Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007838.1 Hibiscus syriacus cultivar Beakdansim tig00110187_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: 3429202
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 13
Found at i:1491896 original size:20 final size:20
Alignment explanation
Indices: 1491865--1491913 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1491855 TTTTCCAAAT
1491865 TCACAACACGAATAGGTAAA
1 TCACAACACGAATAGGTAAA
* * **
1491885 TCGCAACGCGAATTTGTAAA
1 TCACAACACGAATAGGTAAA
1491905 TCACAACAC
1 TCACAACAC
1491914 AGAAGTCAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.43, C:0.24, G:0.14, T:0.18
Consensus pattern (20 bp):
TCACAACACGAATAGGTAAA
Found at i:1491948 original size:19 final size:20
Alignment explanation
Indices: 1491924--1491966 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
1491914 AGAAGTCAAA
*
1491924 TTCGCAAAGCGCA-TTTATT
1 TTCGCAAAGCGAATTTTATT
*
1491943 TTCGCAACGCGAATTTTATT
1 TTCGCAAAGCGAATTTTATT
1491963 TTCG
1 TTCG
1491967 AATTCAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (20 bp):
TTCGCAAAGCGAATTTTATT
Found at i:1494263 original size:21 final size:21
Alignment explanation
Indices: 1494224--1494269 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1494214 GGGGAGTTAA
* * *
1494224 GTGATGAGGTCAATGCTTTGC
1 GTGAGGAGGTCAATACTTTAC
*
1494245 GTGAGGAGGTCAGTACTTTAC
1 GTGAGGAGGTCAATACTTTAC
1494266 GTGA
1 GTGA
1494270 CGACAATTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.22, C:0.13, G:0.35, T:0.30
Consensus pattern (21 bp):
GTGAGGAGGTCAATACTTTAC
Found at i:1494310 original size:21 final size:21
Alignment explanation
Indices: 1494286--1494335 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1494276 TTGTGCATGG
*
1494286 CGTGATGAGGTA-CGGTCTTTA
1 CGTGATGAGGTAGAGGT-TTTA
*
1494307 CGTGGTGAGGTAGAGGTTTTA
1 CGTGATGAGGTAGAGGTTTTA
*
1494328 CGCGATGA
1 CGTGATGA
1494336 CAATGGTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.20, C:0.12, G:0.38, T:0.30
Consensus pattern (21 bp):
CGTGATGAGGTAGAGGTTTTA
Found at i:1494729 original size:42 final size:42
Alignment explanation
Indices: 1494677--1494795 Score: 166
Period size: 42 Copynumber: 2.8 Consensus size: 42
1494667 GATTCACCTG
** * *
1494677 TCATCGTTCAAGAGGCCTTTCCTATCGTTCAAGAGGCCACTA
1 TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCACTA
* *
1494719 TCATCCTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCACTA
**
1494761 TCATCGTTCAAGAGGTTCCTCCCACCGTTCAAGAG
1 TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAG
1494796 CCCGATTCAC
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.24
Consensus pattern (42 bp):
TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:1494789 original size:21 final size:20
Alignment explanation
Indices: 1494681--1494795 Score: 88
Period size: 21 Copynumber: 5.5 Consensus size: 20
1494671 CACCTGTCAT
* * *
1494681 CGTTCAAGAGGCCTTTCCTAT
1 CGTTCAAGAGGCC-CTCCCAC
**
1494702 CGTTCAAGAGGCCACTATCATC
1 CGTTCAAGAGGCC-CTCCCA-C
1494724 C-TTCAAGAGGCCCCTCCCAC
1 CGTTCAAGAGG-CCCTCCCAC
** *
1494744 CGTTCAAGAGGCCACTGTCAT
1 CGTTCAAGAGGCC-CTCCCAC
*
1494765 CGTTCAAGAGGTTCCTCCCAC
1 CGTTCAAGAGG-CCCTCCCAC
1494786 CGTTCAAGAG
1 CGTTCAAGAG
1494796 CCCGATTCAC
Statistics
Matches: 74, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
20 4 0.05
21 66 0.89
22 4 0.05
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (20 bp):
CGTTCAAGAGGCCCTCCCAC
Found at i:1496306 original size:20 final size:20
Alignment explanation
Indices: 1496281--1496324 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1496271 AGGTACACTT
* *
1496281 TCGCAACGTGAAATTCAAAA
1 TCGCAACGCGAAAGTCAAAA
*
1496301 TCGCAACGCGAAAGTCAAAT
1 TCGCAACGCGAAAGTCAAAA
1496321 TCGC
1 TCGC
1496325 GTTGCGATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAAAGTCAAAA
Found at i:1496468 original size:16 final size:16
Alignment explanation
Indices: 1496439--1496474 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1496429 TGTAAATAAG
* *
1496439 AATTGTTTTTTTGTTT
1 AATTGATTTGTTGTTT
1496455 AATTGATTTGTTGTTT
1 AATTGATTTGTTGTTT
1496471 AATT
1 AATT
1496475 TCACTCTGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.14, T:0.67
Consensus pattern (16 bp):
AATTGATTTGTTGTTT
Found at i:1496563 original size:20 final size:20
Alignment explanation
Indices: 1496540--1496611 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
1496530 GAAAGTCAAA
1496540 TTCACATTGCGATTTTGACT
1 TTCACATTGCGATTTTGACT
* * *
1496560 TTCACGTTGCGAGTTTGATT
1 TTCACATTGCGATTTTGACT
* *
1496580 TTCGCATTGCAATTTTGACT
1 TTCACATTGCGATTTTGACT
**
1496600 TTTGCATTGCGA
1 TTCACATTGCGA
1496612 AAGTGTACAT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.18, C:0.18, G:0.19, T:0.44
Consensus pattern (20 bp):
TTCACATTGCGATTTTGACT
Found at i:1499288 original size:24 final size:24
Alignment explanation
Indices: 1499197--1499274 Score: 138
Period size: 24 Copynumber: 3.2 Consensus size: 24
1499187 ATGAAACATC
* *
1499197 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGGGTATTGACCAAG
1499221 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGGGTATTGACCAAG
1499245 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGGGTATTGACCAAG
1499269 ATCAAA
1 ATCAAA
1499275 TTTCGAATAC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (24 bp):
ATCAAAGTCCGGGTATTGACCAAG
Found at i:1500011 original size:16 final size:16
Alignment explanation
Indices: 1499989--1500027 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1499979 GAAATCATTG
*
1499989 AAAAATTATATAGAAA
1 AAAAATTATATAAAAA
* *
1500005 TAAAATTATGTAAAAA
1 AAAAATTATATAAAAA
1500021 AAAAATT
1 AAAAATT
1500028 GAGATGGGGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (16 bp):
AAAAATTATATAAAAA
Found at i:1500209 original size:20 final size:19
Alignment explanation
Indices: 1500184--1500253 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 19
1500174 AAATAAAAGT
1500184 TGTTGCGAAATTAAAATTCG
1 TGTTGCGAAATTAAAA-TCG
1500204 TGTTGC-AAATTTGAAAATCG
1 TGTTGCGAAA-TT-AAAATCG
* * *
1500224 AGTTGCG-ATTTAGAAAATCT
1 TGTTGCGAAATT--AAAATCG
1500244 TGTTGCGAAA
1 TGTTGCGAAA
1500254 AGGAAACTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
19 5 0.12
20 30 0.75
21 5 0.12
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.34
Consensus pattern (19 bp):
TGTTGCGAAATTAAAATCG
Found at i:1500329 original size:20 final size:21
Alignment explanation
Indices: 1500286--1500337 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1500276 TAAATTCGCT
1500286 TTGCGAATTTGAAATTCCGTG
1 TTGCGAATTTGAAATTCCGTG
* *
1500307 TTGCGAATTT-AACTTCTGTG
1 TTGCGAATTTGAAATTCCGTG
*
1500327 TTGCGATTTTG
1 TTGCGAATTTG
1500338 GAAAATCGCG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.19, C:0.13, G:0.23, T:0.44
Consensus pattern (21 bp):
TTGCGAATTTGAAATTCCGTG
Found at i:1500351 original size:41 final size:41
Alignment explanation
Indices: 1500327--1500404 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
1500317 AACTTCTGTG
1500327 TTGCGATTTTGGAAAATCGCGTTGCGATCTACATATTCGGT
1 TTGCGATTTTGGAAAATCGCGTTGCGATCTACATATTCGGT
*
1500368 TTGCGATTTTGGAAAATCGCGTTGCTATCTACATATT
1 TTGCGATTTTGGAAAATCGCGTTGCGATCTACATATT
1500405 ATCGTTGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (41 bp):
TTGCGATTTTGGAAAATCGCGTTGCGATCTACATATTCGGT
Found at i:1500352 original size:21 final size:21
Alignment explanation
Indices: 1500326--1500392 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
1500316 TAACTTCTGT
1500326 GTTGCGATTTTGGAAAATCGC
1 GTTGCGATTTTGGAAAATCGC
* ** * *
1500347 GTTGCGA-TCTACATATTCG-
1 GTTGCGATTTTGGAAAATCGC
1500366 GTTTGCGATTTTGGAAAATCGC
1 G-TTGCGATTTTGGAAAATCGC
1500388 GTTGC
1 GTTGC
1500393 TATCTACATA
Statistics
Matches: 33, Mismatches: 10, Indels: 6
0.67 0.20 0.12
Matches are distributed among these distances:
19 1 0.03
20 13 0.39
21 18 0.55
22 1 0.03
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.36
Consensus pattern (21 bp):
GTTGCGATTTTGGAAAATCGC
Found at i:1507858 original size:15 final size:15
Alignment explanation
Indices: 1507838--1507872 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1507828 GCTTGGTTTA
*
1507838 ATAAATATTAAATGT
1 ATAAATAATAAATGT
1507853 ATAAATAATAAATGT
1 ATAAATAATAAATGT
1507868 -TAAAT
1 ATAAAT
1507873 GTGTAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (15 bp):
ATAAATAATAAATGT
Found at i:1511247 original size:27 final size:27
Alignment explanation
Indices: 1511216--1511274 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
1511206 CAATAGACGT
1511216 AGTTGGAAATTCCGGAACCGAATATAA
1 AGTTGGAAATTCCGGAACCGAATATAA
1511243 AGTTGGAAATTCCGGAACCGAATATAA
1 AGTTGGAAATTCCGGAACCGAATATAA
1511270 AGTTG
1 AGTTG
1511275 TCAAGGCTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.24
Consensus pattern (27 bp):
AGTTGGAAATTCCGGAACCGAATATAA
Found at i:1513576 original size:23 final size:23
Alignment explanation
Indices: 1513546--1513595 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
1513536 GACTCTTTCT
1513546 CCAACTCAAGCAAACAAAATATC
1 CCAACTCAAGCAAACAAAATATC
1513569 CCAACTCAAGCAAACAAAATATC
1 CCAACTCAAGCAAACAAAATATC
1513592 CCAA
1 CCAA
1513596 AATTTTTAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.52, C:0.32, G:0.04, T:0.12
Consensus pattern (23 bp):
CCAACTCAAGCAAACAAAATATC
Found at i:1523491 original size:6 final size:6
Alignment explanation
Indices: 1523481--1523511 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1523471 TGTCTCCTCC
*
1523481 ATTTAC ATTTAA ATTTAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
1523512 AGAGGATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTTAA
Found at i:1524866 original size:15 final size:15
Alignment explanation
Indices: 1524846--1524875 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1524836 CAGAGTGACC
1524846 AATGAATGTTTGATT
1 AATGAATGTTTGATT
1524861 AATGAATGTTTGATT
1 AATGAATGTTTGATT
1524876 GATTGATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (15 bp):
AATGAATGTTTGATT
Found at i:1525370 original size:21 final size:24
Alignment explanation
Indices: 1525344--1525386 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1525334 ATTTTTCAGT
1525344 TATTTT-T-TTAA-ATAATTATTA
1 TATTTTATATTAATATAATTATTA
1525365 TATTTTATATTAATATAATTAT
1 TATTTTATATTAATATAATTAT
1525387 ATAAATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 1 0.05
23 4 0.21
24 8 0.42
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TATTTTATATTAATATAATTATTA
Found at i:1525396 original size:32 final size:30
Alignment explanation
Indices: 1525355--1525460 Score: 85
Period size: 30 Copynumber: 3.5 Consensus size: 30
1525345 ATTTTTTTAA
* *
1525355 ATAATTATTATATTTTATATTAATATAATTAT
1 ATAAATATTAT-TTTT-TATTAAAATAATTAT
1525387 ATAAATATTATTTTTTATTAAAATAA-TAT
1 ATAAATATTATTTTTTATTAAAATAATTAT
* * * *
1525416 TTATATAATTATTATTTATTTAAAT--TTAT
1 ATAAAT-ATTATTTTTTATTAAAATAATTAT
*
1525445 -TAATTAATTATTTTTT
1 ATAAAT-ATTATTTTTT
1525461 GTGCTAATTA
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
28 13 0.21
29 10 0.16
30 26 0.41
31 4 0.06
32 10 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
ATAAATATTATTTTTTATTAAAATAATTAT
Found at i:1525406 original size:30 final size:32
Alignment explanation
Indices: 1525355--1525437 Score: 98
Period size: 33 Copynumber: 2.5 Consensus size: 32
1525345 ATTTTTTTAA
1525355 ATAATTATTATATTTTATATT-AAT-ATAATTAT
1 ATAATTATTAT-TTTT-TATTAAATAATAATTAT
* *
1525387 ATAAATATTATTTTTTATTAAAATAATATTTAT
1 ATAATTATTATTTTTTATT-AAATAATAATTAT
1525420 ATAATTATTATTTATTTA
1 ATAATTATTATTT-TTTA
1525438 AATTTATTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
30 4 0.09
31 4 0.09
32 13 0.30
33 19 0.43
34 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (32 bp):
ATAATTATTATTTTTTATTAAATAATAATTAT
Found at i:1525429 original size:33 final size:30
Alignment explanation
Indices: 1525350--1525460 Score: 95
Period size: 33 Copynumber: 3.6 Consensus size: 30
1525340 CAGTTATTTT
*
1525350 TTTAAATAATTATTATATTTTATATTAATATA
1 TTTATATAATTATTAT-TTTT-TATTAATATA
* *
1525382 ATTATATAAATATTATTTTTTATTAAAATAATA
1 TTTATATAATTATTATTTTTTATT--AAT-ATA
*
1525415 TTTATATAATTATTATTTATTTA--AATTTA
1 TTTATATAATTATTATTT-TTTATTAATATA
*
1525444 TTAAT-TAATTATT-TTTT
1 TTTATATAATTATTATTTT
1525461 GTGCTAATTA
Statistics
Matches: 68, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
26 1 0.01
27 3 0.04
28 8 0.12
29 6 0.09
30 7 0.10
31 4 0.06
32 16 0.24
33 19 0.28
34 4 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
TTTATATAATTATTATTTTTTATTAATATA
Found at i:1527236 original size:21 final size:21
Alignment explanation
Indices: 1527206--1527277 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
1527196 TATGTCATCT
*
1527206 CCGCAAGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
1527227 CCGCAGGGTT-CATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
* * *
1527247 CCGCCA-GGCTACATGCCTAGA
1 CCG-CAGGGTTACATTCCTAGC
1527268 CCGCAGGGTT
1 CCGCAGGGTT
1527278 TTATACCATA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
20 18 0.42
21 25 0.58
ACGTcount: A:0.19, C:0.35, G:0.25, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:1527828 original size:34 final size:34
Alignment explanation
Indices: 1527790--1527889 Score: 155
Period size: 34 Copynumber: 2.9 Consensus size: 34
1527780 AATGTTTTTA
1527790 ACAAATTATAGTATTCGAAATTTAAAATTAAAAT
1 ACAAATTATAGTATTCGAAATTTAAAATTAAAAT
* * *
1527824 ACAAATAATATTATTCGAAATTTAAATTTAAAAT
1 ACAAATTATAGTATTCGAAATTTAAAATTAAAAT
* *
1527858 ATAAATTATAGTATTCGAAATTTAACATTAAA
1 ACAAATTATAGTATTCGAAATTTAAAATTAAA
1527890 TTCAAGTTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 58 1.00
ACGTcount: A:0.52, C:0.06, G:0.05, T:0.37
Consensus pattern (34 bp):
ACAAATTATAGTATTCGAAATTTAAAATTAAAAT
Found at i:1528523 original size:127 final size:127
Alignment explanation
Indices: 1528292--1528695 Score: 664
Period size: 127 Copynumber: 3.2 Consensus size: 127
1528282 ATCTATAGTT
* * **
1528292 CCCCAGGAACGCGCCTTCACGATCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCATGGGG
1 CCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGG
1528357 GACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGC
66 GACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGC
*
1528419 CCCCGGGAACGCGCCTTCACGGTCCCCTAAAGAATAATAGGTATTGACATGAATAGTTCCCGGGG
1 CCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGG
* *
1528484 GACATAAGTGACATAATAGGGTAATAATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCC
66 GACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGGCG---CGC
* * * * *
1528549 CCCCGGGAATGTGCCTTCACGGTCCTCTAAGGAATAATAAGTATTGACATGAATAGTTCCCGAGG
1 CCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGG
1528614 GACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGC
66 GACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGC
*
1528676 CCCCGAGAACGCGCCTTCAC
1 CCCCGGGAACGCGCCTTCAC
1528696 ATGAATAGTA
Statistics
Matches: 256, Mismatches: 18, Indels: 6
0.91 0.06 0.02
Matches are distributed among these distances:
127 137 0.54
130 119 0.46
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (127 bp):
CCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGG
GACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGC
Found at i:1532454 original size:15 final size:15
Alignment explanation
Indices: 1532434--1532462 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1532424 TGGCCGACCG
1532434 AACCGAATTAACCAT
1 AACCGAATTAACCAT
1532449 AACCGAATTAACCA
1 AACCGAATTAACCA
1532463 AACTTTTTTT
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:0.48, C:0.28, G:0.07, T:0.17
Consensus pattern (15 bp):
AACCGAATTAACCAT
Found at i:1532906 original size:183 final size:184
Alignment explanation
Indices: 1532597--1532961 Score: 619
Period size: 183 Copynumber: 2.0 Consensus size: 184
1532587 TTATATAAAA
*
1532597 TTAATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATAAATAATTATAAAATAAAA
1 TTAATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATAAATAATTATAAAATAAAA
* *
1532662 ATTTTAGATAAATTTTTTAATTAATTAATATTGATTTAATTTTAAAAGTTATTGGATCTTAAATT
66 AATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGATCTTAAATT
*
1532727 ATTAATTAGGTTTTAAATGGTTTGGGCTT-AGCCCATATGTTATATATAATATAT
131 ATTAATTAGGTTTTAAATGATTTGGG-TTGAGCCCATATGTTATATATAATATAT
*
1532781 TTAATATTTTTTAATT-AAAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAA
1 TTAATATTTTTTAATTCAAAAAA-AGTTTACAATTAATTTAAATAATAAATAATTATAAAATAAA
*
1532845 AAATTTATAT-AATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGATCTTAAAT
65 AAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGATCTTAAAT
* *
1532909 TATTAATTGGGTTTTTAATGATTTGGGTTGAGCCCATATGTTATATATAATAT
130 TATTAATTAGGTTTTAAATGATTTGGGTTGAGCCCATATGTTATATATAATAT
1532962 TTAAAATTTA
Statistics
Matches: 171, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
182 2 0.01
183 106 0.62
184 63 0.37
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.46
Consensus pattern (184 bp):
TTAATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATAAATAATTATAAAATAAAA
AATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGATCTTAAATT
ATTAATTAGGTTTTAAATGATTTGGGTTGAGCCCATATGTTATATATAATATAT
Found at i:1534930 original size:28 final size:28
Alignment explanation
Indices: 1534899--1534986 Score: 149
Period size: 28 Copynumber: 3.1 Consensus size: 28
1534889 TCAAGTTGTA
1534899 TTTTACAACTCGATTTGAACTTGAAGTT
1 TTTTACAACTCGATTTGAACTTGAAGTT
*
1534927 TTTTACAACTCGATTTGAACTTGAAGAT
1 TTTTACAACTCGATTTGAACTTGAAGTT
* *
1534955 TTTTACAACTCAATTTGAACTTAAAGTT
1 TTTTACAACTCGATTTGAACTTGAAGTT
1534983 TTTT
1 TTTT
1534987 CGAGTTGAGT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 56 1.00
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (28 bp):
TTTTACAACTCGATTTGAACTTGAAGTT
Found at i:1535012 original size:27 final size:27
Alignment explanation
Indices: 1534982--1535053 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 27
1534972 AACTTAAAGT
* * *
1534982 TTTTTCGAGTTGAGTTGAAAAAATCAG
1 TTTTTCGAGTCGAGTCGAAAAAATCAA
* * *
1535009 TTTTTTGAGTCGAGTCGGAAAGATCAA
1 TTTTTCGAGTCGAGTCGAAAAAATCAA
1535036 TTTTTCGAGTCGAGTCGA
1 TTTTTCGAGTCGAGTCGA
1535054 TTTTTGCTCA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.36
Consensus pattern (27 bp):
TTTTTCGAGTCGAGTCGAAAAAATCAA
Found at i:1538218 original size:24 final size:24
Alignment explanation
Indices: 1538191--1538246 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
1538181 TAAACCAACT
1538191 AATTGATAATTAGTCATTCTAGTG
1 AATTGATAATTAGTCATTCTAGTG
*
1538215 AATTGATAATTAGTGATTCTAGTG
1 AATTGATAATTAGTCATTCTAGTG
1538239 AATTGATA
1 AATTGATA
1538247 TTTTAAATGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (24 bp):
AATTGATAATTAGTCATTCTAGTG
Found at i:1546097 original size:75 final size:75
Alignment explanation
Indices: 1545974--1546121 Score: 210
Period size: 75 Copynumber: 2.0 Consensus size: 75
1545964 TAAACAATAA
** * *
1545974 TATTTTAATTATCATTTTTGCTACATTTTGATCATTTAATTATTTTTTTTTAAATCAACGTTATG
1 TATTTTAACCATCATTTTTACTACATTTTGATCATTTAATTA-TTTTTTTTAAATCAACGTTATA
1546039 TTTT-GTTTAG
65 TTTTAGTTTAG
* *
1546049 TATTTTAACCATCATTTTTACTACATTTTGGTCATTTAA-TATTATTTTTTAAATTAACGTTATA
1 TATTTTAACCATCATTTTTACTACATTTTGATCATTTAATTATT-TTTTTTAAATCAACGTTATA
1546113 TTTTAGTTT
65 TTTTAGTTT
1546122 TATTTTTGTC
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
73 2 0.03
74 24 0.37
75 39 0.60
ACGTcount: A:0.27, C:0.09, G:0.07, T:0.57
Consensus pattern (75 bp):
TATTTTAACCATCATTTTTACTACATTTTGATCATTTAATTATTTTTTTTAAATCAACGTTATAT
TTTAGTTTAG
Found at i:1546962 original size:31 final size:31
Alignment explanation
Indices: 1546926--1546984 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1546916 AACTTAAAAG
* *
1546926 AGTTTTGCAATATTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
1546957 AGTTTTATAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
1546985 CCATACAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.46
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:1547032 original size:22 final size:22
Alignment explanation
Indices: 1547005--1547262 Score: 308
Period size: 22 Copynumber: 11.7 Consensus size: 22
1546995 ACAATAATAA
1547005 ATATTTTAAAATAAATCAATCT
1 ATATTTTAAAATAAATCAATCT
*
1547027 ATATTTTAAAATAAATCAATAT
1 ATATTTTAAAATAAATCAATCT
*
1547049 ATATTTTAAAATAAATAAAT-T
1 ATATTTTAAAATAAATCAATCT
*
1547070 CATATTTTAAAATAAATCAATCC
1 -ATATTTTAAAATAAATCAATCT
*
1547093 ATATTTTAAAATAAATCAATCC
1 ATATTTTAAAATAAATCAATCT
* *
1547115 ATATTTAAAAATAAATCAATCC
1 ATATTTTAAAATAAATCAATCT
1547137 ATATTTTAAAATAAATCAATCT
1 ATATTTTAAAATAAATCAATCT
** *
1547159 ATATTTTAAAATAAAAT-TTTTT
1 ATATTTTAAAAT-AAATCAATCT
***
1547181 ATATTTTAAAATAAAATTTTTC-
1 ATATTTTAAAAT-AAATCAATCT
***
1547203 ATATTTTAAAATAAAATTTTTC-
1 ATATTTTAAAAT-AAATCAATCT
*
1547225 ATATTTTAAAATAAATAAATCT
1 ATATTTTAAAATAAATCAATCT
1547247 ATATTTTAAAATAAAT
1 ATATTTTAAAATAAAT
1547263 TTTAAAATAG
Statistics
Matches: 217, Mismatches: 14, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
21 7 0.03
22 203 0.94
23 7 0.03
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (22 bp):
ATATTTTAAAATAAATCAATCT
Found at i:1547615 original size:20 final size:20
Alignment explanation
Indices: 1547586--1547626 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1547576 GATAATCGTT
*
1547586 ACAAAAACATT-TATTTTAA
1 ACAAAAACATTATAGTTTAA
1547605 ACAATAAACATTATAGTTTAA
1 ACAA-AAACATTATAGTTTAA
1547626 A
1 A
1547627 TTCCTAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
21 8 0.42
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (20 bp):
ACAAAAACATTATAGTTTAA
Found at i:1553211 original size:60 final size:59
Alignment explanation
Indices: 1553144--1553304 Score: 198
Period size: 60 Copynumber: 2.7 Consensus size: 59
1553134 ATGAATTAGG
* ** * *
1553144 GGGATGAAATTGGAATATTCAAAAGATTAGGGACTATTTTAGAAAGAGGGTCATAGTTT
1 GGGATGAAATTAGAATATTCAAAAGATTAAAGACTAATTTAGAAAGAGAGTCATAGTTT
* * *
1553203 AGGGATGAAATTAGAATGTTCAAAAGTTTAAAGACTAATTTAGAATGAGAGTCATAGTTT
1 -GGGATGAAATTAGAATATTCAAAAGATTAAAGACTAATTTAGAAAGAGAGTCATAGTTT
* *
1553263 GGGAATAAAATTAGAATATTCAAAAGGTTAAAGA-TCAATTTA
1 GGG-ATGAAATTAGAATATTCAAAAGATTAAAGACT-AATTTA
1553305 AAATGAGTTA
Statistics
Matches: 88, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
59 4 0.05
60 84 0.95
ACGTcount: A:0.42, C:0.05, G:0.22, T:0.30
Consensus pattern (59 bp):
GGGATGAAATTAGAATATTCAAAAGATTAAAGACTAATTTAGAAAGAGAGTCATAGTTT
Found at i:1557727 original size:242 final size:242
Alignment explanation
Indices: 1557302--1557746 Score: 791
Period size: 242 Copynumber: 1.8 Consensus size: 242
1557292 CGAAGTACCG
* *
1557302 CATATATGTTCCAAATGATTACATATATGTCTCGAATGACCACGTAGAACCCTCGACTCTTGGCA
1 CATATATGTTCCAAAGGATTACATATATGTCTCGAATGACCACGTAGAACCCTCGACTCTTAGCA
* * *
1557367 TGCCAACTATACCTCTAGCTCTCAGGACACATATCATGGGCATAATCTTTTATTTCATTTCACAT
66 TGCCAACTATACCTCTAACTCTCAGGACACATAACATGGGCATAATCTTTTATGTCATTTCACAT
*
1557432 ATTCACATAGACACGCAGTTCACTTACACATAACACATTTCCATATAATTCACATATCACATAGC
131 ATTCACATAGACACGCAGTTCACTTACACATAACACATTTCCATAAAATTCACATATCACATAGC
*
1557497 TCATGTCACTTAATCTCTTATGTTCATGTATCACATGTGAATATTCT
196 TAATGTCACTTAATCTCTTATGTTCATGTATCACATGTGAATATTCT
*
1557544 CATATATGTTCTAAAGGATTACATATATGTCTCGAATGACCACGTAGAACCCTCGACTCTTAGCA
1 CATATATGTTCCAAAGGATTACATATATGTCTCGAATGACCACGTAGAACCCTCGACTCTTAGCA
*
1557609 TGCCAACTATACCTCTAACTCTCAGGACACATAACATGGGCATTATCTTTTATGTCATTTCACAT
66 TGCCAACTATACCTCTAACTCTCAGGACACATAACATGGGCATAATCTTTTATGTCATTTCACAT
* *
1557674 ATTCACATAGACACGTAGTTCACTTACACATAACACATTTCCATAAAATTCACATATCACATATC
131 ATTCACATAGACACGCAGTTCACTTACACATAACACATTTCCATAAAATTCACATATCACATAGC
1557739 TAATGTCA
196 TAATGTCA
1557747 TATTCTCATA
Statistics
Matches: 192, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
242 192 1.00
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.32
Consensus pattern (242 bp):
CATATATGTTCCAAAGGATTACATATATGTCTCGAATGACCACGTAGAACCCTCGACTCTTAGCA
TGCCAACTATACCTCTAACTCTCAGGACACATAACATGGGCATAATCTTTTATGTCATTTCACAT
ATTCACATAGACACGCAGTTCACTTACACATAACACATTTCCATAAAATTCACATATCACATAGC
TAATGTCACTTAATCTCTTATGTTCATGTATCACATGTGAATATTCT
Found at i:1564841 original size:32 final size:31
Alignment explanation
Indices: 1564766--1564842 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
1564756 CTAATGTGAC
* * *
1564766 TCTTAGGTAGGCTCTGCGGCCTTGAGATCAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
** **
1564797 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-CAT
1564829 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
1564843 CACGGCCCCA
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.14, C:0.26, G:0.31, T:0.29
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
Found at i:1565836 original size:5 final size:5
Alignment explanation
Indices: 1565828--1565854 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1565818 TGATGTGGTG
1565828 TTCTC TTCTC TTCTC TTCTC TTCTC TT
1 TTCTC TTCTC TTCTC TTCTC TTCTC TT
1565855 ATTCATCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (5 bp):
TTCTC
Found at i:1570511 original size:2 final size:2
Alignment explanation
Indices: 1570504--1570538 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1570494 TTGCCCAAAC
1570504 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1570539 TGAATAGGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1576418 original size:2 final size:2
Alignment explanation
Indices: 1576411--1576459 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1576401 TAATCAGTCC
1576411 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
1576453 AT AT AT A
1 AT AT AT A
1576460 ACTTAAACGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1582064 original size:37 final size:36
Alignment explanation
Indices: 1582005--1582124 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
1581995 ATCCCATTAT
* *
1582005 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAA
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
*
1582040 CTATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 C-ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
*
1582077 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAT
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
1582112 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
1582125 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
35 35 0.45
36 8 0.10
37 34 0.44
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
Found at i:1582080 original size:21 final size:20
Alignment explanation
Indices: 1582053--1582116 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
1582043 TTTTTCAAAG
1582053 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
*
1582073 AAACCATTT-TCAAA----G-
1 AAA-CATTTACCAAACTTTGA
1582088 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
1582108 AAATCATTT
1 AAA-CATTT
1582117 TTTCAAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 1 0.03
19 1 0.03
20 10 0.29
21 10 0.29
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (20 bp):
AAACATTTACCAAACTTTGA
Found at i:1586677 original size:37 final size:36
Alignment explanation
Indices: 1586616--1586702 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 36
1586606 TTATCCCATT
*
1586616 ATCATTTTTC-AACAAACATCTACCAAACTTTGAAAA
1 ATCATTTTTCAAAGAAACATCTACCAAACTTTG-AAA
* *
1586652 ATTATTTTTCAAAGAAACATTTACCAAACTTTGAAA
1 ATCATTTTTCAAAGAAACATCTACCAAACTTTGAAA
1586688 ATCATTTTTTCAAAG
1 ATCA-TTTTTCAAAG
1586703 TTGGTTACCA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
36 15 0.33
37 30 0.67
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.36
Consensus pattern (36 bp):
ATCATTTTTCAAAGAAACATCTACCAAACTTTGAAA
Found at i:1594405 original size:31 final size:32
Alignment explanation
Indices: 1594341--1594411 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
1594331 CCTGAGAGCA
* *
1594341 TACCCAAGAAAGATTCTCGGGGCCACGAGGCC
1 TACCCAAGAAAGATTCTCGGGGCCACAAAGCC
* *
1594373 TACCCAAGAAATA-TCTCGGGGCCGCAAAGCC
1 TACCCAAGAAAGATTCTCGGGGCCACAAAGCC
*
1594404 TATCCAAG
1 TACCCAAG
1594412 GGTTGCCTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 22 0.65
32 12 0.35
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.14
Consensus pattern (32 bp):
TACCCAAGAAAGATTCTCGGGGCCACAAAGCC
Found at i:1598978 original size:149 final size:148
Alignment explanation
Indices: 1598665--1598967 Score: 489
Period size: 149 Copynumber: 2.0 Consensus size: 148
1598655 GAGTCGAGGG
* * * * * * *
1598665 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAATATTTATGAGGTCTTTGAGGCACATA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
* *
1598730 CTTGGTCCTTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGAAATTATTAT
66 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGAAATTATTAT
1598795 ATGGCACTACGGTGCAAT
131 ATGGCACTACGGTGCAAT
* *
1598813 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTT-TAAGACACAT
*
1598878 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
65 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGAAATTATTA
1598943 TATGGCACTACGGTGCAAT
130 TATGGCACTACGGTGCAAT
1598962 TCTACG
1 TCTACG
1598968 TGGCACTTCG
Statistics
Matches: 142, Mismatches: 12, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
148 47 0.33
149 95 0.67
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGAAATTATTAT
ATGGCACTACGGTGCAAT
Found at i:1598979 original size:23 final size:23
Alignment explanation
Indices: 1598945--1598990 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1598935 CATTATTATA
*
1598945 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTATACG
*
1598968 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTATACG
1598991 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATACG
Found at i:1612404 original size:20 final size:20
Alignment explanation
Indices: 1612379--1612416 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1612369 GATGGGTTAG
*
1612379 TGAAATTTCTATTTTTTTAA
1 TGAAATTTCGATTTTTTTAA
*
1612399 TGAAATTTGGATTTTTTT
1 TGAAATTTCGATTTTTTT
1612417 TAATATTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.03, G:0.11, T:0.61
Consensus pattern (20 bp):
TGAAATTTCGATTTTTTTAA
Found at i:1612499 original size:17 final size:16
Alignment explanation
Indices: 1612477--1612510 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1612467 TATTCTATAA
1612477 TATTTTAAAATAGTTTT
1 TATTTTAAAATA-TTTT
*
1612494 TATTTTTAAATATTTT
1 TATTTTAAAATATTTT
1612510 T
1 T
1612511 CTAATTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TATTTTAAAATATTTT
Found at i:1621559 original size:2 final size:2
Alignment explanation
Indices: 1621543--1621583 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
1621533 ATATGTGATG
1621543 TA TA -A TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1621583 T
1 T
1621584 GTACTGACAT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1629956 original size:6 final size:6
Alignment explanation
Indices: 1629945--1630003 Score: 50
Period size: 7 Copynumber: 9.2 Consensus size: 6
1629935 AGAAAAAATG
1629945 AAAGAA AAAGAAGA AAAGAGA AAAGAGA AAATGAA AAATG-A AAA-AA
1 AAAGAA AAAG-A-A AAAGA-A AAAGA-A AAA-GAA AAA-GAA AAAGAA
1629991 AAAGAA AAAGAA A
1 AAAGAA AAAGAA A
1630004 TAAAAGGGGG
Statistics
Matches: 48, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
5 4 0.08
6 17 0.35
7 20 0.42
8 7 0.15
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (6 bp):
AAAGAA
Found at i:1629973 original size:14 final size:14
Alignment explanation
Indices: 1629933--1630002 Score: 56
Period size: 14 Copynumber: 4.9 Consensus size: 14
1629923 AAAAATGGTG
*
1629933 AAAGAAAAA-ATG-
1 AAAGAAAAAGAAGA
1629945 AAAGAAAAAGAAGA
1 AAAGAAAAAGAAGA
1629959 AAAGAGAAAAG-AGA
1 AAAGA-AAAAGAAGA
*
1629973 AAATGAAAAATGAAAAAA
1 AAA-GAAAAA-G--AAGA
1629991 AAAGAAAAAGAA
1 AAAGAAAAAGAA
1630003 ATAAAAGGGG
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
12 9 0.19
13 2 0.04
14 17 0.35
15 8 0.17
16 1 0.02
17 6 0.12
18 5 0.10
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (14 bp):
AAAGAAAAAGAAGA
Found at i:1631331 original size:55 final size:54
Alignment explanation
Indices: 1631262--1631928 Score: 795
Period size: 55 Copynumber: 12.1 Consensus size: 54
1631252 TTTATGAAGA
* *
1631262 TCGAG-TCATATACTCTCTGATA-GAATAGGGAGCGGACCCGTTTATTGAAAATTGT
1 TCGAGTTC-TATACTCTCTGA-AGGAATAGAGAGCGGACCCGTTT-TTGAAGATTGT
* * *
1631317 TCGAGTTATATACTCTCTGATA-GAATAGGGAGCAGACCCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGA-AGGAATAGAGAGCGGACCCGTTT-TTGAAGATTGT
* * * *
1631372 TCGAGTTCTATACTCTCTGATA-GAATAGGGATCGGACCCTTTTATTGAAGATTAT
1 TCGAGTTCTATACTCTCTGA-AGGAATAGAGAGCGGACCCGTTT-TTGAAGATTGT
* *
1631427 TCGAGTTATATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTCATGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TTGAAGATTGT
* *
1631482 TTGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGATCCGTTTTATGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTT-TGAAGATTGT
*
1631537 TCTAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TTGAAGATTGT
* *
1631592 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACCCGTTTTATGAAGATTTT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTT-TGAAGATTGT
* * * * *
1631647 TTGAGTTCTATACTCCCTGAATGAATAGGGAGCGGACTCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TTGAAGATTGT
*
1631702 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACCCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TTGAAGATTGT
** *
1631757 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAAACCTGTTTTATGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTT-TGAAGATTGT
* * * * * * **
1631812 TCGAGTTCTATACTCCCTTAACGAATAGGGTGCGAACTTGTTTTATGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTT-TGAAGATTGT
* * * * *
1631867 CCGAG-TCTTATACTCCCTGAAGGAATAGGGAGCGGACCCGTCATTTGAAGATTTT
1 TCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACCCGT-TTTTGAAGATTGT
*
1631922 TCAAGTT
1 TCGAGTT
1631929 TCATTTATCC
Statistics
Matches: 542, Mismatches: 60, Indels: 19
0.87 0.10 0.03
Matches are distributed among these distances:
54 5 0.01
55 531 0.98
56 6 0.01
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (54 bp):
TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTTGAAGATTGT
Found at i:1633270 original size:2 final size:2
Alignment explanation
Indices: 1633259--1633291 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1633249 ATTTCTTCAA
1633259 AT AT -T 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
1633292 GCGTGTGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1633393 original size:2 final size:2
Alignment explanation
Indices: 1633386--1633418 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1633376 TATAATATCG
*
1633386 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1633419 CGTACTGACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1636661 original size:21 final size:20
Alignment explanation
Indices: 1636636--1636677 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1636626 GAAAATAATG
*
1636636 TAACAAAGAAAATGAAAAAAA
1 TAACAAAAAAAAT-AAAAAAA
*
1636657 TAACAAAAAAAATAACAAAA
1 TAACAAAAAAAATAAAAAAA
1636677 T
1 T
1636678 CAGAAATCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.76, C:0.07, G:0.05, T:0.12
Consensus pattern (20 bp):
TAACAAAAAAAATAAAAAAA
Found at i:1636667 original size:12 final size:12
Alignment explanation
Indices: 1636650--1636676 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1636640 AAAGAAAATG
1636650 AAAAAAATAACA
1 AAAAAAATAACA
1636662 AAAAAAATAACA
1 AAAAAAATAACA
1636674 AAA
1 AAA
1636677 TCAGAAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.85, C:0.07, G:0.00, T:0.07
Consensus pattern (12 bp):
AAAAAAATAACA
Found at i:1642705 original size:27 final size:27
Alignment explanation
Indices: 1642643--1642706 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
1642633 AAAATTACTA
*
1642643 CTTTTTTATTCTTTTGCATAATATGTT
1 CTTTTTTTTTCTTTTGCATAATATGTT
* * *
1642670 CTTTGTTTTTCTTTTTCAT-TTATGATT
1 CTTTTTTTTTCTTTTGCATAATATG-TT
*
1642697 GTTTTTTTTT
1 CTTTTTTTTT
1642707 TTTCTCTCGT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
26 4 0.13
27 26 0.87
ACGTcount: A:0.12, C:0.09, G:0.08, T:0.70
Consensus pattern (27 bp):
CTTTTTTTTTCTTTTGCATAATATGTT
Found at i:1643562 original size:21 final size:21
Alignment explanation
Indices: 1643536--1643585 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
1643526 AGACAGGAGC
1643536 TAAGTGCGTAGCTAGAATTCG
1 TAAGTGCGTAGCTAGAATTCG
1643557 TAAGTGCGTAGCTAGAATTCG
1 TAAGTGCGTAGCTAGAATTCG
*
1643578 GAAGTGCG
1 TAAGTGCG
1643586 GGATTTGGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.14, G:0.32, T:0.26
Consensus pattern (21 bp):
TAAGTGCGTAGCTAGAATTCG
Found at i:1643756 original size:19 final size:19
Alignment explanation
Indices: 1643728--1643765 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1643718 TTGAATCAAA
*
1643728 AAGTTTTAAAATAAATTTT
1 AAGTTATAAAATAAATTTT
*
1643747 AAGTTATAAAATAAGTTTT
1 AAGTTATAAAATAAATTTT
1643766 GAATAACTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (19 bp):
AAGTTATAAAATAAATTTT
Found at i:1646001 original size:22 final size:24
Alignment explanation
Indices: 1645952--1645995 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
1645942 TTTATTTTTT
1645952 TTAAAATCATTATCTTAAAAAAAG
1 TTAAAATCATTATCTTAAAAAAAG
*
1645976 TTAAAAT-ATTA-CTTTAAAAA
1 TTAAAATCATTATCTTAAAAAA
1645996 CATTAAGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 4 0.21
24 7 0.37
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (24 bp):
TTAAAATCATTATCTTAAAAAAAG
Found at i:1647180 original size:36 final size:37
Alignment explanation
Indices: 1647109--1647180 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 37
1647099 TTATATTTTT
*
1647109 ATTTTTGTAAAAAAATTATATAAATATTATGAATTTA
1 ATTTTTGTAAAAAAATTATATAAATATTATCAATTTA
*
1647146 ATTTTT-TAAAGAAAA-TATAT-AATATTTTACAATTT
1 ATTTTTGTAAA-AAAATTATATAAATATTAT-CAATTT
1647181 GTAATATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
35 7 0.23
36 14 0.45
37 10 0.32
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
ATTTTTGTAAAAAAATTATATAAATATTATCAATTTA
Found at i:1647362 original size:20 final size:20
Alignment explanation
Indices: 1647325--1647363 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1647315 AATCCTATTA
* **
1647325 ACTGGTAATCTTTTATTCCC
1 ACTGATAATCTTACATTCCC
1647345 ACTGATAATCTTACATTCC
1 ACTGATAATCTTACATTCC
1647364 GTAAATCAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.08, T:0.41
Consensus pattern (20 bp):
ACTGATAATCTTACATTCCC
Found at i:1647677 original size:13 final size:13
Alignment explanation
Indices: 1647659--1647684 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1647649 ATTTTTATGA
1647659 TTAATTATATTTT
1 TTAATTATATTTT
1647672 TTAATTATATTTT
1 TTAATTATATTTT
1647685 ATCTCATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTAATTATATTTT
Found at i:1647735 original size:31 final size:31
Alignment explanation
Indices: 1647672--1647735 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
1647662 ATTATATTTT
* **
1647672 TTAATTATATTTTATCTCATTATTTTTATGA
1 TTAATTATATTTTATATCATTATTGATATGA
*
1647703 TTAATTATATTTTATAT-TTTATTGATATTGA
1 TTAATTATATTTTATATCATTATTGATA-TGA
1647734 TT
1 TT
1647736 CCATCGATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 7 0.25
31 21 0.75
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (31 bp):
TTAATTATATTTTATATCATTATTGATATGA
Found at i:1649068 original size:64 final size:63
Alignment explanation
Indices: 1648994--1649118 Score: 180
Period size: 64 Copynumber: 2.0 Consensus size: 63
1648984 AATGGAGCTT
*
1648994 TGGTTCGTTCGGGTTGATGACAAGAAACA-GAGAGAAATGAGAGATGGAGGAGGAGGAAGAAAAA
1 TGGTTCGTTCGGGTTGATGAC-AGAAA-AGGAGAGAAATGAGAGATGGAGGAGGAAGAAGAAAAA
* * *
1649058 TGGTTCGTTCGGGTTGATGACAGAAAATGGAGAGAAATGGGAGGTGTAGGAGGAAGAAGAA
1 TGGTTCGTTCGGGTTGATGACAGAAAA-GGAGAGAAATGAGAGATGGAGGAGGAAGAAGAA
1649119 GAAAGAAGAA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
62 1 0.02
63 5 0.09
64 49 0.89
ACGTcount: A:0.38, C:0.06, G:0.39, T:0.18
Consensus pattern (63 bp):
TGGTTCGTTCGGGTTGATGACAGAAAAGGAGAGAAATGAGAGATGGAGGAGGAAGAAGAAAAA
Found at i:1649388 original size:60 final size:60
Alignment explanation
Indices: 1649310--1649424 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 60
1649300 ATATCTCCCT
* * *
1649310 AAACTATGACTTTTATTCTAAATAAATC-CTTAAACTTTTG-ATCATTTCAGTTTCATCGTC
1 AAACTATGACTCTCATTCTAAATAAATCTC-TAAACTTTTGAAT-ATTTCAATTTCATCGTC
*
1649370 AAACTATGACTCTCATTCTAAATTAATCTCTAAACTTTTGAATATTTCAATTTCA
1 AAACTATGACTCTCATTCTAAATAAATCTCTAAACTTTTGAATATTTCAATTTCA
1649425 CCCACAAAGT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
60 46 0.94
61 3 0.06
ACGTcount: A:0.34, C:0.18, G:0.05, T:0.43
Consensus pattern (60 bp):
AAACTATGACTCTCATTCTAAATAAATCTCTAAACTTTTGAATATTTCAATTTCATCGTC
Found at i:1656626 original size:2 final size:2
Alignment explanation
Indices: 1656619--1656658 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1656609 GGAATATTAA
1656619 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
1656659 TTAAGCACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1660723 original size:26 final size:28
Alignment explanation
Indices: 1660669--1660724 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
1660659 AATTGAATAA
* * *
1660669 ATATATAGTATATGGTAAGATGGCTAAT
1 ATATATAGTATATGATAAGATGACAAAT
1660697 ATATATA-TATATGATAAGAT-ACAAAT
1 ATATATAGTATATGATAAGATGACAAAT
1660723 AT
1 AT
1660725 GATCTTGCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 6 0.24
27 12 0.48
28 7 0.28
ACGTcount: A:0.46, C:0.04, G:0.14, T:0.36
Consensus pattern (28 bp):
ATATATAGTATATGATAAGATGACAAAT
Found at i:1664427 original size:39 final size:39
Alignment explanation
Indices: 1664366--1664441 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
1664356 GAAAAAAGTG
* *
1664366 TGATTTTACACTTACCTGGTACAACCCTTTATCAAACTA
1 TGATTTTACACTCACCTCGTACAACCCTTTATCAAACTA
1664405 TGATTTTACACTCACCTCGTACAACCCTTTATCAAAC
1 TGATTTTACACTCACCTCGTACAACCCTTTATCAAAC
1664442 ACCATTGGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.30, C:0.29, G:0.07, T:0.34
Consensus pattern (39 bp):
TGATTTTACACTCACCTCGTACAACCCTTTATCAAACTA
Found at i:1677170 original size:7 final size:7
Alignment explanation
Indices: 1677158--1677186 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1677148 ACAGAACACT
1677158 GTTCAAA
1 GTTCAAA
1677165 GTTCAAA
1 GTTCAAA
1677172 GTTCAAA
1 GTTCAAA
1677179 GTTCAAA
1 GTTCAAA
1677186 G
1 G
1677187 GAGCATGCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (7 bp):
GTTCAAA
Found at i:1683529 original size:19 final size:20
Alignment explanation
Indices: 1683505--1683545 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1683495 ATAATGCTAT
1683505 TTATTTG-TATATTTTTAAA
1 TTATTTGATATATTTTTAAA
*
1683524 TTATTTGATTATTTTTTTAAA
1 TTATTTGA-TATATTTTTAAA
1683545 T
1 T
1683546 CGATCATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
21 12 0.63
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (20 bp):
TTATTTGATATATTTTTAAA
Found at i:1683630 original size:2 final size:2
Alignment explanation
Indices: 1683623--1683708 Score: 163
Period size: 2 Copynumber: 43.0 Consensus size: 2
1683613 ATCTATCATA
1683623 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
*
1683665 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1683707 AT
1 AT
1683709 GGTTATTTGA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1691211 original size:386 final size:386
Alignment explanation
Indices: 1690476--1691252 Score: 1454
Period size: 386 Copynumber: 2.0 Consensus size: 386
1690466 ACCGATAAAA
*
1690476 CATTCTAACTTATTTTATTAAAATAAAATACTATATATATATATTAATACAAGTTTATCAAAATA
1 CATTCAAACTTATTTTATTAAAATAAAATAC-ATATATATATATTAATACAAGTTTATCAAAATA
1690541 ATCAGAGCATACATCACTTGACACTTTGATTACATGACAACATTCATTTACATAACAAAAGGACC
65 ATCA-AGCATACATCACTTGACACTTTGATTACATGACAACATTCATTTACATAACAAAAGGACC
1690606 TACTGCTCAAGTTGCCTCTGATTTGATAGTTGCAGGAGTAATGTTGTCCAGCTGCTTAACATGTC
129 TACTGCTCAAGTTGCCTCTGATTTGATAGTTGCAGGAGTAATGTTGTCCAGCTGCTTAACATGTC
1690671 TCGTCTACTTTCTTGGATCCTACGTGTGAAACACTCACACGCTAAGTCATCGACTTAGTGAGGCA
194 TCGTCTACTTTCTTGGATCCTACGTGTGAAACACTCACACGCTAAGTCATCGACTTAGTGAGGCA
1690736 ATATAATAATAATAATAACAAAGAAATGTAATGGAAATGCCATAATTTAATGGAATGAGATAAAA
259 ATATAATAATAATAATAACAAAGAAATGTAATGGAAATGCCATAATTTAATGGAATGAGATAAAA
1690801 ATCAATGCTAACCATGCAGTTTATATCACCATGTTCTTTACCTGTAAGCATACTATATTGACATT
324 ATCAATGCTAACCATGCAGTTTATATCACCATGTTCTTTACCTGTAAGCATA--ATATTGACATT
1690866 CATTCAAACTTATTTTATTAAAATAAAATAC-TATATATATATTAATACAAGTTTATCAAAATAA
1 CATTCAAACTTATTTTATTAAAATAAAATACATATATATATATTAATACAAGTTTATCAAAATAA
*
1690930 TC-AGCATACATCACTTGACACTTTGATTACATGCCAACATTCATTTACATAACAAAAGGACCTA
66 TCAAGCATACATCACTTGACACTTTGATTACATGACAACATTCATTTACATAACAAAAGGACCTA
1690994 CTGCTCAAGTTGCCTCTGATTTGATAGTTGCAGGAGTAATGTTGTCCAGCTGCTTAACATGTCTC
131 CTGCTCAAGTTGCCTCTGATTTGATAGTTGCAGGAGTAATGTTGTCCAGCTGCTTAACATGTCTC
1691059 GTCTACTTTCTTGGATCCTACGTGTGAAACACTCACACGCTAAGTCATCGACTTAGTGAGGCAAT
196 GTCTACTTTCTTGGATCCTACGTGTGAAACACTCACACGCTAAGTCATCGACTTAGTGAGGCAAT
1691124 AT-ATAATAATAATAACAAAGAAATGTAATGGAAATGCCATAATTTAATGGAATGAGAT-AAAAT
261 ATAATAATAATAATAACAAAGAAATGTAATGGAAATGCCATAATTTAATGGAATGAGATAAAAAT
1691187 CAAATGCTTAACCATGCAGTTTATATCACCATGTTCTTTACCTGTAAGCATAATATTGACATT
326 C-AATGC-TAACCATGCAGTTTATATCACCATGTTCTTTACCTGTAAGCATAATATTGACATT
1691250 CAT
1 CAT
1691253 GAATTCATAT
Statistics
Matches: 383, Mismatches: 2, Indels: 10
0.97 0.01 0.03
Matches are distributed among these distances:
384 20 0.05
385 61 0.16
386 237 0.62
388 35 0.09
390 30 0.08
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.33
Consensus pattern (386 bp):
CATTCAAACTTATTTTATTAAAATAAAATACATATATATATATTAATACAAGTTTATCAAAATAA
TCAAGCATACATCACTTGACACTTTGATTACATGACAACATTCATTTACATAACAAAAGGACCTA
CTGCTCAAGTTGCCTCTGATTTGATAGTTGCAGGAGTAATGTTGTCCAGCTGCTTAACATGTCTC
GTCTACTTTCTTGGATCCTACGTGTGAAACACTCACACGCTAAGTCATCGACTTAGTGAGGCAAT
ATAATAATAATAATAACAAAGAAATGTAATGGAAATGCCATAATTTAATGGAATGAGATAAAAAT
CAATGCTAACCATGCAGTTTATATCACCATGTTCTTTACCTGTAAGCATAATATTGACATT
Found at i:1691385 original size:21 final size:22
Alignment explanation
Indices: 1691361--1691414 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
1691351 ATAAATGCAA
1691361 CGAAGTGCCACGTAGAATT-AC
1 CGAAGTGCCACGTAGAATTCAC
* *
1691382 CGAAGTGTCGCGTAGAATTGCAC
1 CGAAGTGCCACGTAGAATT-CAC
*
1691405 CGTAGTGCCA
1 CGAAGTGCCA
1691415 TATAATATTG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 17 0.65
23 9 0.35
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.20
Consensus pattern (22 bp):
CGAAGTGCCACGTAGAATTCAC
Found at i:1691674 original size:31 final size:30
Alignment explanation
Indices: 1691630--1691690 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 30
1691620 TATTGTATAT
1691630 ACATATAATTTCCAT-ACCTTTATCACATAG
1 ACATATAATTTCCATCA-CTTTATCACATAG
*
1691660 ACATATCATGTTCCATCACTTTATCACATAG
1 ACATATAAT-TTCCATCACTTTATCACATAG
1691691 CTTATATAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 8 0.29
31 19 0.68
32 1 0.04
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (30 bp):
ACATATAATTTCCATCACTTTATCACATAG
Found at i:1692557 original size:3 final size:3
Alignment explanation
Indices: 1692549--1692578 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
1692539 GGTCTCACGG
1692549 GAA GAA GAA GAAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA G-AA GAA GAA GAA GAA GAA GA
1692579 GAAATCTGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1692570 original size:16 final size:17
Alignment explanation
Indices: 1692549--1692581 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1692539 GGTCTCACGG
1692549 GAAGAAGAAGAA-AGAA
1 GAAGAAGAAGAAGAGAA
1692565 GAAGAAGAAGAAGAGAA
1 GAAGAAGAAGAAGAGAA
1692582 ATCTGGAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (17 bp):
GAAGAAGAAGAAGAGAA
Found at i:1694683 original size:21 final size:21
Alignment explanation
Indices: 1694657--1694701 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1694647 GATTTCTGGG
* *
1694657 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1694678 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1694699 CAA
1 CAA
1694702 ACGAACAACA
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1695552 original size:31 final size:31
Alignment explanation
Indices: 1695497--1695620 Score: 189
Period size: 31 Copynumber: 4.0 Consensus size: 31
1695487 AAGGGTCGGG
1695497 GTTTACCTATGTTCTTC-GGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1695527 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1695558 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1695589 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1695620 G
1 G
1695621 GTCCTTCGGG
Statistics
Matches: 87, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
30 17 0.20
31 69 0.79
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1696953 original size:23 final size:23
Alignment explanation
Indices: 1696865--1696945 Score: 135
Period size: 23 Copynumber: 3.5 Consensus size: 23
1696855 TATTATATGG
*
1696865 CACTACGGTGCAATTCTACGCGA
1 CACTTCGGTGCAATTCTACGCGA
1696888 CACTTCGGTGCAATTCTACGCGA
1 CACTTCGGTGCAATTCTACGCGA
* *
1696911 CACTTCGGTGCAATTCTACGTGG
1 CACTTCGGTGCAATTCTACGCGA
1696934 CACTTCGGTGCA
1 CACTTCGGTGCA
1696946 TTTATACGAG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (23 bp):
CACTTCGGTGCAATTCTACGCGA
Found at i:1704314 original size:46 final size:46
Alignment explanation
Indices: 1704257--1704407 Score: 277
Period size: 46 Copynumber: 3.3 Consensus size: 46
1704247 ATGTGTAACC
1704257 ATGT-ATTTCATATCATATCACATGTATCACGTATTACATATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
1704302 ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
*
1704348 ATGTCATTTCATATCATATCACATGTATCACGTATTGCATATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
*
1704394 ATATCATTTCATAT
1 ATGTCATTTCATAT
1704408 AGTCACATAG
Statistics
Matches: 103, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
45 4 0.04
46 99 0.96
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.42
Consensus pattern (46 bp):
ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
Found at i:1704860 original size:35 final size:36
Alignment explanation
Indices: 1704814--1704882 Score: 131
Period size: 35 Copynumber: 1.9 Consensus size: 36
1704804 TTTCATTTAG
1704814 GGGGAATCGATACCCCCCA-GGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCAGGGGGGAATCTGTTCCC
1704849 GGGGAATCGATACCCCCCAGGGGGGAATCTGTTC
1 GGGGAATCGATACCCCCCAGGGGGGAATCTGTTC
1704883 GCCCTGCACA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 19 0.58
36 14 0.42
ACGTcount: A:0.20, C:0.29, G:0.33, T:0.17
Consensus pattern (36 bp):
GGGGAATCGATACCCCCCAGGGGGGAATCTGTTCCC
Found at i:1708193 original size:2 final size:2
Alignment explanation
Indices: 1708186--1708214 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1708176 TCAATCAAAT
1708186 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 T
1708215 TCCAATGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1709820 original size:30 final size:30
Alignment explanation
Indices: 1709784--1709946 Score: 299
Period size: 30 Copynumber: 5.4 Consensus size: 30
1709774 TCTGAAGGAC
1709784 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1709814 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1709844 CTATCCAGAGGTCACAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1709874 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1709904 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
1709934 CTGTCCATAGGTC
1 CTATCCAGAGGTC
1709947 CCGAAGAACC
Statistics
Matches: 129, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 129 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1709902 original size:90 final size:91
Alignment explanation
Indices: 1709784--1709971 Score: 315
Period size: 90 Copynumber: 2.1 Consensus size: 91
1709774 TCTGAAGGAC
1709784 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
* *
1709849 CAGAGGTCACAAAGATCCTCGGT-AA
66 CAGAGGTCACAAAGAACCTAGGTAAA
*
1709874 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTGTC
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
* * *
1709939 CATAGGTCCCGAAGAACCTAGGTAAA
66 CAGAGGTCACAAAGAACCTAGGTAAA
1709965 CTATCCA
1 CTATCCA
1709972 TATGTTCCTT
Statistics
Matches: 91, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
90 82 0.90
91 9 0.10
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (91 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
CAGAGGTCACAAAGAACCTAGGTAAA
Found at i:1709963 original size:30 final size:30
Alignment explanation
Indices: 1709784--1709971 Score: 277
Period size: 30 Copynumber: 6.2 Consensus size: 30
1709774 TCTGAAGGAC
*
1709784 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCTCGGTAA
*
1709814 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCTCGGTAA
1709844 CTATCCAGAGGTCACAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCTCGGTAA
*
1709874 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCTCGGTAA
*
1709904 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCTCGGTAA
* * * * * *
1709934 CTGTCCATAGGTCCCGAAGAACCTAGGTAAA
1 CTATCCAGAGGTCACAAAGATCCTCGGT-AA
1709965 CTATCCA
1 CTATCCA
1709972 TATGTTCCTT
Statistics
Matches: 147, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
30 139 0.95
31 8 0.05
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGATCCTCGGTAA
Found at i:1710207 original size:4 final size:4
Alignment explanation
Indices: 1710198--1710298 Score: 184
Period size: 4 Copynumber: 25.2 Consensus size: 4
1710188 ATATAACCAT
*
1710198 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TATA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
1710246 TATA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1710294 TACA T
1 TACA T
1710299 GTCATCATTT
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 95 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.28
Consensus pattern (4 bp):
TACA
Found at i:1712639 original size:30 final size:30
Alignment explanation
Indices: 1712603--1712849 Score: 485
Period size: 30 Copynumber: 8.2 Consensus size: 30
1712593 TCTGAAGGAC
1712603 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1712633 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1712663 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1712693 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1712723 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1712753 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1712783 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1712813 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1712843 CTGTCCA
1 CTATCCA
1712850 TAGATCCCGA
Statistics
Matches: 216, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 216 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1714639 original size:31 final size:31
Alignment explanation
Indices: 1714601--1714723 Score: 194
Period size: 31 Copynumber: 4.0 Consensus size: 31
1714591 GGGTCGAGGG
*
1714601 TTACCTATGTTCTTCCGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
1714632 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
1714663 TTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
1714694 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
1714724 GTCCTTCGGG
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:1716571 original size:21 final size:20
Alignment explanation
Indices: 1716508--1716571 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
1716498 GCTCGTATAA
1716508 ATGTCCCGAAGGACCTATC-
1 ATGTCCCGAAGGACCTATCT
**
1716527 A--TCCCGAAGGATGTCATCT
1 ATGTCCCGAAGGACCT-ATCT
*
1716546 GTGTCCCGAAGGACCTATCAT
1 ATGTCCCGAAGGACCTATC-T
1716567 ATGTC
1 ATGTC
1716572 TTATATGACA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
17 11 0.32
18 3 0.09
19 1 0.03
20 3 0.09
21 16 0.47
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (20 bp):
ATGTCCCGAAGGACCTATCT
Found at i:1716772 original size:46 final size:46
Alignment explanation
Indices: 1716715--1716911 Score: 360
Period size: 46 Copynumber: 4.3 Consensus size: 46
1716705 ATGTGTAACC
1716715 ATGT-ATTTCATATCATATCACATGTATCACGTATTACATATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
1716760 ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
*
1716806 ATGTCATTTCATATCATATCACATGTATCACATATTACATATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
*
1716852 ATGTCATTTCATATCATATCACATGTATCACGTATTGCATATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
*
1716898 ATATCATTTCATAT
1 ATGTCATTTCATAT
1716912 AGTCACATTA
Statistics
Matches: 147, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
45 4 0.03
46 143 0.97
ACGTcount: A:0.33, C:0.19, G:0.06, T:0.42
Consensus pattern (46 bp):
ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
Found at i:1726410 original size:19 final size:19
Alignment explanation
Indices: 1726388--1726432 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1726378 TTTAACCGGT
1726388 TTTGACCGGTTC-GAACCGA
1 TTTGACCGG-TCAGAACCGA
*
1726407 TTTGACCGGTCAGAACCGG
1 TTTGACCGGTCAGAACCGA
1726426 TTTGACC
1 TTTGACC
1726433 CGACCCGACC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 2 0.08
19 22 0.92
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (19 bp):
TTTGACCGGTCAGAACCGA
Found at i:1735682 original size:22 final size:22
Alignment explanation
Indices: 1735660--1735700 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1735650 TCATAATTAT
1735660 TTAAAAA-ATTAAATAAAAATA
1 TTAAAAATATTAAATAAAAATA
*
1735681 TTAAAAATATTTAATAAAAA
1 TTAAAAATATTAAATAAAAA
1735701 ATAAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
TTAAAAATATTAAATAAAAATA
Found at i:1738581 original size:21 final size:21
Alignment explanation
Indices: 1738555--1738608 Score: 58
Period size: 19 Copynumber: 2.7 Consensus size: 21
1738545 CTTTTAAAAG
* *
1738555 ATAATATTATAAATATATTAT
1 ATAATATTATAAATATATAAA
*
1738576 ATAATATT-T-AATTTATAAA
1 ATAATATTATAAATATATAAA
*
1738595 ATAACATTATAAAT
1 ATAATATTATAAAT
1738609 GTTAGAATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 14 0.52
20 2 0.07
21 11 0.41
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAATATTATAAATATATAAA
Found at i:1739068 original size:10 final size:10
Alignment explanation
Indices: 1739053--1739077 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1739043 ATTCTCTGTA
1739053 AAAAAAAAAG
1 AAAAAAAAAG
1739063 AAAAAAAAAG
1 AAAAAAAAAG
1739073 AAAAA
1 AAAAA
1739078 GGTTATTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:1740775 original size:199 final size:198
Alignment explanation
Indices: 1740429--1741026 Score: 909
Period size: 199 Copynumber: 3.0 Consensus size: 198
1740419 ACATTCCAGA
** * **
1740429 AAAGACACAGGGTCAACCCTGCATAAAGTTAACATTCATCATTTTCCTC--GTCTGGTATCCTAG
1 AAAGACACAGGGTCAGTCCTGCATAAAATTAACATTCATCATTTTCCTCTTGTCTGGGGTCCTAG
* *
1740492 GTATTTACTCGGACTCGTATGCAAGTGTTGCAACATAAGTTTCGAACACGATAATTCAACAAAAA
66 GTGTTTACTCGGACTCGTATGCAAGTGTCGCAACATAAGTTTCGAACACGATAATTCAAC-AAAA
* * * *
1740557 ATCAAGAAACAAAACAACATAGATTTGAATCTAAGTT-TGGCATTTTGAGATGTAGCTTGTATAC
130 ATGAAGAAACAAAACAACATAGATTTGAATCTAAGTTAT-GCATTTTGACAAGTAGCTTGCATAC
1740621 CTAAG
194 CTAAG
1740626 AAAGACACAGGGTCAGTCCTGCATAAAATTAACATTCATCATTTTCCTCTTGTCTGGGGTCCTAG
1 AAAGACACAGGGTCAGTCCTGCATAAAATTAACATTCATCATTTTCCTCTTGTCTGGGGTCCTAG
*
1740691 GTGTTTACTCGGACTCGTATGCAAGTGTCGCAACATAAGTTTCGAACACGATAATTCAAGAAAAT
66 GTGTTTACTCGGACTCGTATGCAAGTGTCGCAACATAAGTTTCGAACACGATAATTCAACAAAA-
* * *
1740756 ATGAAGAAACTACACAACATAGATTTGAATCTAAGTTATGCAGTTTGACAAGTAGCTCT-CATAC
130 ATGAAGAAACAAAACAACATAGATTTGAATCTAAGTTATGCATTTTGACAAGTAGCT-TGCATAC
*
1740820 TTAAG
194 CTAAG
* *
1740825 AATGACACAGGGTCAGTGCTGCATAAAATTAACATTCATCATTTTCCTCTTGTCTGGGGTCCTAG
1 AAAGACACAGGGTCAGTCCTGCATAAAATTAACATTCATCATTTTCCTCTTGTCTGGGGTCCTAG
* * *
1740890 GTGTTTACTCGGACTCGTATGCAAGTGTCGCAACACAAGTTTCGAACACTATAATTTAACAAAAA
66 GTGTTTACTCGGACTCGTATGCAAGTGTCGCAACATAAGTTTCGAACACGATAATTCAACAAAAA
* *
1740955 TGAAGAAACGAAACAACATAG-TTTCAAATCTAAGTTATGCATTTTGACAAGTAGCTTGCATACC
131 TGAAGAAACAAAACAACATAGATTT-GAATCTAAGTTATGCATTTTGACAAGTAGCTTGCATACC
1741019 TAAG
195 TAAG
1741023 AAAG
1 AAAG
1741027 TGGAGAAAGC
Statistics
Matches: 366, Mismatches: 28, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
197 50 0.14
198 65 0.18
199 249 0.68
200 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (198 bp):
AAAGACACAGGGTCAGTCCTGCATAAAATTAACATTCATCATTTTCCTCTTGTCTGGGGTCCTAG
GTGTTTACTCGGACTCGTATGCAAGTGTCGCAACATAAGTTTCGAACACGATAATTCAACAAAAA
TGAAGAAACAAAACAACATAGATTTGAATCTAAGTTATGCATTTTGACAAGTAGCTTGCATACCT
AAG
Found at i:1747719 original size:19 final size:20
Alignment explanation
Indices: 1747691--1747729 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1747681 TATATATTAT
1747691 TATTAGTTTA-TCTTTTGTA
1 TATTAGTTTAGTCTTTTGTA
* *
1747710 TATTATTTTAGTTTTTTGTA
1 TATTAGTTTAGTCTTTTGTA
1747730 AGTAAAATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.21, C:0.03, G:0.10, T:0.67
Consensus pattern (20 bp):
TATTAGTTTAGTCTTTTGTA
Found at i:1748461 original size:9 final size:9
Alignment explanation
Indices: 1748447--1748471 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1748437 TCGATTCGTG
1748447 TCGATTTTT
1 TCGATTTTT
1748456 TCGATTTTT
1 TCGATTTTT
1748465 TCGATTT
1 TCGATTT
1748472 CGTTGCTTAA
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:0.12, C:0.12, G:0.12, T:0.64
Consensus pattern (9 bp):
TCGATTTTT
Found at i:1748615 original size:36 final size:35
Alignment explanation
Indices: 1748564--1748640 Score: 93
Period size: 36 Copynumber: 2.2 Consensus size: 35
1748554 TTCGATTGAA
* * *
1748564 TATAATTTAAATGTTAAT-TTTATAATATTTTATAT
1 TATAATTGAAATGTTAATATTT-GAATATTTTAGAT
*
1748599 TATAATTGGAAATGTTAATATTTGAATATTTTCGAT
1 TATAATT-GAAATGTTAATATTTGAATATTTTAGAT
1748635 TATAAT
1 TATAAT
1748641 AAAAAATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
35 7 0.19
36 26 0.72
37 3 0.08
ACGTcount: A:0.39, C:0.01, G:0.08, T:0.52
Consensus pattern (35 bp):
TATAATTGAAATGTTAATATTTGAATATTTTAGAT
Found at i:1750113 original size:31 final size:31
Alignment explanation
Indices: 1750086--1750162 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
1750076 TTAGGGCCTT
*
1750086 AGAGCCTACCCAAG-ATAGATTTCAGGGCCGC
1 AGAGCCTACCCAAGAAT-GATCTCAGGGCCGC
* *
1750117 AGGGCCTACCCGAGAATGATCTCAGGGCCGC
1 AGAGCCTACCCAAGAATGATCTCAGGGCCGC
*
1750148 AGAGCCTACCTAAGA
1 AGAGCCTACCCAAGA
1750163 GTCACATTAG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 37 0.95
32 2 0.05
ACGTcount: A:0.29, C:0.30, G:0.27, T:0.14
Consensus pattern (31 bp):
AGAGCCTACCCAAGAATGATCTCAGGGCCGC
Found at i:1751476 original size:9 final size:9
Alignment explanation
Indices: 1751462--1751488 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1751452 GTCATAAGGG
1751462 CATTTTGGT
1 CATTTTGGT
1751471 CATTTTGGT
1 CATTTTGGT
1751480 CATTTTGGT
1 CATTTTGGT
1751489 GCTTAACGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.22, T:0.56
Consensus pattern (9 bp):
CATTTTGGT
Found at i:1754221 original size:38 final size:38
Alignment explanation
Indices: 1754165--1754246 Score: 101
Period size: 38 Copynumber: 2.2 Consensus size: 38
1754155 ACTACCCTGC
* *
1754165 AAAATTGACCAACACAATGCCAAGTGCAGAGCAAGAGG
1 AAAAATGACCAACACAATGCCAAGAGCAGAGCAAGAGG
* * * * *
1754203 AAAAATGACCAACTCAATGCTACGAGCAGAGGAGGAGG
1 AAAAATGACCAACACAATGCCAAGAGCAGAGCAAGAGG
1754241 AAAAAT
1 AAAAAT
1754247 AATCATCCTG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.11
Consensus pattern (38 bp):
AAAAATGACCAACACAATGCCAAGAGCAGAGCAAGAGG
Found at i:1755670 original size:31 final size:33
Alignment explanation
Indices: 1755577--1755675 Score: 157
Period size: 33 Copynumber: 3.1 Consensus size: 33
1755567 AATTGGCAAG
*
1755577 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
1755610 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
* *
1755643 TTGGAAAATTC-T-TTGGTAGGTGACCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
1755674 TT
1 TT
1755676 TTTCATGTTT
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
31 19 0.30
32 1 0.02
33 43 0.68
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.38
Consensus pattern (33 bp):
TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
Found at i:1757344 original size:22 final size:22
Alignment explanation
Indices: 1757303--1757369 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
1757293 CTCGTATAAA
1757303 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
1757326 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
1757348 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1757370 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:1759083 original size:21 final size:21
Alignment explanation
Indices: 1759059--1759103 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1759049 TCTTGTTCGT
* *
1759059 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1759080 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1759101 TTG
1 TTG
1759104 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:1760259 original size:7 final size:7
Alignment explanation
Indices: 1760247--1760271 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1760237 TTTCATTTCT
1760247 TTATTCC
1 TTATTCC
1760254 TTATTCC
1 TTATTCC
1760261 TTATTCC
1 TTATTCC
1760268 TTAT
1 TTAT
1760272 ACATTAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.60
Consensus pattern (7 bp):
TTATTCC
Found at i:1762289 original size:22 final size:22
Alignment explanation
Indices: 1762248--1762314 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
1762238 CTCGTATAAA
1762248 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
1762271 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
1762293 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1762315 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:1764021 original size:21 final size:21
Alignment explanation
Indices: 1763997--1764041 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1763987 TCTTGTTCGT
* *
1763997 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1764018 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1764039 TTG
1 TTG
1764042 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:1768395 original size:31 final size:33
Alignment explanation
Indices: 1768331--1768396 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 33
1768321 AGTTGACAAG
* * * *
1768331 TTGGAAATTTCATCTTGGTTGGTGGCCAGCTTA
1 TTGGAAAATTCATCTTGGTAGGTGACCAACTTA
1768364 TTGGAAAATT-AT-TTGGTAGGTGACCAACTTA
1 TTGGAAAATTCATCTTGGTAGGTGACCAACTTA
1768395 TT
1 TT
1768397 TTTCATGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 18 0.62
32 2 0.07
33 9 0.31
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.39
Consensus pattern (33 bp):
TTGGAAAATTCATCTTGGTAGGTGACCAACTTA
Found at i:1769626 original size:17 final size:16
Alignment explanation
Indices: 1769587--1769619 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1769577 AACTCTTATT
*
1769587 TAAATATATTTAAAAA
1 TAAAAATATTTAAAAA
1769603 TAAAAATATTTAAAAA
1 TAAAAATATTTAAAAA
1769619 T
1 T
1769620 GTTAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TAAAAATATTTAAAAA
Found at i:1769941 original size:37 final size:37
Alignment explanation
Indices: 1769891--1769965 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
1769881 GTTTCATGCG
*
1769891 TCTTTCCCAGGTCATACAGAAGACGTTGAGTGCATCA
1 TCTTTCCCAGGTCATACAGAAGACGTTGACTGCATCA
*
1769928 TCTTTCCCAGGTCATACAGAAGACGTTGACTTCATCA
1 TCTTTCCCAGGTCATACAGAAGACGTTGACTGCATCA
1769965 T
1 T
1769966 GCGTCTTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (37 bp):
TCTTTCCCAGGTCATACAGAAGACGTTGACTGCATCA
Found at i:1772053 original size:15 final size:15
Alignment explanation
Indices: 1772028--1772080 Score: 79
Period size: 15 Copynumber: 3.5 Consensus size: 15
1772018 TGAGACATTA
1772028 CCCGCCCCCGCATCCG
1 CCCG-CCCCGCATCCG
1772044 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
* *
1772059 CTCGCCCCACATCCG
1 CCCGCCCCGCATCCG
1772074 CCCGCCC
1 CCCGCCC
1772081 AGCTAAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
15 30 0.88
16 4 0.12
ACGTcount: A:0.08, C:0.68, G:0.17, T:0.08
Consensus pattern (15 bp):
CCCGCCCCGCATCCG
Found at i:1777300 original size:12 final size:12
Alignment explanation
Indices: 1777283--1777307 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1777273 TTAATAATTA
1777283 AAAAATATTTTT
1 AAAAATATTTTT
1777295 AAAAATATTTTT
1 AAAAATATTTTT
1777307 A
1 A
1777308 TTTCAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAAAATATTTTT
Found at i:1777304 original size:38 final size:37
Alignment explanation
Indices: 1777251--1777327 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 37
1777241 GGAGGGGGCC
*
1777251 ATTTTTAAAATTATTTTTAAGTTT--AATAATTAAAAAAT
1 ATTTTTAAAAATATTTTT-A-TTTCAAAT-ATTAAAAAAT
1777289 ATTTTTAAAAATATTTTTATTTCAAATATTAAAAAAT
1 ATTTTTAAAAATATTTTTATTTCAAATATTAAAAAAT
1777326 AT
1 AT
1777328 GGTAATTTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
36 3 0.08
37 13 0.36
38 20 0.56
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (37 bp):
ATTTTTAAAAATATTTTTATTTCAAATATTAAAAAAT
Found at i:1777406 original size:72 final size:71
Alignment explanation
Indices: 1777275--1777411 Score: 177
Period size: 72 Copynumber: 1.9 Consensus size: 71
1777265 TTTTAAGTTT
* * * * *
1777275 AATAATTAAAAAATATTTTTAAAAATATTTTTATTTCAAATATTAAAAAATATGGTAATTTAGTG
1 AATAATTAAAAAATATTTTTAAAAATATTTTTATTTAAAAAACTAAAAAATATGATAATTCAGTG
1777340 GGACTC
66 GGACTC
* **
1777346 AATAATTAAAAAATA-TTTTAAACATCATTTTTTATTTAAAAAACTCGAAAATATGATAATTCAG
1 AATAATTAAAAAATATTTTTAAAAAT-A-TTTTTATTTAAAAAACTAAAAAATATGATAATTCAG
1777410 TG
64 TG
1777412 AACCTCATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
70 9 0.16
71 16 0.29
72 31 0.55
ACGTcount: A:0.47, C:0.06, G:0.07, T:0.39
Consensus pattern (71 bp):
AATAATTAAAAAATATTTTTAAAAATATTTTTATTTAAAAAACTAAAAAATATGATAATTCAGTG
GGACTC
Found at i:1783063 original size:10 final size:10
Alignment explanation
Indices: 1783050--1783079 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
1783040 AATTTTTTTG
1783050 AATAATATAA
1 AATAATATAA
1783060 AATAATTATAA
1 AATAA-TATAA
1783071 AATAATATA
1 AATAATATA
1783080 TATTTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AATAATATAA
Found at i:1783915 original size:32 final size:31
Alignment explanation
Indices: 1783864--1783952 Score: 88
Period size: 32 Copynumber: 2.8 Consensus size: 31
1783854 GATGAAATAG
*
1783864 CATGTACCATGTCACCCAAGGTGATAACGTGA
1 CATGTA-CATGTCATCCAAGGTGATAACGTGA
* * * *
1783896 CATGTATCATATCATCCAAGATAATAACGTGT
1 CATGTA-CATGTCATCCAAGGTGATAACGTGA
* *
1783928 CATAGGACATGTCATCAAAGGTGAT
1 CAT-GTACATGTCATCCAAGGTGAT
1783953 GACTTGAGAT
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
32 43 0.96
33 2 0.04
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (31 bp):
CATGTACATGTCATCCAAGGTGATAACGTGA
Found at i:1785425 original size:17 final size:17
Alignment explanation
Indices: 1785405--1785463 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 17
1785395 ATTATAAAAT
1785405 AATAATATTAATATTGA
1 AATAATATTAATATTGA
1785422 AATAA-ATT-ATA-T-A
1 AATAATATTAATATTGA
1785435 AA-AATATATAATATTG-
1 AATAATAT-TAATATTGA
1785451 -ATAAT-TTAATATT
1 AATAATATTAATATT
1785464 ATTGGATTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 15
0.71 0.00 0.29
Matches are distributed among these distances:
12 2 0.06
13 5 0.14
14 9 0.25
15 8 0.22
16 7 0.19
17 5 0.14
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
AATAATATTAATATTGA
Done.