Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold63
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: 2211945
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 524 characters in sequence are not A, C, G, or T
File 12 of 16
Found at i:1694850 original size:18 final size:18
Alignment explanation
Indices: 1694808--1694843 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1694798 TTTATGTTTT
*
1694808 AAAATTTAATAAAAATAA
1 AAAATTAAATAAAAATAA
1694826 AAAATTAAATAAAAATAA
1 AAAATTAAATAAAAATAA
1694844 CATATTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAATTAAATAAAAATAA
Found at i:1694930 original size:18 final size:18
Alignment explanation
Indices: 1694896--1694933 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1694886 TTATTTATAT
*
1694896 ATAAAATTAAATTTTTAA
1 ATAAAATTAAATCTTTAA
1694914 ATAAAATTTAAA-CTTTAA
1 ATAAAA-TTAAATCTTTAA
1694932 AT
1 AT
1694934 TATCAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAAAATTAAATCTTTAA
Found at i:1694941 original size:26 final size:24
Alignment explanation
Indices: 1694897--1694957 Score: 59
Period size: 26 Copynumber: 2.5 Consensus size: 24
1694887 TATTTATATA
* * *
1694897 TAAAATTAAATTTTTAAATAAAATT
1 TAAATTTAAATTATCAAATAAAA-T
**
1694922 TAAACTTTAAATTATCAAATTTAAT
1 TAAA-TTTAAATTATCAAATAAAAT
1694947 TAAATTTAAAT
1 TAAATTTAAAT
1694958 AAATAAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 7 0.23
25 9 0.30
26 14 0.47
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (24 bp):
TAAATTTAAATTATCAAATAAAAT
Found at i:1694965 original size:24 final size:25
Alignment explanation
Indices: 1694912--1694970 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 25
1694902 TTAAATTTTT
* *
1694912 AAATAAAATTTAAACTTTAAATTATC
1 AAATATAA-TTAAACTTTAAATAATC
*
1694938 AAATTTAATTAAA-TTTAAATAAAT-
1 AAATATAATTAAACTTTAAAT-AATC
1694962 AAATATAAT
1 AAATATAAT
1694971 ATTAATATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 15 0.54
25 7 0.25
26 6 0.21
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (25 bp):
AAATATAATTAAACTTTAAATAATC
Found at i:1700114 original size:2 final size:2
Alignment explanation
Indices: 1700107--1700150 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1700097 TTTTCCGCGG
1700107 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1700149 CT
1 CT
1700151 ATATGTATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1702931 original size:86 final size:86
Alignment explanation
Indices: 1702786--1702958 Score: 208
Period size: 86 Copynumber: 2.0 Consensus size: 86
1702776 ATAGTTGTCA
* * * * * *
1702786 ATATGTTTTCCAGTTTGATTTCTGTGGGGGTTTTCTCTTTAAGCTTGGTCACAATTATTTGT-TG
1 ATATGTCTTCCAGTTTGATCTCTGTGAGGGTTTTCTCTTTAAACTTGGTCACAAGTATTTGTAGG
* *
1702850 TTTTTGCAATTTCATGTTTTTG
66 TTCTT-CAATTTCATATTTTTG
* *
1702872 ATATGTCTTCCAGTTTGATGCT-TGTGATGGTTTTCTCTTTAAAAC-TGGTCACAGGTATTTGTA
1 ATATGTCTTCCAGTTTGAT-CTCTGTGAGGGTTTTCTCTTT-AAACTTGGTCACAAGTATTTGTA
1702935 GGTTCTTCAATTTCATATTTTTG
64 GGTTCTTCAATTTCATATTTTTG
1702958 A
1 A
1702959 GGGTTTTGCG
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
86 65 0.88
87 9 0.12
ACGTcount: A:0.18, C:0.13, G:0.19, T:0.50
Consensus pattern (86 bp):
ATATGTCTTCCAGTTTGATCTCTGTGAGGGTTTTCTCTTTAAACTTGGTCACAAGTATTTGTAGG
TTCTTCAATTTCATATTTTTG
Found at i:1709357 original size:21 final size:20
Alignment explanation
Indices: 1709333--1709380 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1709323 AAATATATCA
*
1709333 ATACATTATATAAATGAATTG
1 ATACATTATAT-AATGAATCG
* *
1709354 ATACATCATATAATGTATCG
1 ATACATTATATAATGAATCG
1709374 ATACATT
1 ATACATT
1709381 TTGTTGGCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (20 bp):
ATACATTATATAATGAATCG
Found at i:1709376 original size:20 final size:21
Alignment explanation
Indices: 1709323--1709379 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
1709313 ATACAAGTAA
* * *
1709323 AAATATATCAATACATTATAT
1 AAATGTATCGATACATCATAT
* *
1709344 AAATGAATTGATACATCATAT
1 AAATGTATCGATACATCATAT
1709365 -AATGTATCGATACAT
1 AAATGTATCGATACAT
1709380 TTTGTTGGCA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.47, C:0.11, G:0.07, T:0.35
Consensus pattern (21 bp):
AAATGTATCGATACATCATAT
Found at i:1709490 original size:20 final size:20
Alignment explanation
Indices: 1709436--1709483 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1709426 ATGCGCATGT
*
1709436 AAATGTATTGATATAATTCA
1 AAATGTATTGATACAATTCA
*
1709456 AAATATATTGATACAATTCA
1 AAATGTATTGATACAATTCA
1709476 AAATGTAT
1 AAATGTAT
1709484 CGTTACATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.38
Consensus pattern (20 bp):
AAATGTATTGATACAATTCA
Found at i:1710021 original size:8 final size:8
Alignment explanation
Indices: 1710008--1710034 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1709998 CTTAGCTTTA
1710008 AATATAAC
1 AATATAAC
1710016 AATATAAC
1 AATATAAC
1710024 AATATAAC
1 AATATAAC
1710032 AAT
1 AAT
1710035 TTTTTAGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (8 bp):
AATATAAC
Found at i:1711162 original size:21 final size:21
Alignment explanation
Indices: 1711087--1711170 Score: 56
Period size: 20 Copynumber: 4.2 Consensus size: 21
1711077 ATAATATTTA
1711087 AAATTTA-TATA-TATTATCAT
1 AAATTTATTATATTATTAT-AT
* *
1711107 ATACTTATTAAATATT-TTA-AT
1 AAATTTATT--ATATTATTATAT
* *
1711128 TAATTTACTA-ATTATTATAT
1 AAATTTATTATATTATTATAT
1711148 AAATTTATTATATTA-TAT-T
1 AAATTTATTATATTATTATAT
1711167 AAAT
1 AAAT
1711171 AAAATATAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 15
0.68 0.11 0.21
Matches are distributed among these distances:
18 3 0.06
19 9 0.18
20 18 0.37
21 12 0.24
23 6 0.12
24 1 0.02
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (21 bp):
AAATTTATTATATTATTATAT
Found at i:1711193 original size:34 final size:34
Alignment explanation
Indices: 1711149--1711215 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
1711139 TTATTATATA
1711149 AATTTATTATATTATATTAAATAAAATATAAATT
1 AATTTATTATATTATATTAAATAAAATATAAATT
*
1711183 AATTTGTTATATTATATTAAATAAAATATAAAT
1 AATTTATTATATTATATTAAATAAAATATAAAT
1711216 ATATTTTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (34 bp):
AATTTATTATATTATATTAAATAAAATATAAATT
Found at i:1711295 original size:19 final size:19
Alignment explanation
Indices: 1711259--1711298 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1711249 AGAGATTAAT
*
1711259 AAAATTTAAAATATTAAAA
1 AAAATTTAAAATAATAAAA
1711278 AAAATTTAAAA-ACATAAAA
1 AAAATTTAAAATA-ATAAAA
1711297 AA
1 AA
1711299 CAAAAAGGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 1 0.05
19 18 0.95
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (19 bp):
AAAATTTAAAATAATAAAA
Found at i:1711584 original size:13 final size:14
Alignment explanation
Indices: 1711566--1711596 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
1711556 TTTGAGTGAA
1711566 AAAAAATAA-TATT
1 AAAAAATAAGTATT
1711579 AAAAAATAAGTATT
1 AAAAAATAAGTATT
1711593 AAAA
1 AAAA
1711597 TTTATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (14 bp):
AAAAAATAAGTATT
Found at i:1711839 original size:18 final size:16
Alignment explanation
Indices: 1711810--1711854 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 16
1711800 AGAATATATA
*
1711810 TATATATATATGTATG
1 TATATGTATATGTATG
*
1711826 TATGCATGTATATGTGTG
1 TAT--ATGTATATGTATG
1711844 TATATGTATAT
1 TATATGTATAT
1711855 CTACACTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 11 0.44
18 14 0.56
ACGTcount: A:0.31, C:0.02, G:0.18, T:0.49
Consensus pattern (16 bp):
TATATGTATATGTATG
Found at i:1713252 original size:47 final size:46
Alignment explanation
Indices: 1713190--1713293 Score: 165
Period size: 47 Copynumber: 2.2 Consensus size: 46
1713180 ATATATTTAT
*
1713190 ATATTAATATAAATATAATATTTTAAATGTATAAAATTTTTTTATAA
1 ATATTAATATAAATATAATATTTTAAATGTAT-AAACTTTTTTATAA
*
1713237 ATATTAATATAAATATAATATTTTAAATGTATAGACTTTTTTATAA
1 ATATTAATATAAATATAATATTTTAAATGTATAAACTTTTTTATAA
1713283 A-ATTAAATATA
1 ATATT-AATATA
1713294 TTTATATTCA
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
45 3 0.06
46 19 0.35
47 32 0.59
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (46 bp):
ATATTAATATAAATATAATATTTTAAATGTATAAACTTTTTTATAA
Found at i:1713478 original size:29 final size:29
Alignment explanation
Indices: 1713445--1713529 Score: 152
Period size: 29 Copynumber: 2.9 Consensus size: 29
1713435 AGATACATCT
1713445 ACTCAAATTTTACTCAAAACAAAAATTAA
1 ACTCAAATTTTACTCAAAACAAAAATTAA
* *
1713474 ACTCAAATTTTACTCAACACAAGAATTAA
1 ACTCAAATTTTACTCAAAACAAAAATTAA
1713503 ACTCAAATTTTACTCAAAACAAAAATT
1 ACTCAAATTTTACTCAAAACAAAAATT
1713530 TTAATTCGAC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.52, C:0.19, G:0.01, T:0.28
Consensus pattern (29 bp):
ACTCAAATTTTACTCAAAACAAAAATTAA
Found at i:1722184 original size:3 final size:3
Alignment explanation
Indices: 1722176--1722203 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1722166 TAGTTTAAGC
1722176 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1722204 GTAGTACTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1722775 original size:34 final size:32
Alignment explanation
Indices: 1722726--1722793 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 32
1722716 ATCAAACAGT
*
1722726 TTTTTAAGGTATGATTTATTTTTAATTATTAAAGTA
1 TTTTTAA-GTATGATTT-GTTTT-ATT-TTAAAGTA
1722762 TTTTTAA-TATGATTTGTTTTATTTTAAAGTA
1 TTTTTAAGTATGATTTGTTTTATTTTAAAGTA
1722793 T
1 T
1722794 GATTTATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
31 9 0.29
32 3 0.10
33 4 0.13
34 8 0.26
36 7 0.23
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (32 bp):
TTTTTAAGTATGATTTGTTTTATTTTAAAGTA
Found at i:1722796 original size:22 final size:22
Alignment explanation
Indices: 1722760--1722813 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 22
1722750 ATTATTAAAG
*
1722760 TATTTTTAATATGATTT-GTTT
1 TATTTTAAATATGATTTAGTTT
*
1722781 TATTTTAAAGTATGATTTATTTT
1 TATTTTAAA-TATGATTTAGTTT
1722804 TATTTGTAAA
1 TATTT-TAAA
1722814 ATTAATTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 8 0.29
22 8 0.29
23 8 0.29
24 4 0.14
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (22 bp):
TATTTTAAATATGATTTAGTTT
Found at i:1722821 original size:23 final size:23
Alignment explanation
Indices: 1722778--1722821 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1722768 ATATGATTTG
* *
1722778 TTTTATTTTAAAGTATGATTTAT
1 TTTTATTTTAAAATATAATTTAT
1722801 TTTTATTTGTAAAAT-TAATTT
1 TTTTATTT-TAAAATATAATTT
1722822 GATTAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (23 bp):
TTTTATTTTAAAATATAATTTAT
Found at i:1723781 original size:18 final size:17
Alignment explanation
Indices: 1723748--1723813 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
1723738 GCTAGAAATT
* *
1723748 AAAAAAAAAATTAAAAT
1 AAAAAAAAAATAAAAAA
*
1723765 AAAAAAAAAAGAAAAAA
1 AAAAAAAAAATAAAAAA
* **
1723782 ACAAGAGAAAAGGAAAAAA
1 A-AA-AAAAAAATAAAAAA
*
1723801 AAAACAAAAATAA
1 AAAAAAAAAATAA
1723814 TGCTGAAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
17 22 0.56
18 4 0.10
19 13 0.33
ACGTcount: A:0.83, C:0.03, G:0.08, T:0.06
Consensus pattern (17 bp):
AAAAAAAAAATAAAAAA
Found at i:1725348 original size:6 final size:7
Alignment explanation
Indices: 1725327--1725351 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1725317 AAATATGAAG
1725327 AATTAAA
1 AATTAAA
1725334 AATTAAA
1 AATTAAA
1725341 AATTAAA
1 AATTAAA
1725348 AATT
1 AATT
1725352 TATTCCTTTT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AATTAAA
Found at i:1726631 original size:16 final size:16
Alignment explanation
Indices: 1726600--1726641 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1726590 GCAAATCGTG
* *
1726600 TATATATATATATATA
1 TATATGTATGTATATA
*
1726616 TGTATGTATGTATATA
1 TATATGTATGTATATA
1726632 TATATGTATG
1 TATATGTATG
1726642 CATTTCTTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (16 bp):
TATATGTATGTATATA
Found at i:1732602 original size:3 final size:3
Alignment explanation
Indices: 1732584--1732620 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
1732574 CTTGTATTGT
* *
1732584 TTG TTC TTG CTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1732621 CATCGTTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.05, G:0.30, T:0.65
Consensus pattern (3 bp):
TTG
Found at i:1735512 original size:81 final size:82
Alignment explanation
Indices: 1735420--1735595 Score: 291
Period size: 82 Copynumber: 2.1 Consensus size: 82
1735410 ATTTTATATA
*
1735420 AAAATATTTTTTACTTATTAAATATTAATGAA-ATAGAATAGATTTCAAAATCTGTGAACAAATT
1 AAAATA-TTTTTACTTATTAAATATTAATGAAGATAGAATAGATTTCAAAATCTATGAACAAATT
1735484 TAATTACTATTATTTTTT
65 TAATTACTATTATTTTTT
* * * *
1735502 AAAATATTTTTACTTATTAAATATTAATTAAGATGGAATATATTTCAAAATTTATGAACAAATTT
1 AAAATATTTTTACTTATTAAATATTAATGAAGATAGAATAGATTTCAAAATCTATGAACAAATTT
1735567 AATTACTATTATTTTTT
66 AATTACTATTATTTTTT
1735584 AAAATATTTTTA
1 AAAATATTTTTA
1735596 AATAAAAAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
81 24 0.27
82 64 0.73
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (82 bp):
AAAATATTTTTACTTATTAAATATTAATGAAGATAGAATAGATTTCAAAATCTATGAACAAATTT
AATTACTATTATTTTTT
Found at i:1743351 original size:204 final size:204
Alignment explanation
Indices: 1743001--1743408 Score: 816
Period size: 204 Copynumber: 2.0 Consensus size: 204
1742991 TATTCCTGCT
1743001 AAAAGAAGATTTGGTTTCTAAAACTCTGTTTCAGTTATCTTAAATAGCAATATATAATTGGTAGA
1 AAAAGAAGATTTGGTTTCTAAAACTCTGTTTCAGTTATCTTAAATAGCAATATATAATTGGTAGA
1743066 CTAATGAATATAATATTGTTGAGGTTGGTTCAGATCTTGTTGAAGCAGATCTTTGTATGAAATGC
66 CTAATGAATATAATATTGTTGAGGTTGGTTCAGATCTTGTTGAAGCAGATCTTTGTATGAAATGC
1743131 TTGATTCAGTTTTATCTCTTAAAAATTGATAGTAACTTACAAATACTGATCTATATTTTTCTCTT
131 TTGATTCAGTTTTATCTCTTAAAAATTGATAGTAACTTACAAATACTGATCTATATTTTTCTCTT
1743196 TGGTGCCTA
196 TGGTGCCTA
1743205 AAAAGAAGATTTGGTTTCTAAAACTCTGTTTCAGTTATCTTAAATAGCAATATATAATTGGTAGA
1 AAAAGAAGATTTGGTTTCTAAAACTCTGTTTCAGTTATCTTAAATAGCAATATATAATTGGTAGA
1743270 CTAATGAATATAATATTGTTGAGGTTGGTTCAGATCTTGTTGAAGCAGATCTTTGTATGAAATGC
66 CTAATGAATATAATATTGTTGAGGTTGGTTCAGATCTTGTTGAAGCAGATCTTTGTATGAAATGC
1743335 TTGATTCAGTTTTATCTCTTAAAAATTGATAGTAACTTACAAATACTGATCTATATTTTTCTCTT
131 TTGATTCAGTTTTATCTCTTAAAAATTGATAGTAACTTACAAATACTGATCTATATTTTTCTCTT
1743400 TGGTGCCTA
196 TGGTGCCTA
1743409 TCACGGATCT
Statistics
Matches: 204, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
204 204 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (204 bp):
AAAAGAAGATTTGGTTTCTAAAACTCTGTTTCAGTTATCTTAAATAGCAATATATAATTGGTAGA
CTAATGAATATAATATTGTTGAGGTTGGTTCAGATCTTGTTGAAGCAGATCTTTGTATGAAATGC
TTGATTCAGTTTTATCTCTTAAAAATTGATAGTAACTTACAAATACTGATCTATATTTTTCTCTT
TGGTGCCTA
Found at i:1747888 original size:21 final size:21
Alignment explanation
Indices: 1747864--1747903 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1747854 ATATTTTATT
*
1747864 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TAAAAAATATA
1747885 TAAATATTAATAAAAAATA
1 TAAATATTAATAAAAAATA
1747904 CTTTTTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATATTAATAAAAAATATA
Found at i:1752407 original size:3 final size:3
Alignment explanation
Indices: 1752399--1752436 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
1752389 TTTAAAACAA
*
1752399 AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1752437 GAAACCTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1752557 original size:27 final size:27
Alignment explanation
Indices: 1752526--1752581 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
1752516 TGTTACTTGG
1752526 ATTTAGAGGTAAATGTTGAATAAAGAT
1 ATTTAGAGGTAAATGTTGAATAAAGAT
*
1752553 ATTTAGAGGTAAATGTTGGATAAAGAT
1 ATTTAGAGGTAAATGTTGAATAAAGAT
1752580 AT
1 AT
1752582 GTGTTTGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.34
Consensus pattern (27 bp):
ATTTAGAGGTAAATGTTGAATAAAGAT
Found at i:1755355 original size:20 final size:20
Alignment explanation
Indices: 1755330--1755395 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1755320 ACATCTAAAA
*
1755330 TTTAATTTGGATGTAGAGTT
1 TTTAATTTGGATATAGAGTT
* * **
1755350 TTTAATTTTGATCTA-A-AA
1 TTTAATTTGGATATAGAGTT
1755368 TTTAATTTGGATATAGAGTT
1 TTTAATTTGGATATAGAGTT
1755388 TTTAATTT
1 TTTAATTT
1755396 TGATCAACTT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
18 13 0.36
19 2 0.06
20 21 0.58
ACGTcount: A:0.30, C:0.02, G:0.15, T:0.53
Consensus pattern (20 bp):
TTTAATTTGGATATAGAGTT
Found at i:1755365 original size:38 final size:38
Alignment explanation
Indices: 1755322--1755400 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
1755312 AATAATTTAC
*
1755322 ATCTAAAATTTAATTTGGATGTAGAGTTTTTAATTTTG
1 ATCTAAAATTTAATTTGGATATAGAGTTTTTAATTTTG
1755360 ATCTAAAATTTAATTTGGATATAGAGTTTTTAATTTTG
1 ATCTAAAATTTAATTTGGATATAGAGTTTTTAATTTTG
1755398 ATC
1 ATC
1755401 AACTTGATGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.33, C:0.04, G:0.14, T:0.49
Consensus pattern (38 bp):
ATCTAAAATTTAATTTGGATATAGAGTTTTTAATTTTG
Found at i:1755373 original size:18 final size:18
Alignment explanation
Indices: 1755322--1755379 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
1755312 AATAATTTAC
1755322 ATCTAAAATTTAATTTGG
1 ATCTAAAATTTAATTTGG
* ** *
1755340 ATGTAGAGTTTTTAATTTTG
1 ATCTA-A-AATTTAATTTGG
1755360 ATCTAAAATTTAATTTGG
1 ATCTAAAATTTAATTTGG
1755378 AT
1 AT
1755380 ATAGAGTTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
18 15 0.50
19 2 0.07
20 13 0.43
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.48
Consensus pattern (18 bp):
ATCTAAAATTTAATTTGG
Found at i:1758037 original size:112 final size:111
Alignment explanation
Indices: 1757840--1758050 Score: 280
Period size: 112 Copynumber: 1.9 Consensus size: 111
1757830 ATGAACATTG
* * *
1757840 CAAATGCCTTTTGCTTTCACATTCTATGTTTTTTCCAACTTGTATCGATATCTTATGTCGGGGGC
1 CAAATGCCTTTTGCTTTCACATTCTATGTTTTCTCCAACTTGTACCGATATCTTATGTCAGGGGC
* * *
1757905 TAGGGGAAAGACATTCAAGTGAGTACTTTTTCTGCTATGATTGAATT
66 TAGGGAAAAGACATACAAGTGAATAC-TTTTCTGCTATGATTGAATT
** * * *
1757952 CAAATGCCTTTTGCTTTCTTATTTTATGTTTTGCTCCAACTTGTACCTATAT-TTATGTTAGGGG
1 CAAATGCCTTTTGCTTTCACATTCTATGTTTT-CTCCAACTTGTACCGATATCTTATGTCAGGGG
* *
1758016 CTTGGGAAAAGATATACAAGTGAATACTTTTCTGC
65 CTAGGGAAAAGACATACAAGTGAATACTTTTCTGC
1758051 CTTGATTCAC
Statistics
Matches: 85, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
111 8 0.09
112 61 0.72
113 16 0.19
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.41
Consensus pattern (111 bp):
CAAATGCCTTTTGCTTTCACATTCTATGTTTTCTCCAACTTGTACCGATATCTTATGTCAGGGGC
TAGGGAAAAGACATACAAGTGAATACTTTTCTGCTATGATTGAATT
Found at i:1766739 original size:2 final size:2
Alignment explanation
Indices: 1766732--1766772 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1766722 AATAAACGTG
*
1766732 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1766773 CAGATCTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1767542 original size:10 final size:10
Alignment explanation
Indices: 1767513--1767569 Score: 61
Period size: 10 Copynumber: 6.1 Consensus size: 10
1767503 CTGGTAACTG
1767513 TAATA-AATA
1 TAATATAATA
*
1767522 TAATTAAAATA
1 TAA-TATAATA
1767533 TAATATAATA
1 TAATATAATA
1767543 TAATA-AATA
1 TAATATAATA
1767552 T-ATATAA-A
1 TAATATAATA
1767560 T-ATATAATA
1 TAATATAATA
1767569 T
1 T
1767570 TTTAAATATC
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
8 11 0.26
9 12 0.28
10 13 0.30
11 7 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
TAATATAATA
Found at i:1767543 original size:21 final size:19
Alignment explanation
Indices: 1767513--1767563 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 19
1767503 CTGGTAACTG
1767513 TAATA-AATATAATTAAAATA
1 TAATATAATATAA-T-AAATA
1767533 TAATATAATATAATAAATA
1 TAATATAATATAATAAATA
1767552 T-ATATAAATATA
1 TAATAT-AATATA
1767564 TAATATTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.14
19 12 0.41
20 6 0.21
21 7 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TAATATAATATAATAAATA
Found at i:1767564 original size:21 final size:20
Alignment explanation
Indices: 1767515--1767568 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
1767505 GGTAACTGTA
*
1767515 ATAAATATA-ATTAAAATAT
1 ATAAATATATAATAAAATAT
*
1767534 A-ATATAATATAATAAATATAT
1 ATAAAT-ATATAATAAA-ATAT
1767555 ATAAATATATAATA
1 ATAAATATATAATA
1767569 TTTTAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 3 0.11
19 4 0.14
20 5 0.18
21 13 0.46
22 3 0.11
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
ATAAATATATAATAAAATAT
Found at i:1767564 original size:26 final size:27
Alignment explanation
Indices: 1767535--1767593 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 27
1767525 TTAAAATATA
*
1767535 ATATAATATAATAAATAT-ATATAAAT
1 ATATAATATAATAAATATCATACAAAT
**
1767561 ATATAATATTTTAAATATCATACAAAT
1 ATATAATATAATAAATATCATACAAAT
1767588 ATATAA
1 ATATAA
1767594 ATTAATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 16 0.55
27 13 0.45
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (27 bp):
ATATAATATAATAAATATCATACAAAT
Found at i:1767591 original size:29 final size:27
Alignment explanation
Indices: 1767513--1767600 Score: 83
Period size: 26 Copynumber: 3.2 Consensus size: 27
1767503 CTGGTAACTG
1767513 TAATAAATATAATTAAAATATAATATAATA
1 TAATAAATAT-A-TAAAATAT-ATATAATA
*
1767543 TAATAAATATATATAA-ATATATAATA
1 TAATAAATATATAAAATATATATAATA
**
1767569 TTTTAAATATCATACAAATATATA-AAT-
1 TAATAAATAT-ATA-AAATATATATAATA
1767596 TAATA
1 TAATA
1767601 TATTAACTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
26 16 0.33
27 8 0.16
28 9 0.18
29 6 0.12
30 10 0.20
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (27 bp):
TAATAAATATATAAAATATATATAATA
Found at i:1767634 original size:16 final size:15
Alignment explanation
Indices: 1767613--1767642 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1767603 TTAACTATAA
1767613 ATAAAAAATAAAAAAT
1 ATAAAAAA-AAAAAAT
1767629 ATAAAAAAAAAAAA
1 ATAAAAAAAAAAAA
1767643 GTAAATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (15 bp):
ATAAAAAAAAAAAAT
Found at i:1767878 original size:24 final size:24
Alignment explanation
Indices: 1767851--1767933 Score: 80
Period size: 25 Copynumber: 3.4 Consensus size: 24
1767841 TTATTTATTT
1767851 TATTTATATTTAAAATATTTTATA
1 TATTTATATTTAAAATATTTTATA
* **
1767875 TATTTTTATACATAAATATTTTATA
1 TATTTATATTTA-AAATATTTTATA
*
1767900 T-TATATAATTTTAAAATA-TTTATA
1 TATTTAT-A-TTTAAAATATTTTATA
*
1767924 TATTAATATT
1 TATTTATATT
1767934 ATATATTAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
23 2 0.04
24 20 0.43
25 22 0.48
26 2 0.04
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (24 bp):
TATTTATATTTAAAATATTTTATA
Found at i:1767935 original size:13 final size:14
Alignment explanation
Indices: 1767815--1767954 Score: 74
Period size: 13 Copynumber: 10.6 Consensus size: 14
1767805 TTTTAATTAA
1767815 TTAT-TATTAA-AT
1 TTATATATTAATAT
*
1767827 TTA-ATAATTTATAT
1 TTATAT-ATTAATAT
* *
1767841 TTATTTATT-TTAT
1 TTATATATTAATAT
1767854 TTATAT-TTAAAATAT
1 TTATATATT--AATAT
*
1767869 TT-TATA-T-ATTT
1 TTATATATTAATAT
* *
1767880 TTATACATAAATAT
1 TTATATATTAATAT
1767894 TT-TATATTATATAAT
1 TTATATATTA-AT-AT
1767909 TT-TA-A--AATAT
1 TTATATATTAATAT
1767919 TTATATATTAATA-
1 TTATATATTAATAT
1767932 TTATATATTAATTAT
1 TTATATATTAA-TAT
1767947 TTATATAT
1 TTATATAT
1767955 AATTATATTA
Statistics
Matches: 98, Mismatches: 11, Indels: 35
0.68 0.08 0.24
Matches are distributed among these distances:
10 4 0.04
11 9 0.09
12 11 0.11
13 28 0.29
14 26 0.27
15 20 0.20
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATATATTAATAT
Found at i:1767954 original size:49 final size:49
Alignment explanation
Indices: 1767831--1767972 Score: 125
Period size: 49 Copynumber: 2.9 Consensus size: 49
1767821 TTAAATTTAA
* *
1767831 TAATTTATAT-TTATTTATTT-TAT-TTATATTTAAAATATTTTATATAT
1 TAATTTATATATTAATTATTTATATATAAT-TTTAAAATATTTTATATAT
* * *
1767878 T--TTTATACATAAATATTTTATATTATATAATTTTAAAATA-TTTATATAT
1 TAATTTATATATTAAT-TATT-TA-TATATAATTTTAAAATATTTTATATAT
*
1767927 TAATATTATATATTAATTATTTATATATAATTATATTAAATATTTT
1 TAAT-TTATATATTAATTATTTATATATAATT-T-TAAAATATTTT
1767973 TATGGCTAAT
Statistics
Matches: 74, Mismatches: 9, Indels: 19
0.73 0.09 0.19
Matches are distributed among these distances:
45 6 0.08
46 3 0.04
47 4 0.05
48 1 0.01
49 19 0.26
50 15 0.20
51 13 0.18
52 13 0.18
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (49 bp):
TAATTTATATATTAATTATTTATATATAATTTTAAAATATTTTATATAT
Found at i:1768850 original size:19 final size:18
Alignment explanation
Indices: 1768826--1768867 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
1768816 AATAAATCAA
1768826 ATATTTATATATTCATATT
1 ATATTTATATATT-ATATT
*
1768845 ATATTTATATATTTTATT
1 ATATTTATATATTATATT
1768863 ATATT
1 ATATT
1768868 ATAATCGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
ATATTTATATATTATATT
Found at i:1769170 original size:17 final size:18
Alignment explanation
Indices: 1769148--1769188 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1769138 TCTAATCAAC
1769148 TTTAAATTA-AT-ATTAAA
1 TTTAAATTAGATCA-TAAA
1769165 TTTAAATTAGATCATAAA
1 TTTAAATTAGATCATAAA
1769183 TTTAAA
1 TTTAAA
1769189 AAAAATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.41
18 12 0.55
19 1 0.05
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
TTTAAATTAGATCATAAA
Found at i:1769246 original size:24 final size:24
Alignment explanation
Indices: 1769201--1769254 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
1769191 AAATTAAATT
*
1769201 AATTAAATTTAATATATCATTTTA
1 AATTAAATTTAAAATATCATTTTA
* *
1769225 AATTATAATTTAAAAT-TTATTTTT
1 AATTA-AATTTAAAATATCATTTTA
1769249 AATTAA
1 AATTAA
1769255 TATTATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 1 0.04
24 16 0.62
25 9 0.35
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
AATTAAATTTAAAATATCATTTTA
Found at i:1769291 original size:21 final size:21
Alignment explanation
Indices: 1769270--1769349 Score: 71
Period size: 17 Copynumber: 3.8 Consensus size: 21
1769260 TATAATTTAT
1769270 AAATAATTTAAATAAA-AAT-
1 AAATAATTTAAATAAATAATA
1769289 --ATAATTTAAATAAATAAATA
1 AAATAATTTAAATAAAT-AATA
1769309 ATAACCTAATTTAAATAAATAA-A
1 A-AA--TAATTTAAATAAATAATA
*
1769332 AAATAACTTAAATCAAAT
1 AAATAATTTAAAT-AAAT
1769350 CAATTTAATA
Statistics
Matches: 51, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
17 14 0.27
19 3 0.06
20 9 0.18
21 4 0.08
22 2 0.04
23 3 0.06
24 2 0.04
25 14 0.27
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATAATTTAAATAAATAATA
Found at i:1769318 original size:25 final size:25
Alignment explanation
Indices: 1769290--1769338 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
1769280 AATAAAAATA
*
1769290 TAATTTAAATAAATAAATAATAACC
1 TAATTTAAATAAATAAAAAATAACC
1769315 TAATTTAAATAAATAAAAAATAAC
1 TAATTTAAATAAATAAAAAATAAC
1769339 TTAAATCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (25 bp):
TAATTTAAATAAATAAAAAATAACC
Found at i:1769349 original size:25 final size:25
Alignment explanation
Indices: 1769296--1769349 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
1769286 AATATAATTT
* * *
1769296 AAATAAATAAATAATAACCTAATTT
1 AAATAAATAAAAAATAACCTAAATC
*
1769321 AAATAAATAAAAAATAACTTAAATC
1 AAATAAATAAAAAATAACCTAAATC
1769346 AAAT
1 AAAT
1769350 CAATTTAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (25 bp):
AAATAAATAAAAAATAACCTAAATC
Found at i:1769875 original size:35 final size:35
Alignment explanation
Indices: 1769814--1769881 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
1769804 AACCACATAA
*
1769814 TTTATTATATTTAAATTTTAAAAATTAATAAATTT
1 TTTATTATATTTAAATTTTAAAAATTAAAAAATTT
* * *
1769849 TTTATTATTTTTATA-TTTATATAATTAAAAAAT
1 TTTATTATATTTAAATTTTA-AAAATTAAAAAAT
1769882 ATTCTAAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 4 0.14
35 24 0.86
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (35 bp):
TTTATTATATTTAAATTTTAAAAATTAAAAAATTT
Found at i:1770906 original size:20 final size:20
Alignment explanation
Indices: 1770861--1770906 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1770851 GAAAAATTAA
*
1770861 TATTTTACATTTTTTTTCCT
1 TATTTTACATTTTTCTTCCT
*
1770881 TTTTTTAACATTTTTCTT-CT
1 TATTTT-ACATTTTTCTTCCT
1770901 TATTTT
1 TATTTT
1770907 GGGTTTTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (20 bp):
TATTTTACATTTTTCTTCCT
Found at i:1771580 original size:17 final size:16
Alignment explanation
Indices: 1771555--1771598 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
1771545 TTGTATACAA
*
1771555 ATATTTATATACTTGT
1 ATATGTATATACTTGT
1771571 GATATGTATATACTTGT
1 -ATATGTATATACTTGT
*
1771588 ACATGTATATA
1 ATATGTATATA
1771599 ATATATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 10 0.40
17 15 0.60
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.48
Consensus pattern (16 bp):
ATATGTATATACTTGT
Found at i:1771595 original size:16 final size:17
Alignment explanation
Indices: 1771560--1771598 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
1771550 TACAAATATT
*
1771560 TATATACTTGTGATATG
1 TATATACTTGTGACATG
1771577 TATATACTTGT-ACATG
1 TATATACTTGTGACATG
1771593 TATATA
1 TATATA
1771599 ATATATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (17 bp):
TATATACTTGTGACATG
Found at i:1780787 original size:29 final size:29
Alignment explanation
Indices: 1780749--1780849 Score: 70
Period size: 28 Copynumber: 3.5 Consensus size: 29
1780739 TTAAAAGTTA
1780749 TTTTATTATTTAAAATATATTAAAAAATAT
1 TTTTA-TATTTAAAATATATTAAAAAATAT
* *
1780779 TTTTATA-TTAATATTTATATT--TAAATAT
1 TTTTATATTTAA-A-ATATATTAAAAAATAT
*
1780807 TTTTATAATT-AAAT-T-TTAAATAAAATAT
1 TTTTATATTTAAAATATATT-AA-AAAATAT
*
1780835 TTTTATTTATTAAAA
1 TTTTATAT-TTAAAA
1780850 AATAATTTAA
Statistics
Matches: 56, Mismatches: 6, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
24 2 0.04
25 1 0.02
26 1 0.02
27 1 0.02
28 30 0.54
29 7 0.12
30 14 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
TTTTATATTTAAAATATATTAAAAAATAT
Found at i:1780793 original size:14 final size:14
Alignment explanation
Indices: 1780774--1780823 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
1780764 TATATTAAAA
1780774 AATATTTTTATATT
1 AATATTTTTATATT
*
1780788 AATATTTATAT-TT
1 AATATTTTTATATT
1780801 AAATATTTTTATAATT
1 -AATATTTTTAT-ATT
1780817 AA-ATTTT
1 AATATTTT
1780824 AAATAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 2 0.06
14 25 0.81
15 2 0.06
16 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
AATATTTTTATATT
Found at i:1780805 original size:28 final size:28
Alignment explanation
Indices: 1780772--1780840 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
1780762 AATATATTAA
*
1780772 AAAATATTTTTAT-ATT-AATATTTATATT
1 AAAATATTTTTATAATTAAAT-TTTA-AAT
*
1780800 TAAATATTTTTATAATTAAATTTTAAAT
1 AAAATATTTTTATAATTAAATTTTAAAT
1780828 AAAATATTTTTAT
1 AAAATATTTTTAT
1780841 TTATTAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 26 0.72
29 7 0.19
30 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
AAAATATTTTTATAATTAAATTTTAAAT
Found at i:1787404 original size:30 final size:29
Alignment explanation
Indices: 1787370--1787440 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 29
1787360 GAAAATTTTT
1787370 ATTATTTATAAAAATTT-AATTAAATTAATA
1 ATTATTTAT-AAAATTTAAATTAAA-TAATA
*
1787400 ATTA--TAT-AAATTTAAATTAAATAATT
1 ATTATTTATAAAATTTAAATTAAATAATA
1787426 ATTATTTATATAAAT
1 ATTATTTATA-AAAT
1787441 ATTTTTTTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
26 14 0.40
27 7 0.20
28 6 0.17
30 8 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
ATTATTTATAAAATTTAAATTAAATAATA
Found at i:1789989 original size:16 final size:17
Alignment explanation
Indices: 1789965--1790005 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
1789955 ATTTTCTTTC
*
1789965 TTTCCTTTCTTTGTT-T
1 TTTCTTTTCTTTGTTCT
*
1789981 TTTCTTTTCTTTTTTCT
1 TTTCTTTTCTTTGTTCT
1789998 TTTCTTTT
1 TTTCTTTT
1790006 TTATCTTGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (17 bp):
TTTCTTTTCTTTGTTCT
Found at i:1789995 original size:12 final size:11
Alignment explanation
Indices: 1789956--1790007 Score: 59
Period size: 12 Copynumber: 4.4 Consensus size: 11
1789946 TATGTAAAAA
1789956 TTTTCTTTCTT
1 TTTTCTTTCTT
*
1789967 TCCTTTCTTTGTT
1 T--TTTCTTTCTT
1789980 TTTTCTTTTCTT
1 TTTTC-TTTCTT
1789992 TTTTCTTTTCTT
1 TTTTC-TTTCTT
1790004 TTTT
1 TTTT
1790008 ATCTTGCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
11 5 0.14
12 21 0.58
13 10 0.28
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (11 bp):
TTTTCTTTCTT
Found at i:1790591 original size:13 final size:13
Alignment explanation
Indices: 1790561--1790591 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
1790551 TAATATTTAT
1790561 ATATTTAAAAATA
1 ATATTTAAAAATA
1790574 A-ATTTAAAAATA
1 ATATTTAAAAATA
1790586 ATATTT
1 ATATTT
1790592 TTTATTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATATTTAAAAATA
Found at i:1791677 original size:23 final size:23
Alignment explanation
Indices: 1791651--1791694 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1791641 TATTTAAAAA
*
1791651 AATTAATATTTATAT-ATTTTTAT
1 AATTAA-ATTTAAATAATTTTTAT
1791674 AATTAAATTTAAATAATTTTT
1 AATTAAATTTAAATAATTTTT
1791695 TATTAGATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
AATTAAATTTAAATAATTTTTAT
Found at i:1793316 original size:29 final size:29
Alignment explanation
Indices: 1793284--1793352 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 29
1793274 ATTAATATTT
*
1793284 ATATATTTTATAATTA-AATTTAAAATAAA
1 ATATATTTTA-AATAATAATTTAAAATAAA
*
1793313 ATATATTATTAAATAATAATTTAAATTAAA
1 ATATATT-TTAAATAATAATTTAAAATAAA
*
1793343 TTA-ATTTTAA
1 ATATATTTTAA
1793353 TTTTTAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 4 0.11
29 14 0.40
30 17 0.49
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
ATATATTTTAAATAATAATTTAAAATAAA
Found at i:1793923 original size:28 final size:29
Alignment explanation
Indices: 1793861--1793940 Score: 119
Period size: 28 Copynumber: 2.8 Consensus size: 29
1793851 AGTTTTTTGT
1793861 AATAAATATATATATATATATATTTTTAC
1 AATAAATATATATATATATATATTTTTAC
* *
1793890 AATAAATATATATA-AGT-TTTTTTTTTAC
1 AATAAATATATATATA-TATATATTTTTAC
1793918 AATAAATATATATATATATATAT
1 AATAAATATATATATATATATAT
1793941 ATATATATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
28 25 0.57
29 19 0.43
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (29 bp):
AATAAATATATATATATATATATTTTTAC
Found at i:1793928 original size:2 final size:2
Alignment explanation
Indices: 1793923--1793954 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1793913 TTTACAATAA
1793923 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
1793955 GCAGAAGGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1795194 original size:23 final size:23
Alignment explanation
Indices: 1795177--1795222 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1795167 TTATTTTTTG
*
1795177 TTCGAGTCATTTCATATTAATTA
1 TTCGAATCATTTCATATTAATTA
*
1795200 TTTGAATCATTTCATATTCAATT
1 TTCGAATCATTTCATATT-AATT
1795223 TTTTTAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (23 bp):
TTCGAATCATTTCATATTAATTA
Found at i:1796121 original size:32 final size:32
Alignment explanation
Indices: 1796085--1796151 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
1796075 AATTATAAAG
**
1796085 ATTTGAATAAAATTATTAAATTTAAAAAATAA
1 ATTTGAATAAAAAAATTAAATTTAAAAAATAA
** *
1796117 ATTTGAATAAAAAAATTTTATTTTAAAAATAA
1 ATTTGAATAAAAAAATTAAATTTAAAAAATAA
1796149 ATT
1 ATT
1796152 AAATTTTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (32 bp):
ATTTGAATAAAAAAATTAAATTTAAAAAATAA
Found at i:1796277 original size:25 final size:24
Alignment explanation
Indices: 1796248--1796294 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
1796238 CACATCTATA
1796248 TAAATTTAAATATTATT-TTTATATC
1 TAAATTTAAA-ATT-TTATTTATATC
1796273 TAAATTTAAAATTTTATTTATA
1 TAAATTTAAAATTTTATTTATA
1796295 AACTATATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 2 0.10
24 9 0.43
25 10 0.48
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
TAAATTTAAAATTTTATTTATATC
Found at i:1798133 original size:40 final size:40
Alignment explanation
Indices: 1798089--1798167 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
1798079 TTTGATGTCA
* *
1798089 TTAAATTTAATT-TAAATTATTATTTATTTA-ATAAAAATAT
1 TTAAATTTAATTATAAA-TA-TATATATTAATATAAAAATAT
1798129 TTAAATTTAATTATAAATATATATATTAATATAAAAATA
1 TTAAATTTAATTATAAATATATATATTAATATAAAAATA
1798168 ATTTTTAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 8 0.23
40 23 0.66
41 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (40 bp):
TTAAATTTAATTATAAATATATATATTAATATAAAAATAT
Found at i:1798166 original size:20 final size:21
Alignment explanation
Indices: 1798119--1798167 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
1798109 TATTTATTTA
*
1798119 ATAAAAATATTTAAATTTAAT
1 ATAAAAATATATAAATTTAAT
* *
1798140 -TATAAATATATATA-TTAAT
1 ATAAAAATATATAAATTTAAT
1798159 ATAAAAATA
1 ATAAAAATA
1798168 ATTTTTAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAAAAATATATAAATTTAAT
Found at i:1800956 original size:27 final size:26
Alignment explanation
Indices: 1800925--1800982 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
1800915 ATTTTTATTC
*
1800925 ATAAATTAA-AAAATTATAATTATTTAA
1 ATAAATCAATAAAATT-TAATT-TTTAA
*
1800952 ATAAATCAATAAAATTTAATTTTTTA
1 ATAAATCAATAAAATTTAATTTTTAA
1800978 ATAAA
1 ATAAA
1800983 AAAATCGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 9 0.32
27 13 0.46
28 6 0.21
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (26 bp):
ATAAATCAATAAAATTTAATTTTTAA
Found at i:1801574 original size:15 final size:16
Alignment explanation
Indices: 1801556--1801585 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1801546 TATTTAATAA
1801556 ATTAAAATTT-TAAAT
1 ATTAAAATTTATAAAT
1801571 ATTAAAATTTATAAA
1 ATTAAAATTTATAAA
1801586 ATTTTAGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATTAAAATTTATAAAT
Found at i:1802176 original size:10 final size:10
Alignment explanation
Indices: 1802163--1802192 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1802153 AAAAGGAAAC
1802163 TTTTTATTTT
1 TTTTTATTTT
1802173 TTTTTA-TTT
1 TTTTTATTTT
1802182 TTTTTATTTT
1 TTTTTATTTT
1802192 T
1 T
1802193 CAATTGACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTTATTTT
Found at i:1802182 original size:9 final size:9
Alignment explanation
Indices: 1802163--1802192 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
1802153 AAAAGGAAAC
1802163 TTTTTATTTT
1 TTTTTA-TTT
1802173 TTTTTATTT
1 TTTTTATTT
1802182 TTTTTATTT
1 TTTTTATTT
1802191 TT
1 TT
1802193 CAATTGACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 14 0.70
10 6 0.30
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTATTT
Found at i:1803032 original size:2 final size:2
Alignment explanation
Indices: 1803025--1803049 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1803015 CCCACCATAC
1803025 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1803050 CTTTCATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1811249 original size:2 final size:2
Alignment explanation
Indices: 1811242--1811272 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1811232 GGAGAAAGTA
*
1811242 AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1811273 ATCTGAGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1811442 original size:3 final size:3
Alignment explanation
Indices: 1811436--1811461 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1811426 AAAAAAAAAG
1811436 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
1811462 GAACCGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1811853 original size:3 final size:3
Alignment explanation
Indices: 1811838--1811879 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
1811828 GTTGTCAAAA
* *
1811838 AAT AAT TAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1811880 TTTTAATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1812138 original size:20 final size:20
Alignment explanation
Indices: 1812101--1812140 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1812091 ATATTTAGAT
1812101 AATATATTTATAAAAATAAA
1 AATATATTTATAAAAATAAA
*
1812121 AATAT-TTTTTAAATAATAAA
1 AATATATTTATAAA-AATAAA
1812141 TTTAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AATATATTTATAAAAATAAA
Found at i:1812173 original size:17 final size:18
Alignment explanation
Indices: 1812134--1812181 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
1812124 ATTTTTTAAA
1812134 TAATAAATTT-AA-TTAT
1 TAATAAATTTAAATTTAT
1812150 TAAATAAATTTAAATTTAT
1 T-AATAAATTTAAATTTAT
*
1812169 T-ATAAATTAAAAT
1 TAATAAATTTAAAT
1812182 AAAACTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 1 0.04
17 20 0.71
18 2 0.07
19 5 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATAAATTTAAATTTAT
Found at i:1814211 original size:25 final size:25
Alignment explanation
Indices: 1814178--1814228 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
1814168 ACCTTTTAAT
*
1814178 TTATAATTTTGTAA-TACAACTTTTA
1 TTATAA-TTTATAAGTACAACTTTTA
* *
1814203 TTATTATTTATAAGTATAACTTTTA
1 TTATAATTTATAAGTACAACTTTTA
1814228 T
1 T
1814229 CATTTATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (25 bp):
TTATAATTTATAAGTACAACTTTTA
Found at i:1814381 original size:18 final size:18
Alignment explanation
Indices: 1814358--1814424 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
1814348 GAATTACAAT
1814358 TTAATAATAAAATTAATA
1 TTAATAATAAAATTAATA
*
1814376 TTAAT-ATAAAAAATAATA
1 TTAATAAT-AAAATTAATA
* *
1814394 TTTTAATAATATAATGAATTA
1 --TTAATAATAAAATTAA-TA
*
1814415 TGAATAATAA
1 TTAATAATAA
1814425 TAGTAAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
17 2 0.05
18 14 0.37
19 8 0.21
20 10 0.26
21 4 0.11
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (18 bp):
TTAATAATAAAATTAATA
Found at i:1815687 original size:2 final size:2
Alignment explanation
Indices: 1815680--1815711 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1815670 AATTTAAACC
1815680 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
1815712 TACTGCCTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1816504 original size:16 final size:17
Alignment explanation
Indices: 1816483--1816583 Score: 69
Period size: 17 Copynumber: 6.5 Consensus size: 17
1816473 TTACGTCATC
1816483 TTAAATCA-TTTAAATT
1 TTAAATCACTTTAAATT
*
1816499 TTAAATCACTTTTAATT
1 TTAAATCACTTTAAATT
*
1816516 TT--A--A--TT-CATT
1 TTAAATCACTTTAAATT
1816526 TTAAATCA-TTTAAATT
1 TTAAATCACTTTAAATT
*
1816542 TTAAATCACTTTCAATT
1 TTAAATCACTTTAAATT
* *
1816559 TCT-AATCATTTTAAAAT
1 T-TAAATCACTTTAAATT
*
1816576 TCAAATCA
1 TTAAATCA
1816584 ATTACTTTTA
Statistics
Matches: 67, Mismatches: 8, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
10 5 0.07
11 2 0.03
12 1 0.01
13 1 0.01
14 1 0.01
15 3 0.04
16 19 0.28
17 34 0.51
18 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.49
Consensus pattern (17 bp):
TTAAATCACTTTAAATT
Found at i:1816517 original size:17 final size:16
Alignment explanation
Indices: 1816483--1816572 Score: 68
Period size: 16 Copynumber: 5.9 Consensus size: 16
1816473 TTACGTCATC
*
1816483 TTAAATCATTTAAATT
1 TTAAATCATTTTAATT
1816499 TTAAATCACTTTTAATT
1 TTAAATCA-TTTTAATT
*
1816516 TT--A--A--TTCATT
1 TTAAATCATTTTAATT
*
1816526 TTAAATCATTTAAATT
1 TTAAATCATTTTAATT
*
1816542 TTAAATCACTTTCAATT
1 TTAAATCA-TTTTAATT
1816559 TCT-AATCATTTTAA
1 T-TAAATCATTTTAA
1816573 AATTCAAATC
Statistics
Matches: 59, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
10 7 0.12
12 1 0.02
13 1 0.02
14 1 0.02
15 1 0.02
16 25 0.42
17 22 0.37
18 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (16 bp):
TTAAATCATTTTAATT
Found at i:1816530 original size:43 final size:42
Alignment explanation
Indices: 1816469--1816573 Score: 156
Period size: 43 Copynumber: 2.4 Consensus size: 42
1816459 TTGTTTTTAA
* * *
1816469 AATTTTACGTCATCTTAAATCATTTAAATTTTAAATCACTTTT
1 AATTTTA-ATCATTTTAAATCATTTAAATTTTAAATCACTTTC
1816512 AATTTTAATTCATTTTAAATCATTTAAATTTTAAATCACTTTC
1 AATTTTAA-TCATTTTAAATCATTTAAATTTTAAATCACTTTC
1816555 AATTTCTAATCATTTTAAA
1 AATTT-TAATCATTTTAAA
1816574 ATTCAAATCA
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
43 54 0.95
44 3 0.05
ACGTcount: A:0.37, C:0.12, G:0.01, T:0.50
Consensus pattern (42 bp):
AATTTTAATCATTTTAAATCATTTAAATTTTAAATCACTTTC
Found at i:1819398 original size:16 final size:15
Alignment explanation
Indices: 1819338--1819402 Score: 53
Period size: 16 Copynumber: 4.1 Consensus size: 15
1819328 ATAATTTGAT
*
1819338 TTAATTTAAATTATTAA
1 TTAATATAAA-TA-TAA
*
1819355 TTAAATAATAAAAATAA
1 TT-AAT-ATAAATATAA
1819372 TTAA-A-AAATATAA
1 TTAATATAAATATAA
1819385 TTGAATATAAATATAA
1 TT-AATATAAATATAA
1819401 TT
1 TT
1819403 TTTTAAGTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
13 9 0.22
14 3 0.08
15 1 0.03
16 12 0.30
17 7 0.17
18 4 0.10
19 4 0.10
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
TTAATATAAATATAA
Found at i:1819785 original size:14 final size:15
Alignment explanation
Indices: 1819766--1819836 Score: 63
Period size: 17 Copynumber: 4.5 Consensus size: 15
1819756 GCTTGGCTTG
1819766 AAATTT-TTTAATTA
1 AAATTTATTTAATTA
1819780 AAATTTATTTAATTTA
1 AAATTTATTTAA-TTA
*
1819796 AATTATTATTTAATTAA
1 AAAT-TTATTTAATT-A
**
1819813 TAAAAATATTTAATTTA
1 -AAATTTATTTAA-TTA
1819830 AAATTTA
1 AAATTTA
1819837 CTATAAAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
14 6 0.13
15 5 0.11
16 13 0.29
17 17 0.38
18 4 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AAATTTATTTAATTA
Found at i:1820138 original size:33 final size:33
Alignment explanation
Indices: 1820086--1820181 Score: 115
Period size: 33 Copynumber: 2.9 Consensus size: 33
1820076 AATTATAAAG
1820086 TAATGAATTAAACATAATTATTGATAAATTTAAT
1 TAAT-AATTAAACATAATTATTGATAAATTTAAT
* *
1820120 TAATAATTAAATAAAATTACTTG-TAAATTTAAT
1 TAATAATTAAACATAATTA-TTGATAAATTTAAT
* * *
1820153 GAAT-ATTAAACATAATTATTAAAAAATTT
1 TAATAATTAAACATAATTATTGATAAATTT
1820182 CCCAATCATT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
31 2 0.04
32 18 0.34
33 26 0.49
34 7 0.13
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.41
Consensus pattern (33 bp):
TAATAATTAAACATAATTATTGATAAATTTAAT
Found at i:1820403 original size:16 final size:16
Alignment explanation
Indices: 1820384--1820414 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1820374 ATATATTGAA
*
1820384 ATATATTGATATCAAT
1 ATATATTAATATCAAT
1820400 ATATATTAATATCAA
1 ATATATTAATATCAA
1820415 AATAAAAGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (16 bp):
ATATATTAATATCAAT
Found at i:1828384 original size:2 final size:2
Alignment explanation
Indices: 1828377--1828411 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1828367 AACAGTGTAC
1828377 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1828412 CACTTCAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1829091 original size:23 final size:23
Alignment explanation
Indices: 1829057--1829137 Score: 83
Period size: 23 Copynumber: 3.3 Consensus size: 23
1829047 TATTATTTCA
1829057 AAATATTCAAATATTATTTTTAT
1 AAATATTCAAATATTATTTTTAT
* *
1829080 AAATATTTAAATTAACTTAACTATTTCA-
1 AAATATTCAAA-T-A-TT-A-T-TTTTAT
1829108 AAATATTCAAATATTATTTTTAT
1 AAATATTCAAATATTATTTTTAT
1829131 AAATATT
1 AAATATT
1829138 TAGATTAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
22 4 0.09
23 18 0.38
24 2 0.04
25 3 0.06
26 3 0.06
27 2 0.04
28 11 0.23
29 4 0.09
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (23 bp):
AAATATTCAAATATTATTTTTAT
Found at i:1829105 original size:51 final size:50
Alignment explanation
Indices: 1829036--1829145 Score: 184
Period size: 51 Copynumber: 2.2 Consensus size: 50
1829026 ATTTGACCCG
*
1829036 TAAATCTAACTTATTATTTCAAAATATTCAAATATTATTTTTATAAATATT
1 TAAAT-TAACTTACTATTTCAAAATATTCAAATATTATTTTTATAAATATT
1829087 TAAATTAACTTAACTATTTCAAAATATTCAAATATTATTTTTATAAATATT
1 TAAATTAACTT-ACTATTTCAAAATATTCAAATATTATTTTTATAAATATT
*
1829138 TAGATTAA
1 TAAATTAA
1829146 ATCAGACTGA
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
50 6 0.11
51 50 0.89
ACGTcount: A:0.45, C:0.07, G:0.01, T:0.47
Consensus pattern (50 bp):
TAAATTAACTTACTATTTCAAAATATTCAAATATTATTTTTATAAATATT
Found at i:1829821 original size:19 final size:18
Alignment explanation
Indices: 1829777--1829824 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
1829767 TAATTATAGA
1829777 AATAT-ATAAATTTTAAT
1 AATATAATAAATTTTAAT
*
1829794 -ATAAAAATAATATTTTAAT
1 AAT-ATAATAA-ATTTTAAT
1829813 AATATAATAAAT
1 AATATAATAAAT
1829825 AGTAAAATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
16 2 0.08
17 1 0.04
18 6 0.24
19 14 0.56
20 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AATATAATAAATTTTAAT
Found at i:1830031 original size:22 final size:20
Alignment explanation
Indices: 1830001--1830040 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1829991 ATTACAATAA
1830001 CATGGATAATATATATTATATT
1 CATGGATAA-A-ATATTATATT
*
1830023 CATGTATAAAATATTATA
1 CATGGATAAAATATTATA
1830041 ATATTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 1 0.06
22 8 0.47
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (20 bp):
CATGGATAAAATATTATATT
Found at i:1830163 original size:3 final size:3
Alignment explanation
Indices: 1830148--1830185 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
1830138 GTGTTCTCAC
*
1830148 AAT AAT AA- CAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1830186 TGATCTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 1 0.03
3 31 0.97
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1830384 original size:2 final size:2
Alignment explanation
Indices: 1830379--1830412 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1830369 AAAAAAGTAG
1830379 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
1830413 TGCTTAACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1830758 original size:20 final size:20
Alignment explanation
Indices: 1830733--1830780 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1830723 ATAAAATAAT
* *
1830733 TTTTTAAAATTTTATATATA
1 TTTTTAAAATATTATAAATA
*
1830753 TTTTTATAATATTATAAATA
1 TTTTTAAAATATTATAAATA
*
1830773 ATTTTAAA
1 TTTTTAAA
1830781 TTTGAATCGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTTTAAAATATTATAAATA
Found at i:1833845 original size:18 final size:18
Alignment explanation
Indices: 1833826--1833894 Score: 66
Period size: 18 Copynumber: 3.6 Consensus size: 18
1833816 TATTTTTATG
*
1833826 ATATATTATATTAATTTG
1 ATATATTATATTAATTTA
* *
1833844 ATATTTTATATAAATTTTA
1 ATATATTATATTAA-TTTA
*
1833863 ATATATTAATAATTTATTTA
1 ATATATT-AT-ATTAATTTA
1833883 ATATAATTATAT
1 ATAT-ATTATAT
1833895 ATATTTATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
18 12 0.29
19 11 0.27
20 12 0.29
21 6 0.15
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (18 bp):
ATATATTATATTAATTTA
Found at i:1833849 original size:39 final size:36
Alignment explanation
Indices: 1833804--1833915 Score: 110
Period size: 39 Copynumber: 3.2 Consensus size: 36
1833794 ATATCAAATA
*
1833804 TTTATTTAATATTATTTTTATGATATATTATATTAAT
1 TTTATTTAATATTAATTTTAT-ATATATTATATTAAT
* *
1833841 TTGATATTTTATATAAATTTTA-ATATATTA-A-TAA-
1 TT--TATTTAATATTAATTTTATATATATTATATTAAT
*
1833875 TTTATTTAATA-TAATTATATATAT-TTATATTAAT
1 TTTATTTAATATTAATTTTATATATATTATATTAAT
*
1833909 TATATTT
1 TTTATTT
1833916 TATTATATTA
Statistics
Matches: 62, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
31 9 0.15
32 13 0.21
33 3 0.05
34 8 0.13
35 3 0.05
36 1 0.02
37 10 0.16
39 15 0.24
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (36 bp):
TTTATTTAATATTAATTTTATATATATTATATTAAT
Found at i:1833881 original size:32 final size:34
Alignment explanation
Indices: 1833821--1833934 Score: 102
Period size: 32 Copynumber: 3.5 Consensus size: 34
1833811 AATATTATTT
1833821 TTATGATATA-TTATATTAATTTGATATTTTATATAAA
1 TTAT-ATATATTTATATTAA-TT-ATATTTTATAT-AA
* *
1833858 TTTTA-ATATATTA-A-TAATT-TATTTAATATAA
1 TTATATATAT-TTATATTAATTATATTTTATATAA
1833889 TTATATATATTTATATTAATTATATTTTAT-T-A
1 TTATATATATTTATATTAATTATATTTTATATAA
1833921 -TAT-TATATTTATAT
1 TTATATATATTTATAT
1833935 CCTATTTTAA
Statistics
Matches: 67, Mismatches: 4, Indels: 19
0.74 0.04 0.21
Matches are distributed among these distances:
30 11 0.16
31 12 0.18
32 15 0.22
33 6 0.09
34 9 0.13
35 6 0.09
36 2 0.03
37 6 0.09
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (34 bp):
TTATATATATTTATATTAATTATATTTTATATAA
Found at i:1833893 original size:40 final size:40
Alignment explanation
Indices: 1833849--1833934 Score: 95
Period size: 40 Copynumber: 2.1 Consensus size: 40
1833839 ATTTGATATT
1833849 TTATATAAATTT-TAATATATTAATAATTTATT-TAATATAA
1 TTATATAAATTTATAATA-ATT-ATAATTTATTATAATATAA
* * * * *
1833889 TTATATATATTTATATTAATTATATTTTATTATATTATAT
1 TTATATAAATTTATAATAATTATAATTTATTATAATATAA
1833929 TTATAT
1 TTATAT
1833935 CCTATTTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
39 9 0.23
40 26 0.67
41 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (40 bp):
TTATATAAATTTATAATAATTATAATTTATTATAATATAA
Found at i:1833901 original size:19 final size:19
Alignment explanation
Indices: 1833849--1833913 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 19
1833839 ATTTGATATT
*
1833849 TTATATAAATTTTAATAT-A
1 TTATATATA-TTTAATATAA
*
1833868 TTAATAATTTATTTAATATAA
1 TT-AT-ATATATTTAATATAA
1833889 TTATATATATTT-ATATTAA
1 TTATATATATTTAATA-TAA
1833908 TTATAT
1 TTATAT
1833914 TTTATTATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 3 0.08
19 18 0.46
20 12 0.31
21 6 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTATATATATTTAATATAA
Found at i:1833912 original size:15 final size:16
Alignment explanation
Indices: 1833801--1833934 Score: 79
Period size: 16 Copynumber: 8.6 Consensus size: 16
1833791 CACATATCAA
1833801 ATATTTAT-TTAATATT
1 ATATTTATATT-ATATT
*
1833817 ATTTTTATGA-TATATT
1 ATATTTAT-ATTATATT
*
1833833 ATATTAAT-TTGATATT
1 ATATTTATATT-ATATT
* * * * *
1833849 TTATATAAATTTTAAT
1 ATATTTATATTATATT
*
1833865 ATATTAATAATT-TATT
1 ATATTTAT-ATTATATT
*
1833881 -TA-ATATAATTATA-T
1 ATATTTAT-ATTATATT
1833895 ATATTTATATTA-ATT
1 ATATTTATATTATATT
1833910 ATATTT-TATTATATT
1 ATATTTATATTATATT
1833925 ATATTTATAT
1 ATATTTATAT
1833935 CCTATTTTAA
Statistics
Matches: 89, Mismatches: 17, Indels: 24
0.68 0.13 0.18
Matches are distributed among these distances:
14 13 0.15
15 27 0.30
16 43 0.48
17 6 0.07
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (16 bp):
ATATTTATATTATATT
Found at i:1833921 original size:19 final size:18
Alignment explanation
Indices: 1833859--1833925 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 18
1833849 TTATATAAAT
*
1833859 TTTAATATATTAA-TA-A
1 TTTATTATATTAATTATA
1833875 TTTATT-TAATATAATTATA
1 TTTATTAT-AT-TAATTATA
*
1833894 TATATTTATATTAATTATA
1 TTTA-TTATATTAATTATA
1833913 TTTTATTATATTA
1 -TTTATTATATTA
1833926 TATTTATATC
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
15 1 0.02
16 7 0.17
17 3 0.07
18 2 0.05
19 20 0.49
20 7 0.17
21 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTATTATATTAATTATA
Found at i:1834486 original size:20 final size:20
Alignment explanation
Indices: 1834458--1834500 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1834448 ATTAGAGAAT
1834458 TTATAAAAA-AATAAATAAAA
1 TTATAAAAATAA-AAATAAAA
* *
1834478 TTATTAAAATAAATATAAAA
1 TTATAAAAATAAAAATAAAA
1834498 TTA
1 TTA
1834501 AAGATATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TTATAAAAATAAAAATAAAA
Found at i:1837630 original size:18 final size:20
Alignment explanation
Indices: 1837604--1837650 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 20
1837594 AAAAAATAAT
*
1837604 ATTACATAAA-ATATTA-TA
1 ATTATATAAATATATTACTA
1837622 ATTATATAAATTATATTATCTA
1 ATTATATAAA-TATATTA-CTA
1837644 ATTATAT
1 ATTATAT
1837651 CAATTTATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 9 0.38
20 6 0.25
22 9 0.38
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTATATAAATATATTACTA
Found at i:1837637 original size:20 final size:21
Alignment explanation
Indices: 1837614--1837655 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1837604 ATTACATAAA
1837614 ATATTA-TAATTATATAAATT
1 ATATTACTAATTATATAAATT
*
1837634 ATATTATCTAATTATATCAATT
1 ATATTA-CTAATTATATAAATT
1837656 TATCATCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
22 13 0.68
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATTACTAATTATATAAATT
Found at i:1840924 original size:24 final size:23
Alignment explanation
Indices: 1840883--1840928 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
1840873 GTTTCAGATA
**
1840883 AGTTATATATTTTTTTTATAATTG
1 AGTTATATATTTAATTTA-AATTG
*
1840907 AGTTATTTATTTAATTTAAATT
1 AGTTATATATTTAATTTAAATT
1840929 TTAAATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.61
Consensus pattern (23 bp):
AGTTATATATTTAATTTAAATTG
Found at i:1841051 original size:22 final size:22
Alignment explanation
Indices: 1840974--1841053 Score: 63
Period size: 22 Copynumber: 3.4 Consensus size: 22
1840964 CTCATTTAAA
1840974 TTAATATTTAATAATAAAAATATT
1 TTAATA-TTAAT-ATAAAAATATT
* * * *
1840998 TTTAT-TTAAATTTAATTATAAAATA
1 TTAATATT-AATATAA--A-AATATT
1841023 TTAATATTAATATAAAAATATT
1 TTAATATTAATATAAAAATATT
1841045 TTAATATTA
1 TTAATATTA
1841054 TAAATAGTAA
Statistics
Matches: 43, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
22 18 0.42
23 4 0.09
24 5 0.12
25 14 0.33
26 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTAATATTAATATAAAAATATT
Found at i:1841611 original size:16 final size:15
Alignment explanation
Indices: 1841592--1841643 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
1841582 GATATTAAAA
1841592 ATATAAATATTTAATT
1 ATATAAAT-TTTAATT
*
1841608 ATATCAAATTTTATATA
1 ATAT-AAATTTTA-ATT
1841625 ATATAAATTATTAA-T
1 ATATAAATT-TTAATT
1841640 ATAT
1 ATAT
1841644 TAAAATTTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 4 0.13
16 14 0.45
17 13 0.42
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATAAATTTTAATT
Found at i:1841628 original size:33 final size:32
Alignment explanation
Indices: 1841591--1841657 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
1841581 TGATATTAAA
* *
1841591 AATATAAA-TATTTAATTATATCAAATTTTATAT
1 AATATAAATTA-TTAA-TATATCAAAATTTACAT
*
1841624 AATATAAATTATTAATATATTAAAATTTACAT
1 AATATAAATTATTAATATATCAAAATTTACAT
1841656 AA
1 AA
1841658 AAATTATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
32 16 0.53
33 12 0.40
34 2 0.07
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (32 bp):
AATATAAATTATTAATATATCAAAATTTACAT
Found at i:1843813 original size:37 final size:37
Alignment explanation
Indices: 1843763--1843840 Score: 147
Period size: 37 Copynumber: 2.1 Consensus size: 37
1843753 TTCATTTACT
1843763 TCTTTTTTGGCTTGATGTTTAGTTTCGTGATTCTTTG
1 TCTTTTTTGGCTTGATGTTTAGTTTCGTGATTCTTTG
*
1843800 TCTTTTTTGGCTTGATGTTTAGTTTCGTGATTCTTTT
1 TCTTTTTTGGCTTGATGTTTAGTTTCGTGATTCTTTG
1843837 TCTT
1 TCTT
1843841 AACTAGTTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.08, C:0.12, G:0.19, T:0.62
Consensus pattern (37 bp):
TCTTTTTTGGCTTGATGTTTAGTTTCGTGATTCTTTG
Found at i:1846294 original size:25 final size:22
Alignment explanation
Indices: 1846249--1846294 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
1846239 GAATTTTTTT
*
1846249 TATTTATAAATTTTAATATTCA
1 TATTTATAAATTTTAACATTCA
1846271 TATTATATAAATTTTGAGACATTC
1 TATT-TATAAATTTT-A-ACATTC
1846295 GGGTATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 10 0.50
24 1 0.05
25 5 0.25
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.50
Consensus pattern (22 bp):
TATTTATAAATTTTAACATTCA
Found at i:1849148 original size:27 final size:24
Alignment explanation
Indices: 1849091--1849148 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
1849081 AAATTTTTAA
* *
1849091 ATATTAATAATTTTTATTTTATAT
1 ATATTAAGAATTTTTATTTTACAT
*
1849115 ATTTTAAGATATTTTTATATTTACATT
1 ATATTAAGA-ATTTTTAT-TTTACA-T
1849142 ATATTAA
1 ATATTAA
1849149 TTTTTAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 7 0.26
25 8 0.30
26 5 0.19
27 7 0.26
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (24 bp):
ATATTAAGAATTTTTATTTTACAT
Found at i:1849416 original size:19 final size:18
Alignment explanation
Indices: 1849394--1849452 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 18
1849384 AAATAATTAA
1849394 AATAAATTAATATAAATAT
1 AATAAATT-ATATAAATAT
*
1849413 AATAAGAATATATAAATAT
1 AATAA-ATTATATAAATAT
*
1849432 ATTAAAATT-TATATAATAT
1 AAT-AAATTATATA-AATAT
1849451 AA
1 AA
1849453 ATTATTAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 4 0.12
19 25 0.76
20 4 0.12
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
AATAAATTATATAAATAT
Found at i:1849469 original size:32 final size:34
Alignment explanation
Indices: 1849409--1849484 Score: 104
Period size: 32 Copynumber: 2.3 Consensus size: 34
1849399 ATTAATATAA
1849409 ATATAATA-AGAATATATAAATATATTAAAATTT
1 ATATAATATAGAATATATAAATATATTAAAATTT
* *
1849442 ATATAATATA-AAT-TATTAATATTTTAAAATTT
1 ATATAATATAGAATATATAAATATATTAAAATTT
1849474 ATATAAATATA
1 ATAT-AATATA
1849485 TGATAATTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
32 21 0.54
33 17 0.44
34 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (34 bp):
ATATAATATAGAATATATAAATATATTAAAATTT
Found at i:1849503 original size:27 final size:26
Alignment explanation
Indices: 1849419--1849512 Score: 70
Period size: 27 Copynumber: 3.6 Consensus size: 26
1849409 ATATAATAAG
*
1849419 AATATATAAATATATTAA-AATTTATA
1 AATATATAAATATA-TAATAATTTAAA
* *
1849445 TA-ATATAAAT-TATTAATATTTTAAA
1 AATATATAAATATA-TAATAATTTAAA
* *
1849470 ATTTATATAAATATATGATAATTTAAA
1 A-ATATATAAATATATAATAATTTAAA
*
1849497 CAATATA-AAAAATATA
1 -AATATATAAATATATA
1849513 CAAATCTAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
24 6 0.11
25 14 0.26
26 8 0.15
27 22 0.42
28 3 0.06
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (26 bp):
AATATATAAATATATAATAATTTAAA
Found at i:1850619 original size:19 final size:20
Alignment explanation
Indices: 1850591--1850634 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
1850581 AATAAAATTA
1850591 ATAT-ATTTTTAAAATATTT
1 ATATAATTTTTAAAATATTT
*
1850610 -TATAATTTTTAATATATTT
1 ATATAATTTTTAAAATATTT
1850629 ATATAA
1 ATATAA
1850635 AAAAACATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 14 0.64
20 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATAATTTTTAAAATATTT
Found at i:1850628 original size:11 final size:11
Alignment explanation
Indices: 1850588--1850628 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
1850578 AATAATAAAA
1850588 TTAATATATTT
1 TTAATATATTT
*
1850599 TTAAAATA-TT
1 TTAATATATTT
1850609 TT-ATA-ATTT
1 TTAATATATTT
1850618 TTAATATATTT
1 TTAATATATTT
1850629 ATATAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
8 1 0.04
9 6 0.24
10 7 0.28
11 11 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTAATATATTT
Done.