Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006484.1 Hibiscus syriacus cultivar Beakdansim tig00015746_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 143820
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:469 original size:30 final size:30
Alignment explanation
Indices: 433--539 Score: 117
Period size: 30 Copynumber: 3.6 Consensus size: 30
423 ATTCTTGACA
* * *
433 TTGCATGTGACTTCGTTCCCCATCATGATT
1 TTGCATGGGACTTCGTTCCCTATCCTGATT
* * * *
463 TTGCATGGGATTTCATT-CCTGTCCCGATT
1 TTGCATGGGACTTCGTTCCCTATCCTGATT
* *
492 CTGCATGGGACTTCGTTCCTTATCCTGATT
1 TTGCATGGGACTTCGTTCCCTATCCTGATT
*
522 TTGCATGAGACTTCGTTC
1 TTGCATGGGACTTCGTTC
540 TCTGTCATTT
Statistics
Matches: 61, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 22 0.36
30 39 0.64
ACGTcount: A:0.15, C:0.25, G:0.20, T:0.40
Consensus pattern (30 bp):
TTGCATGGGACTTCGTTCCCTATCCTGATT
Found at i:639 original size:31 final size:30
Alignment explanation
Indices: 556--652 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 30
546 ATTTTGTATT
* * *
556 GGACCTTGTT-CTCGTCCCGATTCTGCATA
1 GGACCTTGTTCCCCGTCCTGATTCTGCATG
*
585 GGACCTTGTTCCCCGT-CTCGATTCTACATG
1 GGACCTTGTTCCCCGTCCT-GATTCTGCATG
615 GGA-CTTCGTTCCCCCGTCCTGATTCTGCATG
1 GGACCTT-GTT-CCCCGTCCTGATTCTGCATG
646 GGTACCT
1 GG-ACCT
653 CTTCAGAGGG
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
29 14 0.25
30 19 0.34
31 18 0.32
32 3 0.05
33 2 0.04
ACGTcount: A:0.12, C:0.33, G:0.22, T:0.33
Consensus pattern (30 bp):
GGACCTTGTTCCCCGTCCTGATTCTGCATG
Found at i:3508 original size:38 final size:39
Alignment explanation
Indices: 3455--3534 Score: 101
Period size: 38 Copynumber: 2.1 Consensus size: 39
3445 GAATAACATG
* **
3455 AAAACAGTTTCCTTATGA-GGAGCATCATCAGTATCACAA
1 AAAACAGTTTCCTTATGATGG-CCATCATCACCATCACAA
*
3494 AAAAC-GTTTTCTTATGATGGCCATCATCACCATCACAA
1 AAAACAGTTTCCTTATGATGGCCATCATCACCATCACAA
3532 AAA
1 AAA
3535 GCATTGGATC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 29 0.81
39 7 0.19
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (39 bp):
AAAACAGTTTCCTTATGATGGCCATCATCACCATCACAA
Found at i:4119 original size:138 final size:138
Alignment explanation
Indices: 3863--4122 Score: 414
Period size: 138 Copynumber: 1.9 Consensus size: 138
3853 TAAGTGATGT
**
3863 CAAATGATTGAGGCAAGGAAGTTCATCCAAACTTTTGCATGACCTACAGTCAAGGATTTTAAGGT
1 CAAATGATCAAGGCAAGGAAGTTCATCCAAACTTTTGCATGACCTACAGTCAAGGATTTTAAGGT
* * **
3928 TGTTGGCTCCTAATAGATTTGGAATCTTACTTAAATTCTTGCAACCAGAAAGGTCAAGTCTTTCA
66 TGATGGCTCCCAATAGATTTGGAATCTTACTTAAATTCTTGCAAAAAGAAAGGTCAAGTCTTTCA
3993 AGAGATTC
131 AGAGATTC
*
4001 CAAATGATCAAGGCAAGGAAGTTCATCCAACCTTTTGCATGACCTACAGTCAAGGATTTTAAGGT
1 CAAATGATCAAGGCAAGGAAGTTCATCCAAACTTTTGCATGACCTACAGTCAAGGATTTTAAGGT
* * *
4066 TGATGGCTCCCGATAGATTTGGCATCTTCCTTAAATTCTTGCAAAAA-AGAAGGTCAA
66 TGATGGCTCCCAATAGATTTGGAATCTTACTTAAATTCTTGCAAAAAGA-AAGGTCAA
4123 TTTTCTTCAA
Statistics
Matches: 111, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
137 1 0.01
138 110 0.99
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (138 bp):
CAAATGATCAAGGCAAGGAAGTTCATCCAAACTTTTGCATGACCTACAGTCAAGGATTTTAAGGT
TGATGGCTCCCAATAGATTTGGAATCTTACTTAAATTCTTGCAAAAAGAAAGGTCAAGTCTTTCA
AGAGATTC
Found at i:7846 original size:26 final size:26
Alignment explanation
Indices: 7772--7846 Score: 66
Period size: 26 Copynumber: 2.9 Consensus size: 26
7762 TTAACTATTT
*
7772 CAATAATTAAAATTTAT-TTTAATAA
1 CAATAATTAAAATTTATATTTTATAA
* *
7797 CAAAAATTCAAAA--TAAATTATTATAA
1 CAATAATT-AAAATTTATATT-TTATAA
**
7823 TTATAATTAAAATTTATATTTTAT
1 CAATAATTAAAATTTATATTTTAT
7847 TTTATTTTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
24 2 0.05
25 13 0.34
26 18 0.47
27 5 0.13
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (26 bp):
CAATAATTAAAATTTATATTTTATAA
Found at i:10267 original size:65 final size:62
Alignment explanation
Indices: 10130--10269 Score: 174
Period size: 64 Copynumber: 2.2 Consensus size: 62
10120 CAATATTGCC
*
10130 ATAAGATTGTAATTGATAAAAATTAATGAGAATAAAACAGACATATGAAAATAATTGAAACG
1 ATAAGATTGTAATTGATAAAAATTAATGAGAATAAAACAGACATATGAAAACAATTGAAACG
** * * *
10192 ATAAGATTGTAACTT-ATAAAAATGATAATGAGAATTGAATAGACATTTGAATAACAATTGAACC
1 ATAAGATTGTAA-TTGATAAAAAT--TAATGAGAATAAAACAGACATATGAA-AACAATTGAAAC
10256 G
62 G
*
10257 ATAAGGTTGTAAT
1 ATAAGATTGTAAT
10270 CGGTTAAGAA
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
62 20 0.30
63 2 0.03
64 23 0.34
65 22 0.33
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.29
Consensus pattern (62 bp):
ATAAGATTGTAATTGATAAAAATTAATGAGAATAAAACAGACATATGAAAACAATTGAAACG
Found at i:15518 original size:29 final size:31
Alignment explanation
Indices: 15476--15542 Score: 77
Period size: 29 Copynumber: 2.2 Consensus size: 31
15466 TAAATTTATC
15476 ATTAAATTGTATCAA-ATTGTTAAAAAA-TT
1 ATTAAATTGTATCAATATTGTTAAAAAAGTT
* *
15505 ATTAAATT-TCATCAATTTTTTTAAAAAATGTT
1 ATTAAATTGT-ATCAATATTGTTAAAAAA-GTT
15537 ATTAAA
1 ATTAAA
15543 ATATTTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 1 0.03
29 13 0.41
30 10 0.31
32 8 0.25
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.45
Consensus pattern (31 bp):
ATTAAATTGTATCAATATTGTTAAAAAAGTT
Found at i:21920 original size:28 final size:28
Alignment explanation
Indices: 21838--21935 Score: 90
Period size: 28 Copynumber: 3.4 Consensus size: 28
21828 ACAATAAATG
*
21838 ACTTTTATAAATTACAATATACA-ACACAA
1 ACTTTTATAAATTACAATA-AAAGACA-AA
* * * * *
21867 ATTTTTATAAATCACATTTAAGGACAAA
1 ACTTTTATAAATTACAATAAAAGACAAA
*
21895 ACTTTTATAAATTACACTAAAAGACAAA
1 ACTTTTATAAATTACAATAAAAGACAAA
21923 ACATTTTAGTAAA
1 AC-TTTTA-TAAA
21936 AGGACAAAAC
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
28 28 0.51
29 23 0.42
30 4 0.07
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (28 bp):
ACTTTTATAAATTACAATAAAAGACAAA
Found at i:21950 original size:21 final size:20
Alignment explanation
Indices: 21912--21949 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
21902 TAAATTACAC
21912 TAAAAGACAAAACATTTTAG
1 TAAAAGACAAAACATTTTAG
21932 TAAAAGGACAAAAC-TTTT
1 TAAAA-GACAAAACATTTT
21950 TTAAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.26
Consensus pattern (20 bp):
TAAAAGACAAAACATTTTAG
Found at i:21972 original size:51 final size:48
Alignment explanation
Indices: 21886--21985 Score: 119
Period size: 51 Copynumber: 2.0 Consensus size: 48
21876 AATCACATTT
* * *
21886 AAGGACAAAACTTTTATAAATTACACTAAAAGACAAAACATTTTAGTAA
1 AAGGACAAAACTTTTAAAAATTAAAATAAAAGACAAAACATTTTA-TAA
* * *
21935 AAGGACAAAACTTTTTTAAAAATTAAAATTAAGGACAAAACTTTTTATAA
1 AAGGACAAAAC--TTTTAAAAATTAAAATAAAAGACAAAACATTTTATAA
21985 A
1 A
21986 TTAAAATTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
49 11 0.26
50 4 0.09
51 28 0.65
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.29
Consensus pattern (48 bp):
AAGGACAAAACTTTTAAAAATTAAAATAAAAGACAAAACATTTTATAA
Found at i:21989 original size:29 final size:29
Alignment explanation
Indices: 21935--22017 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
21925 ATTTTAGTAA
*
21935 AAGGACAAAACTTTTTTAAAAATTAAAATT
1 AAGGACAAAAC-TTTTTATAAATTAAAATT
21965 AAGGACAAAACTTTTTATAAATTAAAATT
1 AAGGACAAAACTTTTTATAAATTAAAATT
* *
21994 AAGGATAAAACCTTTTATAAATTA
1 AAGGACAAAACTTTTTATAAATTA
22018 TAATAGATAC
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 39 0.78
30 11 0.22
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (29 bp):
AAGGACAAAACTTTTTATAAATTAAAATT
Found at i:22038 original size:29 final size:29
Alignment explanation
Indices: 21935--22046 Score: 122
Period size: 29 Copynumber: 3.8 Consensus size: 29
21925 ATTTTAGTAA
* *
21935 AAGGACAAAACTTTTTTAAAAATTAAAATT
1 AAGGATAAAAC-TTTTTATAAATTAAAATT
*
21965 AAGGACAAAACTTTTTATAAATTAAAATT
1 AAGGATAAAACTTTTTATAAATTAAAATT
* *
21994 AAGGATAAAACCTTTTATAAATTATAA-T
1 AAGGATAAAACTTTTTATAAATTAAAATT
22022 -A-GATACCACAACTTTTTATAAATTA
1 AAGGATA--A-AACTTTTTATAAATTA
22047 CATTAAAGGA
Statistics
Matches: 74, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
26 4 0.05
27 1 0.01
28 2 0.03
29 56 0.76
30 11 0.15
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.35
Consensus pattern (29 bp):
AAGGATAAAACTTTTTATAAATTAAAATT
Found at i:31372 original size:21 final size:21
Alignment explanation
Indices: 31347--31391 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
31337 AATAAAATAA
* *
31347 TTACCGATAATATTATTATTT
1 TTACCGAAAATATCATTATTT
* *
31368 TTACCTAAAATATCATTTTTT
1 TTACCGAAAATATCATTATTT
31389 TTA
1 TTA
31392 ATATTTTCGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.11, G:0.02, T:0.53
Consensus pattern (21 bp):
TTACCGAAAATATCATTATTT
Found at i:33770 original size:23 final size:23
Alignment explanation
Indices: 33735--33784 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
33725 TCATCTAGGG
* *
33735 AAAAAATTATCTATAATTAAGTAT
1 AAAAAATTATCTA-AAATAAATAT
*
33759 AAAAGATT-TCTAAAATAAATAT
1 AAAAAATTATCTAAAATAAATAT
33781 AAAA
1 AAAA
33785 TGTTGTTCGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 12 0.52
23 4 0.17
24 7 0.30
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (23 bp):
AAAAAATTATCTAAAATAAATAT
Found at i:35162 original size:131 final size:135
Alignment explanation
Indices: 34928--35196 Score: 438
Period size: 131 Copynumber: 2.0 Consensus size: 135
34918 CATTCTGCTA
* * *
34928 CAGAAACAAGCACAAGGAGATCAAAGCGGCACAGGATCACAGGTGATTGGAACTTAGCAGTACAT
1 CAGAAACAAGAACAAGGAGATCAAAGCGGCACAGGATCACAGGTGATTGGAACTTAGAAATACAT
*
34993 TTGCTTCTCTATGACATCTGATAACTGCACAAATAAA-T-TA-TAGCTAATCTCTTGTTATATC-
66 TTGCTTCTCTATGACATCTGACAACTGCACAAATAAATTATATTAGCTAATCTCTTGTTATATCA
35054 TTATG
131 TTATG
*
35059 CAGAAACAAGAACAAGGAGATCAAAGCGGCACAGGGTCACAGGTGATTGGAACTTAGAAATACAT
1 CAGAAACAAGAACAAGGAGATCAAAGCGGCACAGGATCACAGGTGATTGGAACTTAGAAATACAT
* *
35124 TTGCTTCTCTATTACATCTGACAACTGCACAAATAAATTAGTATTAGTTAATCTCTTGTTATATC
66 TTGCTTCTCTATGACATCTGACAACTGCACAAATAAATTA-TATTAGCTAATCTCTTGTTATATC
35189 ATTATG
130 ATTATG
35195 CA
1 CA
35197 CGGAATTGAG
Statistics
Matches: 126, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
131 96 0.76
132 1 0.01
134 2 0.02
135 20 0.16
136 7 0.06
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (135 bp):
CAGAAACAAGAACAAGGAGATCAAAGCGGCACAGGATCACAGGTGATTGGAACTTAGAAATACAT
TTGCTTCTCTATGACATCTGACAACTGCACAAATAAATTATATTAGCTAATCTCTTGTTATATCA
TTATG
Found at i:38368 original size:21 final size:21
Alignment explanation
Indices: 38351--38393 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
38341 CATTTTTCAG
38351 TTAAATAGATTAAATTTTAGA
1 TTAAATAGATTAAATTTTAGA
* *
38372 TTAAATATATTAAATTATAGA
1 TTAAATAGATTAAATTTTAGA
38393 T
1 T
38394 GGATGACCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (21 bp):
TTAAATAGATTAAATTTTAGA
Found at i:45444 original size:135 final size:132
Alignment explanation
Indices: 44881--45548 Score: 1068
Period size: 132 Copynumber: 5.0 Consensus size: 132
44871 CATTCTGCTA
* * * *
44881 CAGAAACAAGCACAAGGAGATCAAAGCGGCACAGGATCACAGGTGATTGGAACTTAGCAGTACAT
1 CAGAAACAAGAACAAGGAGATCAAAGCGGCACAGGGTCACAGGTGATTGGAACTTAGAAATACAT
*
44946 TTGCTTCTCTATGACATCTGATAACTGCACAAATAAATTA-TAGTTAATCTCTTGTTATATCTTA
66 TTGCTTCTCTATTACATCTGATAACTGCACAAATAAATTATTAGTTAATCTCTTGTTATATCTTA
45010 TG
131 TG
45012 CAGAAACAAGAACAAGGAGATCAAAGCGGCACAGGGTCACAGGTGATTGGAACTTAGAAATACAT
1 CAGAAACAAGAACAAGGAGATCAAAGCGGCACAGGGTCACAGGTGATTGGAACTTAGAAATACAT
* * * **
45077 TTGCTTCTCTATTACACCTGATAACTGCACAGATAAATTATTAGTTAATTTCTTGTTATATCAGA
66 TTGCTTCTCTATTACATCTGATAACTGCACAAATAAATTATTAGTTAATCTCTTGTTATATCTTA
45142 TG
131 TG
* * * *
45144 CAGAAACAAGAACAAGGAGATCAAAACGGCACAGGGTTACGGGTGATTGGAACTTAGAAATATAT
1 CAGAAACAAGAACAAGGAGATCAAAGCGGCACAGGGTCACAGGTGATTGGAACTTAGAAATACAT
*
45209 TTGCTTCTCTATTACATCTGATAACTGCACAAATAAATTATTAGTTAATTTCTTGTTATATCTTA
66 TTGCTTCTCTATTACATCTGATAACTGCACAAATAAATTATTAGTTAATCTCTTGTTATATCTTA
45274 TG
131 TG
* *
45276 CAGAAACAAGAACGAGGAGATCAAATCGGCACAGGGTCACAGGTGATTGGAACTTAGAAATACAT
1 CAGAAACAAGAACAAGGAGATCAAAGCGGCACAGGGTCACAGGTGATTGGAACTTAGAAATACAT
*
45341 TTGCTTCTCTATTACATCTGACAACTGCACAAATAAATTAGTATTAGTTAATCTCTTGTTATATC
66 TTGCTTCTCTATTACATCTGATAACTGCACAAATAAA-T--TATTAGTTAATCTCTTGTTATATC
45406 TTATG
128 TTATG
* *
45411 CAGAAACAAGAACGAGGAGATCAAATCGGCACAGGGTCACAGGTGATTGGAACTTAGAAATACAT
1 CAGAAACAAGAACAAGGAGATCAAAGCGGCACAGGGTCACAGGTGATTGGAACTTAGAAATACAT
* *
45476 TTACTTCTCTATTACATCTGACAACTGCACAAATAAATTAGTATTAGTTAATCTCTTGTTATATC
66 TTGCTTCTCTATTACATCTGATAACTGCACAAATAAA-T--TATTAGTTAATCTCTTGTTATATC
45541 ATTATG
128 -TTATG
45547 CA
1 CA
45549 CGGAATTGAG
Statistics
Matches: 506, Mismatches: 26, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
131 98 0.19
132 243 0.48
133 1 0.00
135 157 0.31
136 7 0.01
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (132 bp):
CAGAAACAAGAACAAGGAGATCAAAGCGGCACAGGGTCACAGGTGATTGGAACTTAGAAATACAT
TTGCTTCTCTATTACATCTGATAACTGCACAAATAAATTATTAGTTAATCTCTTGTTATATCTTA
TG
Found at i:50185 original size:58 final size:55
Alignment explanation
Indices: 50115--50228 Score: 165
Period size: 58 Copynumber: 2.0 Consensus size: 55
50105 GGTTCCCGTT
*
50115 AAGGGTTATTCAATGTCGATAATATTAGAATAAAATTGAATGTTTTTGGAGTTAGGTG
1 AAGGCTTATTCAATGTCGATAATATTAG--TAAAATTGAAT-TTTTTGGAGTTAGGTG
** *
50173 AAGGCTTATTCAATGTCGATAATATTAGTGTATTTGAATTTTTTGGAGTTAGGTG
1 AAGGCTTATTCAATGTCGATAATATTAGTAAAATTGAATTTTTTGGAGTTAGGTG
50228 A
1 A
50229 CTAAAATATA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
55 17 0.33
56 8 0.15
58 27 0.52
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (55 bp):
AAGGCTTATTCAATGTCGATAATATTAGTAAAATTGAATTTTTTGGAGTTAGGTG
Found at i:51865 original size:64 final size:65
Alignment explanation
Indices: 51753--51912 Score: 211
Period size: 64 Copynumber: 2.5 Consensus size: 65
51743 GTGCACCAAG
* *
51753 TGTGCATCGATGCATAAAATGCACTCGATG-TTTGAAAATAGCCTGAGTGCATCGATGCAT-GAC
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCGATGCATGGA-
51816 T
65 T
* *
51817 TGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCC-GAGTGCATCGATGCATGGA
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATAGCCTGAGTGCATCGATGCATGGA
51880 T
65 T
* * *
51881 AGTGCATCGATGCATGAAATGCATTTGATGTT
1 TGTGCATCGATGCATAAAATGCATTCGATGTT
51913 CAATTAATTC
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
64 74 0.86
65 9 0.10
66 3 0.03
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (65 bp):
TGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCGATGCATGGAT
Found at i:53012 original size:21 final size:21
Alignment explanation
Indices: 52986--53029 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
52976 CTGGAGGAGG
52986 AGGAGGAGCACGAGAAGAACT
1 AGGAGGAGCACGAGAAGAACT
**
53007 AGGAGGAGCTTGAGAAGAACT
1 AGGAGGAGCACGAGAAGAACT
53028 AG
1 AG
53030 CTCATGGAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.39, T:0.09
Consensus pattern (21 bp):
AGGAGGAGCACGAGAAGAACT
Found at i:53853 original size:21 final size:21
Alignment explanation
Indices: 53829--53868 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
53819 TTAATAGGCT
*
53829 ATTAGGAGATTGAGGAACGAG
1 ATTAGGAGATGGAGGAACGAG
*
53850 ATTAGGAGGTGGAGGAACG
1 ATTAGGAGATGGAGGAACG
53869 GGAGGACGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.05, G:0.42, T:0.17
Consensus pattern (21 bp):
ATTAGGAGATGGAGGAACGAG
Found at i:55499 original size:20 final size:20
Alignment explanation
Indices: 55474--55513 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
55464 AGAGATGTCA
55474 TTGAATATGC-TATAAAGAAG
1 TTGAATA-GCATATAAAGAAG
*
55494 TTGAATAGCATATCAAGAAG
1 TTGAATAGCATATAAAGAAG
55514 CGCTTCTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.45, C:0.07, G:0.20, T:0.28
Consensus pattern (20 bp):
TTGAATAGCATATAAAGAAG
Found at i:58927 original size:16 final size:16
Alignment explanation
Indices: 58906--58938 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
58896 TAATAAATAA
58906 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
58922 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
58938 A
1 A
58939 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:59019 original size:10 final size:10
Alignment explanation
Indices: 59004--59071 Score: 58
Period size: 10 Copynumber: 7.1 Consensus size: 10
58994 CATTTAATAA
59004 ATAAACGAAC
1 ATAAACGAAC
59014 ATAAACG-A-
1 ATAAACGAAC
59022 AT--ACGAAC
1 ATAAACGAAC
*
59030 --GAACGAAC
1 ATAAACGAAC
59038 ATAAACGAACAC
1 ATAAACG-A-AC
59050 AATAAACGAAC
1 -ATAAACGAAC
59061 ATAAACGAAC
1 ATAAACGAAC
59071 A
1 A
59072 ACACAAACAC
Statistics
Matches: 48, Mismatches: 1, Indels: 18
0.72 0.01 0.27
Matches are distributed among these distances:
6 3 0.06
7 1 0.02
8 8 0.17
9 1 0.02
10 22 0.46
11 3 0.06
12 3 0.06
13 7 0.15
ACGTcount: A:0.59, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:59061 original size:23 final size:24
Alignment explanation
Indices: 59003--59071 Score: 104
Period size: 23 Copynumber: 2.9 Consensus size: 24
58993 TCATTTAATA
*
59003 AATAAACGAACATAAACGAATACG
1 AATAAACGAACATAAACGAACACG
**
59027 AACGAACGAACATAAACGAACAC-
1 AATAAACGAACATAAACGAACACG
59050 AATAAACGAACATAAACGAACA
1 AATAAACGAACATAAACGAACA
59072 ACACAAACAC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 20 0.50
24 20 0.50
ACGTcount: A:0.59, C:0.20, G:0.12, T:0.09
Consensus pattern (24 bp):
AATAAACGAACATAAACGAACACG
Found at i:59074 original size:13 final size:13
Alignment explanation
Indices: 59027--59079 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
59017 AACGAATACG
59027 AACGAACGAACATA
1 AACGAAC-AACATA
59041 AACGAAC-ACAATA
1 AACGAACAAC-ATA
59054 AACG---AACATA
1 AACGAACAACATA
*
59064 AACGAACAACACA
1 AACGAACAACATA
59077 AAC
1 AAC
59080 ACACACAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
10 7 0.21
11 2 0.06
12 2 0.06
13 15 0.45
14 7 0.21
ACGTcount: A:0.60, C:0.25, G:0.09, T:0.06
Consensus pattern (13 bp):
AACGAACAACATA
Found at i:59079 original size:23 final size:23
Alignment explanation
Indices: 59006--59079 Score: 96
Period size: 23 Copynumber: 3.2 Consensus size: 23
58996 TTTAATAAAT
*
59006 AAACGAACATAAACGAATACGAAC
1 AAACGAACATAAACGAACAC-AAC
* *
59030 GAACGAACATAAACGAACACAAT
1 AAACGAACATAAACGAACACAAC
59053 AAACGAACATAAACGAACA-ACAC
1 AAACGAACATAAACGAACACA-AC
59076 AAAC
1 AAAC
59080 ACACACAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
22 1 0.02
23 25 0.57
24 18 0.41
ACGTcount: A:0.59, C:0.23, G:0.11, T:0.07
Consensus pattern (23 bp):
AAACGAACATAAACGAACACAAC
Found at i:59154 original size:33 final size:31
Alignment explanation
Indices: 59066--59141 Score: 127
Period size: 31 Copynumber: 2.5 Consensus size: 31
59056 CGAACATAAA
*
59066 CGAACAACACAAACACACACAAAAACTTATT
1 CGAACAACACAAACACACAAAAAAACTTATT
59097 CGAACAACACAAACACACAAAAAAACTTATT
1 CGAACAACACAAACACACAAAAAAACTTATT
59128 CGAAC-ACAACAAAC
1 CGAACAAC-ACAAAC
59142 GAATGTAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
30 2 0.05
31 41 0.95
ACGTcount: A:0.57, C:0.29, G:0.04, T:0.11
Consensus pattern (31 bp):
CGAACAACACAAACACACAAAAAAACTTATT
Found at i:59379 original size:14 final size:14
Alignment explanation
Indices: 59360--59405 Score: 74
Period size: 14 Copynumber: 3.1 Consensus size: 14
59350 GCCCTCTGTT
59360 CGAACATAAATGAA
1 CGAACATAAATGAA
59374 CGAACATAAATGAA
1 CGAACATAAATGAA
59388 CGAACATATAATCGAA
1 CGAACATA-AAT-GAA
59404 CG
1 CG
59406 TTCACGAACG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
14 22 0.73
15 3 0.10
16 5 0.17
ACGTcount: A:0.52, C:0.17, G:0.15, T:0.15
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:60265 original size:16 final size:16
Alignment explanation
Indices: 60244--60275 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
60234 ACTATTCACA
*
60244 TGAATAGTGAATTTCG
1 TGAATAGTGAAATTCG
60260 TGAATAGTGAAATTCG
1 TGAATAGTGAAATTCG
60276 GTCGGCAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.34
Consensus pattern (16 bp):
TGAATAGTGAAATTCG
Found at i:62832 original size:21 final size:21
Alignment explanation
Indices: 62806--62864 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
62796 GGGTTTCATA
62806 GGTCCTTCGGGAAAATACAGT
1 GGTCCTTCGGGAAAATACAGT
*
62827 GGTCCTTCGGGACAATACAGT
1 GGTCCTTCGGGAAAATACAGT
*
62848 GGTCATTCGGGACAAAT
1 GGTCCTTCGGGA-AAAT
62865 TTCATATGCC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 31 0.91
22 3 0.09
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (21 bp):
GGTCCTTCGGGAAAATACAGT
Found at i:63679 original size:21 final size:22
Alignment explanation
Indices: 63637--63681 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
63627 TGTAGCAGTA
*
63637 CTGTAGCAGGGGAATCGGTTCC
1 CTGTAGCAGGGGAATCGATTCC
*
63659 CTGTAGCA-GGGTATCGATTCC
1 CTGTAGCAGGGGAATCGATTCC
63680 CT
1 CT
63682 CTTTGTAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.18, C:0.24, G:0.31, T:0.27
Consensus pattern (22 bp):
CTGTAGCAGGGGAATCGATTCC
Found at i:63731 original size:13 final size:13
Alignment explanation
Indices: 63713--63768 Score: 55
Period size: 13 Copynumber: 4.4 Consensus size: 13
63703 TGTAATCGGC
63713 ACTGTAGCAGGTT
1 ACTGTAGCAGGTT
*
63726 ACTGTAGCAGATT
1 ACTGTAGCAGGTT
63739 ACTGTTTA-C-GG-T
1 ACTG--TAGCAGGTT
*
63751 ATTGTAGCAGGTT
1 ACTGTAGCAGGTT
63764 ACTGT
1 ACTGT
63769 TTACTACTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
10 2 0.06
11 1 0.03
12 6 0.18
13 22 0.65
14 1 0.03
15 2 0.06
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.36
Consensus pattern (13 bp):
ACTGTAGCAGGTT
Found at i:70566 original size:354 final size:354
Alignment explanation
Indices: 69911--70835 Score: 1746
Period size: 354 Copynumber: 2.6 Consensus size: 354
69901 TTGTTCTTTG
* *
69911 TTTTCTTTTTTTAACCTTTCTTCGTGGAATCTAATGCACAAATACTATAT-AAAA-AATTGAAGT
1 TTTTC-TTTTTTAACC-AT-TTCATGGAATCTAATGCACAAATACTATATAAAAAGAATTGAAGT
69974 GTAGTTTACCAAGTAAACTTGACATTGCTCTTAACCCATTCATTTGATGCAGCAATGCAATGTGT
63 GTAGTTTACCAAGTAAACTTGACATTGCTCTTAACCCATTCATTTGATGCAGCAATGCAATGTGT
70039 AATTAAAATGAATTTCTTTGATTAAATCATATAGTATAAAAAGGAAGCGTGGTTTACCAAGTAAA
128 AATTAAAATGAATTTCTTTGATTAAATCATATAGTATAAAAAGGAAGCGTGGTTTACCAAGTAAA
70104 CGATGGTGTCCTATCTCATTACATATTATCTTATTAATTATTCGAGATATGCGGATACCATTGTC
193 CGATGGTGTCCTATCTCATTACATATTATCTTATTAATTATTCGAGATATGCGGATACCATTGTC
*
70169 AAATTTCTCGGCGTTTTTTTTCAAATAAGATAATGTTATTTTATTATGGTAGTCAATGTGATGAT
258 AAATTTCTCAGCGTTTTTTTTCAAATAAGATAATGTTATTTTATTATGGTAGTCAATGTGATGAT
70234 GTCCTAATTCATTGGATGTTATCTTTGTTTTA
323 GTCCTAATTCATTGGATGTTATCTTTGTTTTA
70266 TTTTCTTTTTTAACCATTTCATGGAATCTAATGCACAAATACTATATAAAAAGAATTGAAGTGTA
1 TTTTCTTTTTTAACCATTTCATGGAATCTAATGCACAAATACTATATAAAAAGAATTGAAGTGTA
70331 GTTTACCAAGTAAACTTGACATTGCTCTTAACCCATTCATTTGATGCAGCAATGCAATGTGTAAT
66 GTTTACCAAGTAAACTTGACATTGCTCTTAACCCATTCATTTGATGCAGCAATGCAATGTGTAAT
70396 TAAAATGAATTTCTTTGATTAAATCATATAGTATAAAAAGGAAGCGTGGTTTACCAAGTAAACGA
131 TAAAATGAATTTCTTTGATTAAATCATATAGTATAAAAAGGAAGCGTGGTTTACCAAGTAAACGA
*
70461 TGGTGTCCTATCTCATTACATGTTATCTTATTAATTATTCGAGATATGCGGATACCATTGTCAAA
196 TGGTGTCCTATCTCATTACATATTATCTTATTAATTATTCGAGATATGCGGATACCATTGTCAAA
*
70526 TTTCTCATCGTTTTTTTTCAAATAAGATAATGTTATTTTATTATGGTAGTCAATGTGATGATGTC
261 TTTCTCAGCGTTTTTTTTCAAATAAGATAATGTTATTTTATTATGGTAGTCAATGTGATGATGTC
70591 CTAATTCATTGGATGTTATCTTTGTTTTA
326 CTAATTCATTGGATGTTATCTTTGTTTTA
70620 TTTTCTTTTTTAACCATTTCATGGAATCTAATGCACAAATACTATATAAAAAGAATTGAAGTGTA
1 TTTTCTTTTTTAACCATTTCATGGAATCTAATGCACAAATACTATATAAAAAGAATTGAAGTGTA
70685 GTTTACCAAGTAAACTTGACATTGCTCTTAACCCATTCATTTGATGCAGCAATGCAATGTGTAAT
66 GTTTACCAAGTAAACTTGACATTGCTCTTAACCCATTCATTTGATGCAGCAATGCAATGTGTAAT
70750 TAAAATGAATTTCTTTGATTAAATCATATAGTATAAAAAGGAAGCGTGGTTTACCAAGTAAACGA
131 TAAAATGAATTTCTTTGATTAAATCATATAGTATAAAAAGGAAGCGTGGTTTACCAAGTAAACGA
* *
70815 TGGTGTCCTAGCTCTTTACAT
196 TGGTGTCCTATCTCATTACAT
70836 TTCAAATTTC
Statistics
Matches: 561, Mismatches: 7, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
352 29 0.05
353 5 0.01
354 522 0.93
355 5 0.01
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.39
Consensus pattern (354 bp):
TTTTCTTTTTTAACCATTTCATGGAATCTAATGCACAAATACTATATAAAAAGAATTGAAGTGTA
GTTTACCAAGTAAACTTGACATTGCTCTTAACCCATTCATTTGATGCAGCAATGCAATGTGTAAT
TAAAATGAATTTCTTTGATTAAATCATATAGTATAAAAAGGAAGCGTGGTTTACCAAGTAAACGA
TGGTGTCCTATCTCATTACATATTATCTTATTAATTATTCGAGATATGCGGATACCATTGTCAAA
TTTCTCAGCGTTTTTTTTCAAATAAGATAATGTTATTTTATTATGGTAGTCAATGTGATGATGTC
CTAATTCATTGGATGTTATCTTTGTTTTA
Found at i:71559 original size:11 final size:11
Alignment explanation
Indices: 71543--71602 Score: 54
Period size: 11 Copynumber: 5.6 Consensus size: 11
71533 TCATTTCATT
71543 TTATTTTATTA
1 TTATTTTATTA
71554 TTATTTTATTA
1 TTATTTTATTA
* *
71565 TTATCATAATTA
1 TTAT-TTTATTA
*
71577 -AATTTTATTA
1 TTATTTTATTA
*
71587 ATATTTT-TT-
1 TTATTTTATTA
71596 TTATTTT
1 TTATTTT
71603 TTTGTAGGAT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
9 6 0.15
10 7 0.17
11 22 0.55
12 5 0.12
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:71667 original size:3 final size:3
Alignment explanation
Indices: 71661--71694 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
71651 CTACTACCCC
71661 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
71695 TTACGAACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:72318 original size:31 final size:31
Alignment explanation
Indices: 72282--72344 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
72272 ATATAAATAC
72282 ATATACATATATAT-TAAAAAATAAATCTTAA
1 ATATACATATATATATAAAAAATAAAT-TTAA
* *
72313 ATATACATATATATATAATACATAAATTTAA
1 ATATACATATATATATAAAAAATAAATTTAA
72344 A
1 A
72345 AAATAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 19 0.66
32 10 0.34
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (31 bp):
ATATACATATATATATAAAAAATAAATTTAA
Found at i:73325 original size:41 final size:41
Alignment explanation
Indices: 73268--73351 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
73258 AGAATGTACT
*
73268 CTTTTCATCTTTTTAGGATTAGGGAGGTATTTAACGATACA
1 CTTTTCATCTTTTTAGGATTAGGGAGGTATTTAACGAGACA
73309 CTTTTCATCTTTTTAGGATTAGGGAGGTATTTAACGAGACA
1 CTTTTCATCTTTTTAGGATTAGGGAGGTATTTAACGAGACA
73350 CT
1 CT
73352 ATCCTTGACT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.40
Consensus pattern (41 bp):
CTTTTCATCTTTTTAGGATTAGGGAGGTATTTAACGAGACA
Found at i:78521 original size:71 final size:71
Alignment explanation
Indices: 78450--78586 Score: 256
Period size: 71 Copynumber: 1.9 Consensus size: 71
78440 TGCATCTTTG
*
78450 CATTTTTACGTTTGTATTTATATTTTCATTTTTTTTGCATTTGCATTTGCATTTGCATCTTTGCA
1 CATTTTTACGTTTGTATTTACATTTTCATTTTTTTTGCATTTGCATTTGCATTTGCATCTTTGCA
78515 TCTTTG
66 TCTTTG
*
78521 CATTTTTATGTTTGTATTTACATTTTCATTTTTTTTGCATTTGCATTTGCATTTGCATCTTTGCA
1 CATTTTTACGTTTGTATTTACATTTTCATTTTTTTTGCATTTGCATTTGCATTTGCATCTTTGCA
78586 T
66 T
78587 AATTATGTTT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 64 1.00
ACGTcount: A:0.16, C:0.14, G:0.11, T:0.59
Consensus pattern (71 bp):
CATTTTTACGTTTGTATTTACATTTTCATTTTTTTTGCATTTGCATTTGCATTTGCATCTTTGCA
TCTTTG
Found at i:78575 original size:6 final size:6
Alignment explanation
Indices: 78483--78578 Score: 68
Period size: 6 Copynumber: 15.2 Consensus size: 6
78473 TTTCATTTTT
** *
78483 TTTGCA TTTGCA TTTGCA TTTGCA TCTTTGCA TCTTTGCA TTTTTA TGTTTGTA
1 TTTGCA TTTGCA TTTGCA TTTGCA --TTTGCA --TTTGCA TTTGCA --TTTGCA
* * **
78537 TTTACA TTTTCA TTT-TT TTTGCA TTTGCA TTTGCA TTTGCA T
1 TTTGCA TTTGCA TTTGCA TTTGCA TTTGCA TTTGCA TTTGCA T
78579 CTTTGCATAA
Statistics
Matches: 75, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
5 3 0.04
6 53 0.71
8 19 0.25
ACGTcount: A:0.16, C:0.15, G:0.12, T:0.57
Consensus pattern (6 bp):
TTTGCA
Found at i:78576 original size:63 final size:65
Alignment explanation
Indices: 78426--78602 Score: 250
Period size: 71 Copynumber: 2.7 Consensus size: 65
78416 ATCGATAGCT
* *
78426 TTTGCATTTGCATTTGCATCTTTGCATTTTTACGTTTGTATTTATATTTTCATTTTTTTTGCATT
1 TTTGCATTTGCATTTGCATCTTTGCATTTTTATGTTTGTATTTACATTTTCA--TTTTTT--ATT
78491 TGCA
62 TGCA
78495 TTTGCATTTGCATCTTTGCATCTTTGCATTTTTATGTTTGTATTTACATTTTCA-TTTTT-TTTG
1 TTTGCATTTGCA--TTTGCATCTTTGCATTTTTATGTTTGTATTTACATTTTCATTTTTTATTTG
78558 CA
64 CA
**
78560 TTTGCATTTGCATTTGCATCTTTGCATAATTATGTTTGTATTT
1 TTTGCATTTGCATTTGCATCTTTGCATTTTTATGTTTGTATTT
78603 TCAATCCTAC
Statistics
Matches: 102, Mismatches: 4, Indels: 10
0.88 0.03 0.09
Matches are distributed among these distances:
63 29 0.28
65 18 0.18
68 5 0.05
69 12 0.12
71 38 0.37
ACGTcount: A:0.16, C:0.13, G:0.12, T:0.59
Consensus pattern (65 bp):
TTTGCATTTGCATTTGCATCTTTGCATTTTTATGTTTGTATTTACATTTTCATTTTTTATTTGCA
Found at i:82054 original size:9 final size:9
Alignment explanation
Indices: 82042--82066 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
82032 TTTATTTGAT
82042 ATTCATTAA
1 ATTCATTAA
82051 ATTCATTAA
1 ATTCATTAA
82060 ATTCATT
1 ATTCATT
82067 GTTTATGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (9 bp):
ATTCATTAA
Found at i:86105 original size:40 final size:40
Alignment explanation
Indices: 85932--86107 Score: 271
Period size: 40 Copynumber: 4.4 Consensus size: 40
85922 ATTTAATACG
**
85932 AAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAACAA
1 AAGATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAA
*** *
85972 AAGATTTTATCTAATTCAAGATTGTTTTTCCTTGAAACAG
1 AAGATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAA
* *
86012 AAGATTTTATCTCGCTCAAGATTGTTTTTCCTTCAAACAG
1 AAGATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAA
*
86052 AAGACTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAA
1 AAGATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAA
86092 AAGATTTTATCTCGCT
1 AAGATTTTATCTCGCT
86108 TCAGATAGTT
Statistics
Matches: 126, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 126 1.00
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (40 bp):
AAGATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAA
Found at i:86154 original size:37 final size:39
Alignment explanation
Indices: 85932--86165 Score: 122
Period size: 40 Copynumber: 5.9 Consensus size: 39
85922 ATTTAATACG
* * * *
85932 AAGATTTTATCT-CATTCAAGATTGTTTTTCCTTGAAACAA
1 AAGATTTTATCTCCCTTC-AGATAG-TTTCCCTCGAAACAA
** * * * *
85972 AAGATTTTATCT-AATTCAAGATTGTTTTTCCTTGAAACAG
1 AAGATTTTATCTCCCTTC-AGATAG-TTTCCCTCGAAACAA
* * * *
86012 AAGATTTTATCTCGC-TCAAGATTGTTTTTCCTTC-AAACAG
1 AAGATTTTATCTCCCTTC-AGATAG--TTTCCCTCGAAACAA
* * * * *
86052 AAGACTTTATCTCGC-TCAAGATTGTTTTTCCTTGAAACAA
1 AAGATTTTATCTCCCTTC-AGATAG-TTTCCCTCGAAACAA
*
86092 AAGATTTTATCTCGCTTCAGATAGTTTCCCTCGAAAC-A
1 AAGATTTTATCTCCCTTCAGATAGTTTCCCTCGAAACAA
* * * *
86130 AAG-TTTTGTCTCCCTTGAGATAGTTTCTCTTGAAAC
1 AAGATTTTATCTCCCTTCAGATAGTTTCCCTCGAAAC
86166 CTATTTCGTA
Statistics
Matches: 169, Mismatches: 21, Indels: 11
0.84 0.10 0.05
Matches are distributed among these distances:
37 28 0.17
38 4 0.02
39 17 0.10
40 112 0.66
41 8 0.05
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (39 bp):
AAGATTTTATCTCCCTTCAGATAGTTTCCCTCGAAACAA
Found at i:86620 original size:20 final size:20
Alignment explanation
Indices: 86558--86621 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
86548 TTAATGGAGA
86558 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* * ***
86578 -ATC-CAATGAGGAAGAAGAA
1 GTTCATAATGA-GAAGAACTT
86597 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
86617 GTTCA
1 GTTCA
86622 ACCTTGCATC
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
18 5 0.16
19 8 0.26
20 13 0.42
21 5 0.16
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:86819 original size:136 final size:136
Alignment explanation
Indices: 86638--86979 Score: 523
Period size: 136 Copynumber: 2.6 Consensus size: 136
86628 CATCAGTGTC
* *
86638 TCCAAAGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAA
1 TCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTTCATAATGAGAA
* ** * *
86703 GAGCTTGTTCGACCTATCACTCGATTCACGGTATTTCGAATCAGTGACGCCTCGCTTGAGGAATT
66 GAGCTTGTTCGACCTATCACTCGACTCACGACATTTCGAATCAGTGACGCCTCACTTGAGGAATC
86768 GACATT
131 GACATT
* *
86774 TCCAATGGATAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTTCATAATGAAAA
1 TCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTTCATAATGAGAA
*
86839 GAGCTTGTTCGACCTATCACTCGACTCACGACATTTCGAATCAGTGACGCCTCACTTGAGGGATC
66 GAGCTTGTTCGACCTATCACTCGACTCACGACATTTCGAATCAGTGACGCCTCACTTGAGGAATC
86904 GACATT
131 GACATT
* * *
86910 TCCAATGAAGAGTTCATAATGAGAAGAACTCGTCCTA-A-A-GGAG-A-AAGTTCATAATGAGAA
1 TCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTTCATAATGAGAA
*
86970 GAACTTGTTC
66 GAGCTTGTTC
86980 CTTTCAAATC
Statistics
Matches: 190, Mismatches: 16, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
131 24 0.13
132 1 0.01
133 4 0.02
134 1 0.01
135 1 0.01
136 159 0.84
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.24
Consensus pattern (136 bp):
TCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTTCATAATGAGAA
GAGCTTGTTCGACCTATCACTCGACTCACGACATTTCGAATCAGTGACGCCTCACTTGAGGAATC
GACATT
Found at i:87098 original size:242 final size:245
Alignment explanation
Indices: 86784--87224 Score: 685
Period size: 242 Copynumber: 1.8 Consensus size: 245
86774 TCCAATGGAT
*
86784 AGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTTCATAATGAAAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCCAACAGAGGAAGAAGAAGTTCATAATGAAAAGAGCTTGTTC
* * *
86849 GACCTATCACTCGACTCACGACATTTCGAATCAGTGACGCCTCACTTGAGGGATCGACATTTCCA
66 AACCTATCACTCGACTAACGACATTTCGAATCAGTGACGCCTCACTTGAGGAATCGACATTT-CA
*
86914 ATGAAGAGTTCATAATGAGAAGAACTCGTCCTAA-AGG-AG-A-AAGTTCATAATGAGAAGAACT
130 ATGAAGAGTTCATAATGAGAAGAACTCATCC-AAGAGGAAGAAGAAGTTCATAATGAGAAGAACT
86975 TGTTCCTTTCAAATCCATCACAGAAGGAGGTGGATCAACATTTTTAGTGAAG
194 TGTTCCTTTCAAATCCATCACAGAAGGAGGTGGATCAACATTTTTAGTGAAG
* *
87027 AGTTCATAATGAGAAGAACTCATCCAA-AGAGGAAGAAGGAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCCAACAGAGGAAGAAGAAGTTCATAATGAAAAGAGCTTGTTC
* * * * * *
87091 AACCTATCACTCGATTAACGACATTTCGAATCAGTGATGTCTCGCTTGAGGAATTGACATTTTAA
66 AACCTATCACTCGACTAACGACATTTCGAATCAGTGACGCCTCACTTGAGGAATCGACATTTCAA
* *
87156 TGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAATTT
131 TGAAGAGTTCATAATGAGAAGAACTCATCCAA-GAGGAAGAAGAAGTTCATAATGAGAAGAACTT
87221 GTTC
195 GTTC
87225 AACCTTGCAT
Statistics
Matches: 178, Mismatches: 15, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
240 2 0.01
241 30 0.17
242 91 0.51
243 29 0.16
244 1 0.01
245 25 0.14
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.25
Consensus pattern (245 bp):
AGTTCATAATGAGAAGAACTCATCCAACAGAGGAAGAAGAAGTTCATAATGAAAAGAGCTTGTTC
AACCTATCACTCGACTAACGACATTTCGAATCAGTGACGCCTCACTTGAGGAATCGACATTTCAA
TGAAGAGTTCATAATGAGAAGAACTCATCCAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
TTCCTTTCAAATCCATCACAGAAGGAGGTGGATCAACATTTTTAGTGAAG
Found at i:91488 original size:18 final size:18
Alignment explanation
Indices: 91450--91496 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
91440 CAATTTCTCC
* *
91450 CTTTTTCCTTTTTTTCAT
1 CTTTTTTCTTTTTTCCAT
*
91468 CTTTTTTCTTTTTTCCTT
1 CTTTTTTCTTTTTTCCAT
*
91486 CTTCTTTCTTT
1 CTTTTTTCTTT
91497 GTTGGATGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.74
Consensus pattern (18 bp):
CTTTTTTCTTTTTTCCAT
Found at i:98423 original size:21 final size:21
Alignment explanation
Indices: 98365--98423 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
98355 AACCCTAATC
98365 TAATGCTTACAAGTAAATATG
1 TAATGCTTACAAGTAAATATG
* *
98386 TTATGC-GACTAAAGTAAATA-G
1 TAATGCTTAC--AAGTAAATATG
98407 ATAATGCTTACAAGTAA
1 -TAATGCTTACAAGTAA
98424 TACAATTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
20 2 0.07
21 12 0.40
22 14 0.47
23 2 0.07
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (21 bp):
TAATGCTTACAAGTAAATATG
Found at i:101055 original size:23 final size:23
Alignment explanation
Indices: 101020--101069 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
101010 CATCTAGGGA
* *
101020 AAAAAATTATCTATAATTAAGTAT
1 AAAAAATTATCTA-AAATAAATAT
*
101044 AAAAGATT-TCTAAAATAAATAT
1 AAAAAATTATCTAAAATAAATAT
101066 AAAA
1 AAAA
101070 TGTTGTTCGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 12 0.52
23 4 0.17
24 7 0.30
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (23 bp):
AAAAAATTATCTAAAATAAATAT
Found at i:102450 original size:132 final size:132
Alignment explanation
Indices: 102213--102607 Score: 664
Period size: 132 Copynumber: 3.0 Consensus size: 132
102203 CATTCTGCTA
* * *
102213 CAGAAACAAGCACAAGGAGATCAAAGCGGCACAGGATCACAGGTGATTGGAACTTAGAAATACAT
1 CAGAAACAAGAACAAGGAGATCAAAACGGCACAGGGTCACAGGTGATTGGAACTTAGAAATACAT
102278 TTGCTTCTCTATTACATCTGATAACTGCACAAATAAATTATTAGTTAATCTCTTGTTATATCAGA
66 TTGCTTCTCTATTACATCTGATAACTGCACAAATAAATTATTAGTTAATCTCTTGTTATATCAGA
102343 TG
131 TG
* * *
102345 CAGAAACAAGAACAAGGAGATCAAAACGGCACAGGGTTACGGGTGATTGGAACTTAGAAATATAT
1 CAGAAACAAGAACAAGGAGATCAAAACGGCACAGGGTCACAGGTGATTGGAACTTAGAAATACAT
**
102410 TTGCTTCTCTATTACATCTGATAACTGCACAAATAAATTATTAGTTAATCTCTTGTTATATCTTA
66 TTGCTTCTCTATTACATCTGATAACTGCACAAATAAATTATTAGTTAATCTCTTGTTATATCAGA
102475 TG
131 TG
* *
102477 CAGAAACAAGAACGAGGAGATCAAATCGGCACAGGGTCACAGGTGATTGGAACTTAGAAATACAT
1 CAGAAACAAGAACAAGGAGATCAAAACGGCACAGGGTCACAGGTGATTGGAACTTAGAAATACAT
*
102542 TTGCTTCTCTATTACATCTGACAACTGCACAAATAAATTAGTATTAGTTAATCTCTTGTTATATC
66 TTGCTTCTCTATTACATCTGATAACTGCACAAATAAA-T--TATTAGTTAATCTCTTGTTATATC
102607 A
128 A
102608 TTATGCACGG
Statistics
Matches: 245, Mismatches: 15, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
132 220 0.90
133 1 0.00
135 24 0.10
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (132 bp):
CAGAAACAAGAACAAGGAGATCAAAACGGCACAGGGTCACAGGTGATTGGAACTTAGAAATACAT
TTGCTTCTCTATTACATCTGATAACTGCACAAATAAATTATTAGTTAATCTCTTGTTATATCAGA
TG
Found at i:102793 original size:11 final size:11
Alignment explanation
Indices: 102777--102801 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
102767 AACCATAGCA
102777 TAAACTTGGAT
1 TAAACTTGGAT
102788 TAAACTTGGAT
1 TAAACTTGGAT
102799 TAA
1 TAA
102802 TTACAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (11 bp):
TAAACTTGGAT
Found at i:104890 original size:16 final size:16
Alignment explanation
Indices: 104868--104907 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
104858 ATGTCTATTC
104868 TAATTTTAATATTCTTA
1 TAATTTTAATATT-TTA
104885 -AATTTTAATATTTTA
1 TAATTTTAATATTTTA
104900 TAATTTTA
1 TAATTTTA
104908 CCTTATTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.14
16 19 0.86
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
TAATTTTAATATTTTA
Found at i:110910 original size:60 final size:58
Alignment explanation
Indices: 110761--110917 Score: 185
Period size: 61 Copynumber: 2.6 Consensus size: 58
110751 AAAATATAAC
* *
110761 CCTCATTTTAAATTGGTCCTCAAACTTTTGAACATTCTAATTTATCCTTAAATAATGA
1 CCTCATTTTAAATTGGTCCTCAAACTTTTGAACATTCTAATTCATCCTGAAATAATGA
* *
110819 CTCTCAATTTAAATCGGTCC-CTAGGAA-TTTTGAACATTCTAAATTCATCCTGAAACT-ATGA
1 C-CTCATTTTAAATTGGTCCTC-A--AACTTTTGAACATTCT-AATTCATCCTGAAA-TAATGA
*
110880 TCCTCATTTTAAATTAGTCCTCAAACTTTTGAACATTC
1 -CCTCATTTTAAATTGGTCCTCAAACTTTTGAACATTC
110918 CTATAATATC
Statistics
Matches: 83, Mismatches: 7, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
58 2 0.02
59 19 0.23
60 25 0.30
61 34 0.41
62 3 0.04
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (58 bp):
CCTCATTTTAAATTGGTCCTCAAACTTTTGAACATTCTAATTCATCCTGAAATAATGA
Found at i:111135 original size:60 final size:60
Alignment explanation
Indices: 110996--111128 Score: 151
Period size: 60 Copynumber: 2.2 Consensus size: 60
110986 ATATAAAATT
* * * * *
110996 AGGACCATAGTTTAGGGATGGAATTAGAATGATTAAAAGTTTAGAGAACAATTTCGAATA
1 AGGATCATAGTTTAGGGATGAAACTAGAATGATTAAAAATTTAGAGAACAATTTAGAATA
* * * ** *
111056 AGAATTATAGTTTAGGGATGAAACTAGAATGTTTAAAAATTT-GAGGATTAATTTAGAATG
1 AGGATCATAGTTTAGGGATGAAACTAGAATGATTAAAAATTTAGA-GAACAATTTAGAATA
111116 AGGATCATAGTTT
1 AGGATCATAGTTT
111129 GAGGATGTTT
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
59 2 0.03
60 57 0.97
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.32
Consensus pattern (60 bp):
AGGATCATAGTTTAGGGATGAAACTAGAATGATTAAAAATTTAGAGAACAATTTAGAATA
Found at i:117408 original size:60 final size:59
Alignment explanation
Indices: 117252--117410 Score: 137
Period size: 60 Copynumber: 2.6 Consensus size: 59
117242 TAAAACATTC
* * * * *
117252 AAAAGTTTG-GGAACTAATATAGAATTAGGGCCACAGTTTAGGGATGAAATTAGAATGATT
1 AAAAGTTTGAGG-ATTAATTTAGAA-TAGGACCATAGTTTAGGGATGAAACTAGAATGATT
* * **
117312 AAAAGTTT-A-GAGTTCAATTTCGAATAAGAGTTATAGTTTAGGGATGAAACTAGAATG-TT
1 AAAAGTTTGAGGA-TT-AATTTAGAATAGGA-CCATAGTTTAGGGATGAAACTAGAATGATT
*
117371 CGAAAGTTTGAGGATTAATTTAGAATGAGGACCATAGTTT
1 -AAAAGTTTGAGGATTAATTTAGAAT-AGGACCATAGTTT
117411 GAGGACGTTT
Statistics
Matches: 77, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
58 1 0.01
59 7 0.09
60 61 0.79
61 6 0.08
62 2 0.03
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.31
Consensus pattern (59 bp):
AAAAGTTTGAGGATTAATTTAGAATAGGACCATAGTTTAGGGATGAAACTAGAATGATT
Found at i:122528 original size:24 final size:24
Alignment explanation
Indices: 122501--122563 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 24
122491 CGTTCGTGAA
* *
122501 CGTTCGGTTATGTTTGTTTATGTT
1 CGTTCGATTATGTTCGTTTATGTT
122525 CGTTCGATTATGTTCGTTTATGTT
1 CGTTCGATTATGTTCGTTTATGTT
*
122549 CATTC-ATTTATGTTC
1 CGTTCGA-TTATGTTC
122564 ATTCATTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
23 1 0.03
24 34 0.97
ACGTcount: A:0.13, C:0.13, G:0.19, T:0.56
Consensus pattern (24 bp):
CGTTCGATTATGTTCGTTTATGTT
Found at i:122558 original size:14 final size:14
Alignment explanation
Indices: 122541--122576 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
122531 ATTATGTTCG
122541 TTTATGTTCATTCA
1 TTTATGTTCATTCA
122555 TTTATGTTCATTCA
1 TTTATGTTCATTCA
122569 TTTATGTT
1 TTTATGTT
122577 TAACCCAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.19, C:0.11, G:0.08, T:0.61
Consensus pattern (14 bp):
TTTATGTTCATTCA
Found at i:123544 original size:15 final size:16
Alignment explanation
Indices: 123489--123544 Score: 73
Period size: 15 Copynumber: 3.7 Consensus size: 16
123479 CTCCAGTTTA
*
123489 TGTTCG-TTATATTCG
1 TGTTCGTTTATGTTCG
*
123504 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
123520 TGTTCG-TTATGTTCG
1 TGTTCGTTTATGTTCG
123535 TG-TCGTTTAT
1 TGTTCGTTTAT
123545 ATTCATTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
14 3 0.08
15 20 0.56
16 13 0.36
ACGTcount: A:0.11, C:0.12, G:0.21, T:0.55
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:123585 original size:30 final size:30
Alignment explanation
Indices: 123551--123609 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
123541 TTATATTCAT
*
123551 TTATTT-ATTAAATGAACGAACATGAACAAG
1 TTATTTCATT-AATAAACGAACATGAACAAG
*
123581 TTATTTCCTTAATAAACGAACATGAACAA
1 TTATTTCATTAATAAACGAACATGAACAA
123610 AAAAAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 24 0.92
31 2 0.08
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.31
Consensus pattern (30 bp):
TTATTTCATTAATAAACGAACATGAACAAG
Found at i:125246 original size:19 final size:21
Alignment explanation
Indices: 125212--125251 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
125202 TCAACAATAG
125212 CTGCAAAAAGGGGGGCACCGA
1 CTGCAAAAAGGGGGGCACCGA
125233 CTGC-AAAA-GGGGGCACCGA
1 CTGCAAAAAGGGGGGCACCGA
125252 ATTCGGTGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.58
20 4 0.21
21 4 0.21
ACGTcount: A:0.33, C:0.25, G:0.38, T:0.05
Consensus pattern (21 bp):
CTGCAAAAAGGGGGGCACCGA
Found at i:125723 original size:16 final size:16
Alignment explanation
Indices: 125690--125723 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
125680 TTACTATTCA
* *
125690 CGTGAATAGTGAATTT
1 CGTGAATAGTAAAATT
125706 CGTGAATAGTAAAATT
1 CGTGAATAGTAAAATT
125722 CG
1 CG
125724 GTCGGCGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTAAAATT
Found at i:129796 original size:20 final size:22
Alignment explanation
Indices: 129761--129802 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
129751 TCAACAATAG
129761 CTGCAAAAAGGGGGGGCACCGA
1 CTGCAAAAAGGGGGGGCACCGA
129783 CTGC-AAAA-GGGGGGCACCGA
1 CTGCAAAAAGGGGGGGCACCGA
129803 ATTCAGTGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 12 0.60
21 4 0.20
22 4 0.20
ACGTcount: A:0.31, C:0.24, G:0.40, T:0.05
Consensus pattern (22 bp):
CTGCAAAAAGGGGGGGCACCGA
Found at i:130632 original size:79 final size:79
Alignment explanation
Indices: 130493--130644 Score: 286
Period size: 79 Copynumber: 1.9 Consensus size: 79
130483 TAATCACGTT
*
130493 CCGAGTCGTCGAAATTGCCGATTAGTTTCTAATTTACTTTTAACTAATAACCCTGATTTTTAACC
1 CCGAGTCGTCGAAATTGCCGATTAGTTTCTAATTTACTTTTAACTAATAAACCTGATTTTTAACC
130558 ACTTATTTCTAGTC
66 ACTTATTTCTAGTC
*
130572 CCGAGTCGTCGAAATTGCCGATTAGTTTCTAATTTACTTTTAACTAATAAACCTGTTTTTTAACC
1 CCGAGTCGTCGAAATTGCCGATTAGTTTCTAATTTACTTTTAACTAATAAACCTGATTTTTAACC
130637 ACTTATTT
66 ACTTATTT
130645 ATAATATATT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 71 1.00
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (79 bp):
CCGAGTCGTCGAAATTGCCGATTAGTTTCTAATTTACTTTTAACTAATAAACCTGATTTTTAACC
ACTTATTTCTAGTC
Found at i:132301 original size:3 final size:3
Alignment explanation
Indices: 132293--132324 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
132283 GATCATCTAC
132293 ATA ATA ATA ATA ATA ATA ATA ATA ATA TATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA A
132325 GTGTTTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:135139 original size:12 final size:12
Alignment explanation
Indices: 135118--135148 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
135108 TGAATTTTCT
135118 TCTT-TTTTTAA
1 TCTTCTTTTTAA
135129 TCTTCTTTTTAA
1 TCTTCTTTTTAA
135141 TCTTCTTT
1 TCTTCTTT
135149 ATTCTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.21
12 15 0.79
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (12 bp):
TCTTCTTTTTAA
Found at i:135170 original size:17 final size:17
Alignment explanation
Indices: 135136--135167 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
135126 TAATCTTCTT
135136 TTTAATCTTCTTTATTC
1 TTTAATCTTCTTTATTC
135153 TTTAATCTT-TTTATT
1 TTTAATCTTCTTTATT
135168 TCTCTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.19, C:0.12, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTAATCTTCTTTATTC
Found at i:136309 original size:20 final size:21
Alignment explanation
Indices: 136284--136322 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
136274 GGCTCCTGGA
136284 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
136304 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTAACCGGTTT
136323 GACCGGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:136320 original size:10 final size:9
Alignment explanation
Indices: 136285--136375 Score: 65
Period size: 10 Copynumber: 9.3 Consensus size: 9
136275 GCTCCTGGAA
*
136285 ACCGGTTTA
1 ACCGGTTTG
*
136294 ACCGGTTTTCA
1 ACCGG-TTT-G
136305 ACCGGTTCTG
1 ACCGGTT-TG
136315 ACCGGTTTG
1 ACCGGTTTG
*
136324 ACCGGTTTTCA
1 ACCGG-TTT-G
*
136335 ACCGGTTCG
1 ACCGGTTTG
*
136344 AACCGATTTG
1 -ACCGGTTTG
*
136354 ACCGGTTCG
1 ACCGGTTTG
136363 AACCGGTTTG
1 -ACCGGTTTG
136373 ACC
1 ACC
136376 CGACCCGACC
Statistics
Matches: 66, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
9 22 0.33
10 32 0.48
11 12 0.18
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:136321 original size:30 final size:30
Alignment explanation
Indices: 136285--136375 Score: 118
Period size: 30 Copynumber: 3.1 Consensus size: 30
136275 GCTCCTGGAA
*
136285 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGGTTTTCAACCGGTTCTG
136315 ACCGGTTTGACCGGTTTTCAACCGGTTC-G
1 ACCGGTTTGACCGGTTTTCAACCGGTTCTG
*
136344 AACCGATTTGACCGG--TTCGAACCGGTT-TG
1 -ACCGGTTTGACCGGTTTTC-AACCGGTTCTG
136373 ACC
1 ACC
136376 CGACCCGACC
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
28 6 0.11
29 10 0.18
30 40 0.71
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (30 bp):
ACCGGTTTGACCGGTTTTCAACCGGTTCTG
Found at i:136329 original size:19 final size:19
Alignment explanation
Indices: 136286--136375 Score: 85
Period size: 19 Copynumber: 4.6 Consensus size: 19
136276 CTCCTGGAAA
*
136286 CCGGTTTAACCGGTTTTC-AA
1 CCGGTTTGACCGG--TTCGAA
*
136306 CCGGTTCTGACCGGTTTG-A
1 CCGGTT-TGACCGGTTCGAA
*
136325 CCGGTTTTCAACCGGTTCGAA
1 CCGG-TTT-GACCGGTTCGAA
*
136346 CCGATTTGACCGGTTCGAA
1 CCGGTTTGACCGGTTCGAA
136365 CCGGTTTGACC
1 CCGGTTTGACC
136376 CGACCCGACC
Statistics
Matches: 58, Mismatches: 7, Indels: 11
0.76 0.09 0.14
Matches are distributed among these distances:
19 29 0.50
20 19 0.33
21 10 0.17
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.30
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCGAA
Found at i:136399 original size:17 final size:17
Alignment explanation
Indices: 136377--136431 Score: 101
Period size: 17 Copynumber: 3.2 Consensus size: 17
136367 GGTTTGACCC
*
136377 GACCCGACCCGATCGTT
1 GACCCGACCCGACCGTT
136394 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
136411 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
136428 GACC
1 GACC
136432 GTTGACTTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.18, C:0.45, G:0.24, T:0.13
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:143559 original size:20 final size:21
Alignment explanation
Indices: 143534--143572 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
143524 GGCTGCTGGA
143534 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
143554 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTAACCGGTTT
143573 GACCGGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:143570 original size:10 final size:9
Alignment explanation
Indices: 143535--143625 Score: 74
Period size: 10 Copynumber: 9.3 Consensus size: 9
143525 GCTGCTGGAA
*
143535 ACCGGTTTA
1 ACCGGTTTG
*
143544 ACCGGTTTTCA
1 ACCGG-TTT-G
143555 ACCGGTTCTG
1 ACCGGTT-TG
143565 ACCGGTTTG
1 ACCGGTTTG
*
143574 ACCGGTTTCCA
1 ACCGGTTT--G
143585 ACCGGTTTG
1 ACCGGTTTG
*
143594 AACCAGTTTG
1 -ACCGGTTTG
*
143604 ACCGGTCTG
1 ACCGGTTTG
143613 AACCGGTTTG
1 -ACCGGTTTG
143623 ACC
1 ACC
143626 AGCCTGACAC
Statistics
Matches: 68, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
9 25 0.37
10 28 0.41
11 15 0.22
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:143571 original size:30 final size:29
Alignment explanation
Indices: 143535--143625 Score: 112
Period size: 30 Copynumber: 3.1 Consensus size: 29
143525 GCTGCTGGAA
*
143535 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGGTTTTCAACCGGTT-TG
*
143565 ACCGGTTTGACCGGTTTCCAACCGGTTTG
1 ACCGGTTTGACCGGTTTTCAACCGGTTTG
* * *
143594 AACCAGTTTGACCGG-TCTGAACCGGTTTG
1 -ACCGGTTTGACCGGTTTTCAACCGGTTTG
143623 ACC
1 ACC
143626 AGCCTGACAC
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
28 3 0.06
29 13 0.24
30 38 0.70
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (29 bp):
ACCGGTTTGACCGGTTTTCAACCGGTTTG
Found at i:143579 original size:19 final size:19
Alignment explanation
Indices: 143534--143625 Score: 96
Period size: 19 Copynumber: 4.7 Consensus size: 19
143524 GGCTGCTGGA
* *
143534 AACCGGTTTAACCGGTTTTC
1 AACCGGTTTGACCGG-TTTG
143554 AACCGGTTCTGACCGGTTTG
1 AACCGGTT-TGACCGGTTTG
*
143574 -ACCGGTTTCCAACCGGTTTG
1 AACCGGTTT--GACCGGTTTG
* *
143594 AACCAGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTTTG
143613 AACCGGTTTGACC
1 AACCGGTTTGACC
143626 AGCCTGACAC
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
18 1 0.02
19 27 0.44
20 20 0.33
21 13 0.21
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.29
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTTG
Found at i:143632 original size:19 final size:19
Alignment explanation
Indices: 143592--143632 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
143582 CCAACCGGTT
* *
143592 TGAACCAGTTTGACCGGTC
1 TGAACCAGTTTGACCAGCC
*
143611 TGAACCGGTTTGACCAGCC
1 TGAACCAGTTTGACCAGCC
143630 TGA
1 TGA
143633 CACGACCCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (19 bp):
TGAACCAGTTTGACCAGCC
Found at i:143660 original size:22 final size:21
Alignment explanation
Indices: 143628--143690 Score: 62
Period size: 22 Copynumber: 3.1 Consensus size: 21
143618 GTTTGACCAG
*
143628 CCTGACACGACCCGATCGTTGA
1 CCTGACCCGACCCGA-CGTTGA
143650 CCTGACCCGA--C--CGTTGA
1 CCTGACCCGACCCGACGTTGA
*
143667 CCCGACCCGACCCGACCGTTGA
1 CCTGACCCGACCCGA-CGTTGA
143689 CC
1 CC
143691 GTTGACTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
17 15 0.44
19 1 0.03
20 1 0.03
22 17 0.50
ACGTcount: A:0.19, C:0.44, G:0.22, T:0.14
Consensus pattern (21 bp):
CCTGACCCGACCCGACGTTGA
Found at i:143667 original size:12 final size:12
Alignment explanation
Indices: 143652--143690 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
143642 ATCGTTGACC
143652 TGACCCGACCGT
1 TGACCCGACCGT
143664 TGACCCGACC--
1 TGACCCGACCGT
*
143674 CGACCCGACCGT
1 TGACCCGACCGT
143686 TGACC
1 TGACC
143691 GTTGACTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 9 0.39
12 14 0.61
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (12 bp):
TGACCCGACCGT
Found at i:143690 original size:17 final size:17
Alignment explanation
Indices: 143630--143678 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
143620 TTGACCAGCC
* *
143630 TGACACGACCCGATCGT
1 TGACCCGACCCGACCGT
*
143647 TGACCTGACCCGACCGT
1 TGACCCGACCCGACCGT
143664 TGACCCGACCCGACC
1 TGACCCGACCCGACC
143679 CGACCGTTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.20, C:0.43, G:0.22, T:0.14
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Done.