Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 187 of 204
Found at i:55064874 original size:37 final size:37
Alignment explanation
Indices: 55064831--55064905 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
55064821 ATCCATATGA
* *
55064831 TTGGTTATGAATGTAATGGAAAGAATAAAAGAATATT
1 TTGGTTATGAATGAAATGAAAAGAATAAAAGAATATT
55064868 TTGGTTATGAATGAAATGAAAAGAATAAAAGAATATT
1 TTGGTTATGAATGAAATGAAAAGAATAAAAGAATATT
55064905 T
1 T
55064906 GCTCAGAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (37 bp):
TTGGTTATGAATGAAATGAAAAGAATAAAAGAATATT
Found at i:55067015 original size:15 final size:14
Alignment explanation
Indices: 55066995--55067035 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
55066985 TCAGATATAT
55066995 CTAGCCCAACTACAC
1 CTAGCCCAA-TACAC
*
55067010 CTAGCCCAA-ATAC
1 CTAGCCCAATACAC
55067023 CTAGCCCAATACA
1 CTAGCCCAATACA
55067036 ACTATCAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 12 0.52
14 2 0.09
15 9 0.39
ACGTcount: A:0.37, C:0.41, G:0.07, T:0.15
Consensus pattern (14 bp):
CTAGCCCAATACAC
Found at i:55067981 original size:22 final size:22
Alignment explanation
Indices: 55067939--55067981 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
55067929 TCCATTATTT
* *
55067939 ATTTTATTTTGTTTTCTTTTTC
1 ATTTAATTTTGTTTTCATTTTC
*
55067961 ATTTAATTTTGTTTTGATTTT
1 ATTTAATTTTGTTTTCATTTT
55067982 AGCTAAGCTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.14, C:0.05, G:0.07, T:0.74
Consensus pattern (22 bp):
ATTTAATTTTGTTTTCATTTTC
Found at i:55074227 original size:44 final size:43
Alignment explanation
Indices: 55074164--55074305 Score: 212
Period size: 44 Copynumber: 3.2 Consensus size: 43
55074154 AAACCACAAA
* * *
55074164 TCCTATCTACTTGGGCAGCAGTGGAATAGGTTGAAGATAGGTAG
1 TCCTATCTCCTTGGACAGCAGTGGAATAGGTTGAAGAT-TGTAG
55074208 TCCTATCTCCTTGGACAGCAGTGGAATAGGTTGAAGATTGTAAG
1 TCCTATCTCCTTGGACAGCAGTGGAATAGGTTGAAGATTGT-AG
* *
55074252 TCCTATCTCCCTGGACAACAGTGGAATAGGTTGAAGATTGTAG
1 TCCTATCTCCTTGGACAGCAGTGGAATAGGTTGAAGATTGTAG
55074295 ATCCTATCTCC
1 -TCCTATCTCC
55074306 CTAAGCAGTA
Statistics
Matches: 91, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
43 4 0.04
44 87 0.96
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (43 bp):
TCCTATCTCCTTGGACAGCAGTGGAATAGGTTGAAGATTGTAG
Found at i:55074472 original size:44 final size:43
Alignment explanation
Indices: 55074414--55074497 Score: 98
Period size: 44 Copynumber: 1.9 Consensus size: 43
55074404 GTGGAGTAGG
*
55074414 TTAAAACCACAGATC-CTATCTCCCTGAAGTCACAGTAGAGCGGA
1 TTAAAACCACAGATCTC-ATCTCCATGAA-TCACAGTAGAGCGGA
* * * *
55074458 TTAAAATCATAGATCTCATCTCTATGAATTACAGTAGAGC
1 TTAAAACCACAGATCTCATCTCCATGAATCACAGTAGAGC
55074498 AGGTTGCACC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
43 11 0.32
44 22 0.65
45 1 0.03
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (43 bp):
TTAAAACCACAGATCTCATCTCCATGAATCACAGTAGAGCGGA
Found at i:55083137 original size:2 final size:2
Alignment explanation
Indices: 55083130--55083157 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
55083120 AACCACCCTT
55083130 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
55083158 ATTAAGAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55084626 original size:30 final size:27
Alignment explanation
Indices: 55084592--55084675 Score: 71
Period size: 30 Copynumber: 2.9 Consensus size: 27
55084582 AATAAAAGGG
*
55084592 AATAATAAGAGTAAAAACAAAAATAATATA
1 AATAATAA-A-TAAAAACAAAAATAAT-GA
55084622 AATAAT-AATAAAAAACAATAAAATAATGA
1 AATAATAAAT-AAAAAC-A-AAAATAATGA
* *
55084651 AATAATAAAATGAAAATAAAAATAA
1 AATAAT-AAATAAAAACAAAAATAA
55084676 AACAATTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
27 1 0.02
28 14 0.30
29 10 0.22
30 18 0.39
31 3 0.07
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (27 bp):
AATAATAAATAAAAACAAAAATAATGA
Found at i:55084653 original size:8 final size:8
Alignment explanation
Indices: 55084611--55084661 Score: 54
Period size: 8 Copynumber: 6.6 Consensus size: 8
55084601 AGTAAAAACA
55084611 AAAATAAT
1 AAAATAAT
55084619 ATAAATAAT
1 A-AAATAAT
55084628 --AATAA-
1 AAAATAAT
*
55084633 AAAACAAT
1 AAAATAAT
55084641 AAAATAAT
1 AAAATAAT
*
55084649 GAAATAAT
1 AAAATAAT
55084657 AAAAT
1 AAAAT
55084662 GAAAATAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
6 5 0.14
7 4 0.11
8 19 0.54
9 7 0.20
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (8 bp):
AAAATAAT
Found at i:55084654 original size:29 final size:28
Alignment explanation
Indices: 55084604--55084675 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 28
55084594 TAATAAGAGT
*
55084604 AAAAACAAAAATAATATAAATAATAATA
1 AAAAACAAAAATAATAGAAATAATAATA
55084632 AAAAACAATAAAATAAT-GAAATAATAA-A
1 AAAAAC-A-AAAATAATAGAAATAATAATA
*
55084660 ATGAAAATAAAAATAA
1 A--AAAACAAAAATAA
55084676 AACAATTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
28 15 0.39
29 11 0.29
30 12 0.32
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (28 bp):
AAAAACAAAAATAATAGAAATAATAATA
Found at i:55084794 original size:3 final size:3
Alignment explanation
Indices: 55084774--55084921 Score: 95
Period size: 3 Copynumber: 48.7 Consensus size: 3
55084764 ACAATTTAAA
* * * * *
55084774 AAT AAT AAC AAT ATAT AAT AAT AAT AAG AGT AGT AA- AAT AAA AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
55084819 AAT AAT ATT AGT CAT AAT GAA- AAT AAT AAT AAT ACT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * ** *
55084863 AGT AAAT AAT AAT ACGAT GAT AAT AAT AGC AAT AAT AAA AAT AAT AAT
1 AAT -AAT AAT AAT A--AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
55084911 AAT AAA AAT AA
1 AAT AAT AAT AA
55084922 CGATAATATT
Statistics
Matches: 110, Mismatches: 27, Indels: 16
0.72 0.18 0.10
Matches are distributed among these distances:
2 5 0.05
3 96 0.87
4 7 0.06
5 2 0.02
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:55084927 original size:15 final size:15
Alignment explanation
Indices: 55084882--55084929 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
55084872 TAATACGATG
* *
55084882 ATAATAATAGCAATA
1 ATAAAAATAACAATA
*
55084897 ATAAAAATAATAATA
1 ATAAAAATAACAATA
*
55084912 ATAAAAATAACGATA
1 ATAAAAATAACAATA
55084927 ATA
1 ATA
55084930 TTATCAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (15 bp):
ATAAAAATAACAATA
Found at i:55087744 original size:10 final size:10
Alignment explanation
Indices: 55087729--55087793 Score: 60
Period size: 10 Copynumber: 6.6 Consensus size: 10
55087719 AGATTTGTTT
55087729 TAAAAATTTA
1 TAAAAATTTA
* *
55087739 TAAAAAGTAA
1 TAAAAATTTA
* *
55087749 TAGAAATTAA
1 TAAAAATTTA
* *
55087759 TTAAAATTCA
1 TAAAAATTTA
*
55087769 TAAAATTTTA
1 TAAAAATTTA
55087779 T-AAAATTTA
1 TAAAAATTTA
55087788 TAAAAA
1 TAAAAA
55087794 AATAATTTAT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
9 8 0.19
10 35 0.81
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (10 bp):
TAAAAATTTA
Found at i:55087972 original size:17 final size:18
Alignment explanation
Indices: 55087935--55087978 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
55087925 CTATTTATTA
55087935 TTATAATTTTAATAATCTT
1 TTATAATTTT-ATAATCTT
*
55087954 TTATAATTTT-TAATGTT
1 TTATAATTTTATAATCTT
55087971 TTATAATT
1 TTATAATT
55087979 GTAAAATGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 14 0.58
19 10 0.42
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (18 bp):
TTATAATTTTATAATCTT
Found at i:55094594 original size:9 final size:9
Alignment explanation
Indices: 55094580--55094605 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
55094570 ATATATATAT
55094580 ATAATAACA
1 ATAATAACA
55094589 ATAATAACA
1 ATAATAACA
55094598 ATAATAAC
1 ATAATAAC
55094606 TCAAACGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.23
Consensus pattern (9 bp):
ATAATAACA
Found at i:55104897 original size:41 final size:41
Alignment explanation
Indices: 55104850--55105031 Score: 310
Period size: 41 Copynumber: 4.4 Consensus size: 41
55104840 GGTTTTAAAA
* * *
55104850 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
55104891 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
*
55104932 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
* *
55104973 CCTAGCAGGCTAAGTGCCGGTGAACTGGATTAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
55105014 CCTAGCAGGCTAAGTGCC
1 CCTAGCAGGCTAAGTGCC
55105032 AATGAATCTG
Statistics
Matches: 134, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 134 1.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.21
Consensus pattern (41 bp):
CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
Found at i:55106514 original size:59 final size:59
Alignment explanation
Indices: 55106422--55106541 Score: 195
Period size: 59 Copynumber: 2.0 Consensus size: 59
55106412 TTCTTCCAGT
* * * *
55106422 CACGTTATTAATGACATTTCAAATCTAAAATCTTGAAATACTAACGTCAGTACCAATGA
1 CACGTTATTAATGACATTTCAAACCTAAAATCTTGAAATACCAACCTCAATACCAATGA
*
55106481 CACGTTATTAATGACATTTCAAACCTAAAATCTTGAAGTACCAACCTCAATACCAATGA
1 CACGTTATTAATGACATTTCAAACCTAAAATCTTGAAATACCAACCTCAATACCAATGA
55106540 CA
1 CA
55106542 TATTTCAACC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (59 bp):
CACGTTATTAATGACATTTCAAACCTAAAATCTTGAAATACCAACCTCAATACCAATGA
Found at i:55107772 original size:9 final size:9
Alignment explanation
Indices: 55107721--55107779 Score: 59
Period size: 9 Copynumber: 6.3 Consensus size: 9
55107711 TAAAAATTCA
55107721 AAAAATTATT
1 AAAAA-TATT
55107731 AAAAATATAT
1 AAAAATAT-T
55107741 ACAAAATA-T
1 A-AAAATATT
*
55107750 ACAAAATATA
1 A-AAAATATT
55107760 AAAAATATT
1 AAAAATATT
55107769 AAAAA-ATT
1 AAAAATATT
55107777 AAA
1 AAA
55107780 TAAATTCTGA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
8 6 0.14
9 24 0.55
10 8 0.18
11 6 0.14
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.27
Consensus pattern (9 bp):
AAAAATATT
Found at i:55108047 original size:14 final size:13
Alignment explanation
Indices: 55108019--55108061 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
55108009 TGTTGACTTG
55108019 TATTTTTAATAAT
1 TATTTTTAATAAT
55108032 TATTTTTAATACAT
1 TATTTTTAATA-AT
*
55108046 TATGTTGT-ATAAT
1 TAT-TTTTAATAAT
55108059 TAT
1 TAT
55108062 AAAAGAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 16 0.59
14 8 0.30
15 3 0.11
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (13 bp):
TATTTTTAATAAT
Found at i:55112410 original size:12 final size:12
Alignment explanation
Indices: 55112393--55112419 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
55112383 GATTTTGAGA
55112393 AATCCAATTAAG
1 AATCCAATTAAG
55112405 AATCCAATTAAG
1 AATCCAATTAAG
55112417 AAT
1 AAT
55112420 TATTTTGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.15, G:0.07, T:0.26
Consensus pattern (12 bp):
AATCCAATTAAG
Found at i:55119159 original size:16 final size:16
Alignment explanation
Indices: 55119138--55119168 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55119128 TGAATTCTTA
*
55119138 CTTATTAATGATAAAT
1 CTTATTAATAATAAAT
55119154 CTTATTAATAATAAA
1 CTTATTAATAATAAA
55119169 ATTGGAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (16 bp):
CTTATTAATAATAAAT
Found at i:55124451 original size:22 final size:22
Alignment explanation
Indices: 55124410--55124451 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
55124400 TGGGATTCAT
**
55124410 TCATTTGAGTTTAATTTTTAAA
1 TCATTTGAGTTTAAGATTTAAA
55124432 TCATTTGAGTTTAAGATTTA
1 TCATTTGAGTTTAAGATTTA
55124452 TTTTCTAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (22 bp):
TCATTTGAGTTTAAGATTTAAA
Found at i:55134364 original size:14 final size:14
Alignment explanation
Indices: 55134343--55134384 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
55134333 GAATAAGCAA
55134343 ACACATATATATAT
1 ACACATATATATAT
* *
55134357 ATACATATATATGT
1 ACACATATATATAT
*
55134371 ACACATATACATAT
1 ACACATATATATAT
55134385 TTTTGAGAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (14 bp):
ACACATATATATAT
Found at i:55137418 original size:22 final size:23
Alignment explanation
Indices: 55137393--55137437 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
55137383 GTTATCAATT
*
55137393 TTTTTG-AATATTATTG-TTTTCC
1 TTTTTGCAAAATT-TTGATTTTCC
55137415 TTTTTGCAAAATTTTGATTTTCC
1 TTTTTGCAAAATTTTGATTTTCC
55137438 CAAAACTCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.60
Consensus pattern (23 bp):
TTTTTGCAAAATTTTGATTTTCC
Found at i:55139816 original size:37 final size:37
Alignment explanation
Indices: 55139762--55139836 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
55139752 AGCAACAACG
* *
55139762 AAATCAAGACATAAACAATACGGCAAATTTAAAGGGT
1 AAATCAAGACATAAACAATAAGGCAAATTTAAAAGGT
*
55139799 AAATCAAGACATGAACAATAAGGCAAATTTAAAAGGT
1 AAATCAAGACATAAACAATAAGGCAAATTTAAAAGGT
55139836 A
1 A
55139837 GAAGAAATAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.53, C:0.12, G:0.16, T:0.19
Consensus pattern (37 bp):
AAATCAAGACATAAACAATAAGGCAAATTTAAAAGGT
Found at i:55147596 original size:17 final size:17
Alignment explanation
Indices: 55147574--55147606 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
55147564 ACCCAAAATG
*
55147574 AAAACAAGACAAAACCC
1 AAAACAAAACAAAACCC
55147591 AAAACAAAACAAAACC
1 AAAACAAAACAAAACC
55147607 TACCCAATAC
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:0.70, C:0.27, G:0.03, T:0.00
Consensus pattern (17 bp):
AAAACAAAACAAAACCC
Found at i:55154978 original size:25 final size:24
Alignment explanation
Indices: 55154949--55155021 Score: 76
Period size: 26 Copynumber: 3.0 Consensus size: 24
55154939 ATATATATAC
55154949 TCATATACATTTTTTACTATATTTT
1 TCATATACATTTTTTA-TATATTTT
*
55154974 TCATATACATATTCTTTATTTATTTT
1 TCATATACAT-TT-TTTATATATTTT
** *
55155000 AAATACACATTTTTT-TATATTT
1 TCATATACATTTTTTATATATTT
55155022 CATATTTTCA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
23 6 0.15
24 3 0.07
25 12 0.29
26 16 0.39
27 4 0.10
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.59
Consensus pattern (24 bp):
TCATATACATTTTTTATATATTTT
Found at i:55161357 original size:86 final size:87
Alignment explanation
Indices: 55161207--55161389 Score: 260
Period size: 86 Copynumber: 2.1 Consensus size: 87
55161197 ATATCAGTAA
* *
55161207 AGATTGAAGACAAACCTTGCCTCTCTCATTTGTAGCAGAGCTGGTTGAAGATAACAGATCTTGCC
1 AGATCGAAGACAAACATTGCCTCTCTCATTTGTAGCAGAGCTGGTTGAAGATAACAGATCTTGCC
* *
55161272 TTCCTACA-TTGACGGTGAAGC
66 TTCCTACATTTGACAGCGAAGC
** * *
55161293 AGATCGAAGACAAACATTGCCTCTCTTGTTTGTAGTAGAGCTGGTTGAAGATAATAGATCTTGCC
1 AGATCGAAGACAAACATTGCCTCTCTCATTTGTAGCAGAGCTGGTTGAAGATAACAGATCTTGCC
** *
55161358 TTCCTGTATTTGGCAGCGAAGC
66 TTCCTACATTTGACAGCGAAGC
55161380 AGATCGAAGA
1 AGATCGAAGA
55161390 TGGCAGATTT
Statistics
Matches: 85, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
86 65 0.76
87 20 0.24
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (87 bp):
AGATCGAAGACAAACATTGCCTCTCTCATTTGTAGCAGAGCTGGTTGAAGATAACAGATCTTGCC
TTCCTACATTTGACAGCGAAGC
Found at i:55161943 original size:135 final size:134
Alignment explanation
Indices: 55161348--55162411 Score: 1728
Period size: 134 Copynumber: 8.0 Consensus size: 134
55161338 TGAAGATAAT
*
55161348 AGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCCTGACT
1 AGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGACT
* * * *
55161413 ATAGAGGAGTACATTGAAGCCAATAACTCTATCTCCCTG--GTTGGCAGTGGAATAGATTGAAGA
66 ACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAGA
55161476 TTGC
131 TTGC
*
55161480 AGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAAATTTTACCTCCCTGACT
1 AGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGACT
*
55161545 ACAGTGGAGTACATTGAAGCCGATAATTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAGA
66 ACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAGA
55161610 TTGC
131 TTGC
*
55161614 AGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATAGCAGATTTTACCTCCCTGACT
1 AGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGACT
* *
55161679 ACAGTAGAGTACATTGAAGCCGAT-ATTCTATCTCCCTGTATTTGGCAGTGGAATAGATTG-AGA
66 ACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAGA
*
55161742 TTAC
131 TTGC
* * *
55161746 AGATC-TG-CTTTCTGTAATTT-GCAGCGAGGCAGATCAGAGATGGCAGATTTTACCTCCCTGAC
1 AGATCTTGCCTTCCTGT-ATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAC
* * * *
55161808 TACAGTGGAGTACATTGAAGTCGATAATTCTATCTTCCTGTACTTGGCAGTGGAATAGATTGAAG
65 TACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAG
55161873 ATTGC
130 ATTGC
*
55161878 AGATCTTGCCTTCCTGTATTTTGGCAGCGAAGCAGATCAAAGATAGCAGATTTTACCTCCCTGAC
1 AGATCTTGCCTTCCTGTA-TTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAC
* *
55161943 TACAGTAGAGTACATTGAAGCCGATAATTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAG
65 TACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAG
*
55162008 ATTAC
130 ATTGC
* *
55162013 AGATCTTGCCTTCCTGTATTTGGTAGCGAAGCAGATCGAAGATGGCAGATTTTTACCTCCCTGAC
1 AGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGA-TTTTACCTCCCTGAC
*
55162078 TACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAG
65 TACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAG
55162143 ATTGC
130 ATTGC
* * * *
55162148 AGATCTTGCCTTCCTGTATTTGGTAGCGAAGCAGATCGACGATGGCAGATTTTACCTCTCTGACT
1 AGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGACT
* *
55162213 ACAGAGGAGTACATTGAAGCTGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAGA
66 ACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAGA
*
55162278 TTAC
131 TTGC
* *
55162282 AAATATTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGACT
1 AGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGACT
* *
55162347 ACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTAGAATAGAGTGAAGA
66 ACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAGA
55162412 AAACTAGATC
Statistics
Matches: 872, Mismatches: 50, Indels: 18
0.93 0.05 0.02
Matches are distributed among these distances:
130 69 0.08
131 40 0.05
132 120 0.14
133 39 0.04
134 353 0.40
135 251 0.29
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Consensus pattern (134 bp):
AGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGACT
ACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAGA
TTGC
Found at i:55162526 original size:44 final size:44
Alignment explanation
Indices: 55162412--55162532 Score: 153
Period size: 40 Copynumber: 2.8 Consensus size: 44
55162402 AGAGTGAAGA
* * *
55162412 AAACTAGATCTTATCTCCCGAAGCAGTAGTGGAGCAGATCACAT
1 AAACAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAT
55162456 ---CAAG-TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAT
1 AAACAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-AAAT
* *
55162496 AAACCAGATCTTATCTCCCTAAGCAATAGTGGAGCAG
1 AAACAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAG
55162533 GTCGAAGATG
Statistics
Matches: 67, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
39 1 0.01
40 32 0.48
41 3 0.04
43 3 0.04
44 28 0.42
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (44 bp):
AAACAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAT
Found at i:55162638 original size:130 final size:130
Alignment explanation
Indices: 55162500--55163052 Score: 910
Period size: 130 Copynumber: 4.3 Consensus size: 130
55162490 CGAAATAAAC
*
55162500 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGGTCGAAGATGACGGATTTTACCTCCCCGATTA
1 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGGTCGAAGATGGCGGATTTTACCTCCCCGATTA
*
55162565 CGGTGGAGTACATTAAAGCCGGTAGTTCTATCTCCCTGGGCAACAGTGGAATAGAGTGAAGATTA
66 CGGTGGAGTACATTAAAGCTGGTAGTTCTATCTCCCTGGGCAACAGTGGAATAGAGTGAAGATTA
* *
55162630 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGGTCGAAGATGGCGGATTTTACCTCACTGATTA
1 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGGTCGAAGATGGCGGATTTTACCTCCCCGATTA
** * * * *
55162695 TAGTGGAGTACAATGAAGCTGGTAGTTCTATCTCTCTGGGCAACAGTGGAATAGA-TCAAAGATT
66 CGGTGGAGTACATTAAAGCTGGTAGTTCTATCTCCCTGGGCAACAGTGGAATAGAGT-GAAGATT
55162759 A
130 A
*
55162760 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGGTCGAAGATGGCGAATTTTACCTCCCCGATTA
1 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGGTCGAAGATGGCGGATTTTACCTCCCCGATTA
*
55162825 CGGTGGAGTACATTAAAGCTAGTAGTTCTATCTCCCTGGGCAACAGTGGAATAGAGTGAAGATTA
66 CGGTGGAGTACATTAAAGCTGGTAGTTCTATCTCCCTGGGCAACAGTGGAATAGAGTGAAGATTA
* *
55162890 CAGATCTTATCTCCCTAAGTAATAGTGGAGCAGGTCGAAGATGGCGGATTTTACCTCCCTGATTA
1 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGGTCGAAGATGGCGGATTTTACCTCCCCGATTA
* * * **
55162955 CGGTGGAGTACATTGAAGCTGGTAGTTCTATCTCTCGGGGCAACAGTGGAATAGAGTGAAGAGCA
66 CGGTGGAGTACATTAAAGCTGGTAGTTCTATCTCCCTGGGCAACAGTGGAATAGAGTGAAGATTA
*
55163020 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAG
1 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAG
55163053 ATCACATCCA
Statistics
Matches: 390, Mismatches: 31, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
129 1 0.00
130 388 0.99
131 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26
Consensus pattern (130 bp):
CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGGTCGAAGATGGCGGATTTTACCTCCCCGATTA
CGGTGGAGTACATTAAAGCTGGTAGTTCTATCTCCCTGGGCAACAGTGGAATAGAGTGAAGATTA
Found at i:55162670 original size:44 final size:44
Alignment explanation
Indices: 55162622--55162802 Score: 109
Period size: 44 Copynumber: 4.2 Consensus size: 44
55162612 GGAATAGAGT
* *
55162622 GAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGGTC
1 GAAGATGACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATC
* * * * * * **
55162666 GAAGATGGCGGATTTTACCTCACTGA-TTATAGTGGAGTACA-AT-
1 GAAGATGACAGATCTTATCTCCCTAAGCAATAGTGGAG--CAGATC
* ** * * ** * **
55162709 GAAGCTGGTAGTTC-TATCTCTCTGGGCAACAGTGGAATAGATC
1 GAAGATGACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATC
* * *
55162752 AAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGGTC
1 GAAGATGACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATC
55162796 GAAGATG
1 GAAGATG
55162803 GCGAATTTTA
Statistics
Matches: 93, Mismatches: 38, Indels: 12
0.65 0.27 0.08
Matches are distributed among these distances:
41 1 0.01
42 10 0.11
43 33 0.35
44 47 0.51
45 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.27
Consensus pattern (44 bp):
GAAGATGACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATC
Found at i:55169237 original size:29 final size:29
Alignment explanation
Indices: 55169182--55169238 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
55169172 AATTTCATAT
* * *
55169182 ATATATAAATTATTAAAAATTTAAAAAGA
1 ATATATAAAATATAAAAAATGTAAAAAGA
55169211 ATATATAAAATATAAAAAATGGTAAAAA
1 ATATATAAAATATAAAAAAT-GTAAAAA
55169239 AGTAAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (29 bp):
ATATATAAAATATAAAAAATGTAAAAAGA
Found at i:55174559 original size:24 final size:22
Alignment explanation
Indices: 55174525--55174580 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 22
55174515 AAATTATCAA
*
55174525 TTTGGATTTTAAATATTAATAGG
1 TTTGGGTTTTAAATATTAAT-GG
* *
55174548 TATTGTGTTTTAAATTTTAATGG
1 T-TTGGGTTTTAAATATTAATGG
55174571 TTTGGGTTTT
1 TTTGGGTTTT
55174581 TAAGAGTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 8 0.29
23 4 0.14
24 16 0.57
ACGTcount: A:0.25, C:0.00, G:0.20, T:0.55
Consensus pattern (22 bp):
TTTGGGTTTTAAATATTAATGG
Found at i:55176450 original size:21 final size:21
Alignment explanation
Indices: 55176420--55176462 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
55176410 GAGGTGCCTA
*
55176420 TGGGCTGGACCGGGTTTGGGT
1 TGGGCCGGACCGGGTTTGGGT
55176441 TGGGCCGGACCGGGTTTGGGT
1 TGGGCCGGACCGGGTTTGGGT
55176462 T
1 T
55176463 TGGGTTGGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.51, T:0.28
Consensus pattern (21 bp):
TGGGCCGGACCGGGTTTGGGT
Found at i:55180001 original size:2 final size:2
Alignment explanation
Indices: 55179994--55180020 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
55179984 CCTACTCTCG
55179994 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
55180021 CTTAACTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55180671 original size:49 final size:49
Alignment explanation
Indices: 55180614--55180712 Score: 144
Period size: 49 Copynumber: 2.0 Consensus size: 49
55180604 CGTTTTCTCT
* * *
55180614 ATGCCATAGTCCAACTATGGTCTTACATGTAATCACATATCACATACCG
1 ATGCCATAGCCCAACTATGGTCTTACACGGAATCACATATCACATACCG
* * *
55180663 ATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATATCACTTACCG
1 ATGCCATAGCCCAACTATGGTCTTACACGGAATCACATATCACATACCG
55180712 A
1 A
55180713 AAGTACTCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.27
Consensus pattern (49 bp):
ATGCCATAGCCCAACTATGGTCTTACACGGAATCACATATCACATACCG
Found at i:55181667 original size:104 final size:104
Alignment explanation
Indices: 55181483--55181943 Score: 800
Period size: 104 Copynumber: 4.4 Consensus size: 104
55181473 AGCCGTTATC
* * *
55181483 GGTGGATCCCGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
* ** *
55181548 ATCAACACATAGCAACCCCCTTTTTCATTTCAAAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAT
* * *
55181587 GGTGGAT-ATCGCACTTAGCACCACCAATGAATCAGGGAATCAGCACTTAGCAACTCCTCGGGGG
1 GGTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
*
55181651 AATCAGCACATGGCAACCCCCTTTCACATTTCAAAGATAT
65 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAT
55181691 GGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
55181756 ATCAGCACATAGCAACCCCCTTTCACATTTC-AAGATAT
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAT
55181794 GGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
55181859 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAT
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAT
55181898 GGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCAC
1 GGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCAC
55181944 ACAACAACCC
Statistics
Matches: 341, Mismatches: 13, Indels: 6
0.95 0.04 0.02
Matches are distributed among these distances:
103 103 0.30
104 237 0.70
105 1 0.00
ACGTcount: A:0.31, C:0.30, G:0.21, T:0.19
Consensus pattern (104 bp):
GGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAT
Found at i:55181955 original size:207 final size:208
Alignment explanation
Indices: 55181483--55181943 Score: 800
Period size: 207 Copynumber: 2.2 Consensus size: 208
55181473 AGCCGTTATC
* * *
55181483 GGTGGATCCCGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
** *
55181548 ATCAACACATAGCAACCCCCTTTTTCATTTCAAAGATACGGTGGATATCGCACTTAGCACCACCA
66 ATCAACACATAGCAACCCCCTTTCACATTTCAAAGATACGGTGGATATCGCACATAGCACCACCA
* *
55181613 ATGAATCAGGGAATCAGCACTTAGCAACTCCTCGGGGGAATCAGCACATGGCAACCCCCTTTCAC
131 ATGAATCAGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCAC
55181678 ATTTCAAAGATAT
196 ATTTCAAAGATAT
55181691 GGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
* *
55181756 ATCAGCACATAGCAACCCCCTTTCACATTTC-AAGATATGGTGGATCA-CGCACATAGCACCACC
66 ATCAACACATAGCAACCCCCTTTCACATTTCAAAGATACGGTGGAT-ATCGCACATAGCACCACC
*
55181819 AATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCA
130 AATGAATCAGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCA
55181884 CATTTCAAAGATAT
195 CATTTCAAAGATAT
55181898 GGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCAC
1 GGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCAC
55181944 ACAACAACCC
Statistics
Matches: 241, Mismatches: 11, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
207 150 0.62
208 91 0.38
ACGTcount: A:0.31, C:0.30, G:0.21, T:0.19
Consensus pattern (208 bp):
GGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAACACATAGCAACCCCCTTTCACATTTCAAAGATACGGTGGATATCGCACATAGCACCACCA
ATGAATCAGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCAC
ATTTCAAAGATAT
Found at i:55182319 original size:18 final size:19
Alignment explanation
Indices: 55182282--55182319 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
55182272 CATTGGTTTC
* *
55182282 AACTTCCTCTTTGTTCTCA
1 AACTTCCTCTTCGTTATCA
55182301 AACTT-CTCTTCGTTATCA
1 AACTTCCTCTTCGTTATCA
55182319 A
1 A
55182320 CCCTAATTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.21, C:0.29, G:0.05, T:0.45
Consensus pattern (19 bp):
AACTTCCTCTTCGTTATCA
Found at i:55184812 original size:16 final size:16
Alignment explanation
Indices: 55184786--55184818 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
55184776 AAATCAAATT
55184786 TAAAAATTTTTAGAAAA
1 TAAAAATTTTTA-AAAA
55184803 TAAAAA-TTTTAAAAA
1 TAAAAATTTTTAAAAA
55184818 T
1 T
55184819 TTATTTTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 5 0.31
17 6 0.38
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
TAAAAATTTTTAAAAA
Found at i:55186119 original size:3 final size:3
Alignment explanation
Indices: 55186111--55186175 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
55186101 TTTTATCACT
55186111 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
55186159 TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
55186176 TGAAATATGA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:55191353 original size:36 final size:36
Alignment explanation
Indices: 55191306--55191378 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
55191296 AGACTTGGAA
55191306 CTCCCTCCTGAGGTAGAGACACCAAGGGTTAATGCT
1 CTCCCTCCTGAGGTAGAGACACCAAGGGTTAATGCT
55191342 CTCCCTCCTGAGGTAGAGACACCAAGGGTTAATGCT
1 CTCCCTCCTGAGGTAGAGACACCAAGGGTTAATGCT
55191378 C
1 C
55191379 GTTCTTCTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.25, C:0.29, G:0.25, T:0.22
Consensus pattern (36 bp):
CTCCCTCCTGAGGTAGAGACACCAAGGGTTAATGCT
Found at i:55208256 original size:45 final size:45
Alignment explanation
Indices: 55208192--55208292 Score: 159
Period size: 45 Copynumber: 2.2 Consensus size: 45
55208182 GTAACGGTAG
* *
55208192 CAGTAACAGTAACAGTATTCAACACACAAAGT-GCTGAATCTGTAA
1 CAGTAACAGTAACAGTATTCAACACACAAAGTATC-GAATCAGTAA
*
55208237 CAGTAACAGTAACAGTATTCGACACACAAAGTATCGAATCAGTAA
1 CAGTAACAGTAACAGTATTCAACACACAAAGTATCGAATCAGTAA
55208282 CAGTAACAGTA
1 CAGTAACAGTA
55208293 GTCGGCACAT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
45 51 0.98
46 1 0.02
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.21
Consensus pattern (45 bp):
CAGTAACAGTAACAGTATTCAACACACAAAGTATCGAATCAGTAA
Found at i:55209804 original size:16 final size:17
Alignment explanation
Indices: 55209772--55209804 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
55209762 CAATTAACCC
55209772 CTCAATTAATCTAATTTT
1 CTCAATTAA-CTAATTTT
55209790 CTCAATTAA-TAATTT
1 CTCAATTAACTAATTT
55209805 ACCTAGACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
CTCAATTAACTAATTTT
Found at i:55210447 original size:21 final size:21
Alignment explanation
Indices: 55210418--55210459 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
55210408 CTTTTTGTTC
* *
55210418 AATTAATTATCGGAACTTTAA
1 AATTAATTAACGAAACTTTAA
*
55210439 AATTTATTAACGAAACTTTAA
1 AATTAATTAACGAAACTTTAA
55210460 TACTAACTTT
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:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (21 bp):
AATTAATTAACGAAACTTTAA
Found at i:55210942 original size:18 final size:18
Alignment explanation
Indices: 55210915--55210954 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
55210905 TAATTAATTT
55210915 TAATTTTTATA-TAAAAA
1 TAATTTTTATACTAAAAA
*
55210932 TAATATTTTATACTTAAAA
1 TAAT-TTTTATACTAAAAA
55210951 TAAT
1 TAAT
55210955 GAAAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 7 0.35
19 9 0.45
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
TAATTTTTATACTAAAAA
Found at i:55212236 original size:24 final size:24
Alignment explanation
Indices: 55212204--55212260 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
55212194 TTTTATCAAT
* * *
55212204 TTTAAGGGTTAAACTATAATTTTC
1 TTTAGGGGTGAAACTAGAATTTTC
* *
55212228 TTTAGGGGTGAAGCTAGAATTTTT
1 TTTAGGGGTGAAACTAGAATTTTC
55212252 TTTAGGGGT
1 TTTAGGGGT
55212261 AAAATTAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.26, C:0.05, G:0.25, T:0.44
Consensus pattern (24 bp):
TTTAGGGGTGAAACTAGAATTTTC
Found at i:55212928 original size:9 final size:8
Alignment explanation
Indices: 55212909--55212957 Score: 53
Period size: 9 Copynumber: 5.6 Consensus size: 8
55212899 AGATTTGTAA
55212909 AAATATAT
1 AAATATAT
55212917 AAATATTAT
1 AAATA-TAT
55212926 AAATAATAT
1 AAAT-ATAT
55212935 AAAATATATT
1 -AAATATA-T
*
55212945 AAATAAAT
1 AAATATAT
55212953 AAATA
1 AAATA
55212958 AAAATAACAT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
8 11 0.31
9 19 0.53
10 6 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AAATATAT
Found at i:55212939 original size:19 final size:19
Alignment explanation
Indices: 55212906--55212955 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
55212896 ATTAGATTTG
55212906 TAAA-AATATATAAATAT-T
1 TAAATAATATA-AAATATAT
55212924 ATAAATAATATAAAATATAT
1 -TAAATAATATAAAATATAT
55212944 TAAATAA-ATAAA
1 TAAATAATATAAA
55212956 TAAAAATAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.17
19 17 0.59
20 7 0.24
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
TAAATAATATAAAATATAT
Found at i:55212940 original size:27 final size:27
Alignment explanation
Indices: 55212874--55212958 Score: 81
Period size: 27 Copynumber: 3.3 Consensus size: 27
55212864 GATATTAAAA
55212874 ATAAATAATATAAAAT-TATAAA-ATT
1 ATAAATAATATAAAATATATAAATATT
* * **
55212899 A-GATTTGTA-AAAATATATAAATATT
1 ATAAATAATATAAAATATATAAATATT
*
55212924 ATAAATAATATAAAATATATTAAATA-A
1 ATAAATAATATAAAATATA-TAAATATT
55212951 ATAAATAA
1 ATAAATAA
55212959 AAATAACATG
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
23 5 0.11
24 10 0.22
25 5 0.11
26 4 0.09
27 16 0.35
28 6 0.13
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (27 bp):
ATAAATAATATAAAATATATAAATATT
Found at i:55229098 original size:22 final size:21
Alignment explanation
Indices: 55229063--55229120 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
55229053 AAAGGGTATC
* * *
55229063 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCCAAGAT
55229084 TACAAAATCATATCTTCCAAGAT
1 TAC-AAATCATATC-TCCAAGAT
* *
55229107 TGCATATCATATCT
1 TACAAATCATATCT
55229121 AAGATTGCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 4 0.13
22 17 0.57
23 9 0.30
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.34
Consensus pattern (21 bp):
TACAAATCATATCTCCAAGAT
Found at i:55229136 original size:21 final size:20
Alignment explanation
Indices: 55229076--55229154 Score: 81
Period size: 21 Copynumber: 3.9 Consensus size: 20
55229066 AAATTAAATC
* *
55229076 TCTAAGATTACAAAATCATA
1 TCTAAGATTGCAATATCATA
55229096 TCTTCCAAGATTGC-ATATCATA
1 TC-T--AAGATTGCAATATCATA
*
55229118 TCTAAGATTGCATATATCAGA
1 TCTAAGATTGCA-ATATCATA
55229139 TCTAAGATTGC-ATATC
1 TCTAAGATTGCAATATC
55229155 CTTGAAGATA
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
19 13 0.25
20 2 0.04
21 20 0.39
22 9 0.18
23 7 0.14
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (20 bp):
TCTAAGATTGCAATATCATA
Found at i:55231350 original size:4 final size:4
Alignment explanation
Indices: 55231341--55231367 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
55231331 ACTATTCATA
55231341 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
55231368 AATAGCTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:55242475 original size:5 final size:5
Alignment explanation
Indices: 55242465--55242495 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
55242455 TGAGCATTCG
55242465 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
55242496 AATTTTCGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:55243523 original size:9 final size:9
Alignment explanation
Indices: 55243509--55243545 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
55243499 TATAGTTTGA
55243509 TATTCGAAT
1 TATTCGAAT
55243518 TATTCGAAT
1 TATTCGAAT
* *
55243527 TATTTGAGT
1 TATTCGAAT
55243536 TATTCGAAT
1 TATTCGAAT
55243545 T
1 T
55243546 CAAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:55243618 original size:9 final size:9
Alignment explanation
Indices: 55243601--55243631 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
55243591 TCGAGTTGAT
55243601 TCGAATAAC
1 TCGAATAAC
*
55243610 TCGATTAAC
1 TCGAATAAC
55243619 TCGAATAAC
1 TCGAATAAC
55243628 TCGA
1 TCGA
55243632 TTTGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:55255984 original size:13 final size:13
Alignment explanation
Indices: 55255966--55255993 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
55255956 TTATGGTTAT
55255966 TATTATAAAAAAA
1 TATTATAAAAAAA
55255979 TATTATAAAAAAA
1 TATTATAAAAAAA
55255992 TA
1 TA
55255994 ATAAAACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TATTATAAAAAAA
Found at i:55256351 original size:21 final size:20
Alignment explanation
Indices: 55256301--55256356 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 20
55256291 TGCCACGTGT
55256301 TTTTTAAATATATTTATAGTA
1 TTTTTAAATATATTTATAG-A
*
55256322 TTTTCAAATATATTTATA-A
1 TTTTTAAATATATTTATAGA
55256341 TTTAGTTAAATATATT
1 TTT--TTAAATATATT
55256357 ATTTTTGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.13
21 27 0.87
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (20 bp):
TTTTTAAATATATTTATAGA
Found at i:55258065 original size:27 final size:25
Alignment explanation
Indices: 55258013--55258065 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
55258003 TAATGTATTC
* *
55258013 AAATAATGAATTAATAATATTTTAA
1 AAATAATGAATGAATAATATTATAA
*
55258038 AAATAGATGAATGGAATTATATTATAA
1 AAATA-ATGAAT-GAATAATATTATAA
55258065 A
1 A
55258066 TTAAATATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 5 0.22
26 6 0.26
27 12 0.52
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (25 bp):
AAATAATGAATGAATAATATTATAA
Found at i:55260333 original size:29 final size:30
Alignment explanation
Indices: 55260274--55260336 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
55260264 GAATTTCAAT
* *
55260274 AAAAGAAAAGAAAGTGAAAATTATATGAAA
1 AAAAGAAAAGAAAGTGAAAATCAAATGAAA
*
55260304 AAAAG-AAAGAAAGTGAAAATCAAATTAAA
1 AAAAGAAAAGAAAGTGAAAATCAAATGAAA
55260333 AAAA
1 AAAA
55260337 AAATTTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 25 0.83
30 5 0.17
ACGTcount: A:0.70, C:0.02, G:0.14, T:0.14
Consensus pattern (30 bp):
AAAAGAAAAGAAAGTGAAAATCAAATGAAA
Found at i:55260344 original size:13 final size:13
Alignment explanation
Indices: 55260328--55260352 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55260318 GAAAATCAAA
55260328 TTAAAAAAAAAAT
1 TTAAAAAAAAAAT
55260341 TTAAAAAAAAAA
1 TTAAAAAAAAAA
55260353 AACTATTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
TTAAAAAAAAAAT
Found at i:55276424 original size:19 final size:20
Alignment explanation
Indices: 55276402--55276439 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
55276392 TTTGATCTTG
55276402 TTATCTT-TTTTTAATTTCC
1 TTATCTTATTTTTAATTTCC
* *
55276421 TTATGTTATTTTTCATTTC
1 TTATCTTATTTTTAATTTC
55276440 AAATTTAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.16, C:0.13, G:0.03, T:0.68
Consensus pattern (20 bp):
TTATCTTATTTTTAATTTCC
Found at i:55277510 original size:21 final size:21
Alignment explanation
Indices: 55277484--55277542 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
55277474 AACAGCGGTG
**
55277484 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGAAACTGTA
*
55277505 GCGGTGAGATTGGAAACTGTA
1 GCGGTGAGATTAGAAACTGTA
55277526 GCGGTGAGATTAGAAAC
1 GCGGTGAGATTAGAAAC
55277543 AATTGTGGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.29, C:0.10, G:0.36, T:0.25
Consensus pattern (21 bp):
GCGGTGAGATTAGAAACTGTA
Found at i:55279751 original size:5 final size:5
Alignment explanation
Indices: 55279741--55279788 Score: 53
Period size: 5 Copynumber: 9.6 Consensus size: 5
55279731 ATATATATAT
* * *
55279741 ATTCC ATTCC ATACT ATTCC ATGT-C ATACC ATTCC ATTCC ATTCC ATT
1 ATTCC ATTCC ATTCC ATTCC AT-TCC ATTCC ATTCC ATTCC ATTCC ATT
55279789 TTATCAAGCA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
5 34 0.97
6 1 0.03
ACGTcount: A:0.25, C:0.33, G:0.02, T:0.40
Consensus pattern (5 bp):
ATTCC
Found at i:55279787 original size:15 final size:15
Alignment explanation
Indices: 55279741--55279788 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
55279731 ATATATATAT
*
55279741 ATTCCATTCCATACT
1 ATTCCATTCCATACC
55279756 ATTCCATGT-CATACC
1 ATTCCAT-TCCATACC
*
55279771 ATTCCATTCCATTCC
1 ATTCCATTCCATACC
55279786 ATT
1 ATT
55279789 TTATCAAGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 1 0.03
15 27 0.93
16 1 0.03
ACGTcount: A:0.25, C:0.33, G:0.02, T:0.40
Consensus pattern (15 bp):
ATTCCATTCCATACC
Found at i:55280877 original size:51 final size:50
Alignment explanation
Indices: 55280691--55281133 Score: 356
Period size: 51 Copynumber: 8.8 Consensus size: 50
55280681 TCATTCGATA
* * * *
55280691 CACGTAGTAGCCTTCACATAGTACTACATACGTAATC-AATTTTTACGGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTTTT-CGGTT
* *
55280741 CACGTAGTAGCCTTCACATAGCACTACACACGTGATC-AAGTTTTACGGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTTTT-CGGTT
* * * *
55280791 CACGTAGTAGCCTTCACATAGAACTACATACGTGACTAAAGCTTTTCGGTA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAG-TTTTCGGTT
* * * * * **
55280842 CACATAGTAGCCTTCACTTAGTACTATACATGTGACCATCA-TTTATCAATT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCA-AAGTTT-TCGGTT
* *
55280893 CACGTAGTAGCCTTCACAAAGTACTACACACGTGACCAAAGTTTCTCGGTA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTTT-TCGGTT
** * * * * * *
55280944 CATATTGTAGCCTTCACTTAGTACTACGCATGTGACCATTA-TTTATCGATT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCA-AAGTTT-TCGGTT
* * * *
55280995 CACGTAGTAGCCTTCACACAGAACTACACACGTGACCAAAGCTTCTCGGTA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAG-TTTTCGGTT
* * ** * * *** * * *
55281046 CACATTGTAGCCTTCATTTAGTACTACATATGTGACCTTTCG-TTCCAGTA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACC-AAAGTTTTCGGTT
* *
55281096 CACGTAGTAGCCTACACATAGTACTACACACATGACCA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCA
55281134 TCACTTTCAC
Statistics
Matches: 308, Mismatches: 76, Indels: 19
0.76 0.19 0.05
Matches are distributed among these distances:
50 118 0.38
51 181 0.59
52 9 0.03
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (50 bp):
CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTTTTCGGTT
Found at i:55280919 original size:102 final size:102
Alignment explanation
Indices: 55280685--55281133 Score: 473
Period size: 102 Copynumber: 4.4 Consensus size: 102
55280675 CTATTATCAT
* * * * * * * *
55280685 TCGATACACGTAGTAGCCTTCACATAGTACTACATACGTAATC-AA-TTTTTACGGTTCACGTAG
1 TCGATTCACGTAGTAGCCTTCACATAGAACTACACACGTGACCAAAGCTTTT-CGGTACACATAG
* * * * ***
55280748 TAGCCTTCACATAGCACTACACACGTGATCAAGTTTTA
65 TAGCCTTCACTTAGTACTACACATGTGACCATCATTTA
* * *
55280786 -CGGTTCACGTAGTAGCCTTCACATAGAACTACATACGTGACTAAAGCTTTTCGGTACACATAGT
1 TCGATTCACGTAGTAGCCTTCACATAGAACTACACACGTGACCAAAGCTTTTCGGTACACATAGT
*
55280850 AGCCTTCACTTAGTACTATACATGTGACCATCATTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
* * * * *
55280887 TCAATTCACGTAGTAGCCTTCACAAAGTACTACACACGTGACCAAAG-TTTCTCGGTACATATTG
1 TCGATTCACGTAGTAGCCTTCACATAGAACTACACACGTGACCAAAGCTTT-TCGGTACACATAG
* *
55280951 TAGCCTTCACTTAGTACTACGCATGTGACCATTATTTA
65 TAGCCTTCACTTAGTACTACACATGTGACCATCATTTA
* * *
55280989 TCGATTCACGTAGTAGCCTTCACACAGAACTACACACGTGACCAAAGCTTCTCGGTACACATTGT
1 TCGATTCACGTAGTAGCCTTCACATAGAACTACACACGTGACCAAAGCTTTTCGGTACACATAGT
* *
55281054 AGCCTTCATTTAGTACTACATATGTGACC-T--TTCGT-
66 AGCCTTCACTTAGTACTACACATGTGACCATCATT--TA
* * * * *
55281089 TCCAGTACACGTAGTAGCCTACACATAGTACTACACACATGACCA
1 TCGA-TTCACGTAGTAGCCTTCACATAGAACTACACACGTGACCA
55281134 TCACTTTCAC
Statistics
Matches: 298, Mismatches: 42, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
99 2 0.01
100 39 0.13
101 82 0.28
102 173 0.58
103 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (102 bp):
TCGATTCACGTAGTAGCCTTCACATAGAACTACACACGTGACCAAAGCTTTTCGGTACACATAGT
AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
Found at i:55283769 original size:6 final size:6
Alignment explanation
Indices: 55283758--55283782 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
55283748 CTGTCAAAGG
55283758 TCCCTA TCCCTA TCCCTA TCCCTA T
1 TCCCTA TCCCTA TCCCTA TCCCTA T
55283783 TCTTCTACTT
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:0.16, C:0.48, G:0.00, T:0.36
Consensus pattern (6 bp):
TCCCTA
Found at i:55286358 original size:26 final size:26
Alignment explanation
Indices: 55286301--55286360 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
55286291 TGAATTTCAA
* * *
55286301 TAAAAGAAAAGAAAGTGAGAATTATAT
1 TAAAA-AAAAGAAAGTGAAAATGAAAT
*
55286328 GAAAAAAAAGAAAGTGAAAATGAAAT
1 TAAAAAAAAGAAAGTGAAAATGAAAT
55286354 TAAAAAA
1 TAAAAAA
55286361 TAAAAAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 24 0.86
27 4 0.14
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (26 bp):
TAAAAAAAAGAAAGTGAAAATGAAAT
Found at i:55286825 original size:20 final size:21
Alignment explanation
Indices: 55286797--55286844 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
55286787 TATTATTGTT
* *
55286797 ATAAGTAAAAAT-TATTATAA
1 ATAATTAAAAATCTAATATAA
55286817 ATAATT-AAAATCTAATATAA
1 ATAATTAAAAATCTAATATAA
55286837 A-AATTAAA
1 ATAATTAAA
55286845 TTTATTTACT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
ATAATTAAAAATCTAATATAA
Found at i:55286826 original size:19 final size:18
Alignment explanation
Indices: 55286804--55286861 Score: 62
Period size: 20 Copynumber: 3.0 Consensus size: 18
55286794 GTTATAAGTA
55286804 AAAATTATTATAAATAATT
1 AAAATTATTATAAA-AATT
*
55286823 AAAATCTAATATAAAAATT
1 AAAAT-TATTATAAAAATT
*
55286842 AAATTTATTTACTAAAAATT
1 AAAATTA-TTA-TAAAAATT
55286862 TGATTGCTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 2 0.06
19 15 0.45
20 16 0.48
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATTATTATAAAAATT
Found at i:55288761 original size:13 final size:13
Alignment explanation
Indices: 55288745--55288810 Score: 89
Period size: 13 Copynumber: 5.1 Consensus size: 13
55288735 TTTAAACCAA
55288745 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
55288758 ACTTCTCAAAAAC
1 ACTTTTCAAAAGC
*
55288771 ACTTTTCCACAA-C
1 ACTTTT-CAAAAGC
55288784 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
55288797 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
55288810 A
1 A
55288811 ATAAATAACT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
12 4 0.09
13 38 0.83
14 4 0.09
ACGTcount: A:0.39, C:0.27, G:0.05, T:0.29
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:55292765 original size:3 final size:3
Alignment explanation
Indices: 55292757--55292782 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
55292747 TAAAATAACA
55292757 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
55292783 AGATCAATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:55296064 original size:23 final size:23
Alignment explanation
Indices: 55296038--55296128 Score: 82
Period size: 23 Copynumber: 4.1 Consensus size: 23
55296028 TGAAAAGTTA
55296038 GAAGAGTGAAGAGACTTGAATAT
1 GAAGAGTGAAGAGACTTGAATAT
* *
55296061 GAAGAGTGAATAGACTTGAAGAT
1 GAAGAGTGAAGAGACTTGAATAT
* * * * * *
55296084 GAAAAAT-TACACAC---ATTAT
1 GAAGAGTGAAGAGACTTGAATAT
55296103 GAAGAGTGAAGAGACTTGAATAT
1 GAAGAGTGAAGAGACTTGAATAT
55296126 GAA
1 GAA
55296129 AAGTTACACA
Statistics
Matches: 49, Mismatches: 15, Indels: 8
0.68 0.21 0.11
Matches are distributed among these distances:
19 8 0.16
20 4 0.08
22 4 0.08
23 33 0.67
ACGTcount: A:0.46, C:0.07, G:0.25, T:0.22
Consensus pattern (23 bp):
GAAGAGTGAAGAGACTTGAATAT
Found at i:55296105 original size:42 final size:42
Alignment explanation
Indices: 55296058--55296141 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
55296048 GAGACTTGAA
*
55296058 TATGAAGAGTGAATAGACTTGAAGATGAAAAATTACACACAT
1 TATGAAGAGTGAAGAGACTTGAAGATGAAAAATTACACACAT
* *
55296100 TATGAAGAGTGAAGAGACTTGAATATGAAAAGTTACACACAT
1 TATGAAGAGTGAAGAGACTTGAAGATGAAAAATTACACACAT
55296142 GCATGAATAG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.24
Consensus pattern (42 bp):
TATGAAGAGTGAAGAGACTTGAAGATGAAAAATTACACACAT
Found at i:55305193 original size:42 final size:42
Alignment explanation
Indices: 55305146--55305229 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
55305136 GAGGCTTGAA
*
55305146 TATGAAGAGTGAATAGACTTGAAGATGAAAAGTTACACACAT
1 TATGAAGAGTGAAGAGACTTGAAGATGAAAAGTTACACACAT
*
55305188 TATGAAGAGTGAAGAGACTTGAATATGAAAAGTTACACACAT
1 TATGAAGAGTGAAGAGACTTGAAGATGAAAAGTTACACACAT
55305230 GCATGAATAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.45, C:0.10, G:0.21, T:0.24
Consensus pattern (42 bp):
TATGAAGAGTGAAGAGACTTGAAGATGAAAAGTTACACACAT
Found at i:55305216 original size:23 final size:23
Alignment explanation
Indices: 55305126--55305216 Score: 82
Period size: 23 Copynumber: 4.1 Consensus size: 23
55305116 TGAAAAGTTA
*
55305126 GAAGAGTGAAGAGGCTTGAATAT
1 GAAGAGTGAAGAGACTTGAATAT
* *
55305149 GAAGAGTGAATAGACTTGAAGAT
1 GAAGAGTGAAGAGACTTGAATAT
* * * * *
55305172 GAAAAGT-TACACAC---ATTAT
1 GAAGAGTGAAGAGACTTGAATAT
55305191 GAAGAGTGAAGAGACTTGAATAT
1 GAAGAGTGAAGAGACTTGAATAT
55305214 GAA
1 GAA
55305217 AAGTTACACA
Statistics
Matches: 50, Mismatches: 14, Indels: 8
0.69 0.19 0.11
Matches are distributed among these distances:
19 9 0.18
20 4 0.08
22 4 0.08
23 33 0.66
ACGTcount: A:0.44, C:0.07, G:0.27, T:0.22
Consensus pattern (23 bp):
GAAGAGTGAAGAGACTTGAATAT
Found at i:55308216 original size:20 final size:20
Alignment explanation
Indices: 55308193--55308231 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
55308183 TTTGATCTTG
*
55308193 TTATCTTTTTTTTAATTTCC
1 TTATCTTATTTTTAATTTCC
*
55308213 TTATCTTATTTTTCATTTC
1 TTATCTTATTTTTAATTTC
55308232 AAATTTAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (20 bp):
TTATCTTATTTTTAATTTCC
Found at i:55317796 original size:20 final size:20
Alignment explanation
Indices: 55317761--55317799 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
55317751 ACCACCTAAA
**
55317761 CCCAAAACCCCTTTACAAAG
1 CCCAAAACCCAATTACAAAG
55317781 CCCAAAACCCAATTACAAA
1 CCCAAAACCCAATTACAAA
55317800 TAGCCCAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.38, G:0.03, T:0.13
Consensus pattern (20 bp):
CCCAAAACCCAATTACAAAG
Found at i:55318194 original size:14 final size:13
Alignment explanation
Indices: 55318162--55318207 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
55318152 GATTTACTCC
*
55318162 TTTTATTTATCAT
1 TTTTCTTTATCAT
55318175 TTTTCTTTATCAT
1 TTTTCTTTATCAT
55318188 GTTTTC-TTA-CAT
1 -TTTTCTTTATCAT
55318200 TTTT-TTTA
1 TTTTCTTTA
55318208 ACTATTAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 7 0.23
12 3 0.10
13 15 0.50
14 5 0.17
ACGTcount: A:0.17, C:0.11, G:0.02, T:0.70
Consensus pattern (13 bp):
TTTTCTTTATCAT
Found at i:55318885 original size:3 final size:3
Alignment explanation
Indices: 55318877--55318907 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
55318867 AAGTTAGTAC
55318877 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
55318908 TATTCGGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:55319130 original size:23 final size:23
Alignment explanation
Indices: 55319099--55319145 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
55319089 TATATATATG
* *
55319099 TGTACGTATACATTTTTATATTT
1 TGTAAGTATACATATTTATATTT
*
55319122 TGTAAGTATATATATTTATATTT
1 TGTAAGTATACATATTTATATTT
55319145 T
1 T
55319146 AATATACATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.04, G:0.09, T:0.57
Consensus pattern (23 bp):
TGTAAGTATACATATTTATATTT
Found at i:55319248 original size:2 final size:2
Alignment explanation
Indices: 55319128--55319232 Score: 78
Period size: 2 Copynumber: 54.0 Consensus size: 2
55319118 ATTTTGTAAG
* * *
55319128 TA TA TA TA TT TA TA T- TT TA -A TA TA CA TA CTCA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -T-A TA TA TA TA TA
* * *
55319170 TA TA TA TA TA TA TA TA TA TA TA T- TA CA TA T- TA -A AA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
55319209 TA TA CT- TA TA TA TA TA TA TT TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA
55319233 ATTCACATAT
Statistics
Matches: 82, Mismatches: 12, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
1 6 0.07
2 72 0.88
3 3 0.04
4 1 0.01
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55328077 original size:31 final size:29
Alignment explanation
Indices: 55328042--55328105 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
55328032 TGACCGCTTC
*
55328042 GTAACAAAACAATAACATAAGTGACTAAAAT
1 GTAACAAAAC-A-AACATAAGAGACTAAAAT
***
55328073 GTAACATTTCAAACATAAGAGACTAAAAT
1 GTAACAAAACAAACATAAGAGACTAAAAT
55328102 GTAA
1 GTAA
55328106 TCTGAGGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 21 0.72
30 1 0.03
31 7 0.24
ACGTcount: A:0.55, C:0.12, G:0.11, T:0.22
Consensus pattern (29 bp):
GTAACAAAACAAACATAAGAGACTAAAAT
Found at i:55332710 original size:13 final size:13
Alignment explanation
Indices: 55332678--55332716 Score: 64
Period size: 12 Copynumber: 3.2 Consensus size: 13
55332668 CCTAGGGCCC
55332678 AAACCAAATATTA
1 AAACCAAATATTA
55332691 AAA-CAAATATTA
1 AAACCAAATATTA
55332703 AAACCAAAT-TTA
1 AAACCAAATATTA
55332715 AA
1 AA
55332717 TAGTCCACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 17 0.68
13 8 0.32
ACGTcount: A:0.64, C:0.13, G:0.00, T:0.23
Consensus pattern (13 bp):
AAACCAAATATTA
Found at i:55332811 original size:13 final size:13
Alignment explanation
Indices: 55332790--55332822 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
55332780 ACACAATCCT
*
55332790 AACCTAATACTTA
1 AACCCAATACTTA
55332803 AACCCAATACTTA
1 AACCCAATACTTA
55332816 AACCCAA
1 AACCCAA
55332823 AGCCCAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.21
Consensus pattern (13 bp):
AACCCAATACTTA
Found at i:55337826 original size:25 final size:26
Alignment explanation
Indices: 55337793--55337842 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
55337783 ATTTGTTTTA
55337793 AAATCTATTATATATTA-TTATTATG
1 AAATCTATTATATATTATTTATTATG
* * *
55337818 AAATTTATTTTGTATTATTTATTAT
1 AAATCTATTATATATTATTTATTAT
55337843 TATATATTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (26 bp):
AAATCTATTATATATTATTTATTATG
Found at i:55342042 original size:26 final size:27
Alignment explanation
Indices: 55341989--55342043 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
55341979 TATTTTATAA
*
55341989 TTTAATATAAAATATACTTTTAATTTT
1 TTTAATATAAAACATACTTTTAATTTT
* *
55342016 TTTAATAT-AAACATAGTTTTGATTTT
1 TTTAATATAAAACATACTTTTAATTTT
55342042 TT
1 TT
55342044 AATTATTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (27 bp):
TTTAATATAAAACATACTTTTAATTTT
Found at i:55342075 original size:17 final size:17
Alignment explanation
Indices: 55342046--55342091 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
55342036 GATTTTTTAA
55342046 TTATTATTTAATATATT
1 TTATTATTTAATATATT
55342063 TTATT-TTTAAATATATT
1 TTATTATTT-AATATATT
55342080 CTTAATTATTTA
1 -TT-ATTATTTA
55342092 TTTTACATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 3 0.12
17 13 0.52
18 2 0.08
19 4 0.16
20 3 0.12
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (17 bp):
TTATTATTTAATATATT
Found at i:55342079 original size:26 final size:27
Alignment explanation
Indices: 55342039--55342095 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
55342029 TAGTTTTGAT
*
55342039 TTTTTAATTATTA-T-TTAATATATTTTA
1 TTTTTAAATATTATTCTTAAT-TA-TTTA
55342066 TTTTTAAATA-TATTCTTAATTATTTA
1 TTTTTAAATATTATTCTTAATTATTTA
55342092 TTTT
1 TTTT
55342096 ACATATACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 10 0.37
27 12 0.44
28 5 0.19
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTTTAAATATTATTCTTAATTATTTA
Found at i:55344959 original size:21 final size:21
Alignment explanation
Indices: 55344935--55345005 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
55344925 ATTAATTTTT
55344935 TTATATTAATGGGTATGTTAA
1 TTATATTAATGGGTATGTTAA
* *** **
55344956 TTATATTTATTATTAATGTTTT
1 TTATATTAATGGGT-ATGTTAA
*
55344978 TTATATTAATGGGTCTGTTAA
1 TTATATTAATGGGTATGTTAA
55344999 TTATATT
1 TTATATT
55345006 TGCTATTAAT
Statistics
Matches: 36, Mismatches: 13, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
21 21 0.58
22 15 0.42
ACGTcount: A:0.30, C:0.01, G:0.13, T:0.56
Consensus pattern (21 bp):
TTATATTAATGGGTATGTTAA
Found at i:55344991 original size:43 final size:42
Alignment explanation
Indices: 55344918--55345025 Score: 171
Period size: 43 Copynumber: 2.5 Consensus size: 42
55344908 TTTAGTATAC
55344918 ATTTATTATTAATTTTTTTATATTAATGGGTATGTTAATTAT
1 ATTTATTATTAATTTTTTTATATTAATGGGTATGTTAATTAT
*
55344960 ATTTATTATTAATGTTTTTTATATTAATGGGTCTGTTAATTAT
1 ATTTATTATTAAT-TTTTTTATATTAATGGGTATGTTAATTAT
**
55345003 ATTTGCTATTAATTTTTTATATA
1 ATTTATTATTAATTTTTT-TATA
55345026 ATATTAAGAG
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
42 18 0.30
43 43 0.70
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.59
Consensus pattern (42 bp):
ATTTATTATTAATTTTTTTATATTAATGGGTATGTTAATTAT
Found at i:55345382 original size:2 final size:2
Alignment explanation
Indices: 55345377--55345416 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
55345367 AACTGCATAC
55345377 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
55345417 TTACATTGGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55347105 original size:19 final size:20
Alignment explanation
Indices: 55347081--55347119 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
55347071 AATTGTATTC
55347081 TTTATTTTTTATAA-ATAAA
1 TTTATTTTTTATAATATAAA
55347100 TTTATTTTTTATAATATAAA
1 TTTATTTTTTATAATATAAA
55347120 AATAAATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTATTTTTTATAATATAAA
Found at i:55347144 original size:29 final size:27
Alignment explanation
Indices: 55347112--55347173 Score: 70
Period size: 30 Copynumber: 2.2 Consensus size: 27
55347102 TATTTTTTAT
* *
55347112 AATATAAAAATAAATCTTTTATATTTAAA
1 AATATAAAAATAAAT-ATATATA-TTAAA
*
55347141 AATAGTGAAAATAAATATATATATTAAA
1 AATA-TAAAAATAAATATATATATTAAA
55347169 AATAT
1 AATAT
55347174 TATATAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 1 0.03
28 9 0.31
29 9 0.31
30 10 0.34
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (27 bp):
AATATAAAAATAAATATATATATTAAA
Found at i:55350574 original size:3 final size:3
Alignment explanation
Indices: 55350568--55350611 Score: 72
Period size: 3 Copynumber: 14.7 Consensus size: 3
55350558 TGGATAAGAT
55350568 TTA TTA TTA TTA TTA TTA -TA TTTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TT
55350612 TACTTTGGGC
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.90
4 2 0.05
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:55357403 original size:22 final size:21
Alignment explanation
Indices: 55357378--55357425 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
55357368 TTTAATTTAT
* *
55357378 AAATAATTTTTTTATAATATAA
1 AAATAAATCTTTTAT-ATATAA
*
55357400 AAATAAATCTTTTATATTTAA
1 AAATAAATCTTTTATATATAA
55357421 AAATA
1 AAATA
55357426 GTGAAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATAAATCTTTTATATATAA
Found at i:55364234 original size:18 final size:19
Alignment explanation
Indices: 55364208--55364247 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
55364198 TCACATCAAT
55364208 AAATAATTTA-AAAAATATA
1 AAATAATTTATAAAAA-ATA
55364227 AAAT-ATTTATAAAAAATA
1 AAATAATTTATAAAAAATA
55364245 AAA
1 AAA
55364248 ATAAAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AAATAATTTATAAAAAATA
Found at i:55364854 original size:25 final size:24
Alignment explanation
Indices: 55364819--55364876 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
55364809 TTTTAATTAC
*
55364819 CAAGTTTTTTTATTAAG-TTTTGCAT
1 CAAGTTCTTTT-TTAAGCTTTT-CAT
55364844 CAAGTTC-TTTTTAAGCTTTTCAT
1 CAAGTTCTTTTTTAAGCTTTTCAT
55364867 CAAG-TCTTTT
1 CAAGTTCTTTT
55364877 CATCAAGTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 2 0.07
23 15 0.50
24 7 0.23
25 6 0.20
ACGTcount: A:0.22, C:0.14, G:0.10, T:0.53
Consensus pattern (24 bp):
CAAGTTCTTTTTTAAGCTTTTCAT
Found at i:55364877 original size:13 final size:13
Alignment explanation
Indices: 55364859--55364910 Score: 61
Period size: 13 Copynumber: 4.0 Consensus size: 13
55364849 TCTTTTTAAG
55364859 CTTTTCATCAAGT
1 CTTTTCATCAAGT
55364872 CTTTTCATCAAGT
1 CTTTTCATCAAGT
* * *
55364885 GTTTTTAATTAAGT
1 -CTTTTCATCAAGT
55364899 C-TTTCATCAAGT
1 CTTTTCATCAAGT
55364911 TTTCATCTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
12 9 0.28
13 13 0.41
14 10 0.31
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.48
Consensus pattern (13 bp):
CTTTTCATCAAGT
Found at i:55375723 original size:17 final size:18
Alignment explanation
Indices: 55375675--55375726 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
55375665 AGGCATTTGA
*
55375675 TTGTTTGTTTCTTTGTTTC
1 TTGTTT-TTTCTCTGTTTC
*
55375694 TT-TATTTTGCTCTGTTT-
1 TTGT-TTTTTCTCTGTTTC
55375711 TTGTTTTTTCTCTGTT
1 TTGTTTTTTCTCTGTT
55375727 GGTGCTTGCC
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 13 0.46
18 11 0.39
19 4 0.14
ACGTcount: A:0.02, C:0.12, G:0.13, T:0.73
Consensus pattern (18 bp):
TTGTTTTTTCTCTGTTTC
Found at i:55378386 original size:14 final size:14
Alignment explanation
Indices: 55378367--55378396 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
55378357 AATAAATATA
*
55378367 TATTTTTTTATTTT
1 TATTTTTTTAATTT
55378381 TATTTTTTTAATTT
1 TATTTTTTTAATTT
55378395 TA
1 TA
55378397 AAATACTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (14 bp):
TATTTTTTTAATTT
Found at i:55378844 original size:6 final size:6
Alignment explanation
Indices: 55378828--55378870 Score: 56
Period size: 5 Copynumber: 7.5 Consensus size: 6
55378818 TTATTATGTT
55378828 TTTTTA TTTTTTA TTTTTA TTTTTA -TTTTA -TTTTA -TTTTA TTT
1 TTTTTA -TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTT
55378871 ATCAACTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 15 0.43
6 14 0.40
7 6 0.17
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:55389575 original size:21 final size:22
Alignment explanation
Indices: 55389523--55389575 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
55389513 ACAATTATTA
55389523 TTTTTTATTTCTTGTTATACTT
1 TTTTTTATTTCTTGTTATACTT
**
55389545 TTTTGAATTTCTT-TTAT-CTT
1 TTTTTTATTTCTTGTTATACTT
55389565 TTCTTTTATTT
1 TT-TTTTATTT
55389576 TAATTTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 5 0.19
21 10 0.38
22 11 0.42
ACGTcount: A:0.13, C:0.09, G:0.04, T:0.74
Consensus pattern (22 bp):
TTTTTTATTTCTTGTTATACTT
Found at i:55390627 original size:6 final size:6
Alignment explanation
Indices: 55390616--55390661 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
55390606 GTTTATTTTC
55390616 TAATTT TAATTT TAATTT TAATTT TAATTT TAATTT TAATTT TAAT
1 TAATTT TAATTT TAATTT TAATTT TAATTT TAATTT TAATTT TAAT
55390662 AATATGATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
TAATTT
Found at i:55400476 original size:76 final size:75
Alignment explanation
Indices: 55400389--55400530 Score: 212
Period size: 76 Copynumber: 1.9 Consensus size: 75
55400379 AAATCATTTC
** ** * * *
55400389 ATTTTTATGGGGGTTAAAGTGTAATTTTACTATATATTAATTTATAATTTCTTTATTTATAAGAA
1 ATTTTTATGGGGGCCAAAGTACAATTTTACTATATATTAATTTATAACTTCTCTAGTTATAA-AA
55400454 GACTAGAAAAA
65 GACTAGAAAAA
55400465 ATTTTTATGGGGGCCAAAGTACAATTTTACTATATATTAATTTATAACTTCTCTAGTTATAAAAG
1 ATTTTTATGGGGGCCAAAGTACAATTTTACTATATATTAATTTATAACTTCTCTAGTTATAAAAG
55400530 A
66 A
55400531 ACTAAGTTAA
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
75 4 0.07
76 55 0.93
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (75 bp):
ATTTTTATGGGGGCCAAAGTACAATTTTACTATATATTAATTTATAACTTCTCTAGTTATAAAAG
ACTAGAAAAA
Found at i:55402030 original size:4 final size:4
Alignment explanation
Indices: 55402021--55402049 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
55402011 AGAAAAAATG
55402021 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
55402050 ACTTGAAAAT
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:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:55415532 original size:14 final size:15
Alignment explanation
Indices: 55415513--55415547 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
55415503 GATATATGTC
55415513 TTTATTTTTTAA-AT
1 TTTATTTTTTAATAT
55415527 TTTATTTTTTAATAT
1 TTTATTTTTTAATAT
55415542 TTTATT
1 TTTATT
55415548 ATACCTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTATTTTTTAATAT
Found at i:55434582 original size:22 final size:22
Alignment explanation
Indices: 55434554--55434603 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
55434544 TAATTTTTTT
55434554 CTTCTTTTCTTCTGCTTCCTTC
1 CTTCTTTTCTTCTGCTTCCTTC
55434576 CTTCTTTTCTTCTGCTTCCTTC
1 CTTCTTTTCTTCTGCTTCCTTC
55434598 CTTCTT
1 CTTCTT
55434604 CTTTCTTCCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.00, C:0.36, G:0.04, T:0.60
Consensus pattern (22 bp):
CTTCTTTTCTTCTGCTTCCTTC
Found at i:55434718 original size:27 final size:27
Alignment explanation
Indices: 55434669--55434771 Score: 154
Period size: 27 Copynumber: 3.8 Consensus size: 27
55434659 AAAATCACAG
**
55434669 CATTGGCGCCTTTCAG-TATGGCACCAC
1 CATTGGCGCCTCCCAGATA-GGCACCAC
55434696 CATTGGCGCCTCCCAGATAGGCACCAC
1 CATTGGCGCCTCCCAGATAGGCACCAC
*
55434723 CATTGGCGCCTCCCAAATAGGCACCAC
1 CATTGGCGCCTCCCAGATAGGCACCAC
*
55434750 CATTGGCGCCTTCCAGATAGGC
1 CATTGGCGCCTCCCAGATAGGC
55434772 GCCAATACTA
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
27 68 0.97
28 2 0.03
ACGTcount: A:0.21, C:0.37, G:0.22, T:0.19
Consensus pattern (27 bp):
CATTGGCGCCTCCCAGATAGGCACCAC
Found at i:55436134 original size:20 final size:20
Alignment explanation
Indices: 55436089--55436136 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
55436079 TTTGCACCAA
*
55436089 GATGCACCTTATGTGCCAGT
1 GATGCACTTTATGTGCCAGT
*
55436109 -ATGCACTTTGTGTGCCAGT
1 GATGCACTTTATGTGCCAGT
55436128 GATGCACTT
1 GATGCACTT
55436137 CGAGCACCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.19, C:0.23, G:0.25, T:0.33
Consensus pattern (20 bp):
GATGCACTTTATGTGCCAGT
Found at i:55436764 original size:28 final size:28
Alignment explanation
Indices: 55436703--55436765 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 28
55436693 CGCGATTTCG
*
55436703 TGAAAAATGGCCCATTCCGGTAAATAAT
1 TGAAAAACGGCCCATTCCGGTAAATAAT
* *
55436731 TAAAAAACCGGCCCATTCCGGTAAAT-TT
1 TGAAAAA-CGGCCCATTCCGGTAAATAAT
55436759 TGAAAAA
1 TGAAAAA
55436766 AAACGGCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 13 0.43
29 17 0.57
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (28 bp):
TGAAAAACGGCCCATTCCGGTAAATAAT
Found at i:55440399 original size:15 final size:16
Alignment explanation
Indices: 55440379--55440411 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
55440369 TTGATATGTC
55440379 TTTATTTTTTAA-ATT
1 TTTATTTTTTAATATT
55440394 TTTATTTTTTAATATT
1 TTTATTTTTTAATATT
55440410 TT
1 TT
55440412 ATTATACCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTATTTTTTAATATT
Found at i:55443159 original size:16 final size:18
Alignment explanation
Indices: 55443127--55443162 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
55443117 TGTAATGTTT
55443127 TATATTATGTTATATTTA
1 TATATTATGTTATATTTA
55443145 TATATTAT-TTA-ATTTA
1 TATATTATGTTATATTTA
55443161 TA
1 TA
55443163 ACACATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 3 0.17
18 8 0.44
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
TATATTATGTTATATTTA
Found at i:55448589 original size:3 final size:3
Alignment explanation
Indices: 55448581--55448608 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
55448571 AACGGATTCT
55448581 ACC ACC ACC ACC ACC ACC ACC ACC ACC A
1 ACC ACC ACC ACC ACC ACC ACC ACC ACC A
55448609 TCGATAGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.64, G:0.00, T:0.00
Consensus pattern (3 bp):
ACC
Found at i:55451254 original size:19 final size:19
Alignment explanation
Indices: 55451232--55451275 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
55451222 GCTTATATTG
55451232 TTTTTGTAATTTTATAAT-A
1 TTTTTGT-ATTTTATAATAA
* *
55451251 TTTTTCTATTTTTTAATAA
1 TTTTTGTATTTTATAATAA
55451270 TTTTTG
1 TTTTTG
55451276 AAAAATTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTTTGTATTTTATAATAA
Found at i:55456743 original size:22 final size:22
Alignment explanation
Indices: 55456698--55456743 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
55456688 CTTTTTAAAA
* *
55456698 AAAAATTATAAATTAATCTCTT
1 AAAAATTATAAATTAATATATT
*
55456720 AAAAATTATAAATTTATATATT
1 AAAAATTATAAATTAATATATT
55456742 AA
1 AA
55456744 TATAATGAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAAATTATAAATTAATATATT
Found at i:55459876 original size:31 final size:31
Alignment explanation
Indices: 55459824--55459882 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
55459814 ACCTAATGAT
55459824 TTAAATAAAAACTTTCAAATAGTTCAGTGAC
1 TTAAATAAAAACTTTCAAATAGTTCAGTGAC
**
55459855 TTAAATGAAAAA-TTTTGAATAGTTCAGT
1 TTAAAT-AAAAACTTTCAAATAGTTCAGT
55459883 AACTGTTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (31 bp):
TTAAATAAAAACTTTCAAATAGTTCAGTGAC
Found at i:55465193 original size:26 final size:26
Alignment explanation
Indices: 55465138--55465194 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
55465128 TTTTTTTGTT
**
55465138 AATTTGGTAATTATATTTTAAAGTTA
1 AATTTGGTAATTATATTTTAAAGAAA
*
55465164 AATTTGGTAATTATTTTTTAAA-AAA
1 AATTTGGTAATTATATTTTAAAGAAA
55465189 GAATTT
1 -AATTT
55465195 TTTTAAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 1 0.04
26 26 0.96
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (26 bp):
AATTTGGTAATTATATTTTAAAGAAA
Found at i:55465196 original size:15 final size:15
Alignment explanation
Indices: 55465176--55465205 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
55465166 TTTGGTAATT
55465176 ATTTTTTAAAAAAGA
1 ATTTTTTAAAAAAGA
*
55465191 ATTTTTTTAAAAAGA
1 ATTTTTTAAAAAAGA
55465206 GTTGAATTTT
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:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (15 bp):
ATTTTTTAAAAAAGA
Done.