Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 84 of 144
Found at i:19057152 original size:20 final size:20
Alignment explanation
Indices: 19057106--19057208 Score: 73
Period size: 20 Copynumber: 5.0 Consensus size: 20
19057096 AGTTTGAAAC
*
19057106 AATTTTAAAATCAAGTTAAAAT
1 AATTTT-AAA-CAAGTCAAAAT
* *
19057128 GATTTTAAACATGTCAAAAT
1 AATTTTAAACAAGTCAAAAT
* **
19057148 AATTTGAAGTAAGTCAAAAT
1 AATTTTAAACAAGTCAAAAT
* **
19057168 CATTTT-AACACTTCAAAAT
1 AATTTTAAACAAGTCAAAAT
**
19057187 GTTTTTCAAACAAGTCAAAAT
1 AATTTT-AAACAAGTCAAAAT
19057208 A
1 A
19057209 GCTTCAAGCC
Statistics
Matches: 60, Mismatches: 19, Indels: 5
0.71 0.23 0.06
Matches are distributed among these distances:
19 13 0.22
20 28 0.47
21 14 0.23
22 5 0.08
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.34
Consensus pattern (20 bp):
AATTTTAAACAAGTCAAAAT
Found at i:19070859 original size:48 final size:48
Alignment explanation
Indices: 19070788--19070885 Score: 151
Period size: 48 Copynumber: 2.0 Consensus size: 48
19070778 TGTCAACGTA
* * *
19070788 ATTCGTACGTCTGTACTATAATTGCTGAGTCATAAAAAATCAAAGCAT
1 ATTCGTACATCTGTACTACAATTGCTGACTCATAAAAAATCAAAGCAT
* *
19070836 ATTCGTACATCTGTACTGCAATTGCTGACTCATAAAAAATCAAAGTAT
1 ATTCGTACATCTGTACTACAATTGCTGACTCATAAAAAATCAAAGCAT
19070884 AT
1 AT
19070886 CAAGGATTCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (48 bp):
ATTCGTACATCTGTACTACAATTGCTGACTCATAAAAAATCAAAGCAT
Found at i:19072112 original size:15 final size:15
Alignment explanation
Indices: 19072092--19072126 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
19072082 GTCACATAAA
*
19072092 AAAAAGAGAAAAGAG
1 AAAAAGAGAAAAAAG
*
19072107 AAAAAGGGAAAAAAG
1 AAAAAGAGAAAAAAG
19072122 AAAAA
1 AAAAA
19072127 AATATGTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAAAAGAGAAAAAAG
Found at i:19078138 original size:27 final size:28
Alignment explanation
Indices: 19078107--19078200 Score: 88
Period size: 27 Copynumber: 3.5 Consensus size: 28
19078097 AACCAGTGAG
* *
19078107 CCCAGTTTGCCAAGTCC-ACTAGTGAAC
1 CCCAGTTCGCCAAGTCCTTCTAGTGAAC
* * * *
19078134 CCCAGTTCG-TAAGGCCTTCTAG-CAAA
1 CCCAGTTCGCCAAGTCCTTCTAGTGAAC
*
19078160 CCCAGTTCACCAA-TCCTTCTAGTGAAC
1 CCCAGTTCGCCAAGTCCTTCTAGTGAAC
*
19078187 CCCAGTTTGCCAAG
1 CCCAGTTCGCCAAG
19078201 CCCAAACTCC
Statistics
Matches: 50, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
26 23 0.46
27 27 0.54
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (28 bp):
CCCAGTTCGCCAAGTCCTTCTAGTGAAC
Found at i:19082529 original size:4 final size:4
Alignment explanation
Indices: 19082520--19082569 Score: 54
Period size: 4 Copynumber: 13.5 Consensus size: 4
19082510 ATAGACACAA
* *
19082520 TTAT TTAT TTAT TTCT TTA- TTA- TTA- TTAT TT-T TTAT TTTT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
19082564 TTAT TT
1 TTAT TT
19082570 TCATTAAGCA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
3 12 0.30
4 28 0.70
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (4 bp):
TTAT
Found at i:19121227 original size:21 final size:22
Alignment explanation
Indices: 19121201--19121241 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
19121191 TTGCTCTTAC
19121201 TTTCTC-ACAAGTTTATTTTCT
1 TTTCTCTACAAGTTTATTTTCT
* *
19121222 TTTCTCTGCAAGTTTCTTTT
1 TTTCTCTACAAGTTTATTTT
19121242 AACCTTCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.15, C:0.20, G:0.07, T:0.59
Consensus pattern (22 bp):
TTTCTCTACAAGTTTATTTTCT
Found at i:19123219 original size:18 final size:18
Alignment explanation
Indices: 19123193--19123231 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
19123183 ATGCATTTTA
*
19123193 TTTAGTTGTAATTGCATT
1 TTTAGTTGTAACTGCATT
* *
19123211 TTTATTTGTCACTGCATT
1 TTTAGTTGTAACTGCATT
19123229 TTT
1 TTT
19123232 CATATTAGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.10, G:0.13, T:0.59
Consensus pattern (18 bp):
TTTAGTTGTAACTGCATT
Found at i:19123839 original size:6 final size:6
Alignment explanation
Indices: 19123828--19123866 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
19123818 ATGTTGAATG
*
19123828 AGAAAA AGAAAA GGAAAA GAGAAAA AGAGAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA -AGAAAA AGA-AAA AGAAAA A
19123867 AAAGAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 18 0.62
7 11 0.38
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:19123849 original size:19 final size:20
Alignment explanation
Indices: 19123827--19123865 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
19123817 AATGTTGAAT
*
19123827 GAGAAAAAGA-AAAGGAAAA
1 GAGAAAAAGAGAAAAGAAAA
19123846 GAGAAAAAGAGAAAAGAAAA
1 GAGAAAAAGAGAAAAGAAAA
19123866 AAAAGAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (20 bp):
GAGAAAAAGAGAAAAGAAAA
Found at i:19123852 original size:13 final size:14
Alignment explanation
Indices: 19123827--19123873 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
19123817 AATGTTGAAT
19123827 GAGAAAA-AGAAAA
1 GAGAAAAGAGAAAA
19123840 G-GAAAAGAGAAAAA
1 GAGAAAAGAG-AAAA
*
19123854 GAGAAAAGAAAAAA
1 GAGAAAAGAGAAAA
*
19123868 AAGAAA
1 GAGAAA
19123874 TATTGCTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 5 0.17
13 3 0.10
14 14 0.48
15 7 0.24
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (14 bp):
GAGAAAAGAGAAAA
Found at i:19128715 original size:41 final size:38
Alignment explanation
Indices: 19128615--19128718 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
19128605 TTCGAAGCAA
* *
19128615 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
* ** ** * *
19128652 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
19128690 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
19128719 CTCGAGGTCG
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.41
38 10 0.20
40 2 0.04
41 18 0.35
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:19128846 original size:12 final size:13
Alignment explanation
Indices: 19128823--19128860 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
19128813 AATTCATATC
*
19128823 ACTTTCAATTTCA
1 ACTTTCACTTTCA
19128836 AC-TTCACTTTC-
1 ACTTTCACTTTCA
19128847 ACTTTCACTTTCA
1 ACTTTCACTTTCA
19128860 A
1 A
19128861 TTTTGATCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
11 2 0.09
12 17 0.77
13 3 0.14
ACGTcount: A:0.26, C:0.29, G:0.00, T:0.45
Consensus pattern (13 bp):
ACTTTCACTTTCA
Found at i:19139250 original size:17 final size:16
Alignment explanation
Indices: 19139228--19139272 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
19139218 TATGGCAATA
19139228 TTTCTTTTCTTTTCTCT
1 TTTCTTTTCTTTTCT-T
19139245 TTTCTTCTTC-TTTCTT
1 TTTCTT-TTCTTTTCTT
19139261 TTTC-TTTCTTTT
1 TTTCTTTTCTTTT
19139273 GTGATTTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 3 0.12
15 4 0.15
16 5 0.19
17 11 0.42
18 3 0.12
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTCTTTTCTTTTCTT
Found at i:19139271 original size:10 final size:11
Alignment explanation
Indices: 19139228--19139272 Score: 58
Period size: 10 Copynumber: 4.2 Consensus size: 11
19139218 TATGGCAATA
19139228 TTTCTTTTCTT
1 TTTCTTTTCTT
19139239 TTCTCTTTTCTT
1 TT-TCTTTTCTT
*
19139251 CTTC-TTTCTT
1 TTTCTTTTCTT
19139261 TTTC-TTTCTT
1 TTTCTTTTCTT
19139271 TT
1 TT
19139273 GTGATTTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
10 17 0.55
11 4 0.13
12 10 0.32
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:19173359 original size:20 final size:20
Alignment explanation
Indices: 19173334--19173377 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
19173324 TGTCAACGCA
19173334 TTTTTACATTTACTT-TTATC
1 TTTTTACATTTACTTGTT-TC
*
19173354 TTTTTACTTTTACTTGTTTC
1 TTTTTACATTTACTTGTTTC
19173374 TTTT
1 TTTT
19173378 AAATCTTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.14, C:0.14, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTTTACATTTACTTGTTTC
Found at i:19173378 original size:13 final size:14
Alignment explanation
Indices: 19173342--19173378 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
19173332 CATTTTTACA
19173342 TTTACTTTTATCTT
1 TTTACTTTTATCTT
19173356 TTTACTTTTA-CTT
1 TTTACTTTTATCTT
19173369 GTTT-CTTTTA
1 -TTTACTTTTA
19173379 AATCTTATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.14, C:0.14, G:0.03, T:0.70
Consensus pattern (14 bp):
TTTACTTTTATCTT
Found at i:19182517 original size:6 final size:6
Alignment explanation
Indices: 19182506--19182556 Score: 54
Period size: 6 Copynumber: 9.0 Consensus size: 6
19182496 TATCATAAAT
* **
19182506 TTTTTC TTTTTC TTTTTC TTTTTC --TTCC TTTTTC TCATTC -TTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
19182551 TTTTTC
1 TTTTTC
19182557 AAGTGACTGA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
4 3 0.08
5 3 0.08
6 30 0.83
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTTTC
Found at i:19183167 original size:18 final size:18
Alignment explanation
Indices: 19183137--19183191 Score: 53
Period size: 18 Copynumber: 3.0 Consensus size: 18
19183127 TTAACAAAAG
19183137 AAATGCAAG-GACAAAATA
1 AAATGC-AGTGACAAAATA
19183155 AAATGCAGTGACAATAAATAA
1 AAATGCAGTGAC-A-AAAT-A
19183176 AAATGCA-TG-CAAAATA
1 AAATGCAGTGACAAAATA
19183192 TCTATAGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
16 1 0.03
17 6 0.18
18 10 0.30
19 2 0.06
20 6 0.18
21 8 0.24
ACGTcount: A:0.58, C:0.11, G:0.15, T:0.16
Consensus pattern (18 bp):
AAATGCAGTGACAAAATA
Found at i:19183191 original size:21 final size:20
Alignment explanation
Indices: 19183150--19183191 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
19183140 TGCAAGGACA
*
19183150 AAATAAAATGCAGTGACAAT
1 AAATAAAATGCAGTGAAAAT
19183170 AAATAAAAATGCA-TGCAAAAT
1 AAAT-AAAATGCAGTG-AAAAT
19183191 A
1 A
19183192 TCTATAGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.60, C:0.10, G:0.12, T:0.19
Consensus pattern (20 bp):
AAATAAAATGCAGTGAAAAT
Found at i:19191451 original size:22 final size:22
Alignment explanation
Indices: 19191407--19191451 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
19191397 AATAGTTAAT
* *
19191407 ATTGTCAATGCAATCAAAGTTA
1 ATTGTCAAAGCAATCAAAATTA
19191429 ATTGTCAAAGCAA-CAAAAATTA
1 ATTGTCAAAGCAATC-AAAATTA
19191451 A
1 A
19191452 ATCAAAGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.49, C:0.13, G:0.11, T:0.27
Consensus pattern (22 bp):
ATTGTCAAAGCAATCAAAATTA
Found at i:19198478 original size:14 final size:14
Alignment explanation
Indices: 19198459--19198492 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
19198449 GATTACTTTG
*
19198459 ATTCTTATTTGATT
1 ATTCTTATATGATT
*
19198473 ATTCTTATATGTTT
1 ATTCTTATATGATT
19198487 ATTCTT
1 ATTCTT
19198493 GAACTTAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.09, G:0.06, T:0.65
Consensus pattern (14 bp):
ATTCTTATATGATT
Found at i:19207889 original size:187 final size:187
Alignment explanation
Indices: 19207574--19207948 Score: 678
Period size: 187 Copynumber: 2.0 Consensus size: 187
19207564 TTGCTTCATA
*
19207574 ATGAATGGATAGTAGCAATCTTTGAATCTTGCACTACCTTGCTAATTGCAGCGACAATGTATTAA
1 ATGAATGGATAGTAGCAATCTTTGAATCTTGCACTACCTTGCCAATTGCAGCGACAATGTATTAA
19207639 TAAGGAACACTCCAATGTGAGTGCATTGTGACTTATCAAGGGAGAACACTCCACTGCATGTGTTA
66 TAAGGAACACTCCAATGTGAGTGCATTGTGACTTATCAAGGGAGAACACTCCACTGCATGTGTTA
* *
19207704 GAAATATCATCTAGCTAAAGGCTGTCACTGTAAGAGTGTGTGTCAACACAATTACAT
131 GAAATATCATCTAGCCAAAGACTGTCACTGTAAGAGTGTGTGTCAACACAATTACAT
19207761 ATGAATGGATAGTAGCAATCTTTGAATCTTGCACTACCTTGCCAATTGCAGCGACAATGTATTAA
1 ATGAATGGATAGTAGCAATCTTTGAATCTTGCACTACCTTGCCAATTGCAGCGACAATGTATTAA
* *
19207826 TAAGGAACACTCCAATGTGAGTGGATTGTGACTTATCAAGGGAGAACACTCCATTGCATGTGTTA
66 TAAGGAACACTCCAATGTGAGTGCATTGTGACTTATCAAGGGAGAACACTCCACTGCATGTGTTA
* * *
19207891 GAAATATCATCTAGCCGAAGACTGTCACTGTAAGAGTGTGTGTCAGCGCAATTACAT
131 GAAATATCATCTAGCCAAAGACTGTCACTGTAAGAGTGTGTGTCAACACAATTACAT
19207948 A
1 A
19207949 CCTCTTGGGG
Statistics
Matches: 180, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
187 180 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (187 bp):
ATGAATGGATAGTAGCAATCTTTGAATCTTGCACTACCTTGCCAATTGCAGCGACAATGTATTAA
TAAGGAACACTCCAATGTGAGTGCATTGTGACTTATCAAGGGAGAACACTCCACTGCATGTGTTA
GAAATATCATCTAGCCAAAGACTGTCACTGTAAGAGTGTGTGTCAACACAATTACAT
Found at i:19208056 original size:6 final size:6
Alignment explanation
Indices: 19208045--19208086 Score: 59
Period size: 6 Copynumber: 6.8 Consensus size: 6
19208035 ATGTTGAATG
19208045 AGAAAA AG-AAA AGAAAA AGAGAAA AGAGAAA AGAAAA AGAAA
1 AGAAAA AGAAAA AGAAAA AGA-AAA AGA-AAA AGAAAA AGAAA
19208087 TATTGCTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 5 0.15
6 16 0.47
7 13 0.38
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:19208076 original size:20 final size:19
Alignment explanation
Indices: 19208044--19208084 Score: 73
Period size: 20 Copynumber: 2.1 Consensus size: 19
19208034 AATGTTGAAT
19208044 GAGAAAAAGAAAAGAAAAA
1 GAGAAAAAGAAAAGAAAAA
19208063 GAGAAAAGAGAAAAGAAAAA
1 GAGAAAA-AGAAAAGAAAAA
19208083 GA
1 GA
19208085 AATATTGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (19 bp):
GAGAAAAAGAAAAGAAAAA
Found at i:19215593 original size:8 final size:8
Alignment explanation
Indices: 19215580--19215661 Score: 51
Period size: 8 Copynumber: 9.2 Consensus size: 8
19215570 CAATAAATAA
19215580 ATTTTTAT
1 ATTTTTAT
19215588 ATTTTTAT
1 ATTTTTAT
19215596 AATTTATTAGT
1 -ATTT-TTA-T
19215607 -TTTTTAT
1 ATTTTTAT
19215614 AAAGTTTTTAAT
1 --A-TTTTT-AT
19215626 ATTTTTA-
1 ATTTTTAT
19215633 ACTTTTTATTT
1 A-TTTTTA--T
19215644 ATTTTTAT
1 ATTTTTAT
*
19215652 AATTTTAT
1 ATTTTTAT
19215660 AT
1 AT
19215662 AAATTTTAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 24
0.70 0.02 0.28
Matches are distributed among these distances:
7 2 0.03
8 27 0.45
9 12 0.20
10 10 0.17
11 7 0.12
12 2 0.03
ACGTcount: A:0.29, C:0.01, G:0.02, T:0.67
Consensus pattern (8 bp):
ATTTTTAT
Found at i:19215600 original size:9 final size:9
Alignment explanation
Indices: 19215579--19215801 Score: 93
Period size: 9 Copynumber: 23.8 Consensus size: 9
19215569 ACAATAAATA
19215579 AATTTTTAT
1 AATTTTTAT
19215588 -ATTTTTAT
1 AATTTTTAT
19215596 AATTTATTAGT
1 AATTT-TTA-T
19215607 --TTTTTAT
1 AATTTTTAT
19215614 AAAGTTTTTA-
1 -AA-TTTTTAT
19215624 ATATTTTTA-
1 A-ATTTTTAT
*
19215633 ACTTTTTATT
1 AATTTTTA-T
*
19215643 TATTTTTAT
1 AATTTTTAT
19215652 AATTTTATAT
1 AATTTT-TAT
* *
19215662 AAATTTTAA
1 AATTTTTAT
*
19215671 AACTGTTGTA-
1 AA-T-TTTTAT
19215681 ATATTTTTAT
1 A-ATTTTTAT
* *
19215691 TATTTTTTT
1 AATTTTTAT
19215700 AACTTTTTAT
1 AA-TTTTTAT
*
19215710 AATTTATTAA
1 AATTT-TTAT
*
19215720 AATATTTAT
1 AATTTTTAT
*
19215729 AAGATTTTAT
1 AA-TTTTTAT
*
19215739 AAATTTTAT
1 AATTTTTAT
*
19215748 AAGTTTATAT
1 AA-TTTTTAT
**
19215758 AAATTTCCA-
1 -AATTTTTAT
19215767 ATATTTTTAT
1 A-ATTTTTAT
*
19215777 GATTTTTTAT
1 -AATTTTTAT
*
19215787 AACTTTTAT
1 AATTTTTAT
19215796 -ATTTTT
1 AATTTTT
19215802 CATTAGAAAA
Statistics
Matches: 163, Mismatches: 28, Indels: 47
0.68 0.12 0.20
Matches are distributed among these distances:
7 1 0.01
8 23 0.14
9 66 0.40
10 58 0.36
11 15 0.09
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (9 bp):
AATTTTTAT
Found at i:19215668 original size:19 final size:19
Alignment explanation
Indices: 19215646--19215763 Score: 68
Period size: 19 Copynumber: 6.2 Consensus size: 19
19215636 TTTTATTTAT
19215646 TTTTATAATTTTATATAAA
1 TTTTATAATTTTATATAAA
* *
19215665 TTTTAAAACTGTTGTA-AT-AT
1 TTTTATAA-T-TT-TATATAAA
* * *
19215685 TTTTATTATTTT-TTTAACT
1 TTTTATAATTTTATATAA-A
19215704 TTTTATAA-TTTAT-TAAAA
1 TTTTATAATTTTATAT-AAA
*
19215722 TATTTATAAGATTT-TATAAA
1 T-TTTATAA-TTTTATATAAA
*
19215742 TTTTATAAGTTTATATAAA
1 TTTTATAATTTTATATAAA
19215761 TTT
1 TTT
19215764 CCAATATTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 26
0.70 0.07 0.23
Matches are distributed among these distances:
17 2 0.03
18 11 0.14
19 42 0.54
20 13 0.17
21 8 0.10
22 2 0.03
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (19 bp):
TTTTATAATTTTATATAAA
Found at i:19215696 original size:48 final size:48
Alignment explanation
Indices: 19215635--19215763 Score: 129
Period size: 48 Copynumber: 2.7 Consensus size: 48
19215625 TATTTTTAAC
* *
19215635 TTTTTATTTATTTTTATAATTTTATATAAATTTTAAAACT-GTTGTAATA
1 TTTTTA-TTATTTTTATAATTTTATATAAATTTTAAAA-TAGTTATAAGA
* * *
19215684 TTTTTATTATTTTTTTAACTTTT-TATAATTTATTAAAATATTTATAAGA
1 TTTTTATTATTTTTATAA-TTTTATATAAATT-TTAAAATAGTTATAAGA
* * *
19215733 -TTTTATAAATTTTATAAGTTTATATAAATTT
1 TTTTTATTATTTTTATAATTTTATATAAATTT
19215764 CCAATATTTT
Statistics
Matches: 66, Mismatches: 10, Indels: 10
0.77 0.12 0.12
Matches are distributed among these distances:
47 4 0.06
48 40 0.61
49 22 0.33
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.60
Consensus pattern (48 bp):
TTTTTATTATTTTTATAATTTTATATAAATTTTAAAATAGTTATAAGA
Found at i:19215739 original size:10 final size:9
Alignment explanation
Indices: 19215704--19215763 Score: 59
Period size: 10 Copynumber: 6.3 Consensus size: 9
19215694 TTTTTTAACT
*
19215704 TTTTATAAT
1 TTTTATAAA
19215713 TTATTA-AAA
1 TT-TTATAAA
19215722 TATTTATAAGA
1 T-TTTATAA-A
19215733 TTTTATAAA
1 TTTTATAAA
*
19215742 TTTTATAAG
1 TTTTATAAA
19215751 TTTATATAAA
1 TTT-TATAAA
19215761 TTT
1 TTT
19215764 CCAATATTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
9 20 0.47
10 21 0.49
11 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (9 bp):
TTTTATAAA
Found at i:19221785 original size:21 final size:22
Alignment explanation
Indices: 19221756--19221797 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
19221746 GATGACGATA
19221756 ATATGTTTACTTACTTTTTAAC
1 ATATGTTTACTTACTTTTTAAC
* *
19221778 ATAT-TTTATTTTCTTTTTAA
1 ATATGTTTACTTACTTTTTAA
19221798 TTTAATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.26, C:0.10, G:0.02, T:0.62
Consensus pattern (22 bp):
ATATGTTTACTTACTTTTTAAC
Found at i:19225560 original size:23 final size:23
Alignment explanation
Indices: 19225534--19225586 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
19225524 CTAATTCATA
*
19225534 TTTTTCTATTGCTTTTGGACTAC
1 TTTTTCTATTGATTTTGGACTAC
**
19225557 TTTTTCTATTGATTTTGGACTGT
1 TTTTTCTATTGATTTTGGACTAC
19225580 TTTTTCT
1 TTTTTCT
19225587 TTTTTTGATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.11, C:0.13, G:0.13, T:0.62
Consensus pattern (23 bp):
TTTTTCTATTGATTTTGGACTAC
Found at i:19232199 original size:22 final size:23
Alignment explanation
Indices: 19232169--19232211 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
19232159 TAAAGTGGGT
19232169 CATGCAAATTAAATTAATTAAAG
1 CATGCAAATTAAATTAATTAAAG
* *
19232192 CATG-AAATTATATTATTTAA
1 CATGCAAATTAAATTAATTAA
19232212 TGGACATGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (23 bp):
CATGCAAATTAAATTAATTAAAG
Found at i:19233898 original size:5 final size:5
Alignment explanation
Indices: 19233888--19233916 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
19233878 CAATTTGGTT
19233888 TTTTA TTTTA TTTTA -TTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
19233917 CTAACTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:19237326 original size:18 final size:18
Alignment explanation
Indices: 19237300--19237358 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
19237290 CCCAGATAAT
* *
19237300 ATGCGATCACATGACCAG
1 ATGCAATCACATAACCAG
* *
19237318 ATGCAATCACAAAATCAG
1 ATGCAATCACATAACCAG
* *
19237336 ATGCATTCATATAACCAG
1 ATGCAATCACATAACCAG
19237354 ATGCA
1 ATGCA
19237359 GCCACAAGCT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (18 bp):
ATGCAATCACATAACCAG
Found at i:19242881 original size:21 final size:22
Alignment explanation
Indices: 19242843--19242883 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
19242833 CCCAAAAATA
19242843 AATTTTTATTCTGCTTTTAATT
1 AATTTTTATTCTGCTTTTAATT
19242865 AATTTTT-TTCATG-TTTTAA
1 AATTTTTATTC-TGCTTTTAA
19242884 CATTTATAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.24, C:0.07, G:0.05, T:0.63
Consensus pattern (22 bp):
AATTTTTATTCTGCTTTTAATT
Found at i:19244873 original size:15 final size:15
Alignment explanation
Indices: 19244855--19244884 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19244845 CACTTCTCAA
19244855 ATCATTCCTTCATTC
1 ATCATTCCTTCATTC
*
19244870 ATCATTTCTTCATTC
1 ATCATTCCTTCATTC
19244885 CTCTCTCACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.30, G:0.00, T:0.50
Consensus pattern (15 bp):
ATCATTCCTTCATTC
Found at i:19246745 original size:9 final size:9
Alignment explanation
Indices: 19246733--19246760 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
19246723 TGTAACTATC
19246733 CTTTCAACT
1 CTTTCAACT
19246742 CTTTCAACT
1 CTTTCAACT
19246751 CTTTCAACT
1 CTTTCAACT
19246760 C
1 C
19246761 AGTAGGAGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.36, G:0.00, T:0.43
Consensus pattern (9 bp):
CTTTCAACT
Found at i:19249336 original size:17 final size:17
Alignment explanation
Indices: 19249312--19249357 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
19249302 ATGGAAATGA
**
19249312 AATGACAATGTAGATGT
1 AATGACAATAAAGATGT
*
19249329 AGTGACAATAAAGATGT
1 AATGACAATAAAGATGT
19249346 AATGACAATAAA
1 AATGACAATAAA
19249358 AATGCAGGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.50, C:0.07, G:0.20, T:0.24
Consensus pattern (17 bp):
AATGACAATAAAGATGT
Found at i:19249821 original size:15 final size:17
Alignment explanation
Indices: 19249793--19249825 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
19249783 GACAGTAGGT
19249793 TCTTCTCTTATCTCTTC
1 TCTTCTCTTATCTCTTC
19249810 TCTT-TCTT-TCTCTTC
1 TCTTCTCTTATCTCTTC
19249825 T
1 T
19249826 TGTTCCTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 4 0.25
17 4 0.25
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.64
Consensus pattern (17 bp):
TCTTCTCTTATCTCTTC
Found at i:19260599 original size:21 final size:21
Alignment explanation
Indices: 19260575--19260615 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
19260565 TAGTGCAGAC
19260575 TTTTACCGATACAAGTGACAT
1 TTTTACCGATACAAGTGACAT
*
19260596 TTTTACCGATACATGTGACA
1 TTTTACCGATACAAGTGACA
19260616 CTTCAACTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (21 bp):
TTTTACCGATACAAGTGACAT
Found at i:19262648 original size:23 final size:24
Alignment explanation
Indices: 19262621--19262667 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
19262611 AACTATTCAT
19262621 TTTATCTTA-ATTTGC-TATGACAA
1 TTTATCTTATATTTGCGT-TGACAA
*
19262644 TTTATTTTATATTTGCGTTGACAA
1 TTTATCTTATATTTGCGTTGACAA
19262668 ATTAACTCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 12 0.57
25 1 0.05
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.51
Consensus pattern (24 bp):
TTTATCTTATATTTGCGTTGACAA
Found at i:19268951 original size:17 final size:17
Alignment explanation
Indices: 19268929--19268965 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
19268919 GTCATTGCAT
19268929 TTTTATTTGTCACTACA
1 TTTTATTTGTCACTACA
* *
19268946 TTTTATTTGTTAGTACA
1 TTTTATTTGTCACTACA
19268963 TTT
1 TTT
19268966 GCATTGTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.08, T:0.59
Consensus pattern (17 bp):
TTTTATTTGTCACTACA
Found at i:19277271 original size:21 final size:20
Alignment explanation
Indices: 19277245--19277304 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
19277235 AATAGTGCAA
*
19277245 ACTTCTACGGATACAAGTGAC
1 ACTTCTAC-GATACAAGTAAC
*
19277266 AGTTCTATCGATACAAGTAAC
1 ACTTCTA-CGATACAAGTAAC
*
19277287 ACTTCTACTGAAACAAGT
1 ACTTCTAC-GATACAAGT
19277305 CTTACTTCTG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.03
21 31 0.94
22 1 0.03
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.27
Consensus pattern (20 bp):
ACTTCTACGATACAAGTAAC
Found at i:19284763 original size:25 final size:26
Alignment explanation
Indices: 19284719--19284768 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
19284709 TGAAAAATCA
19284719 AAAAGAAAGAAACGATAGT-AGAAAT
1 AAAAGAAAGAAACGATAGTAAGAAAT
19284744 AAAAGAAA-AAATC-ATGAGTAAGAAA
1 AAAAGAAAGAAA-CGAT-AGTAAGAAA
19284769 ATATATGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
24 5 0.23
25 12 0.55
26 5 0.23
ACGTcount: A:0.66, C:0.04, G:0.18, T:0.12
Consensus pattern (26 bp):
AAAAGAAAGAAACGATAGTAAGAAAT
Found at i:19287210 original size:21 final size:22
Alignment explanation
Indices: 19287184--19287231 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
19287174 CCCTTTTAAT
*
19287184 GGTATCACGATATCC-TCTCTG
1 GGTATCACAATATCCTTCTCTG
* *
19287205 GGTATCGCAATATCCTTTTCTG
1 GGTATCACAATATCCTTCTCTG
19287227 GGTAT
1 GGTAT
19287232 TGTGATACCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.38
Consensus pattern (22 bp):
GGTATCACAATATCCTTCTCTG
Found at i:19287446 original size:21 final size:21
Alignment explanation
Indices: 19287405--19287447 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
19287395 TAGTTTTAGG
**
19287405 TTTAGTTTTCTCTAGGTTTTT
1 TTTAGTTTTCTCTAGCATTTT
19287426 TTTAGTTTTTCTCTA-CATTTT
1 TTTAG-TTTTCTCTAGCATTTT
19287447 T
1 T
19287448 CTAGGGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.12, C:0.12, G:0.09, T:0.67
Consensus pattern (21 bp):
TTTAGTTTTCTCTAGCATTTT
Found at i:19287446 original size:22 final size:21
Alignment explanation
Indices: 19287405--19287447 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
19287395 TAGTTTTAGG
**
19287405 TTTAGTTTTCTCTAGGTTTTT
1 TTTAGTTTTCTCTACATTTTT
19287426 TTTAGTTTTTCTCTACATTTTT
1 TTTAG-TTTTCTCTACATTTTT
19287448 CTAGGGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.12, C:0.12, G:0.09, T:0.67
Consensus pattern (21 bp):
TTTAGTTTTCTCTACATTTTT
Found at i:19288714 original size:34 final size:33
Alignment explanation
Indices: 19288610--19288714 Score: 94
Period size: 34 Copynumber: 3.2 Consensus size: 33
19288600 ATATGTGTGG
* *
19288610 CCCATGTGCGAACCCCTAGGTTAGTATGTGCGAA
1 CCCATGTGCAAACCCCTA-GTTAGTATGTGCAAA
* *
19288644 CCCTTGTGAAAACCACC----T-GTATGTGCAAA
1 CCCATGTGCAAACC-CCTAGTTAGTATGTGCAAA
* *
19288673 CCTATGTGCAAACCCCTATGTTAGTATGTGCTAA
1 CCCATGTGCAAACCCCTA-GTTAGTATGTGCAAA
19288707 CCCATGTG
1 CCCATGTG
19288715 TGAGCCCCTT
Statistics
Matches: 55, Mismatches: 9, Indels: 14
0.71 0.12 0.18
Matches are distributed among these distances:
28 2 0.04
29 21 0.38
30 1 0.02
33 1 0.02
34 28 0.51
35 2 0.04
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.27
Consensus pattern (33 bp):
CCCATGTGCAAACCCCTAGTTAGTATGTGCAAA
Found at i:19294147 original size:30 final size:30
Alignment explanation
Indices: 19294109--19294249 Score: 167
Period size: 30 Copynumber: 4.7 Consensus size: 30
19294099 CAGGCTCTTC
* *
19294109 AAGTCAGTCACCCATTGCTCAGTCATCTCT
1 AAGTCAGTCACCTAGTGCTCAGTCATCTCT
* * *
19294139 AAGCCAGTCACCTAGTCCTCAGTCATCTCC
1 AAGTCAGTCACCTAGTGCTCAGTCATCTCT
*
19294169 AAGTCAGTCACCTAGTGCTCAGTCTTCTCT
1 AAGTCAGTCACCTAGTGCTCAGTCATCTCT
* ** *
19294199 AAGTCAATCACCTAGTGCTCAACCTTCT-T
1 AAGTCAGTCACCTAGTGCTCAGTCATCTCT
*
19294228 CAAGTCAGTCACCTAGTCCTCA
1 -AAGTCAGTCACCTAGTGCTCA
19294250 AACTTCTCCT
Statistics
Matches: 96, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
29 1 0.01
30 95 0.99
ACGTcount: A:0.24, C:0.34, G:0.13, T:0.28
Consensus pattern (30 bp):
AAGTCAGTCACCTAGTGCTCAGTCATCTCT
Found at i:19294257 original size:60 final size:60
Alignment explanation
Indices: 19294104--19294249 Score: 193
Period size: 60 Copynumber: 2.4 Consensus size: 60
19294094 TTTGTCAGGC
* * * * **
19294104 TCTTCAAGTCAGTCACCCATTGCTCAGTCATCTCTAAGCCAGTCACCTAGTCCTCAGTCA
1 TCTTCAAGTCAGTCACCTAGTGCTCAGTCTTCTCTAAGCCAATCACCTAGTCCTCAACCA
* * * *
19294164 TCTCCAAGTCAGTCACCTAGTGCTCAGTCTTCTCTAAGTCAATCACCTAGTGCTCAACCT
1 TCTTCAAGTCAGTCACCTAGTGCTCAGTCTTCTCTAAGCCAATCACCTAGTCCTCAACCA
*
19294224 TCTTCAAGTCAGTCACCTAGTCCTCA
1 TCTTCAAGTCAGTCACCTAGTGCTCA
19294250 AACTTCTCCT
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 74 1.00
ACGTcount: A:0.23, C:0.34, G:0.13, T:0.29
Consensus pattern (60 bp):
TCTTCAAGTCAGTCACCTAGTGCTCAGTCTTCTCTAAGCCAATCACCTAGTCCTCAACCA
Found at i:19298024 original size:18 final size:18
Alignment explanation
Indices: 19298001--19298040 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
19297991 TTACTAACTT
*
19298001 AAAATTTTAAAAAATTTA
1 AAAATTTTAAAAAATCTA
*
19298019 AAAATTTTAAAAGATCTA
1 AAAATTTTAAAAAATCTA
19298037 AAAA
1 AAAA
19298041 AAAATTCCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (18 bp):
AAAATTTTAAAAAATCTA
Found at i:19298224 original size:18 final size:17
Alignment explanation
Indices: 19298203--19298243 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
19298193 CAAAAAATAT
*
19298203 TTTTAGGATAAGAAACAC
1 TTTTAAGATAA-AAACAC
*
19298221 TTTTAAGATAAAAACAT
1 TTTTAAGATAAAAACAC
19298238 TTTTAA
1 TTTTAA
19298244 ACAATCTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (17 bp):
TTTTAAGATAAAAACAC
Found at i:19298241 original size:17 final size:17
Alignment explanation
Indices: 19298195--19298243 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
19298185 TTTTGGGACA
* *
19298195 AAAAATATTTTTAGGAT
1 AAAAACATTTTTAAGAT
*
19298212 AAGAAACACTTTTAAGAT
1 AA-AAACATTTTTAAGAT
19298230 AAAAACATTTTTAA
1 AAAAACATTTTTAA
19298244 ACAATCTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (17 bp):
AAAAACATTTTTAAGAT
Found at i:19308587 original size:20 final size:20
Alignment explanation
Indices: 19308559--19308597 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19308549 CCATGACTTT
*
19308559 CATTATTAAGTTTAATTAAC
1 CATTATTAAATTTAATTAAC
*
19308579 CATTTTTAAATTTAATTAA
1 CATTATTAAATTTAATTAA
19308598 ACCTATTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (20 bp):
CATTATTAAATTTAATTAAC
Found at i:19308606 original size:20 final size:20
Alignment explanation
Indices: 19308564--19308608 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
19308554 ACTTTCATTA
* *
19308564 TTAAGTTTAATTAACCATTT
1 TTAAATTTAATTAACCATAT
19308584 TTAAATTTAATTAAACC-TAT
1 TTAAATTTAATT-AACCATAT
19308604 TTAAA
1 TTAAA
19308609 AGTAATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (20 bp):
TTAAATTTAATTAACCATAT
Found at i:19311395 original size:7 final size:7
Alignment explanation
Indices: 19311383--19311420 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
19311373 GAAGTCTCTC
*
19311383 AAAGGGG
1 AAAGGAG
*
19311390 AAAGGGG
1 AAAGGAG
19311397 AAAGGAG
1 AAAGGAG
19311404 AAAGGAG
1 AAAGGAG
19311411 AAAGGAG
1 AAAGGAG
19311418 AAA
1 AAA
19311421 AGTTTTGGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (7 bp):
AAAGGAG
Found at i:19311992 original size:24 final size:24
Alignment explanation
Indices: 19311943--19311992 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
19311933 TAAAGTGGTT
*
19311943 TATTATTTAAATATATCAATGCAA
1 TATTATTTAAATATATCAATGAAA
* *
19311967 TATTTTTTAAATTTAT-AATTGAAA
1 TATTATTTAAATATATCAA-TGAAA
19311991 TA
1 TA
19311993 GATTATTAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (24 bp):
TATTATTTAAATATATCAATGAAA
Found at i:19331370 original size:26 final size:24
Alignment explanation
Indices: 19331324--19331382 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 24
19331314 TATATTTTTA
19331324 TTATATTATTTTAATATTTAATAATT
1 TTATA-TATTTTAATATTTAA-AATT
* *
19331350 TTATATATTTTTATTTATTAAAATT
1 TTATATATTTTAATAT-TTAAAATT
*
19331375 TTTTATAT
1 TTATATAT
19331383 AGTAATCTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 20 0.69
26 9 0.31
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TTATATATTTTAATATTTAAAATT
Found at i:19331847 original size:13 final size:13
Alignment explanation
Indices: 19331814--19331850 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
19331804 ATTTATACAT
19331814 TTTAAAAAATTTA
1 TTTAAAAAATTTA
19331827 -TTAAAAAATTTA
1 TTTAAAAAATTTA
*
19331839 TTTATAAAATTT
1 TTTAAAAAATTT
19331851 TTAATCGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TTTAAAAAATTTA
Found at i:19332624 original size:30 final size:30
Alignment explanation
Indices: 19332590--19332651 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
19332580 AAAATAATCT
*
19332590 TTAAATTAT-GAAAAAATTATATTTTGATTA
1 TTAAATTATCG-AAAAATAATATTTTGATTA
**
19332620 TTAAATTATCGAATTATAATATTTTGATTA
1 TTAAATTATCGAAAAATAATATTTTGATTA
19332650 TT
1 TT
19332652 TTTTTATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (30 bp):
TTAAATTATCGAAAAATAATATTTTGATTA
Found at i:19332822 original size:18 final size:19
Alignment explanation
Indices: 19332799--19332834 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
19332789 ATTTAGAAAA
19332799 AAAATTATCTA-AAATTTT
1 AAAATTATCTAGAAATTTT
19332817 AAAATTATCTAGAAATTT
1 AAAATTATCTAGAAATTT
19332835 ATTTTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (19 bp):
AAAATTATCTAGAAATTTT
Found at i:19346962 original size:19 final size:23
Alignment explanation
Indices: 19346916--19346963 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
19346906 TTTTTCTGTT
19346916 TTATTTTTATTCAAATTATTTAA
1 TTATTTTTATTCAAATTATTTAA
19346939 TTATTTTTA-T-AAA-TATTT-A
1 TTATTTTTATTCAAATTATTTAA
19346958 TTATTT
1 TTATTT
19346964 ATTTTTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.28
20 5 0.20
21 3 0.12
22 1 0.04
23 9 0.36
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (23 bp):
TTATTTTTATTCAAATTATTTAA
Found at i:19346965 original size:23 final size:24
Alignment explanation
Indices: 19346915--19346970 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 24
19346905 TTTTTTCTGT
19346915 TTTATTTTTATTCAAATTATTTAA
1 TTTATTTTTATTCAAATTATTTAA
19346939 -TTATTTTTA-T-AAA-TATTTATTA
1 TTTATTTTTATTCAAATTATTTA--A
19346961 TTTATTTTTA
1 TTTATTTTTA
19346971 ATTAAATCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
20 6 0.21
21 3 0.10
22 2 0.07
23 18 0.62
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (24 bp):
TTTATTTTTATTCAAATTATTTAA
Found at i:19349316 original size:31 final size:29
Alignment explanation
Indices: 19349267--19349338 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 29
19349257 CTATTCACTT
*
19349267 AAAA-AATATTAAAAAATTAATTAAATTA-TA
1 AAAATAATA-TAAAAAATTAACT--ATTATTA
19349297 AAAATAATATAAAATAATTAACTATTATTA
1 AAAATAATATAAAA-AATTAACTATTATTA
19349327 AAAATAAT-TAAA
1 AAAATAATATAAA
19349339 TTATAAAAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
29 8 0.21
30 19 0.50
31 11 0.29
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (29 bp):
AAAATAATATAAAAAATTAACTATTATTA
Found at i:19349341 original size:47 final size:45
Alignment explanation
Indices: 19349266--19349384 Score: 134
Period size: 47 Copynumber: 2.6 Consensus size: 45
19349256 ACTATTCACT
* * *
19349266 TAAAAAATATTAAAAAATTAATTAAATTATAAAAATAATATAAAATAA
1 TAAATAATATT-AAAAA-TAATTAAATTATAAAAACAAAAT-AAATAA
* *
19349314 TTAACTATTATTAAAAATAATTAAATTATAAAAACAAAATAAATAA
1 -TAAATAATATTAAAAATAATTAAATTATAAAAACAAAATAAATAA
*
19349360 TAAATAATA-TAAAAA-AATAAAATTA
1 TAAATAATATTAAAAATAATTAAATTA
19349385 ACTCTTACCA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
43 9 0.15
44 6 0.10
45 7 0.11
46 6 0.10
47 21 0.34
48 5 0.08
49 8 0.13
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (45 bp):
TAAATAATATTAAAAATAATTAAATTATAAAAACAAAATAAATAA
Found at i:19349546 original size:22 final size:22
Alignment explanation
Indices: 19349521--19349572 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
19349511 GAAAGCTTTA
*
19349521 GAGAGAAA-TTTAAAGAGAAATT
1 GAGAGAAAGTTGAAAGA-AAATT
*
19349543 GAGAGAAAGTTGAAATAAAATT
1 GAGAGAAAGTTGAAAGAAAATT
19349565 GAGAGAAA
1 GAGAGAAA
19349573 AATAAAAGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 21 0.78
23 6 0.22
ACGTcount: A:0.56, C:0.00, G:0.25, T:0.19
Consensus pattern (22 bp):
GAGAGAAAGTTGAAAGAAAATT
Found at i:19367877 original size:5 final size:5
Alignment explanation
Indices: 19367878--19367910 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
19367868 AATATAATAT
19367878 TAAAA T-AAA TAAAA TAAAA TAAAA TAAAA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
19367911 TTGAAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:19378378 original size:12 final size:12
Alignment explanation
Indices: 19378363--19378388 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19378353 AATTAAAGAA
19378363 ATAATAGCATTC
1 ATAATAGCATTC
19378375 ATAATAGCATTC
1 ATAATAGCATTC
19378387 AT
1 AT
19378389 CATGATAACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATAATAGCATTC
Found at i:19382611 original size:296 final size:295
Alignment explanation
Indices: 19382064--19382644 Score: 874
Period size: 296 Copynumber: 2.0 Consensus size: 295
19382054 GTCTTGATCA
* * * * *
19382064 ATTAGAAATACCCCAAGGTCGCGATTCTTAAGTAGTAACTCAGACTTTGAATATGCCGCAAAACT
1 ATTACAAATACCCCAAGGTCGAGATTCCTAAGTAATAACTCAGACTTTGAATATACCGCAAAACT
* * *
19382129 TAATCTATATGCATAATAACCTATTATGCCCCTTCTTACGTAGCCTTGACATTGTCCCTTATGAT
66 TAATCTATATGCATAATAACCTATTATGCCCCTTCTTACGTAACCTTGACATCGTCCCTCATGAT
*
19382194 GAAAACCCACAACAATTTACCTGTACATAACAAACACACAGGTAAGTTCATAAGAACTTAGTGAG
131 GAAAACCCACAACAATATACCTGTACATAACAAACACACAGGTAAGTTCATAAGAACTTAGTGAG
* * **
19382259 GAAAACATCGTTTACCTAAGCCGTATTTTCACAATGCGACTGGCAATTTATACAGGTGATCTCAT
196 GAAAACATCGTCTACCTAAGCCGTATTTGCACAATGCGACTAACAATTTATACAGGTGATCTCAT
19382324 CGTTCTTATCCTTCAACTTAATCTTGTCCTAATCT
261 CGTTCTTATCCTTCAACTTAATCTTGTCCTAATCT
* * * *
19382359 ATTACAAATATCCTAAGGTCGAGATTCCTAAGTAATAACTCAGACTTTGAATGTACCGCCAAACT
1 ATTACAAATACCCCAAGGTCGAGATTCCTAAGTAATAACTCAGACTTTGAATATACCGCAAAACT
* * * * * * *
19382424 TGATCTGTATGCATAATAACCTATTATGCCCCTTTTTGGCGTAACCTTGGCATCGTTCCTCATGG
66 TAATCTATATGCATAATAACCTATTATGCCCCTTCTT-ACGTAACCTTGACATCGTCCCTCATGA
* *
19382489 TGAAAACCCACAATAATATACCTGTACATAACAAACACATAGGTAAGTTCATAAGAACTTAGTGA
130 TGAAAACCCACAACAATATACCTGTACATAACAAACACACAGGTAAGTTCATAAGAACTTAGTGA
* **
19382554 GGAAAACATCGTCTACCTGAGTTGTATTTGCACAATGCGACTAACAATTTATACAGGTGATCTCA
195 GGAAAACATCGTCTACCTAAGCCGTATTTGCACAATGCGACTAACAATTTATACAGGTGATCTCA
**
19382619 TTTTTCTTATCCTTCAACTTAATCTT
260 TCGTTCTTATCCTTCAACTTAATCTT
19382645 TGGTGAATAC
Statistics
Matches: 254, Mismatches: 31, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
295 90 0.35
296 164 0.65
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (295 bp):
ATTACAAATACCCCAAGGTCGAGATTCCTAAGTAATAACTCAGACTTTGAATATACCGCAAAACT
TAATCTATATGCATAATAACCTATTATGCCCCTTCTTACGTAACCTTGACATCGTCCCTCATGAT
GAAAACCCACAACAATATACCTGTACATAACAAACACACAGGTAAGTTCATAAGAACTTAGTGAG
GAAAACATCGTCTACCTAAGCCGTATTTGCACAATGCGACTAACAATTTATACAGGTGATCTCAT
CGTTCTTATCCTTCAACTTAATCTTGTCCTAATCT
Found at i:19383223 original size:27 final size:27
Alignment explanation
Indices: 19383193--19383400 Score: 163
Period size: 27 Copynumber: 7.7 Consensus size: 27
19383183 TTCAAAATTC
19383193 GCCACAAAGGCTTTCATTTCATGATTT
1 GCCACAAAGGCTTTCATTTCATGATTT
* *
19383220 GCCACAAAGG-TTTCCTTTCATGGTTT
1 GCCACAAAGGCTTTCATTTCATGATTT
* * * *
19383246 ACCATAAAGACTTTCATTTCGTG-TTT
1 GCCACAAAGGCTTTCATTTCATGATTT
* * * * *
19383272 -CTTCATAATGGTTTTCCTTTCATGATTC
1 GC--CACAAAGGCTTTCATTTCATGATTT
** *
19383300 GTTACAAAGGCTTTCATTTCTTGATTCT
1 GCCACAAAGGCTTTCATTTCATGATT-T
* * *
19383328 -CCATAAAGGCTTTCCTTTCATGATTC
1 GCCACAAAGGCTTTCATTTCATGATTT
* * *
19383354 ACCACAAAGGCTTTCATTTCATGGTTC
1 GCCACAAAGGCTTTCATTTCATGATTT
* *
19383381 GCCACAAAGACTTTCCTTTC
1 GCCACAAAGGCTTTCATTTC
19383401 GTGACGTGTT
Statistics
Matches: 141, Mismatches: 33, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
25 1 0.01
26 24 0.17
27 114 0.81
28 2 0.01
ACGTcount: A:0.23, C:0.24, G:0.13, T:0.40
Consensus pattern (27 bp):
GCCACAAAGGCTTTCATTTCATGATTT
Found at i:19383314 original size:54 final size:54
Alignment explanation
Indices: 19383189--19383400 Score: 221
Period size: 54 Copynumber: 3.9 Consensus size: 54
19383179 TTCTTTCAAA
* * *
19383189 ATTCGCCACAAAGGCTTTCATTTCATGATT-TGCCACAAAGG-TTTCCTTTCATG
1 ATTCACCACAAAGGCTTTCATTTCGTGATTCT-CCATAAAGGCTTTCCTTTCATG
* * * * * * * *
19383242 GTTTACCATAAAGACTTTCATTTCGTGTTTCTTCATAATGGTTTTCCTTTCATG
1 ATTCACCACAAAGGCTTTCATTTCGTGATTCTCCATAAAGGCTTTCCTTTCATG
*** *
19383296 ATTCGTTACAAAGGCTTTCATTTCTTGATTCTCCATAAAGGCTTTCCTTTCATG
1 ATTCACCACAAAGGCTTTCATTTCGTGATTCTCCATAAAGGCTTTCCTTTCATG
* * * * *
19383350 ATTCACCACAAAGGCTTTCATTTCATGGTTCGCCACAAAGACTTTCCTTTC
1 ATTCACCACAAAGGCTTTCATTTCGTGATTCTCCATAAAGGCTTTCCTTTC
19383401 GTGACGTGTT
Statistics
Matches: 127, Mismatches: 30, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
53 29 0.23
54 98 0.77
ACGTcount: A:0.23, C:0.24, G:0.13, T:0.40
Consensus pattern (54 bp):
ATTCACCACAAAGGCTTTCATTTCGTGATTCTCCATAAAGGCTTTCCTTTCATG
Found at i:19383374 original size:81 final size:81
Alignment explanation
Indices: 19383189--19383400 Score: 230
Period size: 81 Copynumber: 2.6 Consensus size: 81
19383179 TTCTTTCAAA
* * *
19383189 ATTCGCCACAAAGGCTTTCATTTCATGATTTGCCACAAAGG-TTTCCTTTCATGGTTTACCATAA
1 ATTCACCACAAAGGCTTTCATTTCATGATTCGCCACAAAGGCTTTCCTTTCATGATTTACCATAA
*
19383253 AGACTTTCATTTCGTG
66 AGACTTTCATTTCATG
* ** * * * * ** * *
19383269 TTTCTTCATAATGGTTTTCCTTTCATGATTCGTTACAAAGGCTTTCATTTCTTGATTCT-CCATA
1 ATTCACCACAAAGGCTTTCATTTCATGATTCGCCACAAAGGCTTTCCTTTCATGATT-TACCATA
* *
19383333 AAGGCTTTCCTTTCATG
65 AAGACTTTCATTTCATG
* *
19383350 ATTCACCACAAAGGCTTTCATTTCATGGTTCGCCACAAAGACTTTCCTTTC
1 ATTCACCACAAAGGCTTTCATTTCATGATTCGCCACAAAGGCTTTCCTTTC
19383401 GTGACGTGTT
Statistics
Matches: 102, Mismatches: 28, Indels: 3
0.77 0.21 0.02
Matches are distributed among these distances:
80 31 0.30
81 70 0.69
82 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.13, T:0.40
Consensus pattern (81 bp):
ATTCACCACAAAGGCTTTCATTTCATGATTCGCCACAAAGGCTTTCCTTTCATGATTTACCATAA
AGACTTTCATTTCATG
Found at i:19384605 original size:58 final size:58
Alignment explanation
Indices: 19384543--19385144 Score: 802
Period size: 58 Copynumber: 10.3 Consensus size: 58
19384533 GGATACCCGG
* * *
19384543 GGGTAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGAAATTTTTGAGGCTTCGA
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAG-TTCGA
* * *
19384601 GGGTAAAATGGT-TTTTTTGATGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTC-A
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGG-AAGTTCGA
19384658 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCGA
1 -GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCGA
19384717 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCGA
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCGA
* * *
19384775 GGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGAAATTTTGGAAGTTCGG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCGA
* *
19384833 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAATTTG-
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCGA
* * * *
19384890 GGAGTAAAATGGTAATTTTTGATGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGG
1 GG-GTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGG-AAGTTCGA
* *
19384950 GGGTAAAATGGTAATTTTTGGTGAAGTCGAGGTTAAAAATGGAATTTTGGAAAGTTCGA
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGG-AAGTTCGA
* * * * * *
19385009 GGGTAAAATGGTAATTTTTAGTGAAATCTGGGTTAAAAATAGAATTTCGAAAAGTTCGG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTG-GAAGTTCGA
* * * ** * *
19385068 GGGTAAAATGGTAATTTTT-G-GAAGTTTCGAGGTTAAAAATGTAATTTTAAAAGGTTTGG
1 GGGTAAAATGGTAATTTTTGGTGAA--ATCGGGGTTAAAAATGGAATTTTGGAA-GTTCGA
19385127 GGGTAAAATGGTAATTTT
1 GGGTAAAATGGTAATTTT
19385145 GGAAGTTTCG
Statistics
Matches: 493, Mismatches: 39, Indels: 23
0.89 0.07 0.04
Matches are distributed among these distances:
57 6 0.01
58 280 0.57
59 205 0.42
60 2 0.00
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCGA
Found at i:19385950 original size:18 final size:19
Alignment explanation
Indices: 19385918--19385954 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
19385908 TTTAAAACTT
*
19385918 TCCTTCTTTTCTTTCAAAA
1 TCCTTCTTTTATTTCAAAA
19385937 TCCTT-TTTTATTTCAAAA
1 TCCTTCTTTTATTTCAAAA
19385955 CAACCAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.24, C:0.22, G:0.00, T:0.54
Consensus pattern (19 bp):
TCCTTCTTTTATTTCAAAA
Found at i:19387036 original size:5 final size:5
Alignment explanation
Indices: 19387026--19387103 Score: 59
Period size: 5 Copynumber: 14.4 Consensus size: 5
19387016 ATATTAAATT
*
19387026 TTAAA TTAAA TTCTAAC TTAAA TTAAA TTTAAA -TAAA TTTAAA TTTAAA
1 TTAAA TTAAA -T-TAAA TTAAA TTAAA -TTAAA TTAAA -TTAAA -TTAAA
* *
19387075 TTAAA TTAAAA TTTAAA ATAAA TTTAA TT
1 TTAAA TT-AAA -TTAAA TTAAA TTAAA TT
19387104 TCGAAGTAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
4 4 0.07
5 29 0.48
6 23 0.38
7 5 0.08
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (5 bp):
TTAAA
Found at i:19387046 original size:17 final size:15
Alignment explanation
Indices: 19387026--19387104 Score: 77
Period size: 17 Copynumber: 4.9 Consensus size: 15
19387016 ATATTAAATT
19387026 TTAAATTAAATTCTAA
1 TTAAATTAAATT-TAA
19387042 CTTAAATTAAATTTAA
1 -TTAAATTAAATTTAA
*
19387058 ATAAATTTAAATTTAAA
1 TTAAA-TTAAATTT-AA
19387075 TTAAATTAAAATTTAAA
1 TTAAATT-AAATTT-AA
* *
19387092 ATAAATTTAATTT
1 TTAAATTAAATTT
19387105 CGAAGTAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
15 4 0.07
16 18 0.33
17 33 0.60
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (15 bp):
TTAAATTAAATTTAA
Found at i:19387059 original size:11 final size:11
Alignment explanation
Indices: 19387043--19387101 Score: 77
Period size: 11 Copynumber: 5.4 Consensus size: 11
19387033 AAATTCTAAC
19387043 TTAAATTAAAT
1 TTAAATTAAAT
19387054 TTAAA-TAAAT
1 TTAAATTAAAT
19387064 TTAAATTTAAA-
1 TTAAA-TTAAAT
19387075 TTAAATTAAAAT
1 TTAAATT-AAAT
*
19387087 TTAAAATAAAT
1 TTAAATTAAAT
19387098 TTAA
1 TTAA
19387102 TTTCGAAGTA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
10 12 0.28
11 21 0.49
12 10 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:19387091 original size:44 final size:46
Alignment explanation
Indices: 19387001--19387101 Score: 127
Period size: 44 Copynumber: 2.2 Consensus size: 46
19386991 AATGGACATT
**
19387001 TTAAATTTACAAATAATATTAAATTTTAAATTAAATTCTAACTTAAA
1 TTAAATTTA-AAATAATATTAAATTTTAAATTAAATTAAAACTTAAA
*
19387048 TTAAATTT-AAATAA-ATTTAAA-TTTAAATTAAATTAAAATTTAAA
1 TTAAATTTAAAATAATA-TTAAATTTTAAATTAAATTAAAACTTAAA
*
19387092 ATAAATTTAA
1 TTAAATTTAA
19387102 TTTCGAAGTA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
44 28 0.58
45 12 0.25
47 8 0.17
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (46 bp):
TTAAATTTAAAATAATATTAAATTTTAAATTAAATTAAAACTTAAA
Found at i:19387518 original size:76 final size:76
Alignment explanation
Indices: 19387391--19388259 Score: 1083
Period size: 76 Copynumber: 11.8 Consensus size: 76
19387381 TGCTCTTTAG
* *
19387391 AGAGATAAAGACTTGCTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCAT
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCTT
19387456 ACTTCAATTTC
66 ACTTCAATTTC
* * * *
19387467 AGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATGGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCTT
19387532 ACTTCAATTTC
66 ACTTCAATTTC
* * * * *
19387543 AGAGATAAAGACGTGATATCCAGCTTTACTTTAATTTCAAGAGGATAGGAAAAGATCTTG--CTT
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCTT
*
19387606 --TT--ACTTC
66 ACTTCAATTTC
* * *
19387613 ------AAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCTT
19387672 ACTTCAATTTC
66 ACTTCAATTTC
* * * * *
19387683 AGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAAGATGGGAAACTATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCTT
19387748 ACTTCAATTTC
66 ACTTCAATTTC
* * * *
19387759 AGAGATAAACACTTGTTATCCAGCTTTACTTCAATTTCAAGAGGATGGGAAACTATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCTT
19387824 ACTTCAATTTC
66 ACTTCAATTTC
* * * *
19387835 AGAGATAAAGACTTGTTATCTAGCTTTACTTTAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCTT
19387900 ACTTCAATTTC
66 ACTTCAATTTC
* * * *
19387911 AGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATGGGAAACTATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCTT
19387976 ACTTCAATTTC
66 ACTTCAATTTC
* * * * * *
19387987 AGAGATAAAGACTTGTTATCCAACTTTACTCCCATTTCAAGAGGATAGGGAATGATGTTGTTCTT
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCTT
19388052 ACTTCAATTTC
66 ACTTCAATTTC
* * * *
19388063 AGAGATAACGACTCGTTTATCCAACTCTACTTCAATTTCAAGCGGAT--G--AC---CTTGCTCT
1 AGAGATAAAGACTTG-TTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCT
19388121 TACTTCAATTTC
65 TACTTCAATTTC
* *
19388133 AGAGATAAAGACATGTTATCC-ACTCTACTTCAATTTCAAGAGGAT--G--ACG---TTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCTT
*
19388190 ACTTCAATTTT
66 ACTTCAATTTC
* * * * *
19388201 AGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGCGGATAGGAAAAGATCTTG
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTG
19388260 GTGTGGTCTG
Statistics
Matches: 710, Mismatches: 62, Indels: 43
0.87 0.08 0.05
Matches are distributed among these distances:
64 52 0.07
66 3 0.00
68 88 0.12
69 6 0.01
70 39 0.05
72 4 0.01
73 1 0.00
74 3 0.00
75 4 0.01
76 483 0.68
77 27 0.04
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (76 bp):
AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCTT
ACTTCAATTTC
Found at i:19388178 original size:68 final size:67
Alignment explanation
Indices: 19388048--19388245 Score: 306
Period size: 68 Copynumber: 2.9 Consensus size: 67
19388038 ATGATGTTGT
*
19388048 TCTTACTTCAATTTCAGAGATAACGACTCGTTTATCCAACTCTACTTCAATTTCAAGCGGATGAC
1 TCTTACTTCAATTTCAGAGATAAAGACT-G-TTATCC-ACTCTACTTCAATTTCAAGCGGATGAC
19388113 CTTGC
63 CTTGC
* *
19388118 TCTTACTTCAATTTCAGAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGAGGATGACGT
1 TCTTACTTCAATTTCAGAGATAAAGAC-TGTTATCCACTCTACTTCAATTTCAAGCGGATGACCT
19388183 TGC
65 TGC
* *
19388186 TCTTACTTCAATTTTAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGCGGAT
1 TCTTACTTCAATTTCAGAGATAAAGAC-TGTTATCCACTCTACTTCAATTTCAAGCGGAT
19388246 AGGAAAAGAT
Statistics
Matches: 120, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
68 86 0.72
69 6 0.05
70 27 0.22
71 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (67 bp):
TCTTACTTCAATTTCAGAGATAAAGACTGTTATCCACTCTACTTCAATTTCAAGCGGATGACCTT
GC
Found at i:19388196 original size:31 final size:31
Alignment explanation
Indices: 19388090--19388199 Score: 103
Period size: 31 Copynumber: 3.4 Consensus size: 31
19388080 TATCCAACTC
* *
19388090 TACTTCAATTTCAAGCGGATGACCTTGCTCT
1 TACTTCAATTTCAAGAGGATGACGTTGCTCT
** * * *
19388121 TACTTCAATTTCAGAGATAAAGACATGTTATCCACT
1 TACTTCAATTTCA-AGAGGATGAC--G-T-TGCTCT
19388157 CTACTTCAATTTCAAGAGGATGACGTTGCTCT
1 -TACTTCAATTTCAAGAGGATGACGTTGCTCT
19388189 TACTTCAATTT
1 TACTTCAATTT
19388200 TAGAGATGAA
Statistics
Matches: 61, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
31 24 0.39
32 10 0.16
33 1 0.02
34 1 0.02
35 1 0.02
36 11 0.18
37 13 0.21
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (31 bp):
TACTTCAATTTCAAGAGGATGACGTTGCTCT
Found at i:19400339 original size:30 final size:30
Alignment explanation
Indices: 19400249--19400399 Score: 98
Period size: 30 Copynumber: 5.1 Consensus size: 30
19400239 AATATGGTAA
* *
19400249 TTTTGGTGAAATCGGGGTTAAAAATGGAAT
1 TTTTGATGAAATCGAGGTTAAAAATGGAAT
*** *
19400279 TTTTGA-GGCTTCGAGGGT-AAAATGGTAAT
1 TTTTGATGAAATCGAGGTTAAAAATGG-AAT
*
19400308 TTTTGATGAAATCAAGGTTAAAAATGGAA-
1 TTTTGATGAAATCGAGGTTAAAAATGGAAT
* * * *
19400337 TTTTG--GAAAGTTTGGGGGT-AAAATGATAAT
1 TTTTGATGAAA--TCGAGGTTAAAAATG-GAAT
* * *
19400367 TTTTGGTTAAATCGGGGTTAAAAATGGAAT
1 TTTTGATGAAATCGAGGTTAAAAATGGAAT
19400397 TTT
1 TTT
19400400 AGAAGTTCGG
Statistics
Matches: 91, Mismatches: 20, Indels: 20
0.69 0.15 0.15
Matches are distributed among these distances:
27 4 0.04
28 13 0.14
29 27 0.30
30 31 0.34
31 13 0.14
32 3 0.03
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (30 bp):
TTTTGATGAAATCGAGGTTAAAAATGGAAT
Found at i:19400341 original size:58 final size:58
Alignment explanation
Indices: 19400234--19400436 Score: 282
Period size: 59 Copynumber: 3.5 Consensus size: 58
19400224 GGATACCCGA
* * *
19400234 GGGGTAATATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTTGAGGCTTCG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAG-TTCG
* * ** * *
19400292 AGGGTAAAATGGTAATTTTTGATGAAATCAAGGTTAAAAATGGAATTTTGGAAAGTTTG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAG-AAGTTCG
* *
19400351 GGGGTAAAATGATAATTTTTGGTTAAATCGGGGTTAAAAATGGAATTTTAGAAGTTCG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGTTCG
19400409 GGGGTAAAATGGTAATTTTTGGTGAAAT
1 GGGGTAAAATGGTAATTTTTGGTGAAAT
19400437 GGAATTTTGG
Statistics
Matches: 125, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
58 45 0.36
59 78 0.62
60 2 0.02
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.34
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGTTCG
Found at i:19400428 original size:29 final size:27
Alignment explanation
Indices: 19400234--19400429 Score: 101
Period size: 29 Copynumber: 6.8 Consensus size: 27
19400224 GGATACCCGA
*
19400234 GGGGTAATATGGTAATTTTGGTGAAATCG
1 GGGGTAAAATGGTAATTTT--TGAAATCG
* **
19400263 GGGTTAAAAATGG-AATTTTTGAGGCTTCG
1 GGGGT-AAAATGGTAATTTTTGA--AATCG
* *
19400292 AGGGTAAAATGGTAATTTTTGATGAAATCA
1 GGGGTAAAATGGTAA-TTTT--TGAAATCG
* * * *
19400322 AGGTTAAAAATGG-AATTTTGGAAAGTTTG
1 GGGGT-AAAATGGTAATTTTTGAAA--TCG
*
19400351 GGGGTAAAATGATAATTTTTGGTTAAATCG
1 GGGGTAAAATGGTAATTTTT-G--AAATCG
* * *
19400381 GGGTTAAAAATGG-AATTTTAGAAGTTCG
1 GGGGT-AAAATGGTAATTTTTGAA-ATCG
19400409 GGGGTAAAATGGTAATTTTTG
1 GGGGTAAAATGGTAATTTTTG
19400430 GTGAAATGGA
Statistics
Matches: 126, Mismatches: 24, Indels: 35
0.68 0.13 0.19
Matches are distributed among these distances:
27 16 0.13
28 27 0.21
29 33 0.26
30 31 0.25
31 13 0.10
32 6 0.05
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (27 bp):
GGGGTAAAATGGTAATTTTTGAAATCG
Found at i:19400456 original size:104 final size:104
Alignment explanation
Indices: 19400329--19400534 Score: 360
Period size: 104 Copynumber: 2.0 Consensus size: 104
19400319 TCAAGGTTAA
* *
19400329 AAATGGAATTTTGGAAAGTTTGGGGGTAAAATGATAATTTTTGGTTAAATCGGGGTTAAAAATGG
1 AAATGGAATTTTGGAAAGTTT-GGGGTAAAATGATAATTTTTGGTGAAATCAGGGTTAAAAATGG
19400394 AATTTTAG-AAGTTCGGGGGTAAAATGGTAATTTTTGGTG
65 AATTTTAGAAAGTTCGGGGGTAAAATGGTAATTTTTGGTG
*
19400433 AAATGGAATTTTGGAAAGTTTGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGA
1 AAATGGAATTTTGGAAAGTTTGGGGTAAAATGATAATTTTTGGTGAAATCAGGGTTAAAAATGGA
*
19400498 ATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
66 ATTTTAGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
19400535 AAGTTTCGGG
Statistics
Matches: 97, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
103 47 0.48
104 50 0.52
ACGTcount: A:0.33, C:0.02, G:0.30, T:0.35
Consensus pattern (104 bp):
AAATGGAATTTTGGAAAGTTTGGGGTAAAATGATAATTTTTGGTGAAATCAGGGTTAAAAATGGA
ATTTTAGAAAGTTCGGGGGTAAAATGGTAATTTTTGGTG
Found at i:19400458 original size:45 final size:45
Alignment explanation
Indices: 19400388--19400481 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 45
19400378 TCGGGGTTAA
19400388 AAATGGAATTTTAGAAGTTCGGGGGTAAAATGGTAATTTTTGGTG
1 AAATGGAATTTTAGAAGTTCGGGGGTAAAATGGTAATTTTTGGTG
* *
19400433 AAATGGAATTTTGGAAAGTT-TGGGGTAAAATGGTAATTTTTGGTG
1 AAATGGAATTTTAG-AAGTTCGGGGGTAAAATGGTAATTTTTGGTG
19400478 AAAT
1 AAAT
19400482 CAGGGTTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
45 41 0.89
46 5 0.11
ACGTcount: A:0.33, C:0.01, G:0.30, T:0.36
Consensus pattern (45 bp):
AAATGGAATTTTAGAAGTTCGGGGGTAAAATGGTAATTTTTGGTG
Found at i:19400475 original size:29 final size:28
Alignment explanation
Indices: 19400433--19400603 Score: 142
Period size: 29 Copynumber: 5.9 Consensus size: 28
19400423 ATTTTTGGTG
19400433 AAATGGAATTTTGGAAAGTTT-GGGGTA
1 AAATGGAATTTTGGAAAGTTTCGGGGTA
*
19400460 AAATGGTAATTTTTGGTGAAA---TCAGGGTTAA
1 AAATGG-AA-TTTT-G-GAAAGTTTC-GGGGT-A
19400491 AAATGGAATTTTGGAAAG-TTCGGGGGTA
1 AAATGGAATTTTGGAAAGTTTC-GGGGTA
19400519 AAATGGTAATTTTTGG-AAGTTTCGGGGTTAA
1 AAATGG-AA-TTTTGGAAAGTTTCGGGG-T-A
* *
19400550 AAATGGAATTTT-AAAAGGTTTGGGGGTA
1 AAATGGAATTTTGGAAA-GTTTCGGGGTA
19400578 AAATGGTAATTTTGG-AAGTTTCGGGG
1 AAATGG-AATTTTGGAAAGTTTCGGGG
19400604 ACCTATAAAC
Statistics
Matches: 119, Mismatches: 7, Indels: 35
0.74 0.04 0.22
Matches are distributed among these distances:
27 10 0.08
28 26 0.22
29 38 0.32
30 27 0.23
31 18 0.15
ACGTcount: A:0.32, C:0.02, G:0.32, T:0.34
Consensus pattern (28 bp):
AAATGGAATTTTGGAAAGTTTCGGGGTA
Found at i:19400532 original size:59 final size:57
Alignment explanation
Indices: 19400433--19400595 Score: 215
Period size: 59 Copynumber: 2.8 Consensus size: 57
19400423 ATTTTTGGTG
*
19400433 AAATGGAATTTTGGAAAGTTTGGGGTAAAATGGTAATTTTTGGTGAA-ATCAGGGTTAA
1 AAATGGAATTTTGGAAAGTTGGGGGTAAAATGGTAATTTTT-G-GAAGATCAGGGTTAA
* *
19400491 AAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGTTTCGGGGTTAA
1 AAATGGAATTTTGGAAAGTT-GGGGGTAAAATGGTAATTTTTGGAAG-ATCAGGGTTAA
*
19400550 AAATGGAATTTT-AAAAGGTTTGGGGGTAAAATGGTAA-TTTTGGAAG
1 AAATGGAATTTTGGAAA-G-TTGGGGGTAAAATGGTAATTTTTGGAAG
19400596 TTTCGGGGAC
Statistics
Matches: 96, Mismatches: 4, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
57 3 0.03
58 33 0.34
59 58 0.60
60 2 0.02
ACGTcount: A:0.34, C:0.02, G:0.31, T:0.34
Consensus pattern (57 bp):
AAATGGAATTTTGGAAAGTTGGGGGTAAAATGGTAATTTTTGGAAGATCAGGGTTAA
Found at i:19400560 original size:162 final size:162
Alignment explanation
Indices: 19400293--19400590 Score: 492
Period size: 162 Copynumber: 1.8 Consensus size: 162
19400283 GAGGCTTCGA
*
19400293 GGGTAAAATGGTAATTTTTGATGAAATCAAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAA
1 GGGTAAAATGGTAATTTTTGATGAAATCAAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAA
*
19400358 AATGATAATTTTTGGTTAAATCGGGGTTAAAAATGGAATTTTAGAA-GTTCGGGGGTAAAATGGT
66 AATGATAATTTTTGG-TAAATCGGGGTTAAAAATGGAATTTTAAAAGGTTCGGGGGTAAAATGGT
19400422 AATTTTTGGTGAAATGGAATTTTGGAAAGTTTG
130 AATTTTTGGTGAAATGGAATTTTGGAAAGTTTG
* *
19400455 GGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAA
1 GGGTAAAATGGTAATTTTTGATGAAATCAAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAA
* * *
19400520 AATGGTAATTTTTGG-AAGTTTCGGGGTTAAAAATGGAATTTTAAAAGGTTTGGGGGTAAAATGG
66 AATGATAATTTTTGGTAA--ATCGGGGTTAAAAATGGAATTTTAAAAGGTTCGGGGGTAAAATGG
19400584 TAATTTT
129 TAATTTT
19400591 GGAAGTTTCG
Statistics
Matches: 126, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
160 2 0.02
162 101 0.80
163 23 0.18
ACGTcount: A:0.34, C:0.02, G:0.29, T:0.35
Consensus pattern (162 bp):
GGGTAAAATGGTAATTTTTGATGAAATCAAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAA
AATGATAATTTTTGGTAAATCGGGGTTAAAAATGGAATTTTAAAAGGTTCGGGGGTAAAATGGTA
ATTTTTGGTGAAATGGAATTTTGGAAAGTTTG
Found at i:19402484 original size:5 final size:5
Alignment explanation
Indices: 19402474--19402551 Score: 59
Period size: 5 Copynumber: 14.4 Consensus size: 5
19402464 ATATTAAATT
*
19402474 TTAAA TTAAA TTCTAAC TTAAA TTAAA TTTAAA -TAAA TTTAAA TTTAAA
1 TTAAA TTAAA -T-TAAA TTAAA TTAAA -TTAAA TTAAA -TTAAA -TTAAA
* *
19402523 TTAAA TTAAAA TTTAAA ATAAA TTTAA TT
1 TTAAA TT-AAA -TTAAA TTAAA TTAAA TT
19402552 TCAAAGTAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
4 4 0.07
5 29 0.48
6 23 0.38
7 5 0.08
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (5 bp):
TTAAA
Found at i:19402507 original size:11 final size:11
Alignment explanation
Indices: 19402491--19402549 Score: 77
Period size: 11 Copynumber: 5.4 Consensus size: 11
19402481 AAATTCTAAC
19402491 TTAAATTAAAT
1 TTAAATTAAAT
19402502 TTAAA-TAAAT
1 TTAAATTAAAT
19402512 TTAAATTTAAA-
1 TTAAA-TTAAAT
19402523 TTAAATTAAAAT
1 TTAAATT-AAAT
*
19402535 TTAAAATAAAT
1 TTAAATTAAAT
19402546 TTAA
1 TTAA
19402550 TTTCAAAGTA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
10 12 0.28
11 21 0.49
12 10 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:19402539 original size:44 final size:46
Alignment explanation
Indices: 19402449--19402549 Score: 127
Period size: 44 Copynumber: 2.2 Consensus size: 46
19402439 AATGGACATT
**
19402449 TTAAATTTACAAATAATATTAAATTTTAAATTAAATTCTAACTTAAA
1 TTAAATTTA-AAATAATATTAAATTTTAAATTAAATTAAAACTTAAA
*
19402496 TTAAATTT-AAATAA-ATTTAAA-TTTAAATTAAATTAAAATTTAAA
1 TTAAATTTAAAATAATA-TTAAATTTTAAATTAAATTAAAACTTAAA
*
19402540 ATAAATTTAA
1 TTAAATTTAA
19402550 TTTCAAAGTA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
44 28 0.58
45 12 0.25
47 8 0.17
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (46 bp):
TTAAATTTAAAATAATATTAAATTTTAAATTAAATTAAAACTTAAA
Found at i:19402561 original size:17 final size:15
Alignment explanation
Indices: 19402449--19402563 Score: 92
Period size: 17 Copynumber: 7.1 Consensus size: 15
19402439 AATGGACATT
19402449 TTAAATTTACAAATAATA
1 TTAAATTT--AAATAA-A
19402467 TTAAATTT---TAAA
1 TTAAATTTAAATAAA
*
19402479 TTAAATTCTAACTTAAA
1 TTAAATT-TAA-ATAAA
19402496 TTAAATTTAAATAAA
1 TTAAATTTAAATAAA
19402511 TTTAAATTTAAATTAAA
1 -TTAAATTTAAA-TAAA
19402528 TTAAAATTTAAAATAAA
1 TT-AAATTT-AAATAAA
*
19402545 TTTAATTTCAAAGTAAA
1 TTAAATTT-AAA-TAAA
19402562 TT
1 TT
19402564 CTAAAATGGT
Statistics
Matches: 84, Mismatches: 3, Indels: 21
0.78 0.03 0.19
Matches are distributed among these distances:
12 8 0.10
13 4 0.05
15 4 0.05
16 24 0.29
17 33 0.39
18 11 0.13
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (15 bp):
TTAAATTTAAATAAA
Found at i:19402562 original size:28 final size:29
Alignment explanation
Indices: 19402513--19402570 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
19402503 TAAATAAATT
*
19402513 TAAATTTAAATTAAATTAAAATT-TAAAA
1 TAAATTTAAATTAAAGTAAAATTCTAAAA
*
19402541 TAAATTTAATTTCAAAGT-AAATTCTAAAA
1 TAAATTTAAATT-AAAGTAAAATTCTAAAA
19402570 T
1 T
19402571 GGTTTGGGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (29 bp):
TAAATTTAAATTAAAGTAAAATTCTAAAA
Found at i:19405547 original size:23 final size:23
Alignment explanation
Indices: 19405521--19405565 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
19405511 ATTAGATTTG
*
19405521 TAAAAAATTATAGATAT-TTTTAA
1 TAAAAAATT-TAAATATATTTTAA
19405544 TAAAAAATTTAAATATATTTTA
1 TAAAAAATTTAAATATATTTTA
19405566 GAATAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TAAAAAATTTAAATATATTTTAA
Found at i:19405549 original size:24 final size:25
Alignment explanation
Indices: 19405522--19405582 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 25
19405512 TTAGATTTGT
* *
19405522 AAAAAATTATAGATATTTT-TAATA
1 AAAAAATTAAAGATATTTTAGAATA
* *
19405546 AAAAATTTAAATATATTTTAGAATA
1 AAAAAATTAAAGATATTTTAGAATA
*
19405571 AAATAAAATAAA
1 AAA-AAATTAAA
19405583 ATCATGAGGA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
24 16 0.55
25 7 0.24
26 6 0.21
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (25 bp):
AAAAAATTAAAGATATTTTAGAATA
Found at i:19411910 original size:18 final size:17
Alignment explanation
Indices: 19411887--19411923 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
19411877 CACGGGCAAT
*
19411887 CACACGACTGTGTGAAGC
1 CACACGACCGTGTG-AGC
19411905 CACACGACCGTGTGAGC
1 CACACGACCGTGTGAGC
19411922 CA
1 CA
19411924 AGAATATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.27, C:0.32, G:0.27, T:0.14
Consensus pattern (17 bp):
CACACGACCGTGTGAGC
Found at i:19417709 original size:18 final size:16
Alignment explanation
Indices: 19417678--19417722 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 16
19417668 CTCAATTAAC
19417678 GTTCTTTCTTTCTTTT
1 GTTCTTTCTTTCTTTT
19417694 GTTCTATTCATTTCTTTT
1 GTTCT-TTC-TTTCTTTT
* *
19417712 ATTTTTTCTTT
1 GTTCTTTCTTT
19417723 TCATTGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 8 0.32
17 6 0.24
18 11 0.44
ACGTcount: A:0.07, C:0.16, G:0.04, T:0.73
Consensus pattern (16 bp):
GTTCTTTCTTTCTTTT
Found at i:19417709 original size:22 final size:22
Alignment explanation
Indices: 19417682--19417736 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
19417672 ATTAACGTTC
19417682 TTTCTTTCTTTTGTTCTATTCA
1 TTTCTTTCTTTTGTTCTATTCA
* *
19417704 TTTCTTT-TATTTTTTCTTTTCA
1 TTTCTTTCT-TTTGTTCTATTCA
*
19417726 TTGTTTTTCTT
1 TT-TCTTTCTT
19417737 CGTGAGTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 1 0.04
22 20 0.74
23 5 0.19
24 1 0.04
ACGTcount: A:0.07, C:0.15, G:0.04, T:0.75
Consensus pattern (22 bp):
TTTCTTTCTTTTGTTCTATTCA
Found at i:19427675 original size:72 final size:72
Alignment explanation
Indices: 19427523--19427696 Score: 170
Period size: 72 Copynumber: 2.4 Consensus size: 72
19427513 AGCTACAGGG
* * * *
19427523 GACACACGAGCGTGTTCCAGACCGTGTGTGTATACTGTTTTGAGAAGTAAGGTATAAGGGACACA
1 GACACACGGGCGTGTGCCAGACCGTGTGTGTATACTGTTTTGACAAGTAAGGTACAAGGGACACA
**
19427588 CGAGTTA
66 CGAGCCA
* * * * ** **
19427595 GGCTCACGGGCGTGTGCCAGACTGTGTGTGTATACTGTTTTG-CAAGTTAAGGTGCACTGGTTAC
1 GACACACGGGCGTGTGCCAGACCGTGTGTGTATACTGTTTTGACAAG-TAAGGTACAAGGGACAC
*
19427659 ACGGGCCA
65 ACGAGCCA
* *
19427667 GACACACGGGCGTGTGTCTAGACCTTGTGT
1 GACACACGGGCGTGTG-CCAGACCGTGTGT
19427697 CACACACGGG
Statistics
Matches: 80, Mismatches: 20, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
71 3 0.04
72 67 0.84
73 10 0.12
ACGTcount: A:0.22, C:0.20, G:0.32, T:0.26
Consensus pattern (72 bp):
GACACACGGGCGTGTGCCAGACCGTGTGTGTATACTGTTTTGACAAGTAAGGTACAAGGGACACA
CGAGCCA
Found at i:19429323 original size:20 final size:21
Alignment explanation
Indices: 19429286--19429324 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19429276 AAACCGAGCA
*
19429286 TCACTGAGTTAGAAAATGCAG
1 TCACTAAGTTAGAAAATGCAG
19429307 TCACTAAGTTA-AAAATGC
1 TCACTAAGTTAGAAAATGC
19429325 TGAAAATGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (21 bp):
TCACTAAGTTAGAAAATGCAG
Found at i:19429693 original size:5 final size:5
Alignment explanation
Indices: 19429678--19429716 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
19429668 TATAAATATA
19429678 TTTCTT TTTCT TTTCT TTTCT TTTCT TCTTCT TTT-T TTT
1 TTTC-T TTTCT TTTCT TTTCT TTTCT T-TTCT TTTCT TTT
19429717 TTACATGTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 4 0.12
5 19 0.59
6 9 0.28
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:19429699 original size:16 final size:17
Alignment explanation
Indices: 19429678--19429717 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
19429668 TATAAATATA
19429678 TTTCTTTTTCTT-TTCT
1 TTTCTTTTTCTTCTTCT
19429694 TTTC-TTTTCTTCTTCT
1 TTTCTTTTTCTTCTTCT
19429710 TTT-TTTTT
1 TTTCTTTTT
19429718 TACATGTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTCTTTTTCTTCTTCT
Found at i:19429704 original size:21 final size:21
Alignment explanation
Indices: 19429678--19429717 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19429668 TATAAATATA
*
19429678 TTTCTTTTTCTTTTCTTTTCT
1 TTTCTTCTTCTTTTCTTTTCT
*
19429699 TTTCTTCTTCTTTTTTTTT
1 TTTCTTCTTCTTTTCTTTT
19429718 TACATGTGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTCTTCTTCTTTTCTTTTCT
Found at i:19438486 original size:46 final size:46
Alignment explanation
Indices: 19438419--19438511 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
19438409 CTGATTGAGA
19438419 TGTCTAATTATATCAACCTAATTTTTAACAATGTCTGAATTATTTC
1 TGTCTAATTATATCAACCTAATTTTTAACAATGTCTGAATTATTTC
*
19438465 TGTCTGAA-TATATCAACCTAATTTTTAACAATGTTTGAATTATTTC
1 TGTCT-AATTATATCAACCTAATTTTTAACAATGTCTGAATTATTTC
19438511 T
1 T
19438512 ATGTATAGGA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 43 0.96
47 2 0.04
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (46 bp):
TGTCTAATTATATCAACCTAATTTTTAACAATGTCTGAATTATTTC
Found at i:19441693 original size:28 final size:29
Alignment explanation
Indices: 19441648--19441703 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
19441638 ACTTGAAGAA
*
19441648 ACGTGGAACTAACTTCTTTGTCGCGACAT
1 ACGTGGAACTAACCTCTTTGTCGCGACAT
*
19441677 ACGT-GAATTAACCTCTTTGTCGCGACA
1 ACGTGGAACTAACCTCTTTGTCGCGACA
19441704 CAAGACTTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (29 bp):
ACGTGGAACTAACCTCTTTGTCGCGACAT
Found at i:19448568 original size:18 final size:18
Alignment explanation
Indices: 19448547--19448594 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
19448537 ACTCAAGCTC
*
19448547 CTTTATTTGCTTTTCTTG
1 CTTTATTTGCTTTCCTTG
*
19448565 CTTTATTTTCTTTCCTTG
1 CTTTATTTGCTTTCCTTG
* *
19448583 TTTTGTTTGCTT
1 CTTTATTTGCTT
19448595 GAGGACAAGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.04, C:0.17, G:0.10, T:0.69
Consensus pattern (18 bp):
CTTTATTTGCTTTCCTTG
Found at i:19465688 original size:39 final size:39
Alignment explanation
Indices: 19465502--19465688 Score: 175
Period size: 39 Copynumber: 4.8 Consensus size: 39
19465492 TCGGTTTGAT
* * *
19465502 AGTGTTTACAGTGTCACTACTTA-CTCAGTA-CGTCATTGC
1 AGTGTTTACAGTGTCACTGC-TAGTTCAGTATTGT-ATTGC
* * * *
19465541 GGTGCTTACAGTGTCACTGTTAGTTC-GATATT-TCTTTGC
1 AGTGTTTACAGTGTCACTGCTAGTTCAG-TATTGT-ATTGC
* * * *
19465580 AGTGTTTACAATATCACTGCTAGTTCGGTATTGTACTGC
1 AGTGTTTACAGTGTCACTGCTAGTTCAGTATTGTATTGC
* *
19465619 AGTGTTTATAGTGTCACTGCTAGTTTAGTATTGTATTGC
1 AGTGTTTACAGTGTCACTGCTAGTTCAGTATTGTATTGC
* *
19465658 AGTGTTTACAGTGTCACTGCCAGTCCAGTAT
1 AGTGTTTACAGTGTCACTGCTAGTTCAGTAT
19465689 GTTGATAATT
Statistics
Matches: 119, Mismatches: 24, Indels: 10
0.78 0.16 0.07
Matches are distributed among these distances:
38 3 0.03
39 114 0.96
40 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (39 bp):
AGTGTTTACAGTGTCACTGCTAGTTCAGTATTGTATTGC
Found at i:19478288 original size:80 final size:79
Alignment explanation
Indices: 19478169--19478325 Score: 269
Period size: 80 Copynumber: 2.0 Consensus size: 79
19478159 ACTAATTTCA
* * * *
19478169 TTTTAACTCTTGTAGGGAAGCTAATGAGTCATGTGTCTTCATTAGGATCTGATGTAGTTAAAAAG
1 TTTTAACTCTTGTAGGAAAGCCAATGAGTCATGTCTCTTCATTAGGATCTGATGTAGCTAAAAAG
19478234 GCATGGCAATTTCGT
66 GCATGGC-ATTTCGT
19478249 TTTTAACTCTTGTAGGAAAGCCAATGAGTCATGTCTCTTCATTAGGATCTGATGTAGCTAAAAAG
1 TTTTAACTCTTGTAGGAAAGCCAATGAGTCATGTCTCTTCATTAGGATCTGATGTAGCTAAAAAG
19478314 GCATGGCATTTC
66 GCATGGCATTTC
19478326 TCTTTAATGA
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
79 5 0.07
80 68 0.93
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (79 bp):
TTTTAACTCTTGTAGGAAAGCCAATGAGTCATGTCTCTTCATTAGGATCTGATGTAGCTAAAAAG
GCATGGCATTTCGT
Found at i:19478823 original size:48 final size:47
Alignment explanation
Indices: 19478766--19478896 Score: 181
Period size: 48 Copynumber: 2.7 Consensus size: 47
19478756 CAAGGCATTT
* *
19478766 AACAAAGATGCATTTAACAAACAAAACAATTAATGATGTAGATTACTA
1 AACAAAGATGCATTTAACAAA-AAAACACTTAATGATGCAGATTACTA
* *
19478814 AATAAAGATGCATTTAACAAATAAAACACTTAATGATGCAGATTATTA
1 AACAAAGATGCATTTAACAAA-AAAACACTTAATGATGCAGATTACTA
* * *
19478862 AACAAATATTCATTTAGCAAAAAAACACTTAATGA
1 AACAAAGATGCATTTAACAAAAAAACACTTAATGA
19478897 AGCATAAATA
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
47 14 0.19
48 60 0.81
ACGTcount: A:0.52, C:0.12, G:0.09, T:0.27
Consensus pattern (47 bp):
AACAAAGATGCATTTAACAAAAAAACACTTAATGATGCAGATTACTA
Found at i:19481459 original size:41 final size:41
Alignment explanation
Indices: 19481361--19481462 Score: 134
Period size: 41 Copynumber: 2.5 Consensus size: 41
19481351 CGAAATAATG
* * * *
19481361 AAAACGCTTTTAGGTGAAAGCATTTTCAACGAATTTGCAGG
1 AAAACGCTTTCAGCTGGAAGCATTTTCAACGAATTTGCAGA
* *
19481402 AAAACGCTTCCAGCTGGAAGCATTTTCAACGTA-TTGACAGA
1 AAAACGCTTTCAGCTGGAAGCATTTTCAACGAATTTG-CAGA
19481443 AAAACGCTTTCAGCTGGAAG
1 AAAACGCTTTCAGCTGGAAG
19481463 TGCTTTCTGT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
40 3 0.06
41 50 0.94
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (41 bp):
AAAACGCTTTCAGCTGGAAGCATTTTCAACGAATTTGCAGA
Found at i:19493203 original size:16 final size:17
Alignment explanation
Indices: 19493182--19493213 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
19493172 ATAGCAAACA
19493182 TTTTTTTC-TTCTTTTC
1 TTTTTTTCTTTCTTTTC
19493198 TTTTTTTCTTTCTTTT
1 TTTTTTTCTTTCTTTT
19493214 TCTCATTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTTTTCTTTCTTTTC
Found at i:19509254 original size:55 final size:56
Alignment explanation
Indices: 19509185--19509295 Score: 143
Period size: 55 Copynumber: 2.0 Consensus size: 56
19509175 CATGTACCTT
* * * *
19509185 AAAATAGTATACACACACAGACTGGCACACGCCCCTGTGTTTG-CCTGTGTGCCTC
1 AAAACAGTATACACACACAGACTGGCACACACCCCTGTGTCTGACCAGTGTGCCTC
** * *
19509240 AAAACAGTATACACACATGGTCTGGCACACACCCGTGTGTCTGACCAGTGTGCCTC
1 AAAACAGTATACACACACAGACTGGCACACACCCCTGTGTCTGACCAGTGTGCCTC
19509296 CTGCAACTTA
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
55 36 0.77
56 11 0.23
ACGTcount: A:0.26, C:0.31, G:0.21, T:0.23
Consensus pattern (56 bp):
AAAACAGTATACACACACAGACTGGCACACACCCCTGTGTCTGACCAGTGTGCCTC
Found at i:19514910 original size:23 final size:23
Alignment explanation
Indices: 19514883--19515095 Score: 318
Period size: 23 Copynumber: 9.3 Consensus size: 23
19514873 TATATCTATT
*
19514883 CTTAAATATTAATATGATTTATG
1 CTTAAATATTAATGTGATTTATG
*
19514906 ATTAAATATTAATGTGATTTATG
1 CTTAAATATTAATGTGATTTATG
*
19514929 CTTAAGTATTAATGTGATTTATG
1 CTTAAATATTAATGTGATTTATG
*
19514952 CTTAAATATTAATGTGATTTGTG
1 CTTAAATATTAATGTGATTTATG
19514975 CTTAAATATTAATGTGATTTATG
1 CTTAAATATTAATGTGATTTATG
**
19514998 CAAAAATATTAATGTGATTTATG
1 CTTAAATATTAATGTGATTTATG
* *
19515021 CTTAAATATTAACGTGATTTGTG
1 CTTAAATATTAATGTGATTTATG
*
19515044 CTTAAATATTAATATGATTTATG
1 CTTAAATATTAATGTGATTTATG
* * *
19515067 ATTAAATATTAATGTGTTTTGTG
1 CTTAAATATTAATGTGATTTATG
19515090 CTTAAA
1 CTTAAA
19515096 GAATTAAGTT
Statistics
Matches: 169, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 169 1.00
ACGTcount: A:0.36, C:0.04, G:0.14, T:0.46
Consensus pattern (23 bp):
CTTAAATATTAATGTGATTTATG
Found at i:19525167 original size:25 final size:25
Alignment explanation
Indices: 19525138--19525196 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
19525128 GCTAGTAGCC
* *
19525138 ATTTCTTTTTGCCAATTTCGTTTCA
1 ATTTCTTTCTGCCAATTTCATTTCA
19525163 ATTTCTTTCTGCCAATTTCATTTCA
1 ATTTCTTTCTGCCAATTTCATTTCA
19525188 ATTTCTTTC
1 ATTTCTTTC
19525197 CATTTCCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.17, C:0.22, G:0.05, T:0.56
Consensus pattern (25 bp):
ATTTCTTTCTGCCAATTTCATTTCA
Found at i:19525180 original size:14 final size:14
Alignment explanation
Indices: 19525138--19525186 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
19525128 GCTAGTAGCC
*
19525138 ATTTCTTTTTGCCA
1 ATTTCTTTCTGCCA
*
19525152 ATTTCGTT-T--CA
1 ATTTCTTTCTGCCA
19525163 ATTTCTTTCTGCCA
1 ATTTCTTTCTGCCA
19525177 ATTTCATTTC
1 ATTTC-TTTC
19525187 AATTTCTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
11 9 0.31
12 1 0.03
13 1 0.03
14 14 0.48
15 4 0.14
ACGTcount: A:0.16, C:0.22, G:0.06, T:0.55
Consensus pattern (14 bp):
ATTTCTTTCTGCCA
Found at i:19534354 original size:13 final size:13
Alignment explanation
Indices: 19534336--19534378 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
19534326 GCCGTGAAGA
19534336 AGAAGAAGAAGTT
1 AGAAGAAGAAGTT
*
19534349 AGAAGAA-AA-AT
1 AGAAGAAGAAGTT
19534360 -GAAGAAGAAGTT
1 AGAAGAAGAAGTT
19534372 AGAAGAA
1 AGAAGAA
19534379 AAATGTGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 6 0.24
11 3 0.12
12 3 0.12
13 13 0.52
ACGTcount: A:0.60, C:0.00, G:0.28, T:0.12
Consensus pattern (13 bp):
AGAAGAAGAAGTT
Found at i:19534363 original size:23 final size:23
Alignment explanation
Indices: 19534337--19534383 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
19534327 CCGTGAAGAA
19534337 GAAGAAGAAGTTAGAAGAAAAAT
1 GAAGAAGAAGTTAGAAGAAAAAT
19534360 GAAGAAGAAGTTAGAAGAAAAAT
1 GAAGAAGAAGTTAGAAGAAAAAT
19534383 G
1 G
19534384 TGATTTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.60, C:0.00, G:0.28, T:0.13
Consensus pattern (23 bp):
GAAGAAGAAGTTAGAAGAAAAAT
Found at i:19539509 original size:19 final size:19
Alignment explanation
Indices: 19539462--19539515 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
19539452 ATCTTTTCTT
* *
19539462 TATTTAGTTATTATTTTAA
1 TATTTATTTTTTATTTTAA
19539481 TATTTATTTTTTATTCTTAA
1 TATTTATTTTTTATT-TTAA
*
19539501 -ATTTCTTTTTT-TTTT
1 TATTTATTTTTTATTTT
19539516 CTTTTTCCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
17 2 0.06
18 2 0.06
19 23 0.74
20 4 0.13
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.72
Consensus pattern (19 bp):
TATTTATTTTTTATTTTAA
Found at i:19540234 original size:12 final size:12
Alignment explanation
Indices: 19540206--19540239 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
19540196 TTTTCTTGGA
19540206 ATTAATT-GTTT
1 ATTAATTGGTTT
19540217 -TTAATTGGTTT
1 ATTAATTGGTTT
19540228 ATTAATTGGTTT
1 ATTAATTGGTTT
19540240 TCTTCTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.29
11 4 0.19
12 11 0.52
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.62
Consensus pattern (12 bp):
ATTAATTGGTTT
Done.