCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACA
Found at i:6602536 original size:19 final size:21
Alignment explanation
Indices: 6602434--6602530 Score: 153
Period size: 21 Copynumber: 4.7 Consensus size: 21
6602424 ATTTTCGAGG
*
6602434 ATATACAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
6602453 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
6602474 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
*
6602495 ATATGCAATTTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
*
6602516 ATATACAATCTTAGA
1 ATATGCAATCTTAGA
6602531 AGATATGATT
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
19 18 0.25
21 54 0.75
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.38
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:6602763 original size:20 final size:18
Alignment explanation
Indices: 6602728--6602771 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
6602718 CTATTTTCTT
*
6602728 TTTTTTCTTTTTCGATTA
1 TTTTTACTTTTTCGATTA
*
6602746 TTTTTACTTATTTACGATTT
1 TTTTTACTT-TTT-CGATTA
6602766 TTTTTA
1 TTTTTA
6602772 AAAAAAGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 8 0.36
19 3 0.14
20 11 0.50
ACGTcount: A:0.16, C:0.09, G:0.05, T:0.70
Consensus pattern (18 bp):
TTTTTACTTTTTCGATTA
Found at i:6603000 original size:3 final size:3
Alignment explanation
Indices: 6602994--6603057 Score: 91
Period size: 3 Copynumber: 22.3 Consensus size: 3
6602984 AATTTTGTTG
6602994 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA -TA TTA -TA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6603038 TTA TATA TTA TTA TTA TTA T
1 TTA T-TA TTA TTA TTA TTA T
6603058 ACCTACATAT
Statistics
Matches: 56, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
2 8 0.14
3 45 0.80
4 3 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:6603069 original size:36 final size:38
Alignment explanation
Indices: 6602998--6603069 Score: 96
Period size: 36 Copynumber: 1.9 Consensus size: 38
6602988 TTGTTGTTAT
* *
6602998 TATTATTATTATTATTATTATTATATTATATTATATTA
1 TATTATTATTATTATTATTATTATACTACATTATATTA
6603036 TATTA-TA-TATTATTATTATTATACCTACA-TATAT
1 TATTATTATTATTATTATTATTATA-CTACATTATAT
6603070 GTGCGCATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 21 0.68
37 5 0.16
38 5 0.16
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (38 bp):
TATTATTATTATTATTATTATTATACTACATTATATTA
Found at i:6609417 original size:17 final size:17
Alignment explanation
Indices: 6609375--6609423 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
6609365 ATTTGAATGC
6609375 AAATT-AATTTGGTATG
1 AAATTGAATTTGGTATG
6609391 AAATTTGAATTTGGT-TG
1 AAA-TTGAATTTGGTATG
6609408 ATAATTGAATTGTGGT
1 A-AATTGAATT-TGGT
6609424 GTCAATGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 3 0.10
17 12 0.41
18 14 0.48
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.45
Consensus pattern (17 bp):
AAATTGAATTTGGTATG
Found at i:6617239 original size:6 final size:6
Alignment explanation
Indices: 6617228--6617252 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6617218 GCATTGATGT
6617228 AAAGGA AAAGGA AAAGGA AAAGGA A
1 AAAGGA AAAGGA AAAGGA AAAGGA A
6617253 TGATTTTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
AAAGGA
Found at i:6629004 original size:4 final size:4
Alignment explanation
Indices: 6628995--6629023 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
6628985 AATAACATTT
6628995 TTTG TTTG TTTG TTTG TTTG TTTG TTTG T
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG T
6629024 CAGTTTTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (4 bp):
TTTG
Found at i:6635191 original size:33 final size:32
Alignment explanation
Indices: 6635147--6635209 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
6635137 TATATTGTTC
*
6635147 CCCCTTAATAAAAGTCATTTTCAATTTAAGCT
1 CCCCTTAATAAAAATCATTTTCAATTTAAGCT
*
6635179 CCCCTTATATAAAAATCATTTTCTATTTAAG
1 CCCCTTA-ATAAAAATCATTTTCAATTTAAG
6635210 GCATAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 7 0.25
33 21 0.75
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.40
Consensus pattern (32 bp):
CCCCTTAATAAAAATCATTTTCAATTTAAGCT
Found at i:6640487 original size:20 final size:20
Alignment explanation
Indices: 6640441--6640489 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
6640431 TGGAGTAGGA
* *
6640441 ATATCGATACCTTAGGAAAT
1 ATATTGATACCTTAAGAAAT
*
6640461 ATTTTGATACCTTAAGAAA-
1 ATATTGATACCTTAAGAAAT
6640480 AGTATTGATA
1 A-TATTGATA
6640490 TTGGATCGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (20 bp):
ATATTGATACCTTAAGAAAT
Found at i:6644426 original size:6 final size:6
Alignment explanation
Indices: 6644415--6644440 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
6644405 TAATTGAATA
6644415 ATAATT ATAATT ATAATT ATAATT AT
1 ATAATT ATAATT ATAATT ATAATT AT
6644441 TATGTATGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATAATT
Found at i:6650687 original size:14 final size:14
Alignment explanation
Indices: 6650647--6650680 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
6650637 ATATTTTAAA
**
6650647 ATTTATATACGTAT
1 ATTTATATATATAT
6650661 ATTTATATATATAT
1 ATTTATATATATAT
6650675 ATTTAT
1 ATTTAT
6650681 TTTTATAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (14 bp):
ATTTATATATATAT
Found at i:6663561 original size:268 final size:267
Alignment explanation
Indices: 6662903--6663726 Score: 1247
Period size: 268 Copynumber: 3.1 Consensus size: 267
6662893 CACCTGAACG
** * *
6662903 TTGCAATAGAAAAGATTGAAGCCGCAATGGCGAATCTTATTTACCCTGACGTTGTAGCGGAGCAG
1 TTGCAATTTAAAAGATTGAAGCCGCAATGGCGAATCTTATTT-CCTTGGCGTTGTAGCGGAGCAG
6662968 ATTGAAGCCACGACGGCGAATCTTATCTCAT-TGGCGTTAAGGCTTGGATTAGCTGAAGTAGAGC
65 ATTGAAGCCACGACGGCGAATCTTATCTC-TCTGGCGTTAAGGCTTGGATTAGCTGAAGTAGAGC
* *
6663032 GGATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTATAGTGGAGCAGATTAAAGCCCCA
129 GGATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTACAGTGGAGCAGATTAAAGCCACA
* * * *
6663097 ATGGTGAATCTTACTCCCCTAGCGGTGTAGTGGAACAGATTGAAGCTACGATGGCGAATCTCGTT
194 ACGGTGAATCTTACTCCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGACGGCAAATCTCGTT
6663162 TCCCCAACA
259 TCCCCAACA
* *
6663171 TTGCAATTTAAAAGATTGAACCCGTAATGGCGAATCTTATTTCCTTGGCGTTGTAGCGGAGCAGA
1 TTGCAATTTAAAAGATTGAAGCCGCAATGGCGAATCTTATTTCCTTGGCGTTGTAGCGGAGCAGA
* * * * *
6663236 TTGAAGCCACGACGGTGAATCTTATCTCCCTGGTGTTAAGGCTTGGATTAGCTGAAGTAAAGCAG
66 TTGAAGCCACGACGGCGAATCTTATCTCTCTGGCGTTAAGGCTTGGATTAGCTGAAGTAGAGCGG
*
6663301 ATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTACAGTGGAGCAGATTAAAGCCGCAAC
131 ATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTACAGTGGAGCAGATTAAAGCCACAAC
** * * * *
6663366 GGCAAATCTTACTCCCCTGGCGGTGTAGTAGAACAAATTGAGGCTACGACGGAAAATCTCGTTTC
196 GGTGAATCTTACTCCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGACGGCAAATCTCGTTT-
6663431 CCCCAACA
260 CCCCAACA
* * *
6663439 TTGCAATTTAAAAGATTGAAGCCACAATGGTGAATCTTATTTCCTTGGCATTGTAGCGGAGCAGA
1 TTGCAATTTAAAAGATTGAAGCCGCAATGGCGAATCTTATTTCCTTGGCGTTGTAGCGGAGCAGA
* * *
6663504 TTGAAGCCACAACGGCAAATCTTATCTCTCTGGCGTTAAGGCTTGGATTAGCTGAAGTGGAGCGG
66 TTGAAGCCACGACGGCGAATCTTATCTCTCTGGCGTTAAGGCTTGGATTAGCTGAAGTAGAGCGG
* ** * *
6663569 ATTAAAGCTGTGGGTAGAAAATCCTATCTCTTTGGCATTACAGTGGAGAAGATTGAAA-CCACGA
131 ATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTACAGTGGAGCAGATT-AAAGCCACAA
* *
6663633 CGGTGAATCTTACTCCCCTGGCGGTGTAGTGGAACAGGTTGAAGCTACGACGGCAAATCTTGTTT
195 CGGTGAATCTTACTCCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGACGGCAAATCTCGTTT
*
6663698 CCCCAGCA
260 CCCCAACA
*
6663706 TTGCAATTTAAAAGACTGAAG
1 TTGCAATTTAAAAGATTGAAG
6663727 ATGGCGAATC
Statistics
Matches: 501, Mismatches: 52, Indels: 7
0.89 0.09 0.01
Matches are distributed among these distances:
267 224 0.45
268 274 0.55
269 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.26
Consensus pattern (267 bp):
TTGCAATTTAAAAGATTGAAGCCGCAATGGCGAATCTTATTTCCTTGGCGTTGTAGCGGAGCAGA
TTGAAGCCACGACGGCGAATCTTATCTCTCTGGCGTTAAGGCTTGGATTAGCTGAAGTAGAGCGG
ATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTACAGTGGAGCAGATTAAAGCCACAAC
GGTGAATCTTACTCCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGACGGCAAATCTCGTTTC
CCCAACA
Found at i:6663788 original size:44 final size:44
Alignment explanation
Indices: 6663733--6664071 Score: 225
Period size: 44 Copynumber: 7.8 Consensus size: 44
6663723 GAAGATGGCG
*
6663733 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* ** **
6663777 AATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATCACA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-AT
* * * * *
6663821 GATCTTATCTCTCTGAAGTTGCAG-AGAGCAGATCT-CA-TC--T
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT-TAAAGCCAAT
* *
6663861 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAG-CAA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTA--AAGCCAAT
* * * * * * * *
6663906 AGTCTTATCCCCCTAAAGTTGCAGTGGGGTAGACTGAAGATGGC--G
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAA-A-GCCAAT
*
6663951 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* ** * **
6663995 AATCCTATCTCCCTGAAGTTATAGTGGAGCGGATTAAAATCACA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-AT
* * * *
6664039 GATCTTATCTCTCTGGAGTTGCAG-AGAGCAGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
6664072 CGCATCAAAT
Statistics
Matches: 233, Mismatches: 44, Indels: 37
0.74 0.14 0.12
Matches are distributed among these distances:
40 21 0.09
41 7 0.03
42 5 0.02
43 16 0.07
44 121 0.52
45 62 0.27
46 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
Found at i:6666294 original size:15 final size:15
Alignment explanation
Indices: 6666271--6666300 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6666261 ATTTCTATGC
*
6666271 CATTGTTGTATTTAT
1 CATTATTGTATTTAT
6666286 CATTATTGTATTTAT
1 CATTATTGTATTTAT
6666301 TATCGCGATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.07, G:0.10, T:0.60
Consensus pattern (15 bp):
CATTATTGTATTTAT
Found at i:6667152 original size:54 final size:54
Alignment explanation
Indices: 6667094--6667200 Score: 205
Period size: 54 Copynumber: 2.0 Consensus size: 54
6667084 AAAGAGAAAG
6667094 AATGAAGCACGGATTTTCTAGACCTCTACCTCCAACAAGTTTTAAGAAGCCCAA
1 AATGAAGCACGGATTTTCTAGACCTCTACCTCCAACAAGTTTTAAGAAGCCCAA
*
6667148 AATGAAGCATGGATTTTCTAGACCTCTACCTCCAACAAGTTTTAAGAAGCCCA
1 AATGAAGCACGGATTTTCTAGACCTCTACCTCCAACAAGTTTTAAGAAGCCCA
6667201 GAGATTAGAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (54 bp):
AATGAAGCACGGATTTTCTAGACCTCTACCTCCAACAAGTTTTAAGAAGCCCAA
Found at i:6677842 original size:19 final size:20
Alignment explanation
Indices: 6677814--6677852 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
6677804 ATATCAAAAT
6677814 TACCACACACATATA-TATA
1 TACCACACACATATACTATA
*
6677833 TACCATACACATATACTATA
1 TACCACACACATATACTATA
6677853 AAACTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (20 bp):
TACCACACACATATACTATA
Found at i:6681914 original size:46 final size:46
Alignment explanation
Indices: 6681839--6682085 Score: 399
Period size: 46 Copynumber: 5.4 Consensus size: 46
6681829 TACGTATGAT
*
6681839 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*
6681883 CACTTATCACTTGGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*
6681929 CACTTATCACTTGGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* * *
6681975 CACTTATCACTTTGTCACTTGATCAGATAAGTGCAGCTAAAGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* * *
6682021 CATTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
6682067 CACTTATCACTTTGTCACT
1 CACTTATCACTTTGTCACT
6682086 GATTAGAAGT
Statistics
Matches: 192, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
44 10 0.05
45 4 0.02
46 178 0.93
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
Found at i:6684994 original size:17 final size:16
Alignment explanation
Indices: 6684974--6685005 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
6684964 TTTAGCTTGC
6684974 TTCTTTTCTTTTTTTTT
1 TTCTTTT-TTTTTTTTT
6684991 TTCTTTTTTTTTTTT
1 TTCTTTTTTTTTTTT
6685006 GACTTGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (16 bp):
TTCTTTTTTTTTTTTT
Found at i:6685005 original size:13 final size:12
Alignment explanation
Indices: 6684977--6685004 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
6684967 AGCTTGCTTC
6684977 TTTTCTTTTTTT
1 TTTTCTTTTTTT
6684989 TTTTCTTTTTTT
1 TTTTCTTTTTTT
6685001 TTTT
1 TTTT
6685005 TGACTTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:6688330 original size:11 final size:10
Alignment explanation
Indices: 6688312--6688350 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
6688302 TTTAAAATCT
6688312 TAATTTTTTA
1 TAATTTTTTA
6688322 TATATTTTTTA
1 TA-ATTTTTTA
*
6688333 -GATTTTTTA
1 TAATTTTTTA
6688342 TAATTTTTT
1 TAATTTTTT
6688351 TAAAATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 8 0.32
10 9 0.36
11 8 0.32
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (10 bp):
TAATTTTTTA
Found at i:6688352 original size:20 final size:20
Alignment explanation
Indices: 6688314--6688350 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6688304 TAAAATCTTA
6688314 ATTTTTTATATATTTTTTAG
1 ATTTTTTATATATTTTTTAG
6688334 ATTTTTTATA-ATTTTTT
1 ATTTTTTATATATTTTTT
6688351 TAAAATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (20 bp):
ATTTTTTATATATTTTTTAG
Found at i:6691299 original size:102 final size:102
Alignment explanation
Indices: 6691107--6691297 Score: 242
Period size: 102 Copynumber: 1.8 Consensus size: 102
6691097 AAGAACATGT
* * * *
6691107 TGGGCTAAGTAACCGGGGTAGGGTGCTTGGGTTGTCATCCTGTTTCGCGTCAAAAGGTTCGATGT
1 TGGGCTAAGTAACCGGGGTAGGGTGCTTGGGCTGTCATCCTGCTTCGCGTCAAAAGGTTCAATAT
* *
6691172 GTTCTTAAGAAAAAAATATAATAAATTAGGAGTCTGC
66 ATTCTAAAGAAAAAAATATAATAAATTAGGAGTCTGC
* * *
6691209 TGGGCTGAGTAACCGGGGTAGGTTGCTT-GGCTGTTATCTCT-CTTCGCGTCAAAAGGTTCAATA
1 TGGGCTAAGTAACCGGGGTAGGGTGCTTGGGCTGTCATC-CTGCTTCGCGTCAAAAGGTTCAATA
6691272 TATTCCTAAAGCATAAAAAAATATAA
65 TATT-CTAAAG---AAAAAAATATAA
6691298 ATAATAAATA
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
101 30 0.40
102 33 0.44
105 12 0.16
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (102 bp):
TGGGCTAAGTAACCGGGGTAGGGTGCTTGGGCTGTCATCCTGCTTCGCGTCAAAAGGTTCAATAT
ATTCTAAAGAAAAAAATATAATAAATTAGGAGTCTGC
Found at i:6691304 original size:17 final size:18
Alignment explanation
Indices: 6691284--6691331 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
6691274 TTCCTAAAGC
*
6691284 ATAAA-AAAATATAAATA
1 ATAAAGAAAATATAAAAA
*
6691301 ATAAATAAAA-ATAAAAA
1 ATAAAGAAAATATAAAAA
*
6691318 AAAAAGAAAATATA
1 ATAAAGAAAATATA
6691332 TATATAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 19 0.73
18 7 0.27
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (18 bp):
ATAAAGAAAATATAAAAA
Found at i:6692883 original size:17 final size:17
Alignment explanation
Indices: 6692858--6692903 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
6692848 TAATTCCTAT
*
6692858 ACATCACTTAGGTATAA
1 ACATTACTTAGGTATAA
*
6692875 ACATTACTTAGGTATAT
1 ACATTACTTAGGTATAA
*
6692892 ATATTACTTAGG
1 ACATTACTTAGG
6692904 CACATGCCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (17 bp):
ACATTACTTAGGTATAA
Found at i:6693802 original size:51 final size:51
Alignment explanation
Indices: 6693723--6693842 Score: 177
Period size: 51 Copynumber: 2.3 Consensus size: 51
6693713 CCAAACACAC
* * * *
6693723 CAGTAACATTAATCAGTAACGGTAACAGTGTTCGACACACAAAGTGTCGAAT
1 CAGTAACAGTAA-CAGTAACAGTAACAGTATTCGACACACAAAGTATCGAAT
* *
6693775 CGGTAACGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTATCGAAT
1 CAGTAACAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTATCGAAT
6693826 CAGTAACAGTAACAGTA
1 CAGTAACAGTAACAGTA
6693843 TTCAACACAC
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
51 51 0.85
52 9 0.15
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (51 bp):
CAGTAACAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTATCGAAT
Found at i:6693841 original size:39 final size:39
Alignment explanation
Indices: 6693787--6693877 Score: 139
Period size: 39 Copynumber: 2.3 Consensus size: 39
6693777 GTAACGGTAA
* *
6693787 CAGTAACAGTAACAGTATTCGACACACAAAGT-ATCGAAT
1 CAGTAACAGTAACAGTATTCAACACACAAAGTGCT-GAAT
6693826 CAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAAT
1 CAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAAT
*
6693865 CTGTAACAGTAAC
1 CAGTAACAGTAAC
6693878 GGTAACAGTA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
39 47 0.98
40 1 0.02
ACGTcount: A:0.43, C:0.21, G:0.15, T:0.21
Consensus pattern (39 bp):
CAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAAT
Found at i:6693886 original size:90 final size:90
Alignment explanation
Indices: 6693733--6693902 Score: 252
Period size: 90 Copynumber: 1.9 Consensus size: 90
6693723 CAGTAACATT
* * * *
6693733 AATCAGTAACGGTAACAGTGTTCGACACACAAAGTGTCGAATCGGTAACGGTAACAGTAACAGTA
1 AATCAGTAACAGTAACAGTATTCAACACACAAAGTGTCGAATCGGTAACAGTAACAGTAACAGTA
*
6693798 ACAGTATTCGACACACAAAGTATCG
66 ACAGTAGTCGACACACAAAGTATCG
* *
6693823 AATCAGTAACAGTAACAGTATTCAACACACAAAGTG-CTGAATCTGTAACAGTAACGGTAACAGT
1 AATCAGTAACAGTAACAGTATTCAACACACAAAGTGTC-GAATCGGTAACAGTAACAGTAACAGT
*
6693887 AACAGTAGTCGGCACA
65 AACAGTAGTCGACACA
6693903 TACGTGCCTG
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
89 1 0.01
90 70 0.99
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (90 bp):
AATCAGTAACAGTAACAGTATTCAACACACAAAGTGTCGAATCGGTAACAGTAACAGTAACAGTA
ACAGTAGTCGACACACAAAGTATCG
Found at i:6696393 original size:28 final size:28
Alignment explanation
Indices: 6696357--6696411 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
6696347 AATTATTGAA
*
6696357 AAATCATTAAATATT-ATAAAAATTTTAG
1 AAATCATTAAAAATTAAT-AAAATTTTAG
*
6696385 AAATGATTAAAAATTAATAAAATTTTA
1 AAATCATTAAAAATTAATAAAATTTTA
6696412 TAAAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (28 bp):
AAATCATTAAAAATTAATAAAATTTTAG
Found at i:6697472 original size:21 final size:21
Alignment explanation
Indices: 6697448--6697504 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
6697438 CACACACGTG
6697448 TGTGTCTTTTAGCCATATGGT
1 TGTGTCTTTTAGCCATATGGT
* *
6697469 TGTGTGTTTCAGCCATATGGT
1 TGTGTCTTTTAGCCATATGGT
6697490 TGTG-CGTTTTAGCCA
1 TGTGTC-TTTTAGCCA
6697505 CACGGCTGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.14, C:0.16, G:0.26, T:0.44
Consensus pattern (21 bp):
TGTGTCTTTTAGCCATATGGT
Found at i:6697514 original size:21 final size:21
Alignment explanation
Indices: 6697454--6697504 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
6697444 CGTGTGTGTC
*
6697454 TTTTAGCCATATGGTTGTGTG
1 TTTTAGCCATATGGTTGTGCG
*
6697475 TTTCAGCCATATGGTTGTGCG
1 TTTTAGCCATATGGTTGTGCG
6697496 TTTTAGCCA
1 TTTTAGCCA
6697505 CACGGCTGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.16, C:0.16, G:0.25, T:0.43
Consensus pattern (21 bp):
TTTTAGCCATATGGTTGTGCG
Found at i:6702038 original size:21 final size:20
Alignment explanation
Indices: 6702001--6702042 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
6701991 CTGGCGTCAT
6702001 ATTCGTTTCCCCCAACAATG
1 ATTCGTTTCCCCCAACAATG
* *
6702021 ATTCGATTTCTCCGAACAATG
1 ATTCG-TTTCCCCCAACAATG
6702042 A
1 A
6702043 ATGAGAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.31
Consensus pattern (20 bp):
ATTCGTTTCCCCCAACAATG
Found at i:6704758 original size:284 final size:284
Alignment explanation
Indices: 6704237--6704784 Score: 893
Period size: 284 Copynumber: 1.9 Consensus size: 284
6704227 ACCAGGAGAA
* *
6704237 AAAAAATCTAATTTGTCATTCTCCTATTAGAAAGGGTAAGGAGGACGTAGAATCACTGTTTCATA
1 AAAAAAGCTAATTTGTCATTCTCCTATTAGAAAGGGTAAGGAGAACGTAGAATCACTGTTTCATA
*
6704302 CAATCCCTTCTCAAGAATTCATATAGAGATGTGATAAGATGTGATTTGAGTATGCTTTGTAGAGT
66 CAATCCCTTCTCAAGAATTCATATAGAGATGTGATAAGATGTGATTTGAGTATGCTTTATAGAGT
* *
6704367 CAACCACAAAGTAATGGGAGATTTATGGGATAAGAAACGAAAATTTTTTATGTGAACTTTGATGG
131 CAACCACAAAGTAATGGGAGATTTATAGGATAAGAAACGAAAATTTTTTAAGTGAACTTTGATGG
* *
6704432 GATTAGATAGCGGCCTACCTGAGAAAGAAATGAAAGCATTTAGTTGGGTGAACATTTTTACAGGC
196 GATTAGATAGCGGCCTACCTGAGAAAGAAATGAAAACATTTAGTTGGGTGAACATTTTTACAGAC
6704497 AAACAAAATGCTAAAAATTAGGAG
261 AAACAAAATGCTAAAAATTAGGAG
* * * *
6704521 AAAAAAGCTTATTTGTCATTCTCCTATTGGAAAGGGT-TGCGATAACGTAGAATCA-TGGTTTCA
1 AAAAAAGCTAATTTGTCATTCTCCTATTAGAAAGGGTAAG-GAGAACGTAGAATCACT-GTTTCA
* * *
6704584 TGCAATCCCTTCTCATGAATTCATATAGATATGTGATAAGATGTGATTTGAGTATGCTTTATAGA
64 TACAATCCCTTCTCAAGAATTCATATAGAGATGTGATAAGATGTGATTTGAGTATGCTTTATAGA
** *
6704649 GTCAACCACAAAGTAATGGGAGATTTATAGGATGCGACACGAAAATTTTTTAAGTGAACTTTGAT
129 GTCAACCACAAAGTAATGGGAGATTTATAGGATAAGAAACGAAAATTTTTTAAGTGAACTTTGAT
* *
6704714 GGGATTAGGTAGCGGCCTACCTGAGAAAGAAATGAAAACATTTAGTTGGGTGAGCATTTTTACAG
194 GGGATTAGATAGCGGCCTACCTGAGAAAGAAATGAAAACATTTAGTTGGGTGAACATTTTTACAG
6704779 ACAAAC
259 ACAAAC
6704785 TCCTTTTTGG
Statistics
Matches: 243, Mismatches: 19, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
283 2 0.01
284 241 0.99
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (284 bp):
AAAAAAGCTAATTTGTCATTCTCCTATTAGAAAGGGTAAGGAGAACGTAGAATCACTGTTTCATA
CAATCCCTTCTCAAGAATTCATATAGAGATGTGATAAGATGTGATTTGAGTATGCTTTATAGAGT
CAACCACAAAGTAATGGGAGATTTATAGGATAAGAAACGAAAATTTTTTAAGTGAACTTTGATGG
GATTAGATAGCGGCCTACCTGAGAAAGAAATGAAAACATTTAGTTGGGTGAACATTTTTACAGAC
AAACAAAATGCTAAAAATTAGGAG
Found at i:6709566 original size:49 final size:49
Alignment explanation
Indices: 6709476--6709572 Score: 113
Period size: 49 Copynumber: 2.0 Consensus size: 49
6709466 TGCCTTAGGA
* * * * * **
6709476 TGGAAATCATCGTTGTCGAGCCATCCGAGATGGTAGGATATGCAAATAG
1 TGGAAACCATCGTTGTAGAGCCACCCAAGATGATAAAATATGCAAATAG
* *
6709525 TGGAAACCATCGTTGTAGGGCCACCCAAGATGATAAAATATGTAAATA
1 TGGAAACCATCGTTGTAGAGCCACCCAAGATGATAAAATATGCAAATA
6709573 ATTAGAACCA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
49 39 1.00
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (49 bp):
TGGAAACCATCGTTGTAGAGCCACCCAAGATGATAAAATATGCAAATAG
Found at i:6711278 original size:16 final size:17
Alignment explanation
Indices: 6711257--6711288 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
6711247 ACTTCACCAT
6711257 TTTATTTA-AATTTTTA
1 TTTATTTATAATTTTTA
6711273 TTTATTTATAATTTTT
1 TTTATTTATAATTTTT
6711289 CTTATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTATTTATAATTTTTA
Found at i:6711426 original size:2 final size:2
Alignment explanation
Indices: 6711419--6711453 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6711409 ATAATAAATT
6711419 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6711454 TAATTTACGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6717544 original size:15 final size:13
Alignment explanation
Indices: 6717516--6717548 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
6717506 ATTTTAAATT
6717516 TTATTATAATTTA
1 TTATTATAATTTA
*
6717529 TTATTATAATAT-
1 TTATTATAATTTA
6717541 TTATTATA
1 TTATTATA
6717549 TCAATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTATTATAATTTA
Found at i:6717558 original size:15 final size:15
Alignment explanation
Indices: 6717516--6717547 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
6717506 ATTTTAAATT
6717516 TTATTAT-A-ATTTA
1 TTATTATAATATTTA
6717529 TTATTATAATATTTA
1 TTATTATAATATTTA
6717544 TTAT
1 TTAT
6717548 ATCAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 1 0.06
15 9 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATTATAATATTTA
Found at i:6720971 original size:9 final size:9
Alignment explanation
Indices: 6720954--6720985 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
6720944 GTTTAGGGTA
6720954 TAATTTAAT
1 TAATTTAAT
*
6720963 TAGTTTAAT
1 TAATTTAAT
6720972 TAATTTAAT
1 TAATTTAAT
6720981 TAATT
1 TAATT
6720986 AAATGAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (9 bp):
TAATTTAAT
Found at i:6721315 original size:15 final size:15
Alignment explanation
Indices: 6721292--6721325 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
6721282 GAACCGAAAA
6721292 TTTTCGATTTTAGAT
1 TTTTCGATTTTAGAT
*
6721307 TTTTGGATTTTAGAT
1 TTTTCGATTTTAGAT
6721322 TTTT
1 TTTT
6721326 TTGAGTTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.03, G:0.15, T:0.65
Consensus pattern (15 bp):
TTTTCGATTTTAGAT
Found at i:6721364 original size:17 final size:17
Alignment explanation
Indices: 6721342--6721375 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
6721332 TGGAAAAAGA
6721342 AATTTTAATTT-ACTTAT
1 AATTTT-ATTTCACTTAT
6721359 AATTTTATTTCACTTAT
1 AATTTTATTTCACTTAT
6721376 TTTTTTCATA
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:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (17 bp):
AATTTTATTTCACTTAT
Found at i:6729185 original size:37 final size:36
Alignment explanation
Indices: 6729100--6729190 Score: 112
Period size: 37 Copynumber: 2.5 Consensus size: 36
6729090 ACACAAGTAG
*
6729100 TCCAACCGA-AACACACCAAACGCTCATAAGAGCTAA
1 TCCAA-CGATAACACGCCAAACGCTCATAAGAGCTAA
* * *
6729136 TCCAAACAATAACACGCCAAGCGCTCATGAGAGCTAA
1 TCC-AACGATAACACGCCAAACGCTCATAAGAGCTAA
6729173 TCCAACTGATAACACGCC
1 TCCAAC-GATAACACGCC
6729191 TCAGCAATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
36 8 0.17
37 39 0.83
ACGTcount: A:0.41, C:0.33, G:0.13, T:0.13
Consensus pattern (36 bp):
TCCAACGATAACACGCCAAACGCTCATAAGAGCTAA
Found at i:6731263 original size:19 final size:19
Alignment explanation
Indices: 6731239--6731278 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
6731229 TTTCATACAG
6731239 TTGAGCTAAACAATATACC
1 TTGAGCTAAACAATATACC
6731258 TTGAGCTAAACAATATACC
1 TTGAGCTAAACAATATACC
6731277 TT
1 TT
6731279 ATGCCATAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (19 bp):
TTGAGCTAAACAATATACC
Found at i:6734709 original size:23 final size:24
Alignment explanation
Indices: 6734683--6734740 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 24
6734673 TTATTTTTAA
*
6734683 AATTTATTG-TTAAATTTTATTTT
1 AATTTATTGTTTAAATTGTATTTT
*
6734706 AATTAATTGTTTTAAATTGTATTTT
1 AATTTATTG-TTTAAATTGTATTTT
6734731 ATTATTTATT
1 A--ATTTATT
6734741 AATTGTTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 8 0.29
25 14 0.50
27 6 0.21
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (24 bp):
AATTTATTGTTTAAATTGTATTTT
Found at i:6737910 original size:36 final size:36
Alignment explanation
Indices: 6737870--6737940 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
6737860 GATTATGTAA
* *
6737870 TCTTAGAGTTTTAATTGTATACATCTTCTAATTGTG
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
* *
6737906 TCTTAGAGTTCTAATTGTATGCAGCTTTTAATTGT
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGT
6737941 AGCCCTTGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.24, C:0.11, G:0.15, T:0.49
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
Found at i:6743206 original size:2 final size:2
Alignment explanation
Indices: 6743199--6743223 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6743189 TTAAATTTAA
6743199 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6743224 AATCTCTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6744919 original size:17 final size:16
Alignment explanation
Indices: 6744897--6744928 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
6744887 TCAAACTTAA
6744897 TCCGAAGTGTATTGTAT
1 TCCGAAGTGT-TTGTAT
6744914 TCCGAAGTGTTTGTA
1 TCCGAAGTGTTTGTA
6744929 CTGAAAGCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.22, C:0.12, G:0.25, T:0.41
Consensus pattern (16 bp):
TCCGAAGTGTTTGTAT
Found at i:6748017 original size:46 final size:46
Alignment explanation
Indices: 6747963--6748057 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 46
6747953 TCTCTTTTCT
*
6747963 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
1 TTTAATTAGGAGATTAAATGCTAAAGTTTAGGAGATAATATTTTGG
6748009 TTTAATTAGGAGATTAAATGCTAAAGTTTAGGAGATAATATTTTGG
1 TTTAATTAGGAGATTAAATGCTAAAGTTTAGGAGATAATATTTTGG
6748055 TTT
1 TTT
6748058 CTATCTTTGT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.35, C:0.02, G:0.22, T:0.41
Consensus pattern (46 bp):
TTTAATTAGGAGATTAAATGCTAAAGTTTAGGAGATAATATTTTGG
Found at i:6752573 original size:22 final size:22
Alignment explanation
Indices: 6752545--6752621 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 22
6752535 TTTCTTTTAA
6752545 TTAGGAGATTAGATGCTAAAGT
1 TTAGGAGATTAGATGCTAAAGT
** * *
6752567 TTAGGAGATAATATTTTGGTTTAA--
1 TTAGGAGAT--TA-GAT-GCTAAAGT
6752591 TTAGGAGATTAGATGCTAAAGT
1 TTAGGAGATTAGATGCTAAAGT
6752613 TTAGGAGAT
1 TTAGGAGAT
6752622 AATATTTTGG
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
20 4 0.10
21 1 0.02
22 20 0.49
24 11 0.27
25 1 0.02
26 4 0.10
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (22 bp):
TTAGGAGATTAGATGCTAAAGT
Found at i:6752594 original size:46 final size:46
Alignment explanation
Indices: 6752540--6752634 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
6752530 TCTCTTTTCT
6752540 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
1 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
6752586 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
1 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
6752632 TTT
1 TTT
6752635 CTATCTTTGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.34, C:0.02, G:0.23, T:0.41
Consensus pattern (46 bp):
TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
Found at i:6757516 original size:41 final size:41
Alignment explanation
Indices: 6757442--6757621 Score: 184
Period size: 41 Copynumber: 4.4 Consensus size: 41
6757432 GGCTTAGGTT
*
6757442 TTTAGCGGCGGTTTTTTAAAAAAGTGCCGCTAATGCTCAGGGC
1 TTTAGCGGC-GTTTTTT-AAAAAGTGCCACTAATGCTCAGGGC
* * **
6757485 TTTAGCGGCGTTTTTTAGAAAGTGCCACTAATACTCTA--TT
1 TTTAGCGGCGTTTTTTAAAAAGTGCCACTAATGCTC-AGGGC
* *
6757525 TTTAGCGGCGTTTTTAAAAAAGTGCCACTAATGCTCGGGGC
1 TTTAGCGGCGTTTTTTAAAAAGTGCCACTAATGCTCAGGGC
* * * * ** * *
6757566 TTTAGCGGCGTTTCTGAAAATGCGCTGCTAATGCTTAAGGC
1 TTTAGCGGCGTTTTTTAAAAAGTGCCACTAATGCTCAGGGC
6757607 TTTAGCGGCGTTTTT
1 TTTAGCGGCGTTTTT
6757622 GAAGAAGCGG
Statistics
Matches: 113, Mismatches: 21, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
40 33 0.29
41 63 0.56
42 8 0.07
43 9 0.08
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTTAAAAAGTGCCACTAATGCTCAGGGC
Found at i:6757547 original size:40 final size:40
Alignment explanation
Indices: 6757439--6757556 Score: 139
Period size: 40 Copynumber: 2.9 Consensus size: 40
6757429 TTGGGCTTAG
* *
6757439 GTTTTTAGCGGCGGTTTTTTAAAAAAGTGCCGCTAATGCTCA
1 GTTTTTAGCGGC-G-TTTTTAAAAAAGTGCCACTAATACTCA
** * *
6757481 GGGCTTTAGCGGCGTTTTTTAGAAAGTGCCACTAATACTCTA
1 -GTTTTTAGCGGCGTTTTTAAAAAAGTGCCACTAATACTC-A
6757523 -TTTTTAGCGGCGTTTTTAAAAAAGTGCCACTAAT
1 GTTTTTAGCGGCGTTTTTAAAAAAGTGCCACTAAT
6757557 GCTCGGGGCT
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
40 30 0.47
41 22 0.34
42 2 0.03
43 10 0.16
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (40 bp):
GTTTTTAGCGGCGTTTTTAAAAAAGTGCCACTAATACTCA
Done.