Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014130.1 Kokia drynarioides strain JFW-HI SEQ_129163, 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: 138050
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 149 characters in sequence are not A, C, G, or T
Found at i:2097 original size:20 final size:20
Alignment explanation
Indices: 2059--2098 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2049 TAATTTATGC
* *
2059 GAGTTCTAAACGCGTGATGA
1 GAGTTCTAAAAGCGGGATGA
*
2079 GAGTTCTAAAAGTGGGATGA
1 GAGTTCTAAAAGCGGGATGA
2099 AAAATACTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.33, T:0.25
Consensus pattern (20 bp):
GAGTTCTAAAAGCGGGATGA
Found at i:8194 original size:96 final size:96
Alignment explanation
Indices: 7888--8271 Score: 440
Period size: 96 Copynumber: 4.0 Consensus size: 96
7878 AATCCTGATA
*
7888 GATGTCAAAAGGTATTTTT-ACTAATCTAGAAGCTTCACATTT-TATGGCTTTAAGAAGCAGCAA
1 GATGTCAAAAGGT-TTTTTGACTAATCTAGAAGCTTCACATTTAT-TGGCTTTAGGAAGCAGCAA
* *
7951 TCTAG-GTGTAAATTGGGTTTCTTATTATGTTTTG
64 TCTAGCGTG--AACTGGGTTTATTATTATGTTTTG
* * * *
7985 GATGTCAAAAGGTTTTTTGACTAGTCTAGAAGCTTCACATTTATTTGTTTTGGGAAGCAGCAATC
1 GATGTCAAAAGGTTTTTTGACTAATCTAGAAGCTTCACATTTATTGGCTTTAGGAAGCAGCAATC
* * *
8050 TAGACGTGAATTGAGTTTATTATTATGTTCTG
66 TAG-CGTGAACTGGGTTTATTATTATGTTTTG
* * * * *
8082 GATGTCAAAAGG-TTTTTGGCTAGTCTAGAAGCTTCACATTTATTGGCTTTGGGAAACAACAA-C
1 GATGTCAAAAGGTTTTTTGACTAATCTAGAAGCTTCACATTTATTGGCTTTAGGAAGCAGCAATC
* *
8145 TACGCGTGGACTGTGTTTATTATTATGTTTTG
66 TA-GCGTGAACTGGGTTTATTATTATGTTTTG
* * * * *
8177 GATGTCAAAAGATTTTTTTACTAATTTAAAAGCTTCACATTTATTGGCTTTAGGAAGCATCAATC
1 GATGTCAAAAGGTTTTTTGACTAATCTAGAAGCTTCACATTTATTGGCTTTAGGAAGCAGCAATC
*
8242 TATG-GT-AGGCTGGGTTTATTATTATGTTTT
66 TA-GCGTGA-ACTGGGTTTATTATTATGTTTT
8272 TGATTTTGGT
Statistics
Matches: 249, Mismatches: 30, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
95 38 0.15
96 115 0.46
97 92 0.37
98 1 0.00
99 3 0.01
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (96 bp):
GATGTCAAAAGGTTTTTTGACTAATCTAGAAGCTTCACATTTATTGGCTTTAGGAAGCAGCAATC
TAGCGTGAACTGGGTTTATTATTATGTTTTG
Found at i:11343 original size:6 final size:6
Alignment explanation
Indices: 11332--11359 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
11322 ATACTTTCGT
11332 TCCGGC TCCGGC TCCGGC TCCGGC TCCG
1 TCCGGC TCCGGC TCCGGC TCCGGC TCCG
11360 TCATCCTGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.50, G:0.32, T:0.18
Consensus pattern (6 bp):
TCCGGC
Found at i:12484 original size:6 final size:6
Alignment explanation
Indices: 12473--12501 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
12463 AGGAGACGGT
12473 GCAGCG GCAGCG GCAGCG GCAGCG GCAGC
1 GCAGCG GCAGCG GCAGCG GCAGCG GCAGC
12502 ATTACCACGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.34, G:0.48, T:0.00
Consensus pattern (6 bp):
GCAGCG
Found at i:13537 original size:15 final size:14
Alignment explanation
Indices: 13517--13552 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 14
13507 AATGGGAGTA
13517 GTGGTGATAGTGGTG
1 GTGGTGA-AGTGGTG
13532 GTGGTGGAAGTGGTG
1 GTGGT-GAAGTGGTG
13547 GTGGTG
1 GTGGTG
13553 GCCGGTGGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 1 0.05
15 17 0.85
16 2 0.10
ACGTcount: A:0.11, C:0.00, G:0.58, T:0.31
Consensus pattern (14 bp):
GTGGTGAAGTGGTG
Found at i:13553 original size:15 final size:15
Alignment explanation
Indices: 13525--13553 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
13515 TAGTGGTGAT
13525 AGTGGTGGTGGTGGA
1 AGTGGTGGTGGTGGA
13540 AGTGGTGGTGGTGG
1 AGTGGTGGTGGTGG
13554 CCGGTGGTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.00, G:0.62, T:0.28
Consensus pattern (15 bp):
AGTGGTGGTGGTGGA
Found at i:28573 original size:86 final size:85
Alignment explanation
Indices: 28414--28575 Score: 202
Period size: 86 Copynumber: 1.9 Consensus size: 85
28404 CTCATCTTTG
* * * * *
28414 TGATGAGATACAGAGAAGTGGATCAAAGCAATGAGGCAATCATCTTCCTTATGAGATACAAAGAA
1 TGATGAGATACAGAGAAGTGAATCAAAACAATAAGACAATCATATTCCTTATGAGATACAAAGAA
28479 GTGAACCAAATTCGTCTTCC
66 GTGAACCAAATTCGTCTTCC
* ** *
28499 TGATGAGATACAGAGAAGTGAAATTAAAACAATAAGACGGTCATATT-CTTGATGAGATACAGAG
1 TGATGAGATACAGAGAAGTG-AATCAAAACAATAAGACAATCATATTCCTT-ATGAGATACAAAG
28563 AAGT-AGACCAAAT
64 AAGTGA-ACCAAAT
28576 CAATGAAACA
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
85 24 0.37
86 41 0.63
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.23
Consensus pattern (85 bp):
TGATGAGATACAGAGAAGTGAATCAAAACAATAAGACAATCATATTCCTTATGAGATACAAAGAA
GTGAACCAAATTCGTCTTCC
Found at i:28644 original size:210 final size:209
Alignment explanation
Indices: 28271--29001 Score: 1022
Period size: 210 Copynumber: 3.5 Consensus size: 209
28261 TAGAGAAAAA
* * *
28271 TGAATCAAATCTGTCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAATGAGGCAGTCATCTT
1 TGAACCAAATCTGTCTTCCTGATGAGATACAGAGAAGTGAATTAAAACAATGAGGCGGTCATCTT
* * * * *
28336 CCTGATAAGATACTGAGAAGTAGACCAAATTAATGAAACAAAACTCAATTTAAGTAAAACTTCAA
66 CCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAACAAAGCTCAATTTAAGTGAAACTTCAA
** * * * * * *
28401 ACCCTCATCTTTGTGATGAGATACAGAGAAGTGGATCAAAGCAATGAGGCAATCATCTTCCTTAT
131 ACCCTCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCAGTTACCTTCCTTAT
*
28466 GAGATACAAAGAAG
196 GAGATACAGAGAAG
* * *
28480 TGAACCAAAT-TCGTCTTCCTGATGAGATACAGAGAAGTGAAATTAAAACAATAAGACGGTCATA
1 TGAACCAAATCT-GTCTTCCTGATGAGATACAGAGAAGTG-AATTAAAACAATGAGGCGGTCATC
* *
28544 TTCTTGATGAGATACAGAGAAGTAGACCAAATCAATGAAACAAAGCTCAATTTGAGTGAAACTTC
64 TTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAACAAAGCTCAATTTAAGTGAAACTTC
* * *
28609 AAACCCCCATCTTCCTGATGAGATATAGAGAAGTGGGTCAAAGCAATAAAGCAGTTACCTTCCTG
129 AAACCCTCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCAGTTACCTTCCTT
28674 ATGAGATACAGAGAAG
194 ATGAGATACAGAGAAG
*
28690 TGAACCAAATCTATCTTCCTGATGAGATACAGAGAAGTGGAATTAAAACAATGAGGCGGTCATCT
1 TGAACCAAATCTGTCTTCCTGATGAGATACAGAGAAGT-GAATTAAAACAATGAGGCGGTCATCT
28755 TCCTGATGAGATACTA-AGAAGTAGACCAAATCAATGAAACAAAG--CAATTTAAGTGAAACTTC
65 TCCTGATGAGATAC-AGAGAAGTAGACCAAATCAATGAAACAAAGCTCAATTTAAGTGAAACTTC
* * * *
28817 AAACCCTCATCTTCCTGATAAGATACAGAGAAGTGGGTTAAAGCAGTAAAGCGGTTACCTT-CTT
129 AAACCCTCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCAGTTACCTTCCTT
*
28881 GATAAGATACAGAGAAG
194 -ATGAGATACAGAGAAG
* * * * *
28898 TGAATCAAATCTGTCTTCCTGATGAGATACAAAAAAGTGGATTAAAATAATGAGGCGGTCATCTT
1 TGAACCAAATCTGTCTTCCTGATGAGATACAGAGAAGTGAATTAAAACAATGAGGCGGTCATCTT
* ** *
28963 CTTGATGAGATATTGAGAAGTAGATCAAATCAATGAAAC
66 CCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAAC
29002 GGAGATCGAT
Statistics
Matches: 466, Mismatches: 49, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
207 61 0.13
208 122 0.26
209 36 0.08
210 244 0.52
211 3 0.01
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (209 bp):
TGAACCAAATCTGTCTTCCTGATGAGATACAGAGAAGTGAATTAAAACAATGAGGCGGTCATCTT
CCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAACAAAGCTCAATTTAAGTGAAACTTCAA
ACCCTCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCAGTTACCTTCCTTAT
GAGATACAGAGAAG
Found at i:28783 original size:86 final size:85
Alignment explanation
Indices: 28617--28786 Score: 218
Period size: 86 Copynumber: 2.0 Consensus size: 85
28607 TCAAACCCCC
* * * *
28617 ATCTTCCTGATGAGATATAGAGAAGTGGGTCAAAGCAATAAAGCAGTTACCTTCCTGATGAGATA
1 ATCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATAAAGCAGTCACCTTCCTGATGAGATA
28682 CAGAGAAGTGAACCAAATCT
66 CAGAGAAGTGAACCAAATCT
* * * * *
28702 ATCTTCCTGATGAGATACAGAGAAGTGGAATTAAAACAATGAGGCGGTCATCTTCCTGATGAGAT
1 ATCTTCCTGATGAGATACAGAGAAGTGG-ATCAAAACAATAAAGCAGTCACCTTCCTGATGAGAT
28767 ACTA-AGAAGT-AGACCAAATC
65 AC-AGAGAAGTGA-ACCAAATC
28787 AATGAAACAA
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
85 28 0.38
86 44 0.60
87 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (85 bp):
ATCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATAAAGCAGTCACCTTCCTGATGAGATA
CAGAGAAGTGAACCAAATCT
Found at i:35745 original size:51 final size:51
Alignment explanation
Indices: 35667--35763 Score: 160
Period size: 51 Copynumber: 1.9 Consensus size: 51
35657 TTATTCTATC
*
35667 AACTTCAATAACAATACTGTAAGTTGCGGTATATGTTGATGATTTCGTATA
1 AACTTCAACAACAATACTGTAAGTTGCGGTATATGTTGATGATTTCGTATA
*
35718 AACTTCAACAACGATACTGTATA-TTGCGGTATATGTTGATGATTTC
1 AACTTCAACAACAATACTGTA-AGTTGCGGTATATGTTGATGATTTC
35764 ATAATCAACG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (51 bp):
AACTTCAACAACAATACTGTAAGTTGCGGTATATGTTGATGATTTCGTATA
Found at i:38076 original size:299 final size:300
Alignment explanation
Indices: 37533--38143 Score: 1100
Period size: 299 Copynumber: 2.0 Consensus size: 300
37523 ACGAATGATA
*
37533 AAAAC-ACAACTTAAGTCAACGATTTCAACTATGCAAGTCGTTTAAAATAGATCGTTAACTCCTT
1 AAAACAACAACTTAAGTCAACGATCTCAACTATGCAAGTCGTTTAAAATAGATCGTTAACTCCTT
*
37597 TGACGTCACCCAACTAAACACCCAATTGAACCACGTTAATTTGTTCTTTGCTAAAATAAAACAAC
66 TGACGTCACCCAACTAAACACCCAATTGAACCACGTCAATTTGTTCTTTGCTAAAATAAAACAAC
* *
37662 AATTACGAATTTAGTTATTTTACCAACAATGCATTGATCCAAGCATCTAACAACGAGCCCTCTTG
131 AATTACGAATTTAATTATTTTACCAACAATGCATTGATCCAAGCATCTAACAACAAGCCCTCTTG
37727 AAACAAATACCTAGGTGAAGAGCAAAGAATGATTTTGGTTCTCACAGTTTTAACACCG-TTTTTT
196 AAACAAATACCTAGGTGAAGAGCAAAGAATGATTTTGGTTCTCACAGTTTTAACACCGTTTTTTT
*
37791 TTTCGGTCTTAACAATCAAAAGTAAGTAGTTAGAACTAAT
261 TTTCGATCTTAACAATCAAAAGTAAGTAGTTAGAACTAAT
*
37831 AAAACAACAACTTAAGTCAACGATCTCAACTGTGCAAGTCGTTTAAAATAGATCGTTAACTCCTT
1 AAAACAACAACTTAAGTCAACGATCTCAACTATGCAAGTCGTTTAAAATAGATCGTTAACTCCTT
* *
37896 TGACGTCACCCAACTACACACCCAATTGAACCACGTCAATTTGTTCTTTGCTAAAATGAAACAAC
66 TGACGTCACCCAACTAAACACCCAATTGAACCACGTCAATTTGTTCTTTGCTAAAATAAAACAAC
* * *
37961 AATTTCGAATTTAATTATTTTACCAACAATGCATTGATCCAAGCATCTAACAATAAGTCCTCTTG
131 AATTACGAATTTAATTATTTTACCAACAATGCATTGATCCAAGCATCTAACAACAAGCCCTCTTG
*
38026 AAACGAATACCTAGGTGAAGAGCAAAGAATGATTTTGGTTCTCACAGTTTTAACACCGTTTTTTT
196 AAACAAATACCTAGGTGAAGAGCAAAGAATGATTTTGGTTCTCACAGTTTTAACACCGTTTTTTT
38091 TTTCGATCTTAACAATCAAAAGTAAGTAGTTAGAACTAAT
261 TTTCGATCTTAACAATCAAAAGTAAGTAGTTAGAACTAAT
38131 AAAACAACAACTT
1 AAAACAACAACTT
38144 TGTTTCTAAC
Statistics
Matches: 299, Mismatches: 12, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
298 5 0.02
299 236 0.79
300 58 0.19
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.30
Consensus pattern (300 bp):
AAAACAACAACTTAAGTCAACGATCTCAACTATGCAAGTCGTTTAAAATAGATCGTTAACTCCTT
TGACGTCACCCAACTAAACACCCAATTGAACCACGTCAATTTGTTCTTTGCTAAAATAAAACAAC
AATTACGAATTTAATTATTTTACCAACAATGCATTGATCCAAGCATCTAACAACAAGCCCTCTTG
AAACAAATACCTAGGTGAAGAGCAAAGAATGATTTTGGTTCTCACAGTTTTAACACCGTTTTTTT
TTTCGATCTTAACAATCAAAAGTAAGTAGTTAGAACTAAT
Found at i:44164 original size:2 final size:2
Alignment explanation
Indices: 44157--44181 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44147 GCAATTTCTC
44157 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
44182 AGCTTCTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49361 original size:21 final size:22
Alignment explanation
Indices: 49325--49367 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
49315 CAGCAAATGA
*
49325 TTTTAAAATTATTAAAATTATT
1 TTTTAAAAATATTAAAATTATT
49347 TTTTAAAAATA-TAAAATTATT
1 TTTTAAAAATATTAAAATTATT
49368 AAAATTATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTTAAAAATATTAAAATTATT
Found at i:53954 original size:20 final size:21
Alignment explanation
Indices: 53923--53970 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
53913 AATTGTGAAT
53923 AAAATATT-AAATAATGTCT-G
1 AAAAT-TTGAAATAATGTCTCG
* *
53943 AAAATTTGAAATGATGTGTCG
1 AAAATTTGAAATAATGTCTCG
53964 AAAATTT
1 AAAATTT
53971 TGCAATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 14 0.58
21 8 0.33
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.35
Consensus pattern (21 bp):
AAAATTTGAAATAATGTCTCG
Found at i:57000 original size:13 final size:14
Alignment explanation
Indices: 56973--57001 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
56963 CTCATAACCC
56973 CAAACCCTCAAACT
1 CAAACCCTCAAACT
56987 CAAACCCT-AAACT
1 CAAACCCTCAAACT
57000 CA
1 CA
57002 TAATCCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.45, C:0.41, G:0.00, T:0.14
Consensus pattern (14 bp):
CAAACCCTCAAACT
Found at i:63387 original size:31 final size:28
Alignment explanation
Indices: 63341--63397 Score: 69
Period size: 31 Copynumber: 1.9 Consensus size: 28
63331 TTGATTTTGA
* *
63341 TTTTTTTTTTTTAATTTGATATTTAAGT
1 TTTTTTTTTTTTAATTTAATACTTAAGT
63369 TTTTTTTTTGTGTCTAATTTAATACTTAA
1 TTTTTTTTT-T-T-TAATTTAATACTTAA
63398 ATTTGGTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 9 0.38
29 1 0.04
30 1 0.04
31 13 0.54
ACGTcount: A:0.23, C:0.04, G:0.07, T:0.67
Consensus pattern (28 bp):
TTTTTTTTTTTTAATTTAATACTTAAGT
Found at i:66264 original size:4 final size:4
Alignment explanation
Indices: 66257--66283 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
66247 GTATGAATGA
66257 ATGC ATGC ATGC ATGC ATGC ATGC ATG
1 ATGC ATGC ATGC ATGC ATGC ATGC ATG
66284 TTCAAGCACT
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:0.22, G:0.26, T:0.26
Consensus pattern (4 bp):
ATGC
Found at i:70615 original size:2 final size:2
Alignment explanation
Indices: 70608--70640 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
70598 TCAATTGCTT
70608 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
70641 TGAAATTTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:73325 original size:2 final size:2
Alignment explanation
Indices: 73318--73352 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
73308 TCATTAATTA
73318 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
73353 ATCCCAGCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:73982 original size:6 final size:6
Alignment explanation
Indices: 73950--73984 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
73940 TTGTGGTTGT
* *
73950 GGTGGC GGCGGC GGCGGC GGTGGC GGTGGC GGTGG
1 GGTGGC GGTGGC GGTGGC GGTGGC GGTGGC GGTGG
73985 GGCTTGTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.20, G:0.69, T:0.11
Consensus pattern (6 bp):
GGTGGC
Found at i:83717 original size:2 final size:2
Alignment explanation
Indices: 83710--83739 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
83700 ATGTAAGAAC
83710 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
83740 TAGTAGTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:84770 original size:20 final size:21
Alignment explanation
Indices: 84731--84772 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
84721 CAACATATGA
*
84731 TTTTAAAATTATTAAAATTAT
1 TTTTAAAAATATTAAAATTAT
*
84752 TTTTAAAAATA-TAATATTAT
1 TTTTAAAAATATTAAAATTAT
84772 T
1 T
84773 AAAATTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTTAAAAATATTAAAATTAT
Found at i:84774 original size:17 final size:17
Alignment explanation
Indices: 84749--84783 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
84739 TTATTAAAAT
*
84749 TATTTTTAAAAATATAA
1 TATTATTAAAAATATAA
*
84766 TATTATTAAAATTATAA
1 TATTATTAAAAATATAA
84783 T
1 T
84784 CATCATCGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TATTATTAAAAATATAA
Found at i:85225 original size:18 final size:15
Alignment explanation
Indices: 85189--85230 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
85179 TAGTTGCGAA
85189 CTGTTGTTTCTTGTT
1 CTGTTGTTTCTTGTT
85204 CTGTTGTTTCTTGTT
1 CTGTTGTTTCTTGTT
*
85219 CTGCTGTTTCTT
1 CTGTTGTTTCTT
85231 TTAGTGTGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.00, C:0.17, G:0.19, T:0.64
Consensus pattern (15 bp):
CTGTTGTTTCTTGTT
Found at i:85505 original size:30 final size:30
Alignment explanation
Indices: 85469--85569 Score: 143
Period size: 29 Copynumber: 3.4 Consensus size: 30
85459 ATTAAAATTA
85469 TTTAATAATTTTTTTATTTTAAAAAATAAT
1 TTTAATAATTTTTTTATTTTAAAAAATAAT
* *
85499 TTTAATAA-TTTTATATTTTAAAAAACAAT
1 TTTAATAATTTTTTTATTTTAAAAAATAAT
* *
85528 TTCAA-ATTTTTTTATATTTTAAAAAATAAT
1 TTTAATAATTTTTT-TATTTTAAAAAATAAT
85558 TTTAATAATTTT
1 TTTAATAATTTT
85570 AAAATCATTT
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
28 1 0.02
29 27 0.45
30 27 0.45
31 5 0.08
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (30 bp):
TTTAATAATTTTTTTATTTTAAAAAATAAT
Found at i:85570 original size:29 final size:29
Alignment explanation
Indices: 85469--85570 Score: 141
Period size: 30 Copynumber: 3.4 Consensus size: 29
85459 ATTAAAATTA
*
85469 TTTAATAATTTTTTTATTTTAAAAAATAAT
1 TTTAATAA-TTTTATATTTTAAAAAATAAT
*
85499 TTTAATAATTTTATATTTTAAAAAACAAT
1 TTTAATAATTTTATATTTTAAAAAATAAT
* **
85528 TTCAAATTTTTTTATATTTTAAAAAATAAT
1 TT-TAATAATTTTATATTTTAAAAAATAAT
85558 TTTAATAATTTTA
1 TTTAATAATTTTA
85571 AAATCATTTG
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
29 29 0.47
30 33 0.53
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (29 bp):
TTTAATAATTTTATATTTTAAAAAATAAT
Found at i:87391 original size:20 final size:21
Alignment explanation
Indices: 87366--87412 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
87356 ATGCAAAGAG
*
87366 AAAAAA-CTATAAAAAATAAA
1 AAAAAAGCTAGAAAAAATAAA
*
87386 AAAAAAGCTAGAAGAAATAAA
1 AAAAAAGCTAGAAAAAATAAA
87407 AAAAAA
1 AAAAAA
87413 AAGTTACGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.79, C:0.04, G:0.06, T:0.11
Consensus pattern (21 bp):
AAAAAAGCTAGAAAAAATAAA
Found at i:88617 original size:38 final size:38
Alignment explanation
Indices: 88550--88623 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
88540 TAATATATAC
*** * *
88550 TAGATAGTTTTTCAATTTTGTTTGTAAAAGTATTAGAG
1 TAGATAGTTTTTCAATTCCATTTGGAAAAGAATTAGAG
88588 TAGATAGTTTTTCAATTCCATTTGGAAAAGAATTAG
1 TAGATAGTTTTTCAATTCCATTTGGAAAAGAATTAG
88624 CTTTTATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (38 bp):
TAGATAGTTTTTCAATTCCATTTGGAAAAGAATTAGAG
Found at i:92135 original size:175 final size:176
Alignment explanation
Indices: 91912--92257 Score: 570
Period size: 175 Copynumber: 2.0 Consensus size: 176
91902 ATATATATAA
* ** *
91912 ATATATATATATCTTTTTTTTTAATATTTATTCTATGTATTATTTATTTATCATTTTATTTTTTT
1 ATATATATATATATCCTTTTTTAATAATTATTCTATGTATTATTTATTTATCATTTTATTTTTTT
* * *
91977 TGTAATAAAGTAATTTAAACGAATAAATAATATAAAAAATGACAGATTTCGAAAGGAAAATACAA
66 CGTAATAAAGAAATATAAACGAATAAATAATATAAAAAATGACAGATTTCGAAAGGAAAATACAA
92042 A-TTTTTTATCAAAATCTTCCTTTTTATGAAAACATAAAATGTAGAT
131 ATTTTTTTATCAAAATCTTCCTTTTT-TGAAAACATAAAATGTAGAT
92088 ATATATATATATATCCTTTTTT-ATAATTATTCTATGTATTATTTATTTATCATTTTATTTTTTT
1 ATATATATATATATCCTTTTTTAATAATTATTCTATGTATTATTTATTTATCATTTTATTTTTTT
*
92152 CGTAATAAAGAAATATAAAGGAATAAATAATATAAAAAATGACAGATTTCGAAAGGAAAATACAA
66 CGTAATAAAGAAATATAAACGAATAAATAATATAAAAAATGACAGATTTCGAAAGGAAAATACAA
*
92217 ATTTTTTTTTATCAAAATCTTCCTTTTTTGAAAACCTAAAA
131 A--TTTTTTTATCAAAATCTTCCTTTTTTGAAAACATAAAA
92258 AGATCTGTTC
Statistics
Matches: 158, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
175 103 0.65
176 19 0.12
177 12 0.08
178 24 0.15
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.45
Consensus pattern (176 bp):
ATATATATATATATCCTTTTTTAATAATTATTCTATGTATTATTTATTTATCATTTTATTTTTTT
CGTAATAAAGAAATATAAACGAATAAATAATATAAAAAATGACAGATTTCGAAAGGAAAATACAA
ATTTTTTTATCAAAATCTTCCTTTTTTGAAAACATAAAATGTAGAT
Found at i:97349 original size:38 final size:38
Alignment explanation
Indices: 97293--97373 Score: 153
Period size: 38 Copynumber: 2.1 Consensus size: 38
97283 TGGAAGAAGC
*
97293 AGAGAAAGGAAAAAACCCTGTAATAAGCCCAAGAGAGG
1 AGAGTAAGGAAAAAACCCTGTAATAAGCCCAAGAGAGG
97331 AGAGTAAGGAAAAAACCCTGTAATAAGCCCAAGAGAGG
1 AGAGTAAGGAAAAAACCCTGTAATAAGCCCAAGAGAGG
97369 AGAGT
1 AGAGT
97374 GAAGACCCTC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.48, C:0.15, G:0.27, T:0.10
Consensus pattern (38 bp):
AGAGTAAGGAAAAAACCCTGTAATAAGCCCAAGAGAGG
Found at i:104964 original size:49 final size:49
Alignment explanation
Indices: 104892--105366 Score: 382
Period size: 49 Copynumber: 9.7 Consensus size: 49
104882 AGATATGCAA
* * *
104892 GGAAAGATTTAAGTCGTAACGGTGAACCTTGTACCTCAGAAACATGAAG
1 GGAAAGATTTAAGCCGCAACGGCGAACCTTGTACCTCAGAAACATGAAG
* * * * **
104941 GGAAAGATTTAAGCCGCAACGGTGAATCTAGTA-C-CATGAAGATATTTAG
1 GGAAAGATTTAAGCCGCAACGGCGAACCTTGTACCTCA-GAA-ACATGAAG
* *
104990 GGAAATG-TTTAAGTCGCAACAGCGAACCTTGTACCTCAGAAACATGAAG
1 GGAAA-GATTTAAGCCGCAACGGCGAACCTTGTACCTCAGAAACATGAAG
* * * * * *
105039 GGAATA-ATTTAAGCAGCAATGGCGAATCC-AGTACCAC-GAAGATATTAAG
1 GGAA-AGATTTAAGCCGCAACGGCGAA-CCTTGTACCTCAGAA-ACATGAAG
* *
105088 GGAAAGATTTAAGCCGCAACGACGAACCTTATACCTCAGAAACATGAAG
1 GGAAAGATTTAAGCCGCAACGGCGAACCTTGTACCTCAGAAACATGAAG
* * * *
105137 GAAAAGATTTAAGCCGCAACGGCGAATCTAGTA--TCACGAAGCTAT-AGAG
1 GGAAAGATTTAAGCCGCAACGGCGAACCTTGTACCTCA-GAAAC-ATGA-AG
* * * *
105186 GGAAAGGTTTAAGTCGCAACGAC-AACCTTGTACCTCAAAAACATGAAG
1 GGAAAGATTTAAGCCGCAACGGCGAACCTTGTACCTCAGAAACATGAAG
* * * * *
105234 GG-AAGAATTTAAGCCGCAACGGCGAATCTAGTACCAC-GAAGATATGGAG
1 GGAAAG-ATTTAAGCCGCAACGGCGAACCTTGTACCTCAGAA-ACATGAAG
* * * * * *
105283 GGAAAGATTTAAGTCGCAACGACGAACCTTATACCT-AAAAACATAAAA
1 GGAAAGATTTAAGCCGCAACGGCGAACCTTGTACCTCAGAAACATGAAG
* * * *
105331 GGAAAGATTAAAGCCGTAACGGCGAATCTTCTACCT
1 GGAAAGATTTAAGCCGCAACGGCGAACCTTGTACCT
105367 TGAAGTTACA
Statistics
Matches: 332, Mismatches: 71, Indels: 47
0.74 0.16 0.10
Matches are distributed among these distances:
47 8 0.02
48 78 0.23
49 227 0.68
50 17 0.05
51 2 0.01
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.20
Consensus pattern (49 bp):
GGAAAGATTTAAGCCGCAACGGCGAACCTTGTACCTCAGAAACATGAAG
Found at i:105049 original size:98 final size:98
Alignment explanation
Indices: 104874--105359 Score: 635
Period size: 98 Copynumber: 5.0 Consensus size: 98
104864 CAGGTTTCAA
* * * **
104874 TACCACAAAGATA-TGCAAGGAAAGATTTAAGTCGTAACGGTGAACCTTGTACCTCAGAAACATG
1 TACCACGAAGATATTG-AGGGAAAGATTTAAGTCGCAACGACGAACCTTGTACCTCAGAAACATG
*
104938 AAGGGAAAGATTTAAGCCGCAACGGTGAATCTAG
65 AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
* *
104972 TACCATGAAGATATTTAGGGAAATG-TTTAAGTCGCAAC-AGCGAACCTTGTACCTCAGAAACAT
1 TACCACGAAGATATTGAGGGAAA-GATTTAAGTCGCAACGA-CGAACCTTGTACCTCAGAAACAT
* * *
105035 GAAGGGAATA-ATTTAAGCAGCAATGGCGAATCCAG
64 GAAGGGAA-AGATTTAAGCCGCAACGGCGAATCTAG
* * *
105070 TACCACGAAGATATTAAGGGAAAGATTTAAGCCGCAACGACGAACCTTATACCTCAGAAACATGA
1 TACCACGAAGATATTGAGGGAAAGATTTAAGTCGCAACGACGAACCTTGTACCTCAGAAACATGA
*
105135 AGGAAAAGATTTAAGCCGCAACGGCGAATCTAG
66 AGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
* * * * *
105168 TATCACGAAGCTATAGAGGGAAAGGTTTAAGTCGCAACGAC-AACCTTGTACCTCAAAAACATGA
1 TACCACGAAGATATTGAGGGAAAGATTTAAGTCGCAACGACGAACCTTGTACCTCAGAAACATGA
105232 AGGG-AAGAATTTAAGCCGCAACGGCGAATCTAG
66 AGGGAAAG-ATTTAAGCCGCAACGGCGAATCTAG
* * * *
105265 TACCACGAAGATATGGAGGGAAAGATTTAAGTCGCAACGACGAACCTTATACCT-AAAAACATAA
1 TACCACGAAGATATTGAGGGAAAGATTTAAGTCGCAACGACGAACCTTGTACCTCAGAAACATGA
* * *
105329 AAGGAAAGATTAAAGCCGTAACGGCGAATCT
66 AGGGAAAGATTTAAGCCGCAACGGCGAATCT
105360 TCTACCTTGA
Statistics
Matches: 341, Mismatches: 37, Indels: 21
0.85 0.09 0.05
Matches are distributed among these distances:
96 3 0.01
97 121 0.35
98 213 0.62
99 4 0.01
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.19
Consensus pattern (98 bp):
TACCACGAAGATATTGAGGGAAAGATTTAAGTCGCAACGACGAACCTTGTACCTCAGAAACATGA
AGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
Found at i:109674 original size:35 final size:35
Alignment explanation
Indices: 109635--109705 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
109625 TAAATAATTA
* ** *
109635 ACTAAATTGTATAGTATTTATTATCATTTATTTAT
1 ACTAAATTATATAAAATTTATTATCAATTATTTAT
*
109670 ACTAAATTATATAAAATTTATTATTAATTATTTAT
1 ACTAAATTATATAAAATTTATTATCAATTATTTAT
109705 A
1 A
109706 TCTAGTCAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (35 bp):
ACTAAATTATATAAAATTTATTATCAATTATTTAT
Found at i:109978 original size:18 final size:19
Alignment explanation
Indices: 109955--109992 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
109945 ATCTATCACC
*
109955 TAAATT-AATTATGAAAAA
1 TAAATTGAATAATGAAAAA
*
109973 TAAATTGAATAATTAAAAA
1 TAAATTGAATAATGAAAAA
109992 T
1 T
109993 CTTGCCATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (19 bp):
TAAATTGAATAATGAAAAA
Found at i:113121 original size:30 final size:30
Alignment explanation
Indices: 113085--113159 Score: 123
Period size: 30 Copynumber: 2.5 Consensus size: 30
113075 CCGTGGAGGA
*
113085 CTTAATTGATTTTTTATTATTTTACGAGAG
1 CTTAATTGATTTTTAATTATTTTACGAGAG
*
113115 CTTAATTGATTTTTAATTATTTTAGGAGAG
1 CTTAATTGATTTTTAATTATTTTACGAGAG
*
113145 CTTAATTTATTTTTA
1 CTTAATTGATTTTTA
113160 GGATTATATA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.28, C:0.05, G:0.12, T:0.55
Consensus pattern (30 bp):
CTTAATTGATTTTTAATTATTTTACGAGAG
Found at i:113365 original size:18 final size:18
Alignment explanation
Indices: 113308--113400 Score: 64
Period size: 18 Copynumber: 5.1 Consensus size: 18
113298 TATTAAAATG
*
113308 TTATAAAAAAATT-GAAAA
1 TTAT-AAAAAATTATAAAA
**
113326 TTATGGAAAATATATCAAAA
1 TTATAAAAAAT-TAT-AAAA
* *
113346 TTATCAAACATTATAAAA
1 TTATAAAAAATTATAAAA
113364 TT-TAAAAAATATATAAAA
1 TTATAAAAAAT-TATAAAA
* * *
113382 CTATTAAATATTATAAAA
1 TTATAAAAAATTATAAAA
113400 T
1 T
113401 ATTATTAATA
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
17 11 0.19
18 26 0.45
19 9 0.16
20 12 0.21
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.33
Consensus pattern (18 bp):
TTATAAAAAATTATAAAA
Found at i:113421 original size:21 final size:20
Alignment explanation
Indices: 113333--113422 Score: 57
Period size: 19 Copynumber: 4.8 Consensus size: 20
113323 AAATTATGGA
* *
113333 AAATA-TATCAAA-ATTATC
1 AAATATTATAAAATATTATT
* **
113351 AAACATTATAAAAT-TTAAA
1 AAATATTATAAAATATTATT
*
113370 AAATA-TAT-AAA-ACTATT
1 AAATATTATAAAATATTATT
113387 AAATATTATAAAATATTATT
1 AAATATTATAAAATATTATT
* *
113407 AATATGTTATGAAATA
1 AA-ATATTATAAAATA
113423 ATGAAAATAT
Statistics
Matches: 54, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
17 10 0.19
18 10 0.19
19 16 0.30
20 7 0.13
21 11 0.20
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (20 bp):
AAATATTATAAAATATTATT
Found at i:113452 original size:11 final size:10
Alignment explanation
Indices: 113332--113450 Score: 67
Period size: 9 Copynumber: 12.4 Consensus size: 10
113322 AAAATTATGG
113332 AAAATA-TAT
1 AAAATATTAT
*
113341 CAAA-ATTAT
1 AAAATATTAT
* *
113350 CAAACATTAT
1 AAAATATTAT
*
113360 AAAAT-TTAA
1 AAAATATTAT
113369 AAAATA-TAT
1 AAAATATTAT
113378 AAAACTA-T-T
1 AAAA-TATTAT
113387 -AAATATTAT
1 AAAATATTAT
113396 AAAATATTATT
1 AAAATATTA-T
* *
113407 AATATGTTAT
1 AAAATATTAT
*
113417 GAAATA--AT
1 AAAATATTAT
*
113425 GAAAATATTAA
1 -AAAATATTAT
113436 ATAAATATTAT
1 A-AAATATTAT
113447 AAAA
1 AAAA
113451 ATTTAGAAAT
Statistics
Matches: 85, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
7 2 0.02
8 7 0.08
9 31 0.36
10 27 0.32
11 18 0.21
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (10 bp):
AAAATATTAT
Found at i:113813 original size:19 final size:18
Alignment explanation
Indices: 113769--113815 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
113759 TTTTAGAACA
113769 TTATAAAAAGTATATAAG
1 TTATAAAAAGTATATAAG
*
113787 TTACTAAAAATTAT-TAAATG
1 TTA-TAAAAAGTATAT-AA-G
113807 TTATAAAAA
1 TTATAAAAA
113816 ATTAAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 4 0.16
19 17 0.68
20 4 0.16
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.36
Consensus pattern (18 bp):
TTATAAAAAGTATATAAG
Found at i:118538 original size:22 final size:20
Alignment explanation
Indices: 118513--118562 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
118503 AAAACTTCTT
118513 AATTTTTTAAATATAAATTTTG
1 AATTTTTTAAA-AT-AATTTTG
* *
118535 AATTTTTGAAAATTATTTTG
1 AATTTTTTAAAATAATTTTG
*
118555 TATTTTTT
1 AATTTTTT
118563 GTTTTGAGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 12 0.50
21 2 0.08
22 10 0.42
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (20 bp):
AATTTTTTAAAATAATTTTG
Found at i:123271 original size:28 final size:28
Alignment explanation
Indices: 123240--123320 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 28
123230 GGATACTCAG
* **
123240 GGGTAAAATGGTAATTTTGGGAAAT-TTA
1 GGGTAAAATGGTAATTTT-AGAAATCCGA
*
123268 GGGTTTAAAATGG-AATTTTAGACATCCGA
1 GGG--TAAAATGGTAATTTTAGAAATCCGA
123297 GGGTAAAATGGTAATTTTTAGAAA
1 GGGTAAAATGGTAA-TTTTAGAAA
123321 AATTAGGATA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
27 8 0.19
28 9 0.21
29 18 0.42
30 8 0.19
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.33
Consensus pattern (28 bp):
GGGTAAAATGGTAATTTTAGAAATCCGA
Found at i:123370 original size:59 final size:58
Alignment explanation
Indices: 123239--123374 Score: 157
Period size: 59 Copynumber: 2.3 Consensus size: 58
123229 TGGATACTCA
* * * * ** *
123239 GGGGTAAAATGGTAA-TTTTGGGAAATTTAGGGTTTAAAATGGAATTTTAGACATCCG
1 GGGGTAAAATGGTAATTTTTAGAAAAATTAGGATAAAAAATGGAATTTTAGAAATCCG
* * *
123296 AGGGTAAAATGGTAATTTTTAGAAAAATTAGGATAAAAAATGGAATTTTTTGAAATTCG
1 GGGGTAAAATGGTAATTTTTAGAAAAATTAGGATAAAAAATGGAA-TTTTAGAAATCCG
*
123355 GGGGTAAAATTGTAATTTTT
1 GGGGTAAAATGGTAATTTTT
123375 GAGAGTTTTG
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
57 14 0.22
58 23 0.35
59 28 0.43
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTAGAAAAATTAGGATAAAAAATGGAATTTTAGAAATCCG
Found at i:123429 original size:58 final size:57
Alignment explanation
Indices: 123226--123433 Score: 202
Period size: 58 Copynumber: 3.6 Consensus size: 57
123216 AAGCGAGACT
* * *
123226 TTTTGGATACTC-AGGGGTAAAATGGTAATTTTGGGAAATTTAGGGTTTAAAATGGAA
1 TTTTGGATATTCGA-GGGTAAAATGGTAATTTTGAGAAATTTAGGGTTAAAAATGGAA
* * * * * * *
123283 TTTTAGACATCCGAGGGTAAAATGGTAATTTTTAGAAAAATTAGGATAAAAAATGGAA
1 TTTTGGATATTCGAGGGTAAAATGGTAATTTTGAG-AAATTTAGGGTTAAAAATGGAA
* * * * ** * *
123341 TTTTTTGAAATTCGGGGGTAAAATTGTAATTTTTGAGAGTTTTGGGGTTAAAAATGGAG
1 -TTTTGGATATTCGAGGGTAAAATGGTAA-TTTTGAGAAATTTAGGGTTAAAAATGGAA
*
123400 TTTTGGATATTCGAGGGTAAAATGATAATTTTGA
1 TTTTGGATATTCGAGGGTAAAATGGTAATTTTGA
123434 AAGTTTCGAC
Statistics
Matches: 119, Mismatches: 28, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
57 33 0.28
58 42 0.35
59 38 0.32
60 6 0.05
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.36
Consensus pattern (57 bp):
TTTTGGATATTCGAGGGTAAAATGGTAATTTTGAGAAATTTAGGGTTAAAAATGGAA
Found at i:123462 original size:30 final size:29
Alignment explanation
Indices: 123331--123617 Score: 196
Period size: 29 Copynumber: 9.8 Consensus size: 29
123321 AATTAGGATA
* * *
123331 AAAAATGGAATTTTTTGAA-ATTCGGGGGT
1 AAAAATGGAATTTTTGGAAGTTTC-GAGGT
* * * *
123360 AAAATTGTAATTTTT-GAGAGTTTTGGGGTT
1 AAAAATGGAATTTTTGGA-AGTTTCGAGG-T
*
123390 AAAAATGG-AGTTTTGG-A-TATTCGAGGGT
1 AAAAATGGAATTTTTGGAAGT-TTCGA-GGT
* * *
123418 -AAAAT-GATAATTTTGAAAGTTTCGACGT
1 AAAAATGGA-ATTTTTGGAAGTTTCGAGGT
* * *
123446 CAAAAATGGATTTTTTGG-AGGTTCGGAAGT
1 -AAAAATGGAATTTTTGGAAGTTTC-GAGGT
*
123476 AAAAATGTAATTTTTGGAAGTTTCGAGGT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGT
* *
123505 AAAAATGTAATTTTTGGAAGTTTTGAGGT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGT
*
123534 CAAAAATGGAATTTTTGGAAGTTT-AAGGGT
1 -AAAAATGGAATTTTTGGAAGTTTCGA-GGT
** * * *
123564 AAAAATATAATTTTTGAAAGTTTTGGGGT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGT
123593 AAAAAATGGAATTTTTGGATAGTTT
1 -AAAAATGGAATTTTTGGA-AGTTT
123618 AGGGACCTCC
Statistics
Matches: 206, Mismatches: 32, Indels: 38
0.75 0.12 0.14
Matches are distributed among these distances:
26 1 0.00
27 6 0.03
28 15 0.07
29 107 0.52
30 70 0.34
31 7 0.03
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.38
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTTCGAGGT
Found at i:123462 original size:58 final size:56
Alignment explanation
Indices: 123297--123523 Score: 176
Period size: 58 Copynumber: 3.9 Consensus size: 56
123287 AGACATCCGA
**
123297 GGGTAAAATGGTAATTTTTAGAAAAATT--AGGATAAAAAATGGAATTTTTT-GAAATTCGG
1 GGGTAAAAT-GTAATTTTT-GAAAGTTTCGAGG-T-AAAAATGG-ATTTTTTGGAAATTC-G
* * * * *
123356 GGGTAAAATTGTAATTTTTGAGAGTTTTGGGGTTAAAAATGGA-GTTTTGGATATTCG
1 GGGTAAAA-TGTAATTTTTGAAAGTTTCGAGG-TAAAAATGGATTTTTTGGAAATTCG
* **
123413 AGGGTAAAATGATAA-TTTTGAAAGTTTCGACGTCAAAAATGGATTTTTTGGAGGTTCG
1 -GGGTAAAATG-TAATTTTTGAAAGTTTCGAGGT-AAAAATGGATTTTTTGGAAATTCG
* * * *
123471 GAAGTAAAAATGTAATTTTTGGAAGTTTCGAGGTAAAAATGTAATTTTTGGAA
1 G-GGT-AAAATGTAATTTTTGAAAGTTTCGAGGTAAAAATGGATTTTTTGGAA
123524 GTTTTGAGGT
Statistics
Matches: 137, Mismatches: 20, Indels: 23
0.76 0.11 0.13
Matches are distributed among these distances:
56 1 0.01
57 30 0.22
58 55 0.40
59 47 0.34
60 4 0.03
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (56 bp):
GGGTAAAATGTAATTTTTGAAAGTTTCGAGGTAAAAATGGATTTTTTGGAAATTCG
Found at i:123526 original size:88 final size:87
Alignment explanation
Indices: 123409--123617 Score: 235
Period size: 88 Copynumber: 2.4 Consensus size: 87
123399 GTTTTGGATA
* * *
123409 TTCGAGGGT-AAAATGATAA-TTTTGAAAGTTTCGACGTCAAAAATGGATTTTTTGGAGGTTCGG
1 TTCGA-GGTAAAAATG-TAATTTTTGGAAGTTTCGACGTCAAAAATGGAATTTTTGGAAGTT--G
* *
123472 AA-GTAAAAATGTAATTTTTGGAAGT
62 AAGGTAAAAATATAATTTTTGAAAGT
* * *
123497 TTCGAGGTAAAAATGTAATTTTTGGAAGTTTTGAGGTCAAAAATGGAATTTTTGGAAGTTTAAGG
1 TTCGAGGTAAAAATGTAATTTTTGGAAGTTTCGACGTCAAAAATGGAATTTTTGGAAGTTGAA-G
123562 GTAAAAATATAATTTTTGAAAGT
65 GTAAAAATATAATTTTTGAAAGT
* * *
123585 TTTGGGGTAAAAAATGGAATTTTTGGATAGTTT
1 TTCGAGGT-AAAAATGTAATTTTTGGA-AGTTT
123618 AGGGACCTCC
Statistics
Matches: 104, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
86 2 0.02
87 6 0.06
88 74 0.71
89 17 0.16
90 5 0.05
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.37
Consensus pattern (87 bp):
TTCGAGGTAAAAATGTAATTTTTGGAAGTTTCGACGTCAAAAATGGAATTTTTGGAAGTTGAAGG
TAAAAATATAATTTTTGAAAGT
Found at i:123539 original size:59 final size:58
Alignment explanation
Indices: 123428--123617 Score: 211
Period size: 59 Copynumber: 3.2 Consensus size: 58
123418 AAAATGATAA
* * * * * ** * *
123428 TTTTGAAAGTTTCGACGTCAAAAATGGATTTTTTGGAGGTTCGGAAGTAAAAATGTAAT
1 TTTTGGAAGTTTCGAGGT-AAAAATGTAATTTTTGGAAGTTTTGAGGTAAAAATGGAAT
123487 TTTTGGAAGTTTCGAGGTAAAAATGTAATTTTTGGAAGTTTTGAGGTCAAAAATGGAAT
1 TTTTGGAAGTTTCGAGGTAAAAATGTAATTTTTGGAAGTTTTGAGGT-AAAAATGGAAT
* * * *
123546 TTTTGGAAGTTT-AAGGGTAAAAATATAATTTTTGAAAGTTTTGGGGTAAAAAATGGAAT
1 TTTTGGAAGTTTCGA-GGTAAAAATGTAATTTTTGGAAGTTTTGAGGT-AAAAATGGAAT
123605 TTTTGGATAGTTT
1 TTTTGGA-AGTTT
123618 AGGGACCTCC
Statistics
Matches: 114, Mismatches: 14, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
58 24 0.21
59 85 0.75
60 5 0.04
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.38
Consensus pattern (58 bp):
TTTTGGAAGTTTCGAGGTAAAAATGTAATTTTTGGAAGTTTTGAGGTAAAAATGGAAT
Found at i:124696 original size:24 final size:24
Alignment explanation
Indices: 124669--124714 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
124659 ATTTAATAAA
124669 TATTATCATTAATAAAATTATTAT
1 TATTATCATTAATAAAATTATTAT
* *
124693 TATTATCATTAGTGAAATTATT
1 TATTATCATTAATAAAATTATT
124715 TAATATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.50
Consensus pattern (24 bp):
TATTATCATTAATAAAATTATTAT
Found at i:124697 original size:18 final size:16
Alignment explanation
Indices: 124642--124694 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
124632 GTTTTCTTTT
124642 TTATTAAT--ATATTAA
1 TTATTAATAAATATT-A
124657 TTATTTAATAAATATTA
1 TTA-TTAATAAATATTA
*
124674 TCATTAATAAA-ATTA
1 TTATTAATAAATATTA
124689 TTATTA
1 TTATTA
124695 TTATCATTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 12 0.36
16 13 0.39
17 3 0.09
18 5 0.15
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
TTATTAATAAATATTA
Found at i:125502 original size:18 final size:16
Alignment explanation
Indices: 125480--125584 Score: 75
Period size: 17 Copynumber: 6.1 Consensus size: 16
125470 ATAATAAGTT
125480 TTAAATTTAAATATAAA
1 TTAAATTTAAA-ATAAA
* *
125497 TCTAAATTTATATTAAA
1 T-TAAATTTAAAATAAA
*
125514 TTTAAATTTTAAAACAAA
1 -TTAAA-TTTAAAATAAA
125532 TTAAAATTTAAAATAAA
1 TT-AAATTTAAAATAAA
* * *
125549 TTTATATTCAAAGTAAA
1 -TTAAATTTAAAATAAA
**
125566 TTTAACCTTAAAATAAA
1 -TTAAATTTAAAATAAA
125583 TT
1 TT
125585 TTAGAATGAG
Statistics
Matches: 69, Mismatches: 14, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
16 2 0.03
17 44 0.64
18 23 0.33
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (16 bp):
TTAAATTTAAAATAAA
Found at i:125526 original size:7 final size:6
Alignment explanation
Indices: 125479--125570 Score: 57
Period size: 6 Copynumber: 15.8 Consensus size: 6
125469 TATAATAAGT
* * *
125479 TTTAAA TTTAAA TATAAA TCTAAA TTTATA -TTAAA TTTAAA TTTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA
** * * * * *
125527 -ACAAA TTAAAA TTTAAA -ATAAA TTTATA TTCAAA -GTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
125571 CCTTAAAATA
Statistics
Matches: 63, Mismatches: 18, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
5 14 0.22
6 43 0.68
7 6 0.10
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:127091 original size:103 final size:103
Alignment explanation
Indices: 126912--127105 Score: 361
Period size: 103 Copynumber: 1.9 Consensus size: 103
126902 TTGAGCCACC
*
126912 AGTACAGTAATGTGGTTTAACCACTAGATAAGGCAGATTATTAAATTGCCAACACTTCCTTCATC
1 AGTACAGTAATGTGGTTTAACCACTAGATAAGGCAGATTATTAAACTGCCAACACTTCCTTCATC
126977 ACATCATTAATCCACCCCAATGGACAATAAACCACCTG
66 ACATCATTAATCCACCCCAATGGACAATAAACCACCTG
*
127015 AGTACAGTAATGTGGTTTAACCACTAGATAAGGCAGATTATTAAACTGCCAACACTTCCTTCGTC
1 AGTACAGTAATGTGGTTTAACCACTAGATAAGGCAGATTATTAAACTGCCAACACTTCCTTCATC
*
127080 ACATCATTAATCCACCCCAATTGACA
66 ACATCATTAATCCACCCCAATGGACA
127106 TGCACATATT
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 88 1.00
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (103 bp):
AGTACAGTAATGTGGTTTAACCACTAGATAAGGCAGATTATTAAACTGCCAACACTTCCTTCATC
ACATCATTAATCCACCCCAATGGACAATAAACCACCTG
Found at i:127432 original size:33 final size:33
Alignment explanation
Indices: 127395--127459 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
127385 GACGGCCTAA
** *
127395 CACAAGCCTGTGTAGCCCACACGGGTTTATTAG
1 CACAAGCCCATGTAGCCCACACGGGTCTATTAG
* *
127428 CACAAGCCCATGTTGCCCACATGGGTCTATTA
1 CACAAGCCCATGTAGCCCACACGGGTCTATTA
127460 ACCCAGCCCG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.25
Consensus pattern (33 bp):
CACAAGCCCATGTAGCCCACACGGGTCTATTAG
Found at i:136047 original size:29 final size:29
Alignment explanation
Indices: 136002--136058 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
135992 CCCTTGCTAT
*
136002 TCTTTAGAGTCCCACTTTCAATTGTGTAA
1 TCTTTAGAGTCCCACTTTCAACTGTGTAA
*
136031 TCTTTAGAGTCCTACTTTCAACTGTGTA
1 TCTTTAGAGTCCCACTTTCAACTGTGTA
136059 CTTATACCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (29 bp):
TCTTTAGAGTCCCACTTTCAACTGTGTAA
Done.