Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A06
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: 115140250
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2234201 characters in sequence are not A, C, G, or T
File 337 of 345
Found at i:112245088 original size:27 final size:25
Alignment explanation
Indices: 112245034--112245088 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
112245024 TAGATGGCCC
* **
112245034 AAAGTAAAAAAATCTAAATATTTTT
1 AAAGTAAAAAAATCTAAATAATCCT
112245059 AAAGTAAAAAAATCTAGATATAATCCT
1 AAAGTAAAAAAATCTA-A-ATAATCCT
112245086 AAA
1 AAA
112245089 AAAAGGCACC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 16 0.64
26 1 0.04
27 8 0.32
ACGTcount: A:0.58, C:0.07, G:0.05, T:0.29
Consensus pattern (25 bp):
AAAGTAAAAAAATCTAAATAATCCT
Found at i:112247064 original size:25 final size:25
Alignment explanation
Indices: 112247036--112247086 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
112247026 ATTTTAATTG
112247036 AATTAAGACTCAATTGACTTAGTTA
1 AATTAAGACTCAATTGACTTAGTTA
112247061 AATTAAGACTCAATTGACTTAGTTA
1 AATTAAGACTCAATTGACTTAGTTA
112247086 A
1 A
112247087 GTTTATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (25 bp):
AATTAAGACTCAATTGACTTAGTTA
Found at i:112255045 original size:17 final size:17
Alignment explanation
Indices: 112255025--112255079 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
112255015 TAAAAGATTG
112255025 ATTACTATAAAAAAATA
1 ATTACTATAAAAAAATA
* *
112255042 ATTACTATAAAAAATTT
1 ATTACTATAAAAAAATA
* *
112255059 ATTAGTATGATAAAAATA
1 ATTACTAT-AAAAAAATA
112255077 ATT
1 ATT
112255080 TCTAGACAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
17 22 0.71
18 9 0.29
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (17 bp):
ATTACTATAAAAAAATA
Found at i:112258580 original size:12 final size:12
Alignment explanation
Indices: 112258563--112258593 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
112258553 GAAGCAGGGG
112258563 AGAAAAAGAGAA
1 AGAAAAAGAGAA
*
112258575 AGAAAAAGGGAA
1 AGAAAAAGAGAA
112258587 AGAAAAA
1 AGAAAAA
112258594 TAAAAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAGAA
Found at i:112259589 original size:38 final size:41
Alignment explanation
Indices: 112259497--112259591 Score: 99
Period size: 38 Copynumber: 2.4 Consensus size: 41
112259487 GACCTCGAGT
**
112259497 CGATGAGACACTGGGTATCACTAAATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTATCACTAAATTTCTTCGGATAGAGC
** * *
112259538 CGATGAGGTACTGGGTA-C-C-AACTTTACTTCGGCTAG-GC
1 CGATGAGACACTGGGTATCACTAAATTT-CTTCGGATAGAGC
112259576 CGATGAGACACTGGGT
1 CGATGAGACACTGGGT
112259592 GTTAACTATT
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
38 19 0.42
39 10 0.22
40 1 0.02
41 15 0.33
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (41 bp):
CGATGAGACACTGGGTATCACTAAATTTCTTCGGATAGAGC
Found at i:112260268 original size:20 final size:20
Alignment explanation
Indices: 112260245--112260282 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
112260235 GTTATTAAGT
112260245 TAAAAATTATGTTA-ATGATA
1 TAAAAATTA-GTTATATGATA
*
112260265 TAAATATTAGTTATATGA
1 TAAAAATTAGTTATATGA
112260283 ATGTGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (20 bp):
TAAAAATTAGTTATATGATA
Found at i:112262491 original size:22 final size:21
Alignment explanation
Indices: 112262455--112262495 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
112262445 TAAGTAAATA
*
112262455 ATATTTTATTATTATATTACT
1 ATATTATATTATTATATTACT
112262476 ATATTATATTTATTATATTA
1 ATATTATA-TTATTATATTA
112262496 GTTAAAAAAA
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:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATTATATTATTATATTACT
Found at i:112262516 original size:9 final size:9
Alignment explanation
Indices: 112262502--112262546 Score: 56
Period size: 9 Copynumber: 4.8 Consensus size: 9
112262492 ATTAGTTAAA
112262502 AAAAGAAAG
1 AAAAGAAAG
112262511 AAAAGAAAG
1 AAAAGAAAG
112262520 AAAA-ACAAG
1 AAAAGA-AAG
112262529 AAAAAGAACAG
1 -AAAAGAA-AG
112262540 AAAAGAA
1 AAAAGAA
112262547 GCGAAAATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 1 0.03
9 16 0.50
10 12 0.38
11 3 0.09
ACGTcount: A:0.78, C:0.04, G:0.18, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:112270368 original size:27 final size:27
Alignment explanation
Indices: 112270311--112270369 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
112270301 ATGACTATTT
** ***
112270311 TGCCCTTATGTGGTAAAATAATTGTTT
1 TGCCCTTATGTGGTAAAATAACAGAAA
*
112270338 TGCCCTTATGTGGTAAAATGACAGAAA
1 TGCCCTTATGTGGTAAAATAACAGAAA
112270365 TGCCC
1 TGCCC
112270370 CTGTATGGTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (27 bp):
TGCCCTTATGTGGTAAAATAACAGAAA
Found at i:112270748 original size:18 final size:18
Alignment explanation
Indices: 112270725--112270777 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
112270715 GGACTTGCAT
*
112270725 ACTGTTTACTGCTACTGC
1 ACTGTTTACTACTACTGC
*
112270743 ACTGTTTACTATTACTGC
1 ACTGTTTACTACTACTGC
* *
112270761 ACTATTTACTATTACTG
1 ACTGTTTACTACTACTG
112270778 AAATAGGCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (18 bp):
ACTGTTTACTACTACTGC
Found at i:112278930 original size:129 final size:129
Alignment explanation
Indices: 112278729--112279055 Score: 501
Period size: 129 Copynumber: 2.5 Consensus size: 129
112278719 AAATCGGAAC
* * * * * * * *
112278729 CCAGCACGATTGGGTACGATTCCTCGAATTTCTAGACATTGAACATTGCCTTCGTTTTAAAATTT
1 CCAGCACGATTGGGCACGATTCCCCAAATTTCCAAACATCGAACGTTGCCTTCATTTTAAAATTT
112278794 TTTAAAACATGAGTGAAATTCCAAAGGAATATTCGATTATTTTGAAAAAACGGGAAATTACAAA
66 TTTAAAACATGAGTGAAATTCCAAAGGAATATTCGATTATTTTGAAAAAACGGGAAATTACAAA
* *
112278858 CCAGCACGATTGGGCACGATTCCCCAAATTTCCAAACATCAAACGTTACCTTCATTTTAAAATTT
1 CCAGCACGATTGGGCACGATTCCCCAAATTTCCAAACATCGAACGTTGCCTTCATTTTAAAATTT
* * *
112278923 TTTAAAACATGAGTGAAATTCCAAAGGAATATTCGATTATTTTGGAAAAACGGGAAATTGCAAC
66 TTTAAAACATGAGTGAAATTCCAAAGGAATATTCGATTATTTTGAAAAAACGGGAAATTACAAA
* *
112278987 CCAGCACGATTGGGCACGATTCCCCAAATTCCCAAACATCGAACGTTGCCTTCGTTTTTAAGAAT
1 CCAGCACGATTGGGCACGATTCCCCAAATTTCCAAACATCGAACGTTGCCTTC-ATTTTAA-AAT
112279052 TTTT
64 TTTT
112279056 AAATGAATAA
Statistics
Matches: 179, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
129 166 0.93
130 6 0.03
131 7 0.04
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.30
Consensus pattern (129 bp):
CCAGCACGATTGGGCACGATTCCCCAAATTTCCAAACATCGAACGTTGCCTTCATTTTAAAATTT
TTTAAAACATGAGTGAAATTCCAAAGGAATATTCGATTATTTTGAAAAAACGGGAAATTACAAA
Found at i:112282938 original size:30 final size:30
Alignment explanation
Indices: 112282902--112282964 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
112282892 ACGTAACAAG
*
112282902 CAAATGTCTCTAAAATAATAACAGAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
*
112282932 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
112282962 CAA
1 CAA
112282965 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.56, C:0.13, G:0.05, T:0.27
Consensus pattern (30 bp):
CAAATGTCTCTAAAATAATAACAAAATTAA
Found at i:112300510 original size:17 final size:17
Alignment explanation
Indices: 112300488--112300522 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
112300478 TAATTTTAAT
112300488 TATTCAAATAAATAAAA
1 TATTCAAATAAATAAAA
* *
112300505 TATTCAATTATATAAAA
1 TATTCAAATAAATAAAA
112300522 T
1 T
112300523 TGTTTTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (17 bp):
TATTCAAATAAATAAAA
Found at i:112313342 original size:16 final size:16
Alignment explanation
Indices: 112313321--112313352 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
112313311 TATATTTGTA
112313321 TTATTTAATAATTATT
1 TTATTTAATAATTATT
*
112313337 TTATTTTATAATTATT
1 TTATTTAATAATTATT
112313353 ATAAAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATTTAATAATTATT
Found at i:112313354 original size:19 final size:20
Alignment explanation
Indices: 112313313--112313352 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 20
112313303 TCTGTGTTTA
112313313 TATTTGTATTATTTAATAAT
1 TATTTGTATTATTTAATAAT
112313333 TATTT-TA-T-TTT-ATAAT
1 TATTTGTATTATTTAATAAT
112313349 TATT
1 TATT
112313353 ATAAAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 9 0.45
17 3 0.15
18 1 0.05
19 2 0.10
20 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (20 bp):
TATTTGTATTATTTAATAAT
Found at i:112316648 original size:3 final size:3
Alignment explanation
Indices: 112316640--112316674 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
112316630 CAAATAATTA
112316640 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
112316675 AGTCTTCTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:112326860 original size:23 final size:24
Alignment explanation
Indices: 112326797--112326860 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 24
112326787 CTTTTGGGAC
*
112326797 AAGATCAAGAGACCATTTTTAACTT
1 AAGATCAAGAGA-CTTTTTTAACTT
* * * *
112326822 AGGA-AAAGAAATTTTTTTAAC-T
1 AAGATCAAGAGACTTTTTTAACTT
112326844 AAGATCAAGAGACTTTT
1 AAGATCAAGAGACTTTT
112326861 GCTATATCCT
Statistics
Matches: 29, Mismatches: 9, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
22 4 0.14
23 17 0.59
24 5 0.17
25 3 0.10
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (24 bp):
AAGATCAAGAGACTTTTTTAACTT
Found at i:112329026 original size:46 final size:46
Alignment explanation
Indices: 112328959--112329051 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
112328949 TGAGGAGGGG
112328959 ATTCATGTAACCAAACTTAACTTCAGGGAACTATGATTGCATACAT
1 ATTCATGTAACCAAACTTAACTTCAGGGAACTATGATTGCATACAT
112329005 ATTCATGTAACCAAACTTAACTTCAGGGAACTATGATTGCATACAT
1 ATTCATGTAACCAAACTTAACTTCAGGGAACTATGATTGCATACAT
112329051 A
1 A
112329052 CATATATAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (46 bp):
ATTCATGTAACCAAACTTAACTTCAGGGAACTATGATTGCATACAT
Found at i:112332489 original size:31 final size:30
Alignment explanation
Indices: 112332427--112332489 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
112332417 GATGAGAAGT
*
112332427 AAATTTTATCCTAGGATTCTCAGGTTTCAG
1 AAATTTTATCCTAGGATTCTCAGCTTTCAG
* * *
112332457 AAATTTTATCTTAGGATTATTGAGCTTTCAG
1 AAATTTTATCCTAGGATT-CTCAGCTTTCAG
112332488 AA
1 AA
112332490 TTAAAATGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 17 0.61
31 11 0.39
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (30 bp):
AAATTTTATCCTAGGATTCTCAGCTTTCAG
Found at i:112334313 original size:31 final size:31
Alignment explanation
Indices: 112334275--112334337 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
112334265 TAAACAACAA
112334275 TAAGAAAGAAGATTGCTACATGTTTGAATTT
1 TAAGAAAGAAGATTGCTACATGTTTGAATTT
112334306 TAAGAAAGAAGATTGCTACATGTTTGAATTT
1 TAAGAAAGAAGATTGCTACATGTTTGAATTT
112334337 T
1 T
112334338 GGTTTTAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.37
Consensus pattern (31 bp):
TAAGAAAGAAGATTGCTACATGTTTGAATTT
Found at i:112338503 original size:18 final size:18
Alignment explanation
Indices: 112338477--112338520 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
112338467 ATAATTTAAA
*
112338477 ATATCAATTTATTAATAT
1 ATATAAATTTATTAATAT
112338495 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
*
112338513 ATGTAAAT
1 ATATAAAT
112338521 ATAGCTTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (18 bp):
ATATAAATTTATTAATAT
Found at i:112338621 original size:19 final size:19
Alignment explanation
Indices: 112338597--112338634 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
112338587 TCCAAACACT
112338597 GGAAAAGTAAATCATTTTC
1 GGAAAAGTAAATCATTTTC
*
112338616 GGAAAAGTAAATTATTTTC
1 GGAAAAGTAAATCATTTTC
112338635 CAAAAATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34
Consensus pattern (19 bp):
GGAAAAGTAAATCATTTTC
Found at i:112338640 original size:19 final size:19
Alignment explanation
Indices: 112338599--112338640 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
112338589 CAAACACTGG
**
112338599 AAAAGTAAATCATTTTCGG
1 AAAAGTAAATCATTTTCCA
*
112338618 AAAAGTAAATTATTTTCCA
1 AAAAGTAAATCATTTTCCA
112338637 AAAA
1 AAAA
112338641 TCATTTTCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.31
Consensus pattern (19 bp):
AAAAGTAAATCATTTTCCA
Found at i:112338646 original size:14 final size:15
Alignment explanation
Indices: 112338624--112338661 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
112338614 TCGGAAAAGT
*
112338624 AAATTATTTTCCA-A
1 AAATCATTTTCCAGA
112338638 AAATCATTTTCCAGA
1 AAATCATTTTCCAGA
112338653 AAA-CATTTT
1 AAATCATTTT
112338662 ACTGGCAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 18 0.82
15 4 0.18
ACGTcount: A:0.42, C:0.16, G:0.03, T:0.39
Consensus pattern (15 bp):
AAATCATTTTCCAGA
Found at i:112339740 original size:21 final size:21
Alignment explanation
Indices: 112339716--112339776 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
112339706 CACCATTGTT
112339716 TCTAATCTCACCGCTACAGTA
1 TCTAATCTCACCGCTACAGTA
*
112339737 TCTAATCTTACCGCTACAGTA
1 TCTAATCTCACCGCTACAGTA
* *
112339758 ACTAATCTCACCGCCACAG
1 TCTAATCTCACCGCTACAG
112339777 CTATTTTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.30, C:0.34, G:0.10, T:0.26
Consensus pattern (21 bp):
TCTAATCTCACCGCTACAGTA
Found at i:112344060 original size:4 final size:4
Alignment explanation
Indices: 112344051--112344110 Score: 84
Period size: 4 Copynumber: 15.0 Consensus size: 4
112344041 ATCAAAGTTC
* * *
112344051 CATA CATA CATA CACA CATA CATG CATA CATA CATA TATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
112344099 TATA CATA CATA
1 CATA CATA CATA
112344111 TACATATGTA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.48, C:0.23, G:0.02, T:0.27
Consensus pattern (4 bp):
CATA
Found at i:112349123 original size:30 final size:30
Alignment explanation
Indices: 112349089--112349157 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
112349079 ACTAGTAATT
*
112349089 AAAGTATAGGACGAAAATTTTAAAATTTAA
1 AAAGTATAGGACGAAAATTGTAAAATTTAA
* ** *
112349119 AAAGTATAGGACTAAAATTGTCGATTTTAA
1 AAAGTATAGGACGAAAATTGTAAAATTTAA
112349149 AAAGTATAG
1 AAAGTATAG
112349158 AGATTAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.49, C:0.04, G:0.16, T:0.30
Consensus pattern (30 bp):
AAAGTATAGGACGAAAATTGTAAAATTTAA
Found at i:112355262 original size:12 final size:13
Alignment explanation
Indices: 112355245--112355276 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
112355235 CCGACAAATT
112355245 AAACAAAAACC-A
1 AAACAAAAACCAA
112355257 AAACAAAAACCAA
1 AAACAAAAACCAA
112355270 AAACAAA
1 AAACAAA
112355277 TTACAATCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (13 bp):
AAACAAAAACCAA
Found at i:112355828 original size:27 final size:28
Alignment explanation
Indices: 112355771--112355827 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
112355761 ACATCAAATC
112355771 TTCTCGGAGTTTAAAACAAAAATAATTT
1 TTCTCGGAGTTTAAAACAAAAATAATTT
112355799 TTCTCGGAGTTTAAAACAAAAATAATTT
1 TTCTCGGAGTTTAAAACAAAAATAATTT
112355827 T
1 T
112355828 CCACTTCACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (28 bp):
TTCTCGGAGTTTAAAACAAAAATAATTT
Found at i:112358939 original size:2 final size:2
Alignment explanation
Indices: 112358932--112358965 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
112358922 TTGAATTGTA
112358932 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
112358966 GTTATAATTT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:112371801 original size:52 final size:49
Alignment explanation
Indices: 112371716--112372082 Score: 440
Period size: 46 Copynumber: 7.6 Consensus size: 49
112371706 TTTGAGTACT
* **
112371716 TCTGATCAAGTG---ATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
* *
112371762 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
112371814 TCTGATCAAGTG---ATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
112371860 TCTGATCAAGTGAC---AAAGTGATAAGTGATAGCTTCAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
112371906 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
112371958 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
* **
112372010 TCTGATCAAGAGAC---AAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
112372056 TCTGATCAAGAGAC---AAAGTGATAAGTG
1 TCTGATCAAGTGACAATAAAGTGATAAGTG
112372083 GCTACACTTA
Statistics
Matches: 292, Mismatches: 15, Indels: 28
0.87 0.04 0.08
Matches are distributed among these distances:
46 155 0.53
48 1 0.00
49 2 0.01
50 1 0.00
52 133 0.46
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (49 bp):
TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
Found at i:112371836 original size:98 final size:97
Alignment explanation
Indices: 112371716--112372082 Score: 501
Period size: 98 Copynumber: 3.7 Consensus size: 97
112371706 TTTGAGTACT
* *
112371716 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT-
*
112371781 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
65 GAAAGTGATAAGTGATAGCTTCGGCTATACTTA
* *
112371814 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* *
112371874 AAAGTGATAAGTGATAGCTTCAGCTACACTTA
66 AAAGTGATAAGTGATAGCTTCGGCTATACTTA
*
112371906 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 TCTGATCAAGTG---A-T--AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGA
112371971 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
60 CAAGTG-AAAGTGATAAGTGATAGCTTCGGCTATACTTA
* * * *
112372010 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC-AAGT
112372075 GATAAGTG
65 GA-AAGTG
112372083 GCTACACTTA
Statistics
Matches: 240, Mismatches: 15, Indels: 27
0.85 0.05 0.10
Matches are distributed among these distances:
92 41 0.17
95 1 0.00
96 1 0.00
98 145 0.60
99 10 0.04
101 1 0.00
104 41 0.17
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (97 bp):
TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
AAAGTGATAAGTGATAGCTTCGGCTATACTTA
Found at i:112372064 original size:196 final size:196
Alignment explanation
Indices: 112371730--112372082 Score: 607
Period size: 196 Copynumber: 1.8 Consensus size: 196
112371720 ATCAAGTGAT
* * *
112371730 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTA
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
* * * *
112371795 ATAGCTTCGGCTATACTTATCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
112371860 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
131 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
112371925 G
196 G
* *
112371926 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
*
112371991 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
66 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
112372056 TCTGATCAAGAGACAAAGTGATAAGTG
131 TCTGATCAAGAGACAAAGTGATAAGTG
112372083 GCTACACTTA
Statistics
Matches: 146, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
196 146 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (196 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
G
Found at i:112372090 original size:37 final size:37
Alignment explanation
Indices: 112372046--112372191 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
112372036 GATAGCTTTA
*
112372046 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
112372083 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
112372120 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
112372157 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
112372192 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:112372119 original size:150 final size:149
Alignment explanation
Indices: 112371716--112372071 Score: 467
Period size: 150 Copynumber: 2.4 Consensus size: 149
112371706 TTTGAGTACT
* * * * *
112371716 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
* * * *
112371781 GAAAGTGATAAGTAATAGCTTC-G---GCTATACTTATC---TGATCAAGTGATAAAGTGATAAG
66 GAAAGTGATAACT-ATAGCTTCAGCAAACTAAACTGATCAAGTGA-CAAGTGATAAAGTGATAAG
112371839 TGATAGCTTCGGCTATACTTA
129 TGATAGCTTCGGCTATACTTA
* *
112371860 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
* * * * *
112371925 GAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA-AAAGTGATAAG
66 GAAAGTGATAACT-ATAGCTTCAGC-AAACTAAACTGATCAAGTGACAAGTGATAAAGTGATAAG
112371989 TGATAGCTTCGGCTATACTTA
129 TGATAGCTTCGGCTATACTTA
*
112372010 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAA
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAA
112372072 AGTGATAAGT
Statistics
Matches: 192, Mismatches: 12, Indels: 10
0.90 0.06 0.05
Matches are distributed among these distances:
144 83 0.43
145 1 0.01
149 7 0.04
150 91 0.47
151 7 0.04
152 3 0.02
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (149 bp):
TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
GAAAGTGATAACTATAGCTTCAGCAAACTAAACTGATCAAGTGACAAGTGATAAAGTGATAAGTG
ATAGCTTCGGCTATACTTA
Found at i:112375779 original size:53 final size:53
Alignment explanation
Indices: 112375705--112375855 Score: 196
Period size: 53 Copynumber: 2.8 Consensus size: 53
112375695 CTTACACGGT
* * *
112375705 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATTACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
112375760 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** * *
112375813 TCACATTGCACCGATGCCATAGCCCAGCTACGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
112375856 GCACACTTAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
52 1 0.01
53 79 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:112381452 original size:3 final size:3
Alignment explanation
Indices: 112381444--112381583 Score: 113
Period size: 3 Copynumber: 46.7 Consensus size: 3
112381434 CAAAGAAAAT
* * * *
112381444 ATA ATA ATA ATA ATA ATA GTA ATA AT- ACA ATA GTA ATA ATA ATA ACA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
112381491 AAA ATA GTA ATA ATA ATA GTA ATA GTA ATA ATA ACGA A-A ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA
* ** * *
112381536 GTA ATA ATA GGA ATA AAA ATA ATA GTA ATA ATA ATA ATAA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
112381582 AT
1 AT
112381584 GTTAAAATTA
Statistics
Matches: 107, Mismatches: 26, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
2 3 0.03
3 99 0.93
4 5 0.05
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:112389582 original size:13 final size:13
Alignment explanation
Indices: 112389564--112389602 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
112389554 CAACCCAAAT
112389564 ACCACCCCACTAA
1 ACCACCCCACTAA
112389577 ACCACCCCACTAA
1 ACCACCCCACTAA
*
112389590 ACCATCCCACTAA
1 ACCACCCCACTAA
112389603 CTCCATCACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.38, C:0.51, G:0.00, T:0.10
Consensus pattern (13 bp):
ACCACCCCACTAA
Found at i:112389994 original size:3 final size:3
Alignment explanation
Indices: 112389971--112390113 Score: 80
Period size: 3 Copynumber: 48.0 Consensus size: 3
112389961 GGGGAGAGTG
* * * * * * *
112389971 TTA TTT TTA ATA TTG TTA TTA TTA TTA TTA TT- GTA TTA CTG TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
**
112390018 TTA TT- TTA -TA TATA TTTA TTA CCA TTA TTTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA -TTA TTA TTA TTA -TTA -TTA TTA TTA TTA TTA
* ** * * *
112390065 GTA ACA -TA TTT TTA TTT TTA TTA TT- TTA TTA TTA TTA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
112390111 TTA
1 TTA
112390114 CCATGGTACT
Statistics
Matches: 104, Mismatches: 28, Indels: 16
0.70 0.19 0.11
Matches are distributed among these distances:
2 8 0.08
3 84 0.81
4 11 0.11
5 1 0.01
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:112390033 original size:26 final size:26
Alignment explanation
Indices: 112389984--112390114 Score: 67
Period size: 26 Copynumber: 5.0 Consensus size: 26
112389974 TTTTTAATAT
* *
112389984 TGTTATTATTATTATTATTGTATTAC
1 TGTTACTATTATTATTATTATATTAC
112390010 TGTTACTATTATT-TTATATATATT--
1 TGTTACTATTATTATTAT-TATATTAC
* * *
112390034 TATTACCATTATTTATTTATTATTATTAT
1 TGTTACTATTA-TTA-TTATTA-TATTAC
* *
112390063 TAGTAACATATTTTTATT-TT-TATTA-
1 T-GTTAC-TATTATTATTATTATATTAC
* * *
112390088 TTTTATTATTATTATTTTTATTATTAC
1 TGTTACTATTATTATTATTA-TATTAC
112390115 CATGGTACTA
Statistics
Matches: 80, Mismatches: 12, Indels: 25
0.68 0.10 0.21
Matches are distributed among these distances:
23 9 0.11
24 13 0.16
25 7 0.09
26 29 0.36
27 8 0.10
28 2 0.03
29 3 0.04
30 6 0.08
31 3 0.04
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (26 bp):
TGTTACTATTATTATTATTATATTAC
Found at i:112390057 original size:24 final size:23
Alignment explanation
Indices: 112390012--112390061 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
112390002 TGTATTACTG
*
112390012 TTACTATTATTTTATATATATTTA
1 TTACCATTATTTTATATATA-TTA
*
112390036 TTACCATTA-TTTATTTATTATTA
1 TTACCATTATTTTATATA-TATTA
112390059 TTA
1 TTA
112390062 TTAGTAACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (23 bp):
TTACCATTATTTTATATATATTA
Found at i:112395461 original size:19 final size:19
Alignment explanation
Indices: 112395437--112395473 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
112395427 AGGCAGCCAA
112395437 AAAGAAAGAAAC-ACAAAAG
1 AAAGAAA-AAACAACAAAAG
112395456 AAAGAAAAAACAACAAAA
1 AAAGAAAAAACAACAAAA
112395474 AAATAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.78, C:0.11, G:0.11, T:0.00
Consensus pattern (19 bp):
AAAGAAAAAACAACAAAAG
Found at i:112395487 original size:11 final size:11
Alignment explanation
Indices: 112395460--112395489 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
112395450 CAAAAGAAAG
*
112395460 AAAAAACAACA
1 AAAAAATAACA
112395471 AAAAAATAACA
1 AAAAAATAACA
112395482 AAAAAATA
1 AAAAAATA
112395490 TTGTGGAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.83, C:0.10, G:0.00, T:0.07
Consensus pattern (11 bp):
AAAAAATAACA
Found at i:112397530 original size:84 final size:84
Alignment explanation
Indices: 112397402--112397667 Score: 247
Period size: 84 Copynumber: 3.1 Consensus size: 84
112397392 AAGCAGACTG
* *
112397402 AAAATTACAGATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCGAAGACGGT-AAGCCTTAACCC
1 AAAATTACAGA---TAT-TCCCTAAACAGTAGTAGAGCAGATCGAAGAC-ATCAAGCCTTAACCC
* *
112397466 CCTAAGCAATAGGGTAACAGGCTGG
61 CCTAAGCAATAGGGTAACAAGCT-A
* *
112397491 AAAA-TACAGATATTCCCTAAACAGTAGTGGAGCATATCGAAGACATCAAGCCTTAACCCCCTAA
1 AAAATTACAGATATTCCCTAAACAGTAGTAGAGCAGATCGAAGACATCAAGCCTTAACCCCCTAA
*
112397555 GCAGTAGGGTAACAAGCTA
66 GCAATAGGGTAACAAGCTA
* * ** * *
112397574 AAAATTACAGATCTTATCTCCCTAAATAGTAG-CGAAGCAGATTAAAGAC-T--AGCCTTATCTC
1 AAAATTACAGA---TAT-TCCCTAAACAGTAGTAG-AGCAGATCGAAGACATCAAGCCTTAACCC
* **
112397635 CCTAAGCAATAGGGAAACGGGCTA
61 CCTAAGCAATAGGGTAACAAGCTA
112397659 AAAATTACA
1 AAAATTACA
112397668 AATCATATCT
Statistics
Matches: 152, Mismatches: 18, Indels: 18
0.81 0.10 0.10
Matches are distributed among these distances:
83 5 0.03
84 67 0.44
85 41 0.27
87 5 0.03
88 30 0.20
89 4 0.03
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (84 bp):
AAAATTACAGATATTCCCTAAACAGTAGTAGAGCAGATCGAAGACATCAAGCCTTAACCCCCTAA
GCAATAGGGTAACAAGCTA
Found at i:112397597 original size:44 final size:42
Alignment explanation
Indices: 112397549--112397690 Score: 101
Period size: 44 Copynumber: 3.3 Consensus size: 42
112397539 AGCCTTAACC
112397549 CCCTAAGCAGTAGGGTAACAAGCTAAAAATTACAGATCTTATCT
1 CCCTAAGCAGTAGGG-AAC-AGCTAAAAATTACAGATCTTATCT
** * * * * *
112397593 CCCTAAATAGTAGCGAAGCAGAT-TAAA-GACTAG-CCTTATCT
1 CCCTAAGCAGTAGGGAA-CAGCTAAAAATTAC-AGATCTTATCT
* * * *
112397634 CCCTAAGCAATAGGGAAACGGGCTAAAAATTACAAATCATATCT
1 CCCTAAGCAGTAGGG-AAC-AGCTAAAAATTACAGATCTTATCT
*
112397678 CCCTAAGCGGTAG
1 CCCTAAGCAGTAG
112397691 CGGAGCAGAT
Statistics
Matches: 71, Mismatches: 20, Indels: 14
0.68 0.19 0.13
Matches are distributed among these distances:
41 21 0.30
42 9 0.13
43 9 0.13
44 32 0.45
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.23
Consensus pattern (42 bp):
CCCTAAGCAGTAGGGAACAGCTAAAAATTACAGATCTTATCT
Found at i:112397701 original size:85 final size:87
Alignment explanation
Indices: 112397402--112397700 Score: 324
Period size: 85 Copynumber: 3.5 Consensus size: 87
112397392 AAGCAGACTG
* * **
112397402 AAAATTACAGATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCGAAGACGGTAAGCCTTAACCCC
1 AAAATTACAGATCATATCTCCCTAAACAGTAGCGGAGCAGATCGAAGAC-GTAAGCCTTAACCCC
*
112397467 CTAAGCAATAGGGTAACAGGCTGG
65 CTAAGCAATAGGGTAACAGGCT-A
* * *
112397491 AAAA-TACAG---ATAT-TCCCTAAACAGTAGTGGAGCATATCGAAGACATCAAGCCTTAACCCC
1 AAAATTACAGATCATATCTCCCTAAACAGTAGCGGAGCAGATCGAAGACGT-AAGCCTTAACCCC
* *
112397551 CTAAGCAGTAGGGTAACAAGCTA
65 CTAAGCAATAGGGTAACAGGCTA
* * * ** * *
112397574 AAAATTACAGATCTTATCTCCCTAAATAGTAGCGAAGCAGATTAAAGAC-T-AGCCTTATCTCCC
1 AAAATTACAGATCATATCTCCCTAAACAGTAGCGGAGCAGATCGAAGACGTAAGCCTTAACCCCC
* *
112397637 TAAGCAATAGGGAAACGGGCTA
66 TAAGCAATAGGGTAACAGGCTA
* * *
112397659 AAAATTACAAATCATATCTCCCTAAGCGGTAGCGGAGCAGAT
1 AAAATTACAGATCATATCTCCCTAAACAGTAGCGGAGCAGAT
112397701 TTAAACAAAA
Statistics
Matches: 177, Mismatches: 27, Indels: 16
0.80 0.12 0.07
Matches are distributed among these distances:
83 5 0.03
84 66 0.37
85 68 0.38
87 4 0.02
88 30 0.17
89 4 0.02
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.21
Consensus pattern (87 bp):
AAAATTACAGATCATATCTCCCTAAACAGTAGCGGAGCAGATCGAAGACGTAAGCCTTAACCCCC
TAAGCAATAGGGTAACAGGCTA
Found at i:112397955 original size:13 final size:13
Alignment explanation
Indices: 112397937--112398017 Score: 85
Period size: 13 Copynumber: 6.0 Consensus size: 13
112397927 CAACCCAAGT
112397937 ACCACCCCACTAA
1 ACCACCCCACTAA
112397950 ACCACCCCACTAA
1 ACCACCCCACTAA
*
112397963 CTCCAACACCCTACTAA
1 -ACC-AC-CCC-ACTAA
*
112397980 ACTGA--CCACTAA
1 AC-CACCCCACTAA
112397992 ACCACCCCACTAA
1 ACCACCCCACTAA
112398005 ACCACCCCACTAA
1 ACCACCCCACTAA
112398018 CTCCATCACC
Statistics
Matches: 57, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
11 1 0.02
12 7 0.12
13 35 0.61
14 2 0.04
15 2 0.04
16 5 0.09
17 5 0.09
ACGTcount: A:0.38, C:0.49, G:0.01, T:0.11
Consensus pattern (13 bp):
ACCACCCCACTAA
Found at i:112397979 original size:30 final size:30
Alignment explanation
Indices: 112397939--112398032 Score: 101
Period size: 30 Copynumber: 3.3 Consensus size: 30
112397929 ACCCAAGTAC
*
112397939 CACCCCACTAAACCACCCCACTAACTCCAA
1 CACCCTACTAAACCACCCCACTAACTCCAA
* *
112397969 CACCCTACTAAACTGA--CCACTAA-ACC-A
1 CACCCTACTAAAC-CACCCCACTAACTCCAA
*
112397996 C-CCC-ACTAAACCACCCCACTAACTCCAT
1 CACCCTACTAAACCACCCCACTAACTCCAA
112398024 CACCCTACT
1 CACCCTACT
112398033 TGCCTACAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
24 1 0.02
25 7 0.14
26 10 0.20
27 4 0.08
28 3 0.06
29 10 0.20
30 15 0.29
31 1 0.02
ACGTcount: A:0.35, C:0.50, G:0.01, T:0.14
Consensus pattern (30 bp):
CACCCTACTAAACCACCCCACTAACTCCAA
Found at i:112398410 original size:3 final size:3
Alignment explanation
Indices: 112398387--112398520 Score: 80
Period size: 3 Copynumber: 45.0 Consensus size: 3
112398377 GGGGAGAGTG
* * * * * *
112398387 TTA TTT TTA ATA TTG TTA TTA TTA TT- TTA TTA CTG TTA CTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** * **
112398433 TTA -TA TATA TTTA TTA CCA TTA TTTA TTTA TTA TTA TTA TTA GTA ACA
1 TTA TTA T-TA -TTA TTA TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA
* *
112398481 -TA TTT TTA TTT TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
112398521 CCATGGTACT
Statistics
Matches: 99, Mismatches: 24, Indels: 16
0.71 0.17 0.12
Matches are distributed among these distances:
2 9 0.09
3 78 0.79
4 11 0.11
5 1 0.01
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:112398467 original size:24 final size:23
Alignment explanation
Indices: 112398422--112398471 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
112398412 TTTATTACTG
*
112398422 TTACTATTATTTTATATATATTTA
1 TTACCATTATTTTATATATA-TTA
*
112398446 TTACCATTA-TTTATTTATTATTA
1 TTACCATTATTTTATATA-TATTA
112398469 TTA
1 TTA
112398472 TTAGTAACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (23 bp):
TTACCATTATTTTATATATATTA
Found at i:112398471 original size:17 final size:17
Alignment explanation
Indices: 112398426--112398519 Score: 58
Period size: 17 Copynumber: 5.8 Consensus size: 17
112398416 TTACTGTTAC
112398426 TATTATT-TTATATATATT
1 TATTATTATTAT-T-TATT
**
112398444 TATTACCATTATTTATT
1 TATTATTATTATTTATT
*
112398461 TATTATTATTA-TTA-G
1 TATTATTATTATTTATT
**
112398476 TAACA-TATT-TTTATT
1 TATTATTATTATTTATT
*
112398491 T-TTATTATTTTATTA-T
1 TATTATTATTAT-TTATT
112398507 TATTATTATTATT
1 TATTATTATTATT
112398520 ACCATGGTAC
Statistics
Matches: 58, Mismatches: 11, Indels: 16
0.68 0.13 0.19
Matches are distributed among these distances:
14 8 0.14
15 8 0.14
16 7 0.12
17 25 0.43
18 6 0.10
19 4 0.07
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (17 bp):
TATTATTATTATTTATT
Found at i:112398517 original size:20 final size:20
Alignment explanation
Indices: 112398387--112398519 Score: 87
Period size: 20 Copynumber: 6.7 Consensus size: 20
112398377 GGGGAGAGTG
* *
112398387 TTATTTTTAATATTGTTATTA
1 TTATTATTATTATT-TTATTA
* *
112398408 TTATT-TTATTACTGTTACTA
1 TTATTATTATTA-TTTTATTA
112398428 TTATT-TTATATATATTTATTA
1 TTATTATTAT-TAT-TTTATTA
**
112398449 CCATTA-T-TTA-TTTATTA
1 TTATTATTATTATTTTATTA
* *** *
112398466 TTATTATTAGTAACATATTT
1 TTATTATTATTATTTTATTA
*
112398486 TTATTTTTATTATTTTATTA
1 TTATTATTATTATTTTATTA
112398506 TTATTATTATTATT
1 TTATTATTATTATT
112398520 ACCATGGTAC
Statistics
Matches: 85, Mismatches: 20, Indels: 15
0.71 0.17 0.12
Matches are distributed among these distances:
17 11 0.13
18 1 0.01
19 4 0.05
20 52 0.61
21 17 0.20
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (20 bp):
TTATTATTATTATTTTATTA
Found at i:112398675 original size:3 final size:3
Alignment explanation
Indices: 112398667--112398707 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
112398657 TTTTCCCTTA
* *
112398667 TAT TAT TAT TAT TTT TAT TAA TA- TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
112398708 CTTCTATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:112400628 original size:21 final size:21
Alignment explanation
Indices: 112400589--112400639 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
112400579 TAATAATATT
*
112400589 AAAAATATGATGATAATAACA
1 AAAAATATGATGACAATAACA
* *
112400610 AAAAATATGTTGACGATAACA
1 AAAAATATGATGACAATAACA
**
112400631 TTAAATATG
1 AAAAATATG
112400640 GGGGATAATA
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:0.55, C:0.06, G:0.12, T:0.27
Consensus pattern (21 bp):
AAAAATATGATGACAATAACA
Found at i:112400858 original size:17 final size:14
Alignment explanation
Indices: 112400820--112400876 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
112400810 CTTCGCTTAA
112400820 AAATATATATATATAT
1 AAATATATA-ATA-AT
* *
112400836 ATATATTTACATAAT
1 AAATATATA-ATAAT
112400851 AAATATATAATAAT
1 AAATATATAATAAT
*
112400865 AAATAAATAATA
1 AAATATATAATA
112400877 TAATAATATG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 16 0.46
15 9 0.26
16 10 0.29
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATATATAATAAT
Found at i:112400877 original size:19 final size:18
Alignment explanation
Indices: 112400848--112400884 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
112400838 ATATTTACAT
112400848 AATAAATATATAATAATA
1 AATAAATATATAATAATA
112400866 AATAAATAATATAATAATA
1 AATAAAT-ATATAATAATA
112400885 TGAAACATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AATAAATATATAATAATA
Found at i:112401126 original size:22 final size:21
Alignment explanation
Indices: 112401086--112401126 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
112401076 CTTTTCCCTT
112401086 CAAAGAAAAAAATGTGAATGC
1 CAAAGAAAAAAATGTGAATGC
112401107 CAAAGTAAACAAAAT-TGAAT
1 CAAAG-AAA-AAAATGTGAAT
112401127 AATATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 8 0.44
23 5 0.28
ACGTcount: A:0.59, C:0.10, G:0.15, T:0.17
Consensus pattern (21 bp):
CAAAGAAAAAAATGTGAATGC
Found at i:112401317 original size:29 final size:29
Alignment explanation
Indices: 112401273--112401342 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
112401263 GGTGATGGAG
*
112401273 TTAGTGGGGGCGATGGAGGTAGTGGAT-GGT
1 TTAGT-GGGGTGATGGAGGTAGTGG-TCGGT
* *
112401303 TTAGTTGGGTGATGGAGTTAGTGGTCGGT
1 TTAGTGGGGTGATGGAGGTAGTGGTCGGT
112401332 TTAGTGGGGTG
1 TTAGTGGGGTG
112401343 TTTAATTTGG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 1 0.03
29 29 0.83
30 5 0.14
ACGTcount: A:0.14, C:0.03, G:0.50, T:0.33
Consensus pattern (29 bp):
TTAGTGGGGTGATGGAGGTAGTGGTCGGT
Found at i:112405858 original size:35 final size:35
Alignment explanation
Indices: 112405816--112405886 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
112405806 TTTCAAATTT
112405816 AAAAATTTCAGTCTTCACCAAACGATAATTGTTAA
1 AAAAATTTCAGTCTTCACCAAACGATAATTGTTAA
112405851 AAAAATTTCAGTCTTCACCAAACGATAATTGTTAA
1 AAAAATTTCAGTCTTCACCAAACGATAATTGTTAA
112405886 A
1 A
112405887 TTTATTAAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (35 bp):
AAAAATTTCAGTCTTCACCAAACGATAATTGTTAA
Found at i:112419990 original size:46 final size:44
Alignment explanation
Indices: 112419886--112419993 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
112419876 TGTCTTTGAC
** * * *
112419886 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
112419930 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
112419976 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
112419994 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:112425173 original size:14 final size:14
Alignment explanation
Indices: 112425154--112425183 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
112425144 GCTGAGGTAA
*
112425154 TTTCAATTTATGTT
1 TTTCAATTTATATT
112425168 TTTCAATTTATATT
1 TTTCAATTTATATT
112425182 TT
1 TT
112425184 GCAAAAATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.07, G:0.03, T:0.67
Consensus pattern (14 bp):
TTTCAATTTATATT
Found at i:112425225 original size:87 final size:86
Alignment explanation
Indices: 112425096--112425483 Score: 512
Period size: 87 Copynumber: 4.5 Consensus size: 86
112425086 TTACTGTTTG
*
112425096 TCAAAAAGTCGACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAAT
1 TCAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAAT
*
112425161 TTATGTTTTTCAATTTATATTT
65 TTCTGTTTTTCAATTTATATTT
* * *
112425183 TGCAAAAATCTACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTATTTTCAAT
1 T-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAAT
* * *
112425248 TTCTGTTCTT-AATGTCTATTT
65 TTCTGTTTTTCAATTTATATTT
* * * *
112425269 T--TAAATCAACTCATAGTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTATTTTCAATT
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
*
112425332 TTTGTTTTTTTCCAATTTATATTTT
66 TCTG--TTTTT-CAATTTATA-TTT
* * * *
112425357 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCGGGGCACGCTGAGATAATTTCAATT
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
* *
112425422 TCTGTTTTTCAATTTCTGCTTT
66 TCTGTTTTTCAATTTAT-ATTT
112425444 TCAAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 TCAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCT
112425484 TTTAATTCAT
Statistics
Matches: 265, Mismatches: 26, Indels: 19
0.85 0.08 0.06
Matches are distributed among these distances:
83 62 0.23
85 4 0.02
86 10 0.04
87 86 0.32
88 46 0.17
90 57 0.22
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.37
Consensus pattern (86 bp):
TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
TCTGTTTTTCAATTTATATTT
Found at i:112425425 original size:173 final size:174
Alignment explanation
Indices: 112425098--112425483 Score: 555
Period size: 173 Copynumber: 2.2 Consensus size: 174
112425088 ACTGTTTGTC
*
112425098 AAAAAGTCGACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
1 AAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
*
112425163 ATGTTTTTCAATTTATATTTTGCAAAAATCTACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA
66 ATGTTTTTCAATTTATATTTTGCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA
* * *
112425228 CACGTTGAGGTATTTTCAATTTCTGTTCTT-AATGTCT-ATTTT
131 CACGCTGAGATAATTTCAATTTCTGTTCTTCAATGTCTGATTTT
* * * *
112425270 -TAAA-TCAACTCATAGTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTATTTTCAATTT
1 AAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
* * * *
112425333 TTGTTTTTTTCCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCG
66 ATG--TTTTT-CAATTTATATTTTGCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
* * * *
112425398 GGGCACGCTGAGATAATTTCAATTTCTGTTTTTCAATTTCTGCTTTT
128 GGACACGCTGAGATAATTTCAATTTCTGTTCTTCAATGTCTGATTTT
112425445 CAAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 -AAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCT
112425484 TTTAATTCAT
Statistics
Matches: 187, Mismatches: 19, Indels: 10
0.87 0.09 0.05
Matches are distributed among these distances:
170 57 0.30
171 3 0.02
172 5 0.03
173 78 0.42
174 6 0.03
175 4 0.02
177 3 0.02
178 31 0.17
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.37
Consensus pattern (174 bp):
AAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
ATGTTTTTCAATTTATATTTTGCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA
CACGCTGAGATAATTTCAATTTCTGTTCTTCAATGTCTGATTTT
Found at i:112425433 original size:14 final size:14
Alignment explanation
Indices: 112425414--112425447 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
112425404 GCTGAGATAA
*
112425414 TTTCAATTTCTGTT
1 TTTCAATTTCTGCT
112425428 TTTCAATTTCTGCT
1 TTTCAATTTCTGCT
112425442 TTTCAA
1 TTTCAA
112425448 AAAGTCAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.18, C:0.18, G:0.06, T:0.59
Consensus pattern (14 bp):
TTTCAATTTCTGCT
Found at i:112425525 original size:54 final size:54
Alignment explanation
Indices: 112425427--112425591 Score: 269
Period size: 54 Copynumber: 3.0 Consensus size: 54
112425417 CAATTTCTGT
*
112425427 TTTTCAATTTCTGCTTTTCAAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCC
1 TTTT-AATTTCTGTTTTTCAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCC
*
112425483 TTTTAA-TTCATGTTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCC
1 TTTTAATTTC-TGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
*
112425537 TTTTAATTTCTGTTTTTCAAAAATCAATTCATATTGCGAGAGGTGAGTTGAGCC
1 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
112425591 T
1 T
112425592 CGGGGCACGC
Statistics
Matches: 103, Mismatches: 4, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
54 82 0.80
55 17 0.17
56 4 0.04
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (54 bp):
TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
Found at i:112425627 original size:13 final size:13
Alignment explanation
Indices: 112425609--112425638 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
112425599 CGCTGAGGTA
112425609 TTTTCAATTTCTG
1 TTTTCAATTTCTG
*
112425622 TTTTCAGTTTCTG
1 TTTTCAATTTCTG
112425635 TTTT
1 TTTT
112425639 TCAAAAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.13, G:0.10, T:0.67
Consensus pattern (13 bp):
TTTTCAATTTCTG
Found at i:112425754 original size:168 final size:170
Alignment explanation
Indices: 112425555--112425869 Score: 490
Period size: 168 Copynumber: 1.9 Consensus size: 170
112425545 TCTGTTTTTC
* * * * *
112425555 AAAAATCAATTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
* *** * *
112425620 TG-TTTTCAGTTTCTGTTTTTCAAAAATCAACTCATATTGTGAGAGGTGAGTTGAG-CCTTTTAA
66 TGTTTTTCAATTTCTACCTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCCTTTCAA
*
112425683 TTTCTGTTTTTCAAAATCTACTTTTCAAATCAAGTTTCAA
131 TTTATGTTTTTCAAAATCTACTTTTCAAATCAAGTTTCAA
*
112425723 AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
112425788 TGTTTTTTCAATTTCTACCTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCCTTTCA
66 TG-TTTTTCAATTTCTACCTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCCTTTCA
112425853 ATTTATGTTTTTCAAAA
130 ATTTATGTTTTTCAAAA
112425870 AAAAAAATCA
Statistics
Matches: 131, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
168 61 0.47
170 48 0.37
171 22 0.17
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (170 bp):
AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
TGTTTTTCAATTTCTACCTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCCTTTCAA
TTTATGTTTTTCAAAATCTACTTTTCAAATCAAGTTTCAA
Found at i:112425822 original size:88 final size:86
Alignment explanation
Indices: 112425551--112425846 Score: 284
Period size: 82 Copynumber: 3.5 Consensus size: 86
112425541 AATTTCTGTT
* * *
112425551 TTTCAAAAATCAATTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAA
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA
* ***
112425616 TTTCTGTTTTCAGTTTCTGTT
66 TTTCTGTTTTCAATTTCTAAC
* *** **
112425637 TTTCAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCT-TTTA-ATTTCT---GT-TTTTCA
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA-CGCTGAGGTATTTTCA
** * * *
112425696 AAATCTACTTTTCAA-ATC-AAG
65 ATTTCT-GTTTTCAATTTCTAAC
* *
112425717 TTTCAAAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
1 TTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC
* *
112425782 AATTTTTGTTTTTTCAATTTCTACC
64 AATTTCTG--TTTTCAATTTCTAAC
112425807 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
112425847 CTTTCAATTT
Statistics
Matches: 164, Mismatches: 32, Indels: 26
0.74 0.14 0.12
Matches are distributed among these distances:
80 4 0.02
81 12 0.07
82 43 0.26
83 3 0.02
84 2 0.01
85 2 0.01
86 41 0.25
87 8 0.05
88 42 0.26
89 2 0.01
90 5 0.03
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (86 bp):
TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA
TTTCTGTTTTCAATTTCTAAC
Found at i:112425936 original size:55 final size:55
Alignment explanation
Indices: 112425807--112425984 Score: 259
Period size: 61 Copynumber: 3.1 Consensus size: 55
112425797 AATTTCTACC
* *
112425807 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCCTTTCAATTTATGTT
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCCTTTAAATTCATGTT
*
112425862 TTTCAAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAAATTCATGTT
1 TTTC------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCCTTTAAATTCATGTT
*
112425923 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCCTTTAATTTC-TGTT
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCCTTTAAATTCATGTT
112425977 TTTCAAAA
1 TTTCAAAA
112425985 TCTGCTTTTA
Statistics
Matches: 112, Mismatches: 5, Indels: 13
0.86 0.04 0.10
Matches are distributed among these distances:
54 12 0.11
55 48 0.43
61 52 0.46
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (55 bp):
TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCCTTTAAATTCATGTT
Found at i:112429438 original size:7 final size:7
Alignment explanation
Indices: 112429426--112429459 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
112429416 ACTGTATTAA
112429426 AAAAAAT
1 AAAAAAT
112429433 AAAAAAT
1 AAAAAAT
112429440 AAAAAAT
1 AAAAAAT
112429447 AAAAAAT
1 AAAAAAT
112429454 AAAAAA
1 AAAAAA
112429460 AGATAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:112431544 original size:14 final size:15
Alignment explanation
Indices: 112431525--112431557 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
112431515 TACAAAATAT
112431525 TTTGAATTAAACTA-
1 TTTGAATTAAACTAC
112431539 TTTGAATTAAACTAC
1 TTTGAATTAAACTAC
112431554 TTTG
1 TTTG
112431558 TGTTGATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (15 bp):
TTTGAATTAAACTAC
Found at i:112436238 original size:21 final size:22
Alignment explanation
Indices: 112436214--112436264 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
112436204 AATTTATATT
* *
112436214 TATAATAAA-ATAATTATATAA
1 TATAATAAATATAAGTATAAAA
112436235 TATATATAAATATAAGTATAAAA
1 TATA-ATAAATATAAGTATAAAA
112436258 TA-AATAA
1 TATAATAA
112436265 TTAATGATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 8 0.31
22 6 0.23
23 12 0.46
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
TATAATAAATATAAGTATAAAA
Found at i:112436512 original size:20 final size:20
Alignment explanation
Indices: 112436487--112436638 Score: 82
Period size: 20 Copynumber: 7.2 Consensus size: 20
112436477 GAAAGTGTAT
112436487 ATATGTAAAAATAATATATA
1 ATATGTAAAAATAATATATA
112436507 ATATGTATAAATAATTAATAAATATACA
1 ATATG--TAAA-AA-TAAT--ATAT--A
* *
112436535 ATACAAGTAAAAAATATATAGATA
1 AT--ATGT-AAAAATA-ATATATA
*
112436559 ATAATGT-AAAATATTA-ATA
1 AT-ATGTAAAAATAATATATA
*
112436578 ATTTGTGAAAAATAATATATA
1 ATATGT-AAAAATAATATATA
*
112436599 ATATATAATAAATAATA-ATA
1 ATATGTAA-AAATAATATATA
112436619 ATATG---AAATAATATATA
1 ATATGTAAAAATAATATATA
112436636 ATA
1 ATA
112436639 AAATAATTTT
Statistics
Matches: 105, Mismatches: 10, Indels: 37
0.69 0.07 0.24
Matches are distributed among these distances:
16 8 0.08
17 6 0.06
18 3 0.03
19 5 0.05
20 24 0.23
21 21 0.20
22 4 0.04
23 5 0.05
24 7 0.07
26 7 0.07
27 2 0.02
28 8 0.08
29 3 0.03
30 2 0.02
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.34
Consensus pattern (20 bp):
ATATGTAAAAATAATATATA
Found at i:112436594 original size:3 final size:3
Alignment explanation
Indices: 112436588--112436645 Score: 50
Period size: 3 Copynumber: 19.0 Consensus size: 3
112436578 ATTTGTGAAA
*
112436588 AAT AAT ATAT AAT ATAT AAT AAAT AAT AAT AAT -AT GA- AAT AAT ATAT
1 AAT AAT A-AT AAT A-AT AAT -AAT AAT AAT AAT AAT AAT AAT AAT A-AT
112436635 AAT AA- AAT AAT
1 AAT AAT AAT AAT
112436646 TTTATAATAT
Statistics
Matches: 47, Mismatches: 1, Indels: 14
0.76 0.02 0.23
Matches are distributed among these distances:
2 5 0.11
3 30 0.64
4 12 0.26
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:112436601 original size:7 final size:7
Alignment explanation
Indices: 112436589--112436663 Score: 71
Period size: 7 Copynumber: 10.1 Consensus size: 7
112436579 TTTGTGAAAA
112436589 ATAATAT
1 ATAATAT
112436596 ATAATAT
1 ATAATAT
*
112436603 ATAATAA
1 ATAATAT
112436610 ATAATA-
1 ATAATAT
112436616 ATAATAT
1 ATAATAT
112436623 GAAATAATAT
1 ---ATAATAT
*
112436633 ATAATAAA
1 ATAAT-AT
*
112436641 ATAATTTT
1 ATAA-TAT
112436649 ATAATAT
1 ATAATAT
112436656 ATAATAT
1 ATAATAT
112436663 A
1 A
112436664 AAAATAAGGT
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
6 6 0.11
7 34 0.60
8 9 0.16
9 1 0.02
10 7 0.12
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (7 bp):
ATAATAT
Found at i:112436636 original size:23 final size:23
Alignment explanation
Indices: 112436603--112436661 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
112436593 TATATAATAT
*
112436603 ATAATAAATAATAATAAT-ATGAA
1 ATAATATATAATAA-AATAATGAA
***
112436626 ATAATATATAATAAAATAATTTT
1 ATAATATATAATAAAATAATGAA
112436649 ATAATATATAATA
1 ATAATATATAATA
112436662 TAAAAATAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 3 0.10
23 28 0.90
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
ATAATATATAATAAAATAATGAA
Found at i:112436660 original size:30 final size:27
Alignment explanation
Indices: 112436588--112436663 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 27
112436578 ATTTGTGAAA
112436588 AATAATATATAATATATAATAAATAAT
1 AATAATATATAATATATAATAAATAAT
112436615 AATAATATGAAATAATATATAATAAAATAATTT
1 AATAATAT---ATAATATATAAT-AAATAA--T
*
112436648 TATAATATATAATATA
1 AATAATATATAATATA
112436664 AAAATAAGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
27 8 0.19
30 20 0.48
31 6 0.14
33 8 0.19
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (27 bp):
AATAATATATAATATATAATAAATAAT
Found at i:112438696 original size:206 final size:205
Alignment explanation
Indices: 112438288--112438996 Score: 835
Period size: 206 Copynumber: 3.5 Consensus size: 205
112438278 AAATCTGCTT
** ** * * *
112438288 CTTCGATTCATTCTCTGGCAATGCAGAGACGACAAATCATCTTAGACTTGCTTCATCGTAAGCAC
1 CTTCGATTTGTTCTCTAACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
* * * *
112438353 GCGAAAGCCAAATCAGC--TA---T-GATTTGTTCCTTATAAGCACAAGAATGCCAAATCATCTT
66 GTGAAAGCCAAATCAGCTATATCTTCGATTTGTTCCTTGTAAGTACAAGGATGCCAAATCATCTT
* *
112438412 GGATCTGCTTCAGCATAATCATCTGAAGGTGAGATCTGCTGTGTATCTACTCTCCATTAAAGTGG
131 GGATCTGCTTCAGCATAATCATCTGAAGGTGAGATCTACTGTGTATCTGCTCTCCATTAAAGTGG
* *
112438477 AGAAGCTAGA
196 AGATGCCAGA
* * *
112438487 CTTCGATTTGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTTATCGTAAACAC
1 CTTCGATTTGTTCTCTAACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
*
112438552 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGTACAAGGATGCCAAATCATCTT
66 GTGAAAGCCAAATCAGCTATATCTTCGATTTGTTCCTTGTAAGTACAAGGATGCCAAATCATCTT
* * * *
112438617 GGATCTTGCTTCAGTC-TAATCGTTTGAAGGTCAGATCTACTGTGTATCTGCTCTCCATTGAAGT
131 GGATC-TGCTTCAG-CATAATCATCTGAAGGTGAGATCTACTGTGTATCTGCTCTCCATTAAAGT
112438681 GGAGATGCCAGA
194 GGAGATGCCAGA
* *
112438693 CTTCGATTTGTTCTCTAAAAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAATAC
1 CTTCGATTTGTTCTCTAACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
** * * ** * * **
112438758 GTGAAAGCCAAATCAGCTATATCTTTAATCTGCTCCCCGCCGAA-TACAGAGAGATAAGATC-TG
66 GTGAAAGCCAAATCAGCTATATCTTCGATTTGTTCCTTG--TAAGTACA-AG-GAT--G-CCAAA
* * * ** * *
112438821 TCATCTTGGATCTGCTTCAGCGTAAACATCTGAAGGTGAGATTTTTTATGTGTCTGC-CTTCCAT
124 TCATCTTGGATCTGCTTCAGCATAATCATCTGAAGGTGAGATCTACTGTGTATCTGCTC-TCCAT
* * * *
112438885 CAAAGTAGAAATACCAGA
188 TAAAGTGGAGATGCCAGA
*
112438903 CTTCGATTTGTTCTCTAACAATACAGAGATGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
1 CTTCGATTTGTTCTCTAACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
112438968 GTGAAAGCCAAATCAGCTATATCTTCGAT
66 GTGAAAGCCAAATCAGCTATATCTTCGAT
112438997 CTGCTCCCTG
Statistics
Matches: 437, Mismatches: 56, Indels: 23
0.85 0.11 0.04
Matches are distributed among these distances:
199 73 0.17
201 1 0.00
204 1 0.00
205 41 0.09
206 152 0.35
207 5 0.01
208 4 0.01
209 5 0.01
210 141 0.32
211 13 0.03
212 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (205 bp):
CTTCGATTTGTTCTCTAACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
GTGAAAGCCAAATCAGCTATATCTTCGATTTGTTCCTTGTAAGTACAAGGATGCCAAATCATCTT
GGATCTGCTTCAGCATAATCATCTGAAGGTGAGATCTACTGTGTATCTGCTCTCCATTAAAGTGG
AGATGCCAGA
Found at i:112438939 original size:210 final size:209
Alignment explanation
Indices: 112438405--112439074 Score: 881
Period size: 210 Copynumber: 3.2 Consensus size: 209
112438395 GAATGCCAAA
* * * *
112438405 TCATCTTGGATCTGCTTCAGCATAATCATCTGAAGGTGAGATCTGCTGTGTATCTACTCTCCATT
1 TCATCTTGGATCTGCTTCAGCGTAAACATCTGAAGGTGAGATCTACTGTGTATCTGCTCTCCATT
* *
112438470 AAAGTGGAGAA-GCTAGACTTCGATTTGTTCTCTGACAATACAGAGATGACAAATCATCTTAGAT
66 AAAGTGGA-AATGCCAGACTTCGATTTGTTCTCTAACAATACAGAGATGACAAATCATCTTAGAT
* * * * * *
112438534 TTGCTTTATCGTAAACACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTG-TAAGTAC
130 TTGCTTCATCGTAAACACGTGAAAGCCAAATCAGCTATATCTTCGATCTGCTCCCTGCGAA-TAC
* **
112438598 A-AG-GAT--G-CCAAA
194 AGAGAGATAAGATC-TG
* * * *
112438610 TCATCTTGGATCTTGCTTCAGTC-TAATCGTTTGAAGGTCAGATCTACTGTGTATCTGCTCTCCA
1 TCATCTTGGATC-TGCTTCAG-CGTAAACATCTGAAGGTGAGATCTACTGTGTATCTGCTCTCCA
* * * *
112438674 TTGAAGTGGAGATGCCAGACTTCGATTTGTTCTCTAAAAATACAGAGACGACAAATCATCTTAGA
64 TTAAAGTGGAAATGCCAGACTTCGATTTGTTCTCTAACAATACAGAGATGACAAATCATCTTAGA
* ** *
112438739 TTTGCTTCATCGTAAATACGTGAAAGCCAAATCAGCTATATCTTTAATCTGCTCCCCGCCGAATA
129 TTTGCTTCATCGTAAACACGTGAAAGCCAAATCAGCTATATCTTCGATCTGCTCCCTG-CGAATA
112438804 CAGAGAGATAAGATCTG
193 CAGAGAGATAAGATCTG
* ** * *
112438821 TCATCTTGGATCTGCTTCAGCGTAAACATCTGAAGGTGAGATTTTTTATGTGTCTGC-CTTCCAT
1 TCATCTTGGATCTGCTTCAGCGTAAACATCTGAAGGTGAGATCTACTGTGTATCTGCTC-TCCAT
* * *
112438885 CAAAGTAGAAATACCAGACTTCGATTTGTTCTCTAACAATACAGAGATGACAAATCATCTTAGAT
65 TAAAGTGGAAATGCCAGACTTCGATTTGTTCTCTAACAATACAGAGATGACAAATCATCTTAGAT
112438950 TTGCTTCATCGTAAACACGTGAAAGCCAAATCAGCTATATCTTCGATCTGCTCCCTGCTGAATAC
130 TTGCTTCATCGTAAACACGTGAAAGCCAAATCAGCTATATCTTCGATCTGCTCCCTGC-GAATAC
112439015 AGAGAGATAAGATCTG
194 AGAGAGATAAGATCTG
*
112439031 TCATCTTGGATCTGCTTCAGCGTAAACAGCTGAAGGTGAGATCT
1 TCATCTTGGATCTGCTTCAGCGTAAACATCTGAAGGTGAGATCT
112439075 GCTATGCTGC
Statistics
Matches: 406, Mismatches: 46, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
205 13 0.03
206 150 0.37
207 5 0.01
208 4 0.01
209 6 0.01
210 214 0.53
211 13 0.03
212 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (209 bp):
TCATCTTGGATCTGCTTCAGCGTAAACATCTGAAGGTGAGATCTACTGTGTATCTGCTCTCCATT
AAAGTGGAAATGCCAGACTTCGATTTGTTCTCTAACAATACAGAGATGACAAATCATCTTAGATT
TGCTTCATCGTAAACACGTGAAAGCCAAATCAGCTATATCTTCGATCTGCTCCCTGCGAATACAG
AGAGATAAGATCTG
Found at i:112445280 original size:38 final size:38
Alignment explanation
Indices: 112445194--112445388 Score: 203
Period size: 38 Copynumber: 5.0 Consensus size: 38
112445184 AAACTCAAAC
* * ***
112445194 ATAACACCAGCACGAAGCCTACGGGACTTTAAACTTAGAT
1 ATAATACCAGCACGAAGCCTGCGGGA-TTT-AACCCGGAT
* * * * *
112445234 ATATTACCAGCACTAGGCCTGCGAGATTTAAGCCGGAT
1 ATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGAT
112445272 ATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGAT
1 ATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGAT
* *
112445310 ATATTACCAGCACGAAGTCTGCGGGATTTAACCCGGAT
1 ATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGAT
* * *
112445348 ATAATTCCAGCA-TATAGCCTGCGGGTCTTTAAGCCCGGAT
1 ATAATACCAGCACGA-AGCCTGCGGG-ATTTAA-CCCGGAT
112445388 A
1 A
112445389 CACATCAAAT
Statistics
Matches: 130, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
37 1 0.01
38 93 0.72
39 8 0.06
40 28 0.22
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.23
Consensus pattern (38 bp):
ATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGAT
Found at i:112451195 original size:14 final size:16
Alignment explanation
Indices: 112451160--112451196 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
112451150 TAAATGATAT
112451160 GATG-AAATGCTATGA
1 GATGCAAATGCTATGA
112451175 GATGCAAATGC-ATGA
1 GATGCAAATGCTATGA
112451190 -ATGCAAA
1 GATGCAAA
112451197 AAGGATATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.33
15 8 0.38
16 6 0.29
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.22
Consensus pattern (16 bp):
GATGCAAATGCTATGA
Found at i:112454882 original size:19 final size:20
Alignment explanation
Indices: 112454848--112454895 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
112454838 TATAATACAC
*
112454848 ATAAAATATGGTATTTAATA
1 ATAAAATATAGTATTTAATA
112454868 ATAAAA-ATAGTATTTAAT-
1 ATAAAATATAGTATTTAATA
*
112454886 ATACAATATA
1 ATAAAATATA
112454896 TAATATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.20
19 14 0.56
20 6 0.24
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (20 bp):
ATAAAATATAGTATTTAATA
Found at i:112455387 original size:7 final size:7
Alignment explanation
Indices: 112455375--112455446 Score: 67
Period size: 7 Copynumber: 10.1 Consensus size: 7
112455365 TTTGTGAAAA
112455375 ATAATAT
1 ATAATAT
112455382 ATAATAT
1 ATAATAT
*
112455389 ATAATAA
1 ATAATAT
112455396 ATAATA-
1 ATAATAT
*
112455402 AT-ATGAA
1 ATAAT-AT
112455409 ATAATAT
1 ATAATAT
*
112455416 ATAATAAA
1 ATAAT-AT
*
112455424 ATAATTTT
1 ATAA-TAT
112455432 ATAATAT
1 ATAATAT
112455439 ATAATAT
1 ATAATAT
112455446 A
1 A
112455447 AAAATAAGGT
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
5 2 0.04
6 3 0.06
7 37 0.69
8 11 0.20
9 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (7 bp):
ATAATAT
Found at i:112455422 original size:10 final size:11
Alignment explanation
Indices: 112455373--112455419 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 11
112455363 AATTTGTGAA
112455373 AAATAATATAT
1 AAATAATATAT
112455384 -AAT-ATATAAT
1 AAATAATAT-AT
112455394 AAATAATAATAT
1 AAATAAT-ATAT
112455406 GAAATAATATAT
1 -AAATAATATAT
112455418 AA
1 AA
112455420 TAAAATAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
9 4 0.13
10 5 0.16
11 5 0.16
12 8 0.26
13 9 0.29
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (11 bp):
AAATAATATAT
Found at i:112459643 original size:17 final size:17
Alignment explanation
Indices: 112459621--112459654 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
112459611 TTAATTTAAA
112459621 TAAATAAATTTCTCAAT
1 TAAATAAATTTCTCAAT
112459638 TAAATAAATTTCTCAAT
1 TAAATAAATTTCTCAAT
112459655 GCAATTCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATAAATTTCTCAAT
Found at i:112476707 original size:3 final size:3
Alignment explanation
Indices: 112476699--112476734 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
112476689 ACGTTTTTAA
112476699 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
112476735 CTACTATTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:112478647 original size:22 final size:23
Alignment explanation
Indices: 112478602--112478650 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
112478592 TCAATATCTG
* *
112478602 AATTTAGTTTTAATTTGTAATTA
1 AATTTAGTTTCAATATGTAATTA
112478625 AATTTAGTTTCAATAT-TAATTA
1 AATTTAGTTTCAATATGTAATTA
112478647 AATT
1 AATT
112478651 GTTTAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (23 bp):
AATTTAGTTTCAATATGTAATTA
Found at i:112478743 original size:13 final size:13
Alignment explanation
Indices: 112478713--112478762 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
112478703 AAAATAATAA
112478713 AAAATTTAAATATT
1 AAAA-TTAAATATT
112478727 -AAATTAAATATT
1 AAAATTAAATATT
*
112478739 AAAATCAAAT-TT
1 AAAATTAAATATT
*
112478751 AATAATAAAATA
1 AA-AATTAAATA
112478763 GAAGTTACCA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 13 0.42
13 18 0.58
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAATTAAATATT
Found at i:112478748 original size:18 final size:18
Alignment explanation
Indices: 112478714--112478761 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
112478704 AAATAATAAA
*
112478714 AAAT-TTAAATATTAAATT
1 AAATATTAAA-ATCAAATT
112478732 AAATATTAAAATCAAATT
1 AAATATTAAAATCAAATT
* *
112478750 TAATAATAAAAT
1 AAATATTAAAAT
112478762 AGAAGTTACC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 21 0.81
19 5 0.19
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATATTAAAATCAAATT
Found at i:112483150 original size:21 final size:21
Alignment explanation
Indices: 112483112--112483165 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
112483102 TTGGGGTTTT
112483112 GGATTTGAA-GTTTAAAGTTAA
1 GGATTT-AAGGTTTAAAGTTAA
* * *
112483133 GGGTTTAAGGTTTGAAGTTTA
1 GGATTTAAGGTTTAAAGTTAA
*
112483154 GGATTTAGGGTT
1 GGATTTAAGGTT
112483166 CTAGGTTAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.28, C:0.00, G:0.31, T:0.41
Consensus pattern (21 bp):
GGATTTAAGGTTTAAAGTTAA
Found at i:112492476 original size:30 final size:30
Alignment explanation
Indices: 112492442--112492502 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
112492432 ATTGGTTGAA
112492442 AGCTTCAATTTTTGAGTAGATGCATGGCAT
1 AGCTTCAATTTTTGAGTAGATGCATGGCAT
112492472 AGCTTCAATTTTTGAGTAGATGCATGGCAT
1 AGCTTCAATTTTTGAGTAGATGCATGGCAT
112492502 A
1 A
112492503 TGGAACTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (30 bp):
AGCTTCAATTTTTGAGTAGATGCATGGCAT
Found at i:112494028 original size:37 final size:37
Alignment explanation
Indices: 112493986--112494060 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
112493976 TTTTGATAAG
*
112493986 TAAATTGGTTTGGTTTAGTGGTTAAGTGTTTTAGTTA
1 TAAATTGGTTTGGTTTAGTGGTTAAATGTTTTAGTTA
112494023 TAAATTGGTTTGGTTTAGTGGTTAAATGTTTTAGTTA
1 TAAATTGGTTTGGTTTAGTGGTTAAATGTTTTAGTTA
112494060 T
1 T
112494061 GTATTAAGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.52
Consensus pattern (37 bp):
TAAATTGGTTTGGTTTAGTGGTTAAATGTTTTAGTTA
Found at i:112494202 original size:47 final size:47
Alignment explanation
Indices: 112494133--112494234 Score: 161
Period size: 47 Copynumber: 2.2 Consensus size: 47
112494123 ATATTTGGAC
*
112494133 ATGTGGTTTATCAGTTAGATTCAGTCCATTGATGACAACAATGAGTT
1 ATGTGGTTTATAAGTTAGATTCAGTCCATTGATGACAACAATGAGTT
* *
112494180 ATGTGGTTTATAAGTTAGATTCAGTCTATTGATGACAAGAATGAGTT
1 ATGTGGTTTATAAGTTAGATTCAGTCCATTGATGACAACAATGAGTT
112494227 -TGTTGGTT
1 ATG-TGGTT
112494235 CAATGGTTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
46 2 0.04
47 49 0.96
ACGTcount: A:0.28, C:0.09, G:0.24, T:0.39
Consensus pattern (47 bp):
ATGTGGTTTATAAGTTAGATTCAGTCCATTGATGACAACAATGAGTT
Found at i:112501143 original size:131 final size:131
Alignment explanation
Indices: 112500959--112501226 Score: 369
Period size: 131 Copynumber: 2.0 Consensus size: 131
112500949 CATTTTAGAA
* * * * *
112500959 TTTAAAGAACATGAGTGAAATTCTAAAGGGATATTCGATTATTTTGAATAAACGAGAAGTTGCAA
1 TTTAAAGAACATGAGCGAAATTCTAAAGGAATATTCGATTATTTTGAACAAACGAGAAATCGCAA
* * * *
112501024 CCCAGCACGACAGGGCACGATTCCCCGAGTTGCCAAACATCGAACATTACCTTCGTTTTGAAGAA
66 CCCAGCACGACAGGGCACGATT-CCCGAATCGCCAAACATCGAAAATTACCTTCGTTTCGAAGAA
112501089 TT
130 TT
* * *
112501091 TTTAAAG-AGATGAGCGAAATT-TCAAAGGAATATTCGATTGTTTTGAACAAACGGGAAATCGCA
1 TTTAAAGAACATGAGCGAAATTCT-AAAGGAATATTCGATTATTTTGAACAAACGAGAAATCGCA
* * *
112501154 ACCCAGCACGATAGGGTACGATTCCCGAATCGCCAAACATCGAAAATTGCCTTCGTTTCGAAGAA
65 ACCCAGCACGACAGGGCACGATTCCCGAATCGCCAAACATCGAAAATTACCTTCGTTTCGAAGAA
112501219 TT
130 TT
112501221 TTTAAA
1 TTTAAA
112501227 TGGATAATTA
Statistics
Matches: 120, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
130 46 0.38
131 67 0.56
132 7 0.06
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (131 bp):
TTTAAAGAACATGAGCGAAATTCTAAAGGAATATTCGATTATTTTGAACAAACGAGAAATCGCAA
CCCAGCACGACAGGGCACGATTCCCGAATCGCCAAACATCGAAAATTACCTTCGTTTCGAAGAAT
T
Found at i:112503574 original size:31 final size:31
Alignment explanation
Indices: 112503536--112503715 Score: 272
Period size: 31 Copynumber: 5.8 Consensus size: 31
112503526 ACAAATGACA
*
112503536 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* * *
112503567 AGTGAAAAGTGGTTGCTTCTGCTACCTGAGC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
112503598 AGTGAAAAGTGGTAG-TTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTT-CGGCTACCTGATC
112503629 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* * *
112503660 AGTGAAAAATGGTAGCTCCGGCTATCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
112503691 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
112503716 AAGTGACAAG
Statistics
Matches: 134, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
30 2 0.01
31 130 0.97
32 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:112503894 original size:42 final size:42
Alignment explanation
Indices: 112503787--112503901 Score: 144
Period size: 42 Copynumber: 2.7 Consensus size: 42
112503777 TATGTGATTC
* *
112503787 GTGTAAGACCATAGCT-AGGCTGTGGCATCGATATATGAATAT
1 GTGTAAGACCATAGCTGA-GCTATGGCATCGATATATGAAGAT
* *
112503829 GTGTAAGACCATAGCTGGGCTATGGCATC-ATTATGTGAAGAT
1 GTGTAAGACCATAGCTGAGCTATGGCATCGA-TATATGAAGAT
* *
112503871 GTGTAAGACCATAGTTGAACTATGGCATCGA
1 GTGTAAGACCATAGCTGAGCTATGGCATCGA
112503902 GAAAACGAAG
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
41 1 0.02
42 61 0.97
43 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (42 bp):
GTGTAAGACCATAGCTGAGCTATGGCATCGATATATGAAGAT
Found at i:112507929 original size:21 final size:21
Alignment explanation
Indices: 112507903--112507966 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
112507893 TTTGGGCGGA
* *
112507903 TCAGCTATCACGAGCTTTTGT
1 TCAGCTCTCACGAGCTTCTGT
112507924 TCAGCTCTCACGAGCTTCTGT
1 TCAGCTCTCACGAGCTTCTGT
*
112507945 TCAGCTCTCATGAGCTTCTGT
1 TCAGCTCTCACGAGCTTCTGT
112507966 T
1 T
112507967 GGAGTGTTCG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.16, C:0.28, G:0.19, T:0.38
Consensus pattern (21 bp):
TCAGCTCTCACGAGCTTCTGT
Found at i:112512759 original size:16 final size:16
Alignment explanation
Indices: 112512738--112512770 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
112512728 TCCAAAAGAT
112512738 AGATTTATCACCAGAA
1 AGATTTATCACCAGAA
*
112512754 AGATTTATTACCAGAA
1 AGATTTATCACCAGAA
112512770 A
1 A
112512771 TTAAGCTAAG
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:0.45, C:0.15, G:0.12, T:0.27
Consensus pattern (16 bp):
AGATTTATCACCAGAA
Found at i:112513402 original size:19 final size:21
Alignment explanation
Indices: 112513358--112513404 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 21
112513348 ATTGAGTGGT
112513358 TAATTAGACTTTAATTAAGTA
1 TAATTAGACTTTAATTAAGTA
*
112513379 AAATTAG-C-TTAATTAAG-A
1 TAATTAGACTTTAATTAAGTA
112513397 GTAATTAG
1 -TAATTAG
112513405 TGGAAAGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 1 0.04
19 15 0.65
20 1 0.04
21 6 0.26
ACGTcount: A:0.45, C:0.04, G:0.13, T:0.38
Consensus pattern (21 bp):
TAATTAGACTTTAATTAAGTA
Found at i:112513675 original size:24 final size:24
Alignment explanation
Indices: 112513633--112513690 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
112513623 ATTGTATGGT
112513633 AATTAAA-AATACATGTGTAATA-
1 AATTAAATAATACATGTGTAATAC
112513655 AATTAAATACATACACT-TGTAATAC
1 AATTAAATA-ATACA-TGTGTAATAC
*
112513680 AACTAAATAAT
1 AATTAAATAAT
112513691 TACTTAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
22 7 0.23
23 1 0.03
24 14 0.45
25 9 0.29
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.31
Consensus pattern (24 bp):
AATTAAATAATACATGTGTAATAC
Found at i:112513737 original size:5 final size:5
Alignment explanation
Indices: 112513713--112513768 Score: 67
Period size: 5 Copynumber: 10.6 Consensus size: 5
112513703 AAGAAATTGT
* *
112513713 TATTA TATGA TATTA TTATTA TATTA TAGTA TATTA TATTATA TATTA
1 TATTA TATTA TATTA -TATTA TATTA TATTA TATTA TA-T-TA TATTA
112513761 TATTA TAT
1 TATTA TAT
112513769 AAATAAGTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
5 33 0.75
6 7 0.16
7 4 0.09
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (5 bp):
TATTA
Found at i:112513759 original size:12 final size:12
Alignment explanation
Indices: 112513716--112513769 Score: 65
Period size: 12 Copynumber: 4.3 Consensus size: 12
112513706 AAATTGTTAT
*
112513716 TATATGATATTA
1 TATATTATATTA
112513728 T-TATTATATTATA
1 TATATTATA-T-TA
112513741 GTATATTATATTA
1 -TATATTATATTA
112513754 TATATTATATTA
1 TATATTATATTA
112513766 TATA
1 TATA
112513770 AATAAGTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
11 6 0.16
12 18 0.49
13 4 0.11
14 2 0.05
15 7 0.19
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (12 bp):
TATATTATATTA
Found at i:112515695 original size:22 final size:22
Alignment explanation
Indices: 112515670--112515712 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
112515660 CAATCCTTTA
112515670 ATCAATTCAAA-TCAAAATTTCT
1 ATCAATT-AAACTCAAAATTTCT
*
112515692 ATCAATTAAACTCATAATTTC
1 ATCAATTAAACTCAAAATTTC
112515713 ATTATTAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (22 bp):
ATCAATTAAACTCAAAATTTCT
Found at i:112515902 original size:26 final size:26
Alignment explanation
Indices: 112515873--112515927 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
112515863 CAAACCCTAA
* *
112515873 TTTCTCAT-TTTTCTTTTCTTTTCTTC
1 TTTCT-ATCTTTTCATTTCGTTTCTTC
*
112515899 TTTCTTTCTTTTCATTTCGTTTCTTC
1 TTTCTATCTTTTCATTTCGTTTCTTC
112515925 TTT
1 TTT
112515928 GTAACTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 1 0.04
26 24 0.96
ACGTcount: A:0.04, C:0.22, G:0.02, T:0.73
Consensus pattern (26 bp):
TTTCTATCTTTTCATTTCGTTTCTTC
Found at i:112516117 original size:3 final size:3
Alignment explanation
Indices: 112516109--112516143 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
112516099 TTAGTTGATA
112516109 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
112516144 GTTAATATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:112518131 original size:29 final size:28
Alignment explanation
Indices: 112518098--112518155 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 28
112518088 TTTATTTTAA
112518098 GTTTTTTTGTATATTATTTATATTAAATT
1 GTTTTTTT-TATATTATTTATATTAAATT
*
112518127 G----TTTTATATTATTTATTTTAAATT
1 GTTTTTTTTATATTATTTATATTAAATT
112518151 GTTTT
1 GTTTT
112518156 AGATATTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 9
0.71 0.03 0.26
Matches are distributed among these distances:
24 20 0.83
25 3 0.12
29 1 0.04
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (28 bp):
GTTTTTTTTATATTATTTATATTAAATT
Found at i:112518139 original size:24 final size:24
Alignment explanation
Indices: 112518085--112518248 Score: 123
Period size: 26 Copynumber: 6.4 Consensus size: 24
112518075 TTAAACTATT
* *
112518085 TTATTTATTTTAAGTTTTTTTGTATA
1 TTATTTATTTTAA-ATTGTTT-TATA
*
112518111 TTATTTATATTAAATTGTTTTATA
1 TTATTTATTTTAAATTGTTTTATA
112518135 TTATTTATTTTAAATTGTTTTAGATA
1 TTATTTATTTTAAATTGTTTT--ATA
* * * *
112518161 TTATCTATTTTAAATCGATTCATACA
1 TTATTTATTTTAAATTG-TT-TTATA
* * *
112518187 TTATTTATTTTGAACTGCTTTATAAA
1 TTATTTATTTTAAATTG-TTT-TATA
*
112518213 TTATTTTATTTTAAAATTGTTTCATA
1 TTA-TTTATTTT-AAATTGTTTTATA
112518239 -TATATTATTT
1 TTAT-TTATTT
112518249 GTTTTAGATT
Statistics
Matches: 111, Mismatches: 19, Indels: 17
0.76 0.13 0.12
Matches are distributed among these distances:
24 25 0.23
25 13 0.12
26 55 0.50
27 13 0.12
28 5 0.05
ACGTcount: A:0.30, C:0.04, G:0.05, T:0.60
Consensus pattern (24 bp):
TTATTTATTTTAAATTGTTTTATA
Found at i:112518162 original size:50 final size:50
Alignment explanation
Indices: 112518085--112518351 Score: 144
Period size: 50 Copynumber: 5.0 Consensus size: 50
112518075 TTAAACTATT
* * *
112518085 TTATTTATTTTAAGTT-TTTTTGTATATTATTTATATTAAATTGTTTTATA
1 TTATTTATTTTAAATTGTTTTAG-ATATTATTTATTTTAAATTGTTTTATA
* * * *
112518135 TTATTTATTTTAAATTGTTTTAGATATTATCTATTTTAAATCGATTCATACA
1 TTATTTATTTTAAATTGTTTTAGATATTATTTATTTTAAATTG-TT-TTATA
* * * * *
112518187 TTATTTATTTTGAACTGCTTTATAAATTATTTTATTTTAAAATTGTTTCATATATA
1 TTATTTATTTTAAATTGTTTTAGATATTA-TTTATTTT-AAATTG-TT--T-TATA
* * * * * *
112518243 TTATTTGTTTTAGATTTTTTTTACATATTATTTCTTTTTGTAAAAAAATGCTTTATATA
1 TTATTTATTTTA-AATTGTTTTAGATATTA-TT-TATTT-T---AAATTG-TTT-TATA
* * * * *
112518302 TTATTTATTTTAAATTGCTTTAG--CTTATTTATTTCAAACTGTTTTGTA
1 TTATTTATTTTAAATTGTTTTAGATATTATTTATTTTAAATTGTTTTATA
112518350 TT
1 TT
112518352 TTATTTGTGT
Statistics
Matches: 166, Mismatches: 39, Indels: 26
0.72 0.17 0.11
Matches are distributed among these distances:
48 5 0.03
49 3 0.02
50 37 0.22
51 7 0.04
52 27 0.16
53 7 0.04
54 11 0.07
55 2 0.01
56 16 0.10
57 14 0.08
58 11 0.07
59 18 0.11
61 8 0.05
ACGTcount: A:0.29, C:0.05, G:0.06, T:0.59
Consensus pattern (50 bp):
TTATTTATTTTAAATTGTTTTAGATATTATTTATTTTAAATTGTTTTATA
Found at i:112518247 original size:52 final size:51
Alignment explanation
Indices: 112518110--112518248 Score: 138
Period size: 52 Copynumber: 2.7 Consensus size: 51
112518100 TTTTTTGTAT
* * * * *
112518110 ATTATTTATATTAAATTGTTTTATAT-TATTTATTTTAAATTGTTTTAGAT
1 ATTATTTATTTTAAATTGTTTCATATATATTTATTTTAAACTGCTTTAGAA
* * * * * *
112518160 ATTATCTATTTTAAATCGATTCATACATTATTTATTTTGAACTGCTTTATAA
1 ATTATTTATTTTAAATTGTTTCATATA-TATTTATTTTAAACTGCTTTAGAA
112518212 ATTATTTTATTTTAAAATTGTTTCATATATA-TTATTT
1 ATTA-TTTATTTT-AAATTGTTTCATATATATTTATTT
112518249 GTTTTAGATT
Statistics
Matches: 70, Mismatches: 15, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
50 20 0.29
52 29 0.41
53 9 0.13
54 12 0.17
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (51 bp):
ATTATTTATTTTAAATTGTTTCATATATATTTATTTTAAACTGCTTTAGAA
Found at i:112518462 original size:25 final size:25
Alignment explanation
Indices: 112518422--112518494 Score: 92
Period size: 26 Copynumber: 2.8 Consensus size: 25
112518412 TTATTAAAAA
*
112518422 AAACTTTTTTCATATATTATTTATTTC
1 AAAC-TTTTT-ATATATTATTTACTTC
112518449 AAACTTTTTATATATTATTTACTTC
1 AAACTTTTTATATATTATTTACTTC
* *
112518474 GAATTGTTTTATATATTATTT
1 AAACT-TTTTATATATTATTT
112518495 TGTTTCGTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
25 18 0.43
26 20 0.48
27 4 0.10
ACGTcount: A:0.30, C:0.08, G:0.03, T:0.59
Consensus pattern (25 bp):
AAACTTTTTATATATTATTTACTTC
Found at i:112519280 original size:16 final size:16
Alignment explanation
Indices: 112519259--112519297 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
112519249 ATTAAAACGA
112519259 TCAATCATAAGGTGAC
1 TCAATCATAAGGTGAC
112519275 TCAATCATAAGGTGAC
1 TCAATCATAAGGTGAC
112519291 TCAATCA
1 TCAATCA
112519298 CACCTCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (16 bp):
TCAATCATAAGGTGAC
Found at i:112520555 original size:3 final size:3
Alignment explanation
Indices: 112520549--112520582 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
112520539 CCAACTCATT
112520549 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
112520583 GCTTTATACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:112521404 original size:41 final size:40
Alignment explanation
Indices: 112521359--112521440 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 40
112521349 TCAACTTAAC
* *
112521359 ACTTTTTCTTTTTCTAATTTGGTATCTAATTTTTTTTATCT
1 ACTTTTTCTTTTTCTAATGTGGCATCTAA-TTTTTTTATCT
112521400 ACTTTTTCTTTTTCTAATGTGGCATCTAATTTTTTTATCT
1 ACTTTTTCTTTTTCTAATGTGGCATCTAATTTTTTTATCT
112521440 A
1 A
112521441 ATTTGGTATC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 12 0.31
41 27 0.69
ACGTcount: A:0.18, C:0.13, G:0.06, T:0.62
Consensus pattern (40 bp):
ACTTTTTCTTTTTCTAATGTGGCATCTAATTTTTTTATCT
Found at i:112524223 original size:10 final size:10
Alignment explanation
Indices: 112524204--112524253 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
112524194 TGAAATTCTA
112524204 AAAGATAAAT
1 AAAGATAAAT
*
112524214 GCAA-ATAAAT
1 -AAAGATAAAT
112524224 AAAGATAAAT
1 AAAGATAAAT
112524234 AAAGATAAAT
1 AAAGATAAAT
112524244 GAAA-ATAAAT
1 -AAAGATAAAT
112524254 CCTAGAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
9 2 0.06
10 28 0.80
11 5 0.14
ACGTcount: A:0.68, C:0.02, G:0.10, T:0.20
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:112525808 original size:3 final size:3
Alignment explanation
Indices: 112525800--112525850 Score: 56
Period size: 3 Copynumber: 18.0 Consensus size: 3
112525790 ACATCCAAAA
*
112525800 AAT AAT AAT AAT AAT AAT AAT -AT AAT AAAT AGT AA- AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
112525843 AA- AAT AAT
1 AAT AAT AAT
112525851 TAAATTAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
2 8 0.20
3 30 0.73
4 3 0.07
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:112525811 original size:6 final size:6
Alignment explanation
Indices: 112525800--112525850 Score: 56
Period size: 5 Copynumber: 9.0 Consensus size: 6
112525790 ACATCCAAAA
*
112525800 AATAAT AATAAT AATAAT AAT-AT AATAAAT AGTAA- AATAA- AATAA-
1 AATAAT AATAAT AATAAT AATAAT AAT-AAT AATAAT AATAAT AATAAT
112525845 AATAAT
1 AATAAT
112525851 TAAATTAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
5 19 0.47
6 17 0.43
7 4 0.10
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (6 bp):
AATAAT
Found at i:112525817 original size:12 final size:11
Alignment explanation
Indices: 112525798--112525880 Score: 64
Period size: 12 Copynumber: 7.4 Consensus size: 11
112525788 CAACATCCAA
112525798 AAAATAATAAT
1 AAAATAATAAT
112525809 AATAATAATAAT
1 AA-AATAATAAT
* *
112525821 ATAATAAATAGT
1 AAAAT-AATAAT
112525833 AAAATAA-AAT
1 AAAATAATAAT
112525843 AAAATAAT--T
1 AAAATAATAAT
*
112525852 AAATTAAATTAAT
1 AAAAT-AA-TAAT
*
112525865 AAAAATAAAAAT
1 -AAAATAATAAT
112525877 AAAA
1 AAAA
112525881 AAATTGGGTT
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
9 5 0.09
10 11 0.19
11 12 0.21
12 22 0.39
13 3 0.05
14 4 0.07
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.28
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:112525826 original size:17 final size:17
Alignment explanation
Indices: 112525804--112525850 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
112525794 CCAAAAAATA
112525804 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
*
112525821 ATAATAAATAGTAA-AAT
1 ATAAT-AATAATAATAAT
*
112525838 AAAATAA-AATAAT
1 ATAATAATAATAAT
112525851 TAAATTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 4 0.16
16 2 0.08
17 12 0.48
18 7 0.28
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (17 bp):
ATAATAATAATAATAAT
Found at i:112525859 original size:14 final size:14
Alignment explanation
Indices: 112525798--112525874 Score: 50
Period size: 14 Copynumber: 5.3 Consensus size: 14
112525788 CAACATCCAA
112525798 AAAATAA-TAATAAT
1 AAAATAATTAA-AAT
*
112525812 AATAATAA-TATAAT
1 AA-AATAATTAAAAT
*
112525826 AAATAGTAAAATAAAAT
1 AAA-A-T-AATTAAAAT
*
112525843 AAAATAATTAAATT
1 AAAATAATTAAAAT
* *
112525857 AAATTAATAAAAAT
1 AAAATAATTAAAAT
112525871 AAAA
1 AAAA
112525875 ATAAAAAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
13 1 0.02
14 29 0.58
15 9 0.18
16 3 0.06
17 8 0.16
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (14 bp):
AAAATAATTAAAAT
Found at i:112525874 original size:5 final size:5
Alignment explanation
Indices: 112525798--112525880 Score: 53
Period size: 5 Copynumber: 15.8 Consensus size: 5
112525788 CAACATCCAA
*
112525798 AAAAT AATAAT AATAAT AATAAT ATAAT AAATAGT AAAAT AAAAT AAAAT
1 AAAAT AA-AAT AA-AAT AA-AAT AAAAT AAA-A-T AAAAT AAAAT AAAAT
* * * *
112525848 -AATT AAATT AAATT AATA- AAAAT AAAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAA
112525881 AAATTGGGTT
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
4 6 0.09
5 33 0.50
6 23 0.35
7 4 0.06
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.28
Consensus pattern (5 bp):
AAAAT
Done.