Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008522.1 Hibiscus syriacus cultivar Beakdansim tig00111390_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: 1416293
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 8
Found at i:1296177 original size:21 final size:21
Alignment explanation
Indices: 1296128--1296178 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1296118 CTCTTACTAG
*
1296128 GTATCAATACACCTTGAATGT
1 GTATCGATACACCTTGAATGT
**
1296149 GTGCCGATACACCTTGAATGT
1 GTATCGATACACCTTGAATGT
1296170 GTATCGATA
1 GTATCGATA
1296179 TCCCATCGAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (21 bp):
GTATCGATACACCTTGAATGT
Found at i:1297539 original size:18 final size:18
Alignment explanation
Indices: 1297516--1297552 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1297506 AAAAACCCCC
1297516 GGTGCTAGCTCTTCACGA
1 GGTGCTAGCTCTTCACGA
1297534 GGTGCTAGCTCTTCACGA
1 GGTGCTAGCTCTTCACGA
1297552 G
1 G
1297553 CTACCCCGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.27, G:0.30, T:0.27
Consensus pattern (18 bp):
GGTGCTAGCTCTTCACGA
Found at i:1298597 original size:21 final size:21
Alignment explanation
Indices: 1298571--1298624 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
1298561 AAATAAGGAG
1298571 GTATCGATACCCTCTTAATGA
1 GTATCGATACCCTCTTAATGA
1298592 GTATCGATACCCTCTTAATGA
1 GTATCGATACCCTCTTAATGA
1298613 GTATCGATACCC
1 GTATCGATACCC
1298625 CTCAAACATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (21 bp):
GTATCGATACCCTCTTAATGA
Found at i:1298692 original size:24 final size:23
Alignment explanation
Indices: 1298665--1298724 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 23
1298655 TACCCCACAG
1298665 GGTACCGATACCCCTATA-CAAAGA
1 GGTACCGATACCCCTA-ACCAAA-A
*
1298689 GGTACCGATA--CCTAACCCAAA
1 GGTACCGATACCCCTAACCAAAA
1298710 GGTACCGATACCCCT
1 GGTACCGATACCCCT
1298725 CGTGTTGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
21 12 0.38
22 7 0.22
23 3 0.09
24 10 0.31
ACGTcount: A:0.33, C:0.33, G:0.17, T:0.17
Consensus pattern (23 bp):
GGTACCGATACCCCTAACCAAAA
Found at i:1300296 original size:29 final size:31
Alignment explanation
Indices: 1300228--1300287 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
1300218 CTAATATTAG
1300228 ATTATTTATACA--TAGGTCCCTAGACTTTAT
1 ATTATTT-TACACTTAGGTCCCTAGACTTTAT
1300258 ATTATTTTACACTTAGGTCCCTAGACTTTA
1 ATTATTTTACACTTAGGTCCCTAGACTTTA
1300288 GTTTTTTACA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 4 0.14
30 7 0.25
31 17 0.61
ACGTcount: A:0.28, C:0.18, G:0.10, T:0.43
Consensus pattern (31 bp):
ATTATTTTACACTTAGGTCCCTAGACTTTAT
Found at i:1303028 original size:23 final size:22
Alignment explanation
Indices: 1302989--1303033 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
1302979 TTATTATATT
*
1302989 TTTAATATTTTGTATTTAATTTA
1 TTTAATATTTTGAATTT-ATTTA
1303012 TTTAAGTATTTT-AATTTATTTA
1 TTTAA-TATTTTGAATTTATTTA
1303034 ATATTTTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 9 0.45
24 6 0.30
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (22 bp):
TTTAATATTTTGAATTTATTTA
Found at i:1303040 original size:17 final size:18
Alignment explanation
Indices: 1303003--1303041 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1302993 ATATTTTGTA
1303003 TTTAATTTATTTAAGTAT
1 TTTAATTTATTTAAGTAT
1303021 TTTAATTTATTTAA-TAT
1 TTTAATTTATTTAAGTAT
1303038 TTTA
1 TTTA
1303042 CTTATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTAATTTATTTAAGTAT
Found at i:1305780 original size:6 final size:6
Alignment explanation
Indices: 1305729--1305779 Score: 93
Period size: 6 Copynumber: 8.5 Consensus size: 6
1305719 CACTGTTTGG
*
1305729 GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA GAGAGA
1 GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA
1305777 GAG
1 GAG
1305780 AAAAGTGAAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
GAGGGA
Found at i:1312275 original size:21 final size:21
Alignment explanation
Indices: 1312251--1312290 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1312241 CAATGGGATT
*
1312251 AGGATTAGGAATTGGATTTTG
1 AGGATTAGGAAGTGGATTTTG
*
1312272 AGGATTTGGAAGTGGATTT
1 AGGATTAGGAAGTGGATTT
1312291 GGTTGACGGT
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:0.28, C:0.00, G:0.35, T:0.38
Consensus pattern (21 bp):
AGGATTAGGAAGTGGATTTTG
Found at i:1312997 original size:21 final size:21
Alignment explanation
Indices: 1312973--1313027 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
1312963 CAGAACACCA
*
1312973 GGGGGTATCGATTCCCCT-AT
1 GGGGGGATCGATTCCCCTCAT
*
1312993 GGGGGGAATCGGTT-CCCTCAT
1 GGGGGG-ATCGATTCCCCTCAT
1313014 GGGGGGATCGATTC
1 GGGGGGATCGATTC
1313028 GCTCTGCACC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.15, C:0.22, G:0.38, T:0.25
Consensus pattern (21 bp):
GGGGGGATCGATTCCCCTCAT
Found at i:1313010 original size:20 final size:22
Alignment explanation
Indices: 1312973--1313027 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
1312963 CAGAACACCA
*
1312973 GGGGGTATCGATTCCCCT-ATG
1 GGGGGAATCGATTCCCCTCATG
*
1312994 GGGGGAATCGGTT-CCCTCATG
1 GGGGGAATCGATTCCCCTCATG
1313015 GGGGG-ATCGATTC
1 GGGGGAATCGATTC
1313028 GCTCTGCACC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 10 0.34
21 19 0.66
ACGTcount: A:0.15, C:0.22, G:0.38, T:0.25
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTCATG
Found at i:1319805 original size:35 final size:34
Alignment explanation
Indices: 1319720--1319806 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
1319710 AAAATAATTT
*
1319720 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
1319754 TAAATGATAACCAAATTACAATAATTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
1319792 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
1319807 ACTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.54, C:0.09, G:0.08, T:0.29
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:1326443 original size:57 final size:57
Alignment explanation
Indices: 1326355--1326543 Score: 303
Period size: 57 Copynumber: 3.4 Consensus size: 57
1326345 CCATGACAAG
1326355 CATAATCTAAGAGTTGAAGAAACACTGAGCAAAAAACACATTTGGTCAGATGGCAAA
1 CATAATCTAAGAGTTGAAGAAACACTGAGCAAAAAACACATTTGGTCAGATGGCAAA
1326412 CATAATCTAAGAGTTGAAGAAACACTGAGCAAAAAACACATTTGGTCAGATGGCAAA
1 CATAATCTAAGAGTTGAAGAAACACTGAGCAAAAAACACATTTGGTCAGATGGCAAA
* * * * *
1326469 CATAATCTAAGAGTTGCAGAAACCCTGAGC---AAGCACATTTGATCAGATGGCAAG
1 CATAATCTAAGAGTTGAAGAAACACTGAGCAAAAAACACATTTGGTCAGATGGCAAA
*
1326523 CATAATCTAAGAGTTGCAGAA
1 CATAATCTAAGAGTTGAAGAA
1326544 TGAGCAAGTA
Statistics
Matches: 127, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
54 42 0.33
57 85 0.67
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (57 bp):
CATAATCTAAGAGTTGAAGAAACACTGAGCAAAAAACACATTTGGTCAGATGGCAAA
Found at i:1326569 original size:50 final size:52
Alignment explanation
Indices: 1326351--1326574 Score: 229
Period size: 57 Copynumber: 4.1 Consensus size: 52
1326341 TATACCATGA
* *
1326351 CAAGCATAATCTAAGAGTTGAAGAAACACTGAGCAAAAAACACATTTGGTCAGATGG
1 CAAGCATAATCTAAGAGTTGCAG-AA-ACTGAGC---AAGCACATTTGGTCAGATGG
* * *
1326408 CAAACATAATCTAAGAGTTGAAGAAACACTGAGCAAAAAACACATTTGGTCAGATGG
1 CAAGCATAATCTAAGAGTTGCAG-AA-ACTGAGC---AAGCACATTTGGTCAGATGG
* *
1326465 CAAACATAATCTAAGAGTTGCAGAAACCCTGAGCAAGCACATTTGATCAGATGG
1 CAAGCATAATCTAAGAGTTGCAGAAA--CTGAGCAAGCACATTTGGTCAGATGG
* *
1326519 CAAGCATAATCTAAGAGTTGCAG-AA-TGAGCAAGTATATTTGG-CTAGATGG
1 CAAGCATAATCTAAGAGTTGCAGAAACTGAGCAAGCACATTTGGTC-AGATGG
1326569 CAAGCA
1 CAAGCA
1326575 GCTCATCTTT
Statistics
Matches: 156, Mismatches: 8, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
49 1 0.01
50 26 0.17
53 2 0.01
54 40 0.26
55 1 0.01
56 2 0.01
57 84 0.54
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.21
Consensus pattern (52 bp):
CAAGCATAATCTAAGAGTTGCAGAAACTGAGCAAGCACATTTGGTCAGATGG
Found at i:1327364 original size:46 final size:46
Alignment explanation
Indices: 1327297--1327396 Score: 173
Period size: 46 Copynumber: 2.2 Consensus size: 46
1327287 TAAGTTAGGT
*
1327297 TTCATTTGGTTAAATTATATTATCCATCACTCAATTATTTTCTTAA
1 TTCATTTGGTTAAATTATATTATCCATCACTCAAATATTTTCTTAA
*
1327343 TTCATTTGGTTAAATTATATTATCCATCACTCAAATATTTTCTTAC
1 TTCATTTGGTTAAATTATATTATCCATCACTCAAATATTTTCTTAA
1327389 TTCTATTT
1 TTC-ATTT
1327397 TGATAACCAA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
46 47 0.92
47 4 0.08
ACGTcount: A:0.29, C:0.16, G:0.04, T:0.51
Consensus pattern (46 bp):
TTCATTTGGTTAAATTATATTATCCATCACTCAAATATTTTCTTAA
Found at i:1327549 original size:16 final size:16
Alignment explanation
Indices: 1327521--1327564 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
1327511 GTGGTATAAT
*
1327521 TTTAAATTTATATTTTA
1 TTTAAA-TTATATATTA
1327538 TTTAAATTATATATTA
1 TTTAAATTATATATTA
* *
1327554 ATAAAATTATA
1 TTTAAATTATA
1327565 ATAAAAATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTAAATTATATATTA
Found at i:1330323 original size:33 final size:34
Alignment explanation
Indices: 1330269--1330342 Score: 107
Period size: 33 Copynumber: 2.2 Consensus size: 34
1330259 CACTTTAAGC
*
1330269 TTTTTAATCTTTTAAAATTTTATTTTTTTTAT-T
1 TTTTTAATCTCTTAAAATTTTATTTTTTTTATCT
*
1330302 TCTTTTAA-CTCTTAAATTTTTATTTTTTTTATCT
1 T-TTTTAATCTCTTAAAATTTTATTTTTTTTATCT
1330336 TTTTTAA
1 TTTTTAA
1330343 ATAAAATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
33 29 0.78
34 8 0.22
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (34 bp):
TTTTTAATCTCTTAAAATTTTATTTTTTTTATCT
Found at i:1330529 original size:31 final size:31
Alignment explanation
Indices: 1330494--1330557 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
1330484 AAAAATATAT
1330494 ATATGATCACTTTCGTTTTTATTTAATTAAG
1 ATATGATCACTTTCGTTTTTATTTAATTAAG
*
1330525 ATATGGTCACTTTCGTTTTTATTTAATTAAG
1 ATATGATCACTTTCGTTTTTATTTAATTAAG
1330556 AT
1 AT
1330558 GTAGTCACCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.28, C:0.09, G:0.11, T:0.52
Consensus pattern (31 bp):
ATATGATCACTTTCGTTTTTATTTAATTAAG
Found at i:1330565 original size:31 final size:31
Alignment explanation
Indices: 1330500--1330565 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
1330490 ATATATATGA
*
1330500 TCACTTTCGTTTTTATTTAATTAAGATATGG
1 TCACTTTCGTTTTTATTTAATTAAGATATAG
*
1330531 TCACTTTCGTTTTTATTTAATTAAGATGTAG
1 TCACTTTCGTTTTTATTTAATTAAGATATAG
1330562 TCAC
1 TCAC
1330566 CACGGGTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.50
Consensus pattern (31 bp):
TCACTTTCGTTTTTATTTAATTAAGATATAG
Found at i:1338113 original size:23 final size:21
Alignment explanation
Indices: 1338080--1338127 Score: 53
Period size: 24 Copynumber: 2.2 Consensus size: 21
1338070 ATTTATTATA
*
1338080 TATTTTTCT-AATTAAAATACT
1 TATTTTTCTAAACTAAAATA-T
1338101 TATTTTTACCTAAACTAAAATAT
1 TATTTTT--CTAAACTAAAATAT
1338124 TATT
1 TATT
1338128 AGATTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 7 0.30
23 7 0.30
24 9 0.39
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (21 bp):
TATTTTTCTAAACTAAAATAT
Found at i:1341381 original size:31 final size:31
Alignment explanation
Indices: 1341343--1341472 Score: 190
Period size: 31 Copynumber: 4.2 Consensus size: 31
1341333 CCCGAAGGAC
* *
1341343 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
1341374 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
1341405 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
1341436 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1341467 CAGTCC
1 CAGTCC
1341473 TCGACCCTTG
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 90 0.99
32 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:1341968 original size:16 final size:18
Alignment explanation
Indices: 1341947--1341987 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1341937 GCATGTTAAC
1341947 ACATATAA-TCATG-CAT
1 ACATATAATTCATGTCAT
1341963 ACATATAATTCATGTCAT
1 ACATATAATTCATGTCAT
*
1341981 TCATATA
1 ACATATA
1341988 CGTATAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.36
17 5 0.23
18 9 0.41
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (18 bp):
ACATATAATTCATGTCAT
Found at i:1342372 original size:21 final size:21
Alignment explanation
Indices: 1342342--1342386 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1342332 ATTCTGTCGT
* *
1342342 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1342363 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1342384 TTG
1 TTG
1342387 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1345465 original size:31 final size:31
Alignment explanation
Indices: 1345427--1345582 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
1345417 CCCGAAGGAC
* *
1345427 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
1345458 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
1345489 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
1345520 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
1345551 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1345582 C
1 C
1345583 CCTTGACCCT
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:1346080 original size:16 final size:18
Alignment explanation
Indices: 1346059--1346099 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1346049 GCATGTTAAC
1346059 ACATATAA-TCATG-CAT
1 ACATATAATTCATGTCAT
1346075 ACATATAATTCATGTCAT
1 ACATATAATTCATGTCAT
*
1346093 TCATATA
1 ACATATA
1346100 CGTATAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.36
17 5 0.23
18 9 0.41
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (18 bp):
ACATATAATTCATGTCAT
Found at i:1346486 original size:21 final size:21
Alignment explanation
Indices: 1346456--1346500 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1346446 ATTCTGTCGT
* *
1346456 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1346477 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1346498 TTG
1 TTG
1346501 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1347476 original size:21 final size:21
Alignment explanation
Indices: 1347450--1347589 Score: 201
Period size: 21 Copynumber: 6.7 Consensus size: 21
1347440 CATATGAAAT
*
1347450 TTGTCCCGAATGACCACTGTA
1 TTGTCCCGAAGGACCACTGTA
1347471 TTGTCCCGAAGGACCACTGTA
1 TTGTCCCGAAGGACCACTGTA
*
1347492 TTGTCCCAAAGGACC-CTGTA
1 TTGTCCCGAAGGACCACTGTA
*
1347512 TTATCCCGAAGGACCACTGTA
1 TTGTCCCGAAGGACCACTGTA
* *
1347533 TTGTCCTGAATGACCACTGTA
1 TTGTCCCGAAGGACCACTGTA
* *
1347554 TTATCCCGAAGGACCATTGTA
1 TTGTCCCGAAGGACCACTGTA
*
1347575 TTATCCCGAAGGACC
1 TTGTCCCGAAGGACC
1347590 TATGAAACCC
Statistics
Matches: 107, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
20 18 0.17
21 89 0.83
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (21 bp):
TTGTCCCGAAGGACCACTGTA
Found at i:1347550 original size:62 final size:63
Alignment explanation
Indices: 1347453--1347589 Score: 213
Period size: 62 Copynumber: 2.2 Consensus size: 63
1347443 ATGAAATTTG
* *
1347453 TCCCGAATGACCACTGTATTGTCCCGAAGGACCACTGTATTGTCCCAAAGGACC-CTGTATTA
1 TCCCGAAGGACCACTGTATTGTCCCGAAGGACCACTGTATTATCCCAAAGGACCACTGTATTA
* * * *
1347515 TCCCGAAGGACCACTGTATTGTCCTGAATGACCACTGTATTATCCCGAAGGACCATTGTATTA
1 TCCCGAAGGACCACTGTATTGTCCCGAAGGACCACTGTATTATCCCAAAGGACCACTGTATTA
1347578 TCCCGAAGGACC
1 TCCCGAAGGACC
1347590 TATGAAACCC
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
62 49 0.72
63 19 0.28
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (63 bp):
TCCCGAAGGACCACTGTATTGTCCCGAAGGACCACTGTATTATCCCAAAGGACCACTGTATTA
Found at i:1347867 original size:40 final size:40
Alignment explanation
Indices: 1347820--1347899 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
1347810 CTTATGTTCA
1347820 CATGACATATAATGCATACAAATTATATTCACATATGCCT
1 CATGACATATAATGCATACAAATTATATTCACATATGCCT
1347860 CATGACATATAATGCATACAAATTATATTCACATATGCCT
1 CATGACATATAATGCATACAAATTATATTCACATATGCCT
1347900 TTACTCGTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (40 bp):
CATGACATATAATGCATACAAATTATATTCACATATGCCT
Found at i:1347897 original size:23 final size:23
Alignment explanation
Indices: 1347831--1347897 Score: 56
Period size: 23 Copynumber: 3.2 Consensus size: 23
1347821 ATGACATATA
1347831 ATGCATACAAATTATATTCACAT
1 ATGCATACAAATTATATTCACAT
* * * *
1347854 ATGCCT-C--ATGACA-T-ATA-
1 ATGCATACAAATTATATTCACAT
1347871 ATGCATACAAATTATATTCACAT
1 ATGCATACAAATTATATTCACAT
1347894 ATGC
1 ATGC
1347898 CTTTACTCGT
Statistics
Matches: 30, Mismatches: 8, Indels: 12
0.60 0.16 0.24
Matches are distributed among these distances:
17 5 0.17
18 3 0.10
19 1 0.03
20 8 0.27
21 1 0.03
22 3 0.10
23 9 0.30
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.33
Consensus pattern (23 bp):
ATGCATACAAATTATATTCACAT
Found at i:1348392 original size:43 final size:41
Alignment explanation
Indices: 1348327--1348410 Score: 96
Period size: 43 Copynumber: 2.0 Consensus size: 41
1348317 TTCACATAAA
** * *
1348327 CATATATATATCATTTAATTCATGTCTTATTCTTATATCAT
1 CATATATATATCATTTAATTCATCACTTAATCTCATATCAT
**
1348368 CATATATATATCATCTATGTTTCATCACTTAATCTCATATCAT
1 CATATATATATCAT-T-TAATTCATCACTTAATCTCATATCAT
1348411 ATAACATGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
41 14 0.40
42 1 0.03
43 20 0.57
ACGTcount: A:0.32, C:0.18, G:0.02, T:0.48
Consensus pattern (41 bp):
CATATATATATCATTTAATTCATCACTTAATCTCATATCAT
Found at i:1349701 original size:23 final size:23
Alignment explanation
Indices: 1349663--1349736 Score: 76
Period size: 23 Copynumber: 3.1 Consensus size: 23
1349653 AATGACCGAT
1349663 AAAAAAAGATGAAAAAACATACCAC
1 AAAAAAAGA-G-AAAAACATACCAC
** **
1349688 AAAAAAAGAGAAAAATGTGTCAC
1 AAAAAAAGAGAAAAACATACCAC
**
1349711 AAAAGTAGAGAAAAACATACCAC
1 AAAAAAAGAGAAAAACATACCAC
1349734 AAA
1 AAA
1349737 GACAGAATTA
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
23 29 0.74
24 1 0.03
25 9 0.23
ACGTcount: A:0.65, C:0.14, G:0.12, T:0.09
Consensus pattern (23 bp):
AAAAAAAGAGAAAAACATACCAC
Found at i:1349849 original size:17 final size:17
Alignment explanation
Indices: 1349827--1349861 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1349817 TGTCGTCGAC
*
1349827 GGCTAAATAAAATCAAT
1 GGCTAAACAAAATCAAT
1349844 GGCTAAACAAAATCAAT
1 GGCTAAACAAAATCAAT
1349861 G
1 G
1349862 AAGATAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.51, C:0.14, G:0.14, T:0.20
Consensus pattern (17 bp):
GGCTAAACAAAATCAAT
Found at i:1350039 original size:31 final size:31
Alignment explanation
Indices: 1350001--1350066 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
1349991 AGCTCGTAAT
* *
1350001 TAGCAAATAATAA-CAACTGCAGGCTGAATAG
1 TAGCAAATAATAATC-ACTACAGGCTGAATAC
1350032 TAGCAAATAATAATCACTACAGGCTGAATAC
1 TAGCAAATAATAATCACTACAGGCTGAATAC
1350063 TAGC
1 TAGC
1350067 TTAGTAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.44, C:0.18, G:0.17, T:0.21
Consensus pattern (31 bp):
TAGCAAATAATAATCACTACAGGCTGAATAC
Found at i:1350589 original size:60 final size:60
Alignment explanation
Indices: 1350484--1350597 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
1350474 ATAGTCGGAT
* *
1350484 GACCATTTTATAAGTTTAAATAGTCGGGAGACTCAACAAAGTAACACTCTATAGCTGGGG
1 GACCATTTTATAAGTTTAAATAGTCGGGAGACTCAACAAAATAACACCCTATAGCTGGGG
* * * * * *
1350544 GACCATTTTATAATTTTCAATAGTTGATG-GACTTAATAAAATAACACCCTATAG
1 GACCATTTTATAAGTTTAAATAGTCG-GGAGACTCAACAAAATAACACCCTATAG
1350598 TCGAGGGACC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
60 44 0.98
61 1 0.02
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.31
Consensus pattern (60 bp):
GACCATTTTATAAGTTTAAATAGTCGGGAGACTCAACAAAATAACACCCTATAGCTGGGG
Found at i:1350606 original size:60 final size:60
Alignment explanation
Indices: 1350484--1350615 Score: 135
Period size: 60 Copynumber: 2.2 Consensus size: 60
1350474 ATAGTCGGAT
* * *
1350484 GACCATTTTATAAGTTTAAATAGTCGGGAGACTCAACAAAGTAACACTCTATAGCTGGGG
1 GACCATTTTATAAGTTTAAATAGTCGGGAGACTCAACAAAATAACACCCTATAGCTGAGG
* * * * * *
1350544 GACCATTTTATAATTTTCAATAGTTGATG-GACTTAATAAAATAACACCCTATAG-TCGAGG
1 GACCATTTTATAAGTTTAAATAGTCG-GGAGACTCAACAAAATAACACCCTATAGCT-GAGG
1350604 GACC-TTTCTATA
1 GACCATTT-TATA
1350616 CTTTACCCTT
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
59 4 0.07
60 55 0.92
61 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (60 bp):
GACCATTTTATAAGTTTAAATAGTCGGGAGACTCAACAAAATAACACCCTATAGCTGAGG
Found at i:1352903 original size:3 final size:3
Alignment explanation
Indices: 1352897--1352937 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1352887 TTGTACTTAT
1352897 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1352938 TAGCTTACCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1360213 original size:16 final size:17
Alignment explanation
Indices: 1360182--1360214 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1360172 GACTTTGACC
*
1360182 AAAAAGTCAATTTTTTA
1 AAAAAGTCAATATTTTA
1360199 AAAAAGTC-ATATTTTA
1 AAAAAGTCAATATTTTA
1360215 TATTTTCCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (17 bp):
AAAAAGTCAATATTTTA
Found at i:1367634 original size:21 final size:21
Alignment explanation
Indices: 1367591--1367634 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1367581 GGATGAACTG
* *
1367591 TGGCTTTGTAAAAGTGTTGCT
1 TGGCTTTGTAAAAATGTTCCT
1367612 TGGCTTTGTAACAAAT-TTCCT
1 TGGCTTTGTAA-AAATGTTCCT
1367633 TG
1 TG
1367635 ATTTTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.20, C:0.14, G:0.23, T:0.43
Consensus pattern (21 bp):
TGGCTTTGTAAAAATGTTCCT
Found at i:1374004 original size:20 final size:20
Alignment explanation
Indices: 1373975--1374022 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1373965 CCCTCGAGTA
*
1373975 TCGATACCAACTAGATAGTG
1 TCGATACCAACTAGACAGTG
* *
1373995 TCGATGCCAACTGGACAGTG
1 TCGATACCAACTAGACAGTG
1374015 TCGATACC
1 TCGATACC
1374023 CTGTAAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (20 bp):
TCGATACCAACTAGACAGTG
Found at i:1375302 original size:31 final size:30
Alignment explanation
Indices: 1375267--1375341 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 30
1375257 AAAAGTTTTT
* *
1375267 AAAGTTAATTGGCCAAAATAGAAA-CACGATA
1 AAAGTTAA-TGACCAAAATA-AAAGCACAATA
1375298 AAAGTTGAATGACCAAAATAAAAGCACAATA
1 AAAGTT-AATGACCAAAATAAAAGCACAATA
1375329 AAAGTTAAATGAC
1 AAAGTT-AATGAC
1375342 TAAATGTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
30 3 0.08
31 34 0.87
32 2 0.05
ACGTcount: A:0.55, C:0.12, G:0.15, T:0.19
Consensus pattern (30 bp):
AAAGTTAATGACCAAAATAAAAGCACAATA
Found at i:1377322 original size:9 final size:9
Alignment explanation
Indices: 1377292--1377346 Score: 53
Period size: 9 Copynumber: 6.3 Consensus size: 9
1377282 GAAAAGATTA
1377292 ATTTT-TAT
1 ATTTTATAT
*
1377300 ATTTTGTA-
1 ATTTTATAT
*
1377308 AATTTATAT
1 ATTTTATAT
1377317 ATTTTATA-
1 ATTTTATAT
*
1377325 ATTTTAAAAT
1 ATTTT-ATAT
1377335 ATTTTATAT
1 ATTTTATAT
1377344 ATT
1 ATT
1377347 AGCTTATATT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
8 16 0.42
9 17 0.45
10 5 0.13
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (9 bp):
ATTTTATAT
Found at i:1377330 original size:17 final size:17
Alignment explanation
Indices: 1377290--1377371 Score: 69
Period size: 17 Copynumber: 4.6 Consensus size: 17
1377280 AAGAAAAGAT
*
1377290 TAATTTT-TATATTTTG
1 TAATTTTATATATTTTA
*
1377306 TAAATTTATATATTTTA
1 TAATTTTATATATTTTA
*
1377323 TAATTTTAAAATATTTTA
1 TAATTTT-ATATATTTTA
1377341 TATATTAGCTTATAT-TTTTA
1 TA-ATT---TTATATATTTTA
1377361 TAATTCTTATA
1 TAATT-TTATA
1377372 GTTCTTTAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
16 6 0.11
17 20 0.36
18 11 0.20
19 6 0.11
20 7 0.13
21 3 0.05
22 2 0.04
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (17 bp):
TAATTTTATATATTTTA
Found at i:1377433 original size:16 final size:18
Alignment explanation
Indices: 1377395--1377427 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1377385 TTTTTTCTTA
1377395 TAATTTTCTATAGATTTG
1 TAATTTTCTATAGATTTG
1377413 TAATTTT-TAT-GATTT
1 TAATTTTCTATAGATTT
1377428 TAAATTGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 3 0.20
18 7 0.47
ACGTcount: A:0.27, C:0.03, G:0.09, T:0.61
Consensus pattern (18 bp):
TAATTTTCTATAGATTTG
Found at i:1377848 original size:22 final size:22
Alignment explanation
Indices: 1377822--1377865 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1377812 ACATTAAACT
*
1377822 ATATATATTATTTTTATCTTAA
1 ATATATATTATTCTTATCTTAA
* *
1377844 ATATATTTTATTCTTATTTTAA
1 ATATATATTATTCTTATCTTAA
1377866 CTTAAAAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (22 bp):
ATATATATTATTCTTATCTTAA
Found at i:1377902 original size:30 final size:28
Alignment explanation
Indices: 1377833--1377936 Score: 122
Period size: 29 Copynumber: 3.6 Consensus size: 28
1377823 TATATATTAT
* *
1377833 TTTTATCTT-AAATATATTTTATTCTTA
1 TTTTAACTTAAAAAATATTTTATTCTTA
*
1377860 TTTTAACTTAAAAAGATATGTTATTCTTA
1 TTTTAACTTAAAAA-ATATTTTATTCTTA
1377889 TTTTAACCTTAAAAATATATTTTAGTT-TTA
1 TTTTAA-CTTAAAAA-ATATTTTA-TTCTTA
*
1377919 TCTTAACTTAAAAAATAT
1 TTTTAACTTAAAAAATAT
1377937 AATATATTCT
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
27 8 0.12
28 7 0.10
29 27 0.40
30 23 0.34
31 2 0.03
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.52
Consensus pattern (28 bp):
TTTTAACTTAAAAAATATTTTATTCTTA
Found at i:1377937 original size:30 final size:29
Alignment explanation
Indices: 1377842--1377979 Score: 136
Period size: 30 Copynumber: 4.7 Consensus size: 29
1377832 TTTTTATCTT
1377842 AAATATATTTTATTCTTATTTTAACTTAA
1 AAATATATTTTATTCTTATTTTAACTTAA
* *
1377871 AAAGATATGTTATTCTTATTTTAACCTTAA
1 AAATATATTTTATTCTTATTTTAA-CTTAA
*
1377901 AAATATATTTTAGTT-TTATCTTAACTTAAA
1 AAATATATTTTA-TTCTTATTTTAACTT-AA
* * * *
1377931 AAATATAATATATTCTTACCTTAAAC-TAA
1 AAATATATTTTATTCTTA-TTTTAACTTAA
* *
1377960 ATATTTATATTTATTCTTAT
1 AAATATAT-TTTATTCTTAT
1377980 AATATTTTAA
Statistics
Matches: 88, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
29 34 0.39
30 48 0.55
31 6 0.07
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (29 bp):
AAATATATTTTATTCTTATTTTAACTTAA
Found at i:1378347 original size:31 final size:30
Alignment explanation
Indices: 1378312--1378402 Score: 96
Period size: 31 Copynumber: 3.0 Consensus size: 30
1378302 ATTTTTTATG
1378312 TTATAATTTATTTTTATTTTTATTT-AAAA
1 TTATAATTTATTTTTATTTTTATTTAAAAA
* * *
1378341 TTTTATATGTTATTCTTATTTTAATTTAAAAA
1 TTATA-AT-TTATTTTTATTTTTATTTAAAAA
* * *
1378373 ATATATTTTATTTTTATCTTT-TTTAAAAA
1 TTATAATTTATTTTTATTTTTATTTAAAAA
1378402 T
1 T
1378403 AAAACATAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
29 12 0.24
30 13 0.27
31 17 0.35
32 7 0.14
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (30 bp):
TTATAATTTATTTTTATTTTTATTTAAAAA
Found at i:1381462 original size:2 final size:2
Alignment explanation
Indices: 1381455--1381497 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1381445 AACCCACATA
1381455 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1381497 A
1 A
1381498 ATAAAATCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1381905 original size:2 final size:2
Alignment explanation
Indices: 1381898--1381931 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1381888 ATCAAATTTA
1381898 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1381932 TGATATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1382060 original size:17 final size:16
Alignment explanation
Indices: 1382040--1382073 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1382030 ACTTTGACTC
1382040 ATTATTAATTAAAATTT
1 ATTATTAA-TAAAATTT
*
1382057 ATTATTGATAAAATTT
1 ATTATTAATAAAATTT
1382073 A
1 A
1382074 AAATATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
ATTATTAATAAAATTT
Found at i:1383239 original size:31 final size:31
Alignment explanation
Indices: 1383177--1383265 Score: 135
Period size: 31 Copynumber: 2.9 Consensus size: 31
1383167 GGTGTTTAAC
* *
1383177 TTTTTTCCATTACACTTTTAAGTG-TTAATA
1 TTTTCTCCGTTACACTTTTAAGTGCTTAATA
1383207 TTTTCTCCGTTACACTTTTAAGTGCTTAATA
1 TTTTCTCCGTTACACTTTTAAGTGCTTAATA
* *
1383238 TTTTCTTCGTTACACTTTTAGGTGCTTA
1 TTTTCTCCGTTACACTTTTAAGTGCTTA
1383266 TACAGTAACG
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
30 22 0.41
31 32 0.59
ACGTcount: A:0.21, C:0.17, G:0.10, T:0.52
Consensus pattern (31 bp):
TTTTCTCCGTTACACTTTTAAGTGCTTAATA
Found at i:1385737 original size:23 final size:23
Alignment explanation
Indices: 1385710--1385807 Score: 106
Period size: 23 Copynumber: 4.3 Consensus size: 23
1385700 TTTTGGTTGT
* *
1385710 CGAACATGTTCGCAAATGATAAA
1 CGAACATGTTCGAAAATGTTAAA
* *
1385733 AGAACATGTTAGAAAATGTTAAA
1 CGAACATGTTCGAAAATGTTAAA
** *
1385756 CGAACATGTTCGTGAACGTTAAA
1 CGAACATGTTCGAAAATGTTAAA
** *
1385779 CGAACATGTTCGTGAACGTTAAA
1 CGAACATGTTCGAAAATGTTAAA
1385802 CGAACA
1 CGAACA
1385808 AACAAAAACA
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 66 1.00
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.23
Consensus pattern (23 bp):
CGAACATGTTCGAAAATGTTAAA
Found at i:1386521 original size:86 final size:86
Alignment explanation
Indices: 1386376--1386547 Score: 317
Period size: 86 Copynumber: 2.0 Consensus size: 86
1386366 TAAAAACTAC
* *
1386376 AGTGGAGATGGTTTACCTACAATCTATCTTCATTGTTCACCGATTTACTATTCTAATCCAGGGGT
1 AGTGGAGATGGTTTACATACAATCGATCTTCATTGTTCACCGATTTACTATTCTAATCCAGGGGT
*
1386441 AATCTGGTGCAAAGGTAGACG
66 AATCTGGTGCAAAGGCAGACG
1386462 AGTGGAGATGGTTTACATACAATCGATCTTCATTGTTCACCGATTTACTATTCTAATCCAGGGGT
1 AGTGGAGATGGTTTACATACAATCGATCTTCATTGTTCACCGATTTACTATTCTAATCCAGGGGT
1386527 AATCTGGTGCAAAGGCAGACG
66 AATCTGGTGCAAAGGCAGACG
1386548 GGTGCAAGGG
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
86 83 1.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (86 bp):
AGTGGAGATGGTTTACATACAATCGATCTTCATTGTTCACCGATTTACTATTCTAATCCAGGGGT
AATCTGGTGCAAAGGCAGACG
Found at i:1386562 original size:10 final size:10
Alignment explanation
Indices: 1386547--1386575 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
1386537 AAAGGCAGAC
1386547 GGGTGCAAGG
1 GGGTGCAAGG
1386557 GGGTGCAAGG
1 GGGTGCAAGG
1386567 GGGTGCAAG
1 GGGTGCAAG
1386576 AGGTGCAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.10, G:0.59, T:0.10
Consensus pattern (10 bp):
GGGTGCAAGG
Found at i:1387546 original size:10 final size:10
Alignment explanation
Indices: 1387525--1387562 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
1387515 TATTATTAAA
1387525 AAATATATAT
1 AAATATATAT
1387535 AAGATA-ATAT
1 AA-ATATATAT
1387545 AAATATATAT
1 AAATATATAT
1387555 AAATATAT
1 AAATATAT
1387563 TTTTTTTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 3 0.12
10 20 0.77
11 3 0.12
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (10 bp):
AAATATATAT
Found at i:1387967 original size:24 final size:22
Alignment explanation
Indices: 1387913--1387967 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 22
1387903 TATTTTAATT
1387913 TAATTAATATAAATAAATATTTA
1 TAATTAAT-TAAATAAATATTTA
1387936 T-ATT--TTAAATTAAATATGTTA
1 TAATTAATTAAA-TAAATAT-TTA
1387957 TAATTAATTAA
1 TAATTAATTAA
1387968 TTTGATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
19 4 0.15
20 8 0.30
21 4 0.15
22 6 0.22
23 1 0.04
24 4 0.15
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TAATTAATTAAATAAATATTTA
Found at i:1393388 original size:134 final size:135
Alignment explanation
Indices: 1393099--1393685 Score: 704
Period size: 134 Copynumber: 4.4 Consensus size: 135
1393089 GCGAATCGAA
* ** * *
1393099 CTCGATTTAATCTTCCCTGAAGAATTGTGGAATGAATCAAAATTTCCAGATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCTAGATCTGATTTTCCCTCA
* * * * * *
1393164 AGAAACAGTGAAA-AAAT-CCTTTTTTTTCCATAATTGATCATCCCTAAGGAAAAGTGGAACAAG
66 AGAAACAGCGAAACAAATCCCTCTTTTTTCCATATTTGATCTTCCCTGAGGAACAGTGGAACAAG
*
1393227 TCTAA
131 TCTAC
* * * * * * *
1393232 ATC-ATTCAATATTCCCTAAAGAATAGTGGAAAGAATCAACATTTCTAGATCTGATTTTGCCTTA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCTAGATCTGATTTTCCCTCA
* * *
1393296 AGAAGCAGCGAAACATATCGCTCTTTTTTCCATATTTGATCTTCCCT-AGGAACAGTGGAACAAG
66 AGAAACAGCGAAACAAATCCCTCTTTTTTCCATATTTGATCTTCCCTGAGGAACAGTGGAACAAG
*
1393360 TCTGC
131 TCTAC
* * *
1393365 CTCGATTCAATCTTCCCTGAAGAACACTGGAATGAATCAACATTTCCAGATCT--TTTTCCCTTA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCTAGATCTGATTTTCCCTCA
* * * * * *
1393428 AGAAACAGCGGAACAGACCCCTCTTTTTTCCAAGATTTAATCTTCCCTGAGGAATAGTGGAACAA
66 AGAAACAGCGAAACAAATCCCTCTTTTTTCC-ATATTTGATCTTCCCTGAGGAACAGTGGAACAA
*
1393493 GTCTGC
130 GTCTAC
* * *
1393499 CTCTATTCAATCTTCCCTGAAGAACAGTGAAATGAATCAACATTTTTAGATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCTAGATCTGATTTTCCCTCA
* * * *
1393564 AGAAGCAGCGGAACAAATCCCTCTTTTTT-TATATTTGATCTTCCCTGAGGAACAGTGTAACAAG
66 AGAAACAGCGAAACAAATCCCTCTTTTTTCCATATTTGATCTTCCCTGAGGAACAGTGGAACAAG
*
1393628 TTTAC
131 TCTAC
** *
1393633 CAAGATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAACATTT-TCAGATCT
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCT-AGATCT
1393686 CTTTTCAGAC
Statistics
Matches: 389, Mismatches: 57, Indels: 15
0.84 0.12 0.03
Matches are distributed among these distances:
132 98 0.25
133 41 0.11
134 215 0.55
136 35 0.09
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (135 bp):
CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCTAGATCTGATTTTCCCTCA
AGAAACAGCGAAACAAATCCCTCTTTTTTCCATATTTGATCTTCCCTGAGGAACAGTGGAACAAG
TCTAC
Found at i:1393883 original size:3 final size:3
Alignment explanation
Indices: 1393877--1393908 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1393867 TTATTATCAT
1393877 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1393909 GAATCATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1393920 original size:3 final size:3
Alignment explanation
Indices: 1393914--1393955 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
1393904 TAATAGAATC
* *
1393914 ATT ATT ATT ATT ATT ATT ATT ATT AGT ATT AGT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1393956 TATTGTAGGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1398533 original size:23 final size:23
Alignment explanation
Indices: 1398490--1398533 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1398480 TGTTTGTTAA
* *
1398490 TTTATTTTTCTTTGTTTTATTTC
1 TTTATTTTTATTTGTTATATTTC
1398513 TTTATTTTTATTT-TTAATATT
1 TTTATTTTTATTTGTT-ATATT
1398534 ATTTCTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (23 bp):
TTTATTTTTATTTGTTATATTTC
Found at i:1403704 original size:132 final size:132
Alignment explanation
Indices: 1403432--1403766 Score: 490
Period size: 132 Copynumber: 2.5 Consensus size: 132
1403422 CGGATGAAGC
*
1403432 AATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTGCT
1 AATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATT-AT
* * * * * * * *
1403497 AGTTTCTCTCTCGAATCAATAATCATTTTTAAGAAGGAATAGTGATGTCTCTTCATTTCGATTGG
65 CGTTTTTCACTCGAATCAATAATCAATTTTAAGAAGAAATAGTGATATCTCTTCATTTCAATTAG
1403562 AGT
130 AGT
* * * * * *
1403565 AATAAATGACTACTTTAGGGCATAAGAGGTCATTTATTCTCGATTGAAAATCATTATATATTATC
1 AATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATC
* * *
1403630 GTTTTTCACTCGAATCAATATTGAATTTTAAGACGAAATAGTGATATCTCTTCATTTCAATTAGA
66 GTTTTTCACTCGAATCAATAATCAATTTTAAGAAGAAATAGTGATATCTCTTCATTTCAATTAGA
1403695 GT
131 GT
1403697 AATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATC
1 AATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATC
*
1403762 ATTTT
66 GTTTT
1403767 CTCTCTTAGA
Statistics
Matches: 177, Mismatches: 25, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
132 121 0.68
133 56 0.32
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.38
Consensus pattern (132 bp):
AATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATC
GTTTTTCACTCGAATCAATAATCAATTTTAAGAAGAAATAGTGATATCTCTTCATTTCAATTAGA
GT
Found at i:1408254 original size:16 final size:16
Alignment explanation
Indices: 1408230--1408260 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1408220 TATATTTTCT
*
1408230 TTTTTATTATTTATTA
1 TTTTAATTATTTATTA
1408246 TTTTAATTATTTATT
1 TTTTAATTATTTATT
1408261 TTATTTGAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTAATTATTTATTA
Found at i:1414080 original size:32 final size:32
Alignment explanation
Indices: 1414044--1414116 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
1414034 ACGACTGGTA
* * * *
1414044 TGATATTGGTCCGACTCTAAAAGT-GACTGATT
1 TGATATTGATCCGA-TCCAAAAATCGACCGATT
*
1414076 TGATATTGATCTGATCCAAAAATCGACCGATT
1 TGATATTGATCCGATCCAAAAATCGACCGATT
1414108 TGATATTGA
1 TGATATTGA
1414117 CTCAAATAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 7 0.20
32 28 0.80
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (32 bp):
TGATATTGATCCGATCCAAAAATCGACCGATT
Found at i:1415110 original size:2 final size:2
Alignment explanation
Indices: 1415103--1415152 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
1415093 GAAACCCTGA
1415103 AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1415144 AT -T AT AT AT
1 AT AT AT AT AT
1415153 CAAGTGAACT
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1415137 original size:25 final size:25
Alignment explanation
Indices: 1415103--1415152 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1415093 GAAACCCTGA
1415103 ATATATATATATATATATTATATAT
1 ATATATATATATATATATTATATAT
1415128 ATATATATATATATATATTATATAT
1 ATATATATATATATATATTATATAT
1415153 CAAGTGAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
ATATATATATATATATATTATATAT
Done.