Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A13
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: 109233746
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2708888 characters in sequence are not A, C, G, or T
File 45 of 332
Found at i:13522958 original size:3 final size:3
Alignment explanation
Indices: 13522950--13522975 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
13522940 ATGTTCTCTT
13522950 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
13522976 TACTAAAATG
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:13529425 original size:21 final size:20
Alignment explanation
Indices: 13529395--13529437 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
13529385 TTATATTTAA
13529395 ATAAAATTCTTA-TATTTATTT
1 ATAAAATTC-TAGTATTT-TTT
*
13529416 ATAAATTTCTAGTATTTTTT
1 ATAAAATTCTAGTATTTTTT
13529436 AT
1 AT
13529438 TTCACAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (20 bp):
ATAAAATTCTAGTATTTTTT
Found at i:13538410 original size:6 final size:6
Alignment explanation
Indices: 13538399--13538444 Score: 56
Period size: 6 Copynumber: 7.3 Consensus size: 6
13538389 TACTTTTATA
* *
13538399 AATTTT AATTTT AATTTT AATTTT AAAATTT AAGTTT AATTGTT AA
1 AATTTT AATTTT AATTTT AATTTT -AATTTT AATTTT AATT-TT AA
13538445 CATCATTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
6 26 0.74
7 9 0.26
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (6 bp):
AATTTT
Found at i:13540864 original size:65 final size:65
Alignment explanation
Indices: 13540760--13540889 Score: 215
Period size: 65 Copynumber: 2.0 Consensus size: 65
13540750 CTTTTGGTAG
* * *
13540760 CTGTTTAATTCTATGTACATAGGGGTGCTTTTCTAGCACTGAATTTTAGTATGGGAGACGTTTGA
1 CTGTTTAATTCTATGTACATAGGGATACTTTTCTAGCACTGAATTTTAGTATGGAAGACGTTTGA
* *
13540825 CTGTTTAATTCTATGTACATAGGGATACTTTTCTAGCACTGAATTTTTGTATGGAAGATGTTTGA
1 CTGTTTAATTCTATGTACATAGGGATACTTTTCTAGCACTGAATTTTAGTATGGAAGACGTTTGA
13540890 TATAATGTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 60 1.00
ACGTcount: A:0.25, C:0.12, G:0.22, T:0.42
Consensus pattern (65 bp):
CTGTTTAATTCTATGTACATAGGGATACTTTTCTAGCACTGAATTTTAGTATGGAAGACGTTTGA
Found at i:13548407 original size:39 final size:40
Alignment explanation
Indices: 13548351--13548432 Score: 123
Period size: 40 Copynumber: 2.1 Consensus size: 40
13548341 TTTCAGCAAG
*
13548351 AGTTTGACTTGGAACCAGA-GTTGTATACTGAATAAATAA
1 AGTTTGACTTGGAACCAGAGGATGTATACTGAATAAATAA
*
13548390 AGTTTGACTT-GACACCAGAGGATGTATACTGAATAAATGA
1 AGTTTGACTTGGA-ACCAGAGGATGTATACTGAATAAATAA
13548430 AGT
1 AGT
13548433 GCTGTGGAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
38 2 0.05
39 16 0.41
40 21 0.54
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (40 bp):
AGTTTGACTTGGAACCAGAGGATGTATACTGAATAAATAA
Found at i:13558582 original size:24 final size:24
Alignment explanation
Indices: 13558531--13558582 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
13558521 TTGTGCAGAT
* *
13558531 AAAATTTTAAGATTCAAAAGGAGT
1 AAAATTTGAAGATTCAAAAGGAGA
* * *
13558555 AAAATTTGACGATTCAAGAGTAGA
1 AAAATTTGAAGATTCAAAAGGAGA
13558579 AAAA
1 AAAA
13558583 GATTTATTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.06, G:0.17, T:0.25
Consensus pattern (24 bp):
AAAATTTGAAGATTCAAAAGGAGA
Found at i:13560464 original size:8 final size:8
Alignment explanation
Indices: 13560451--13560476 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
13560441 GTTTCAATAT
13560451 ATGTTTTA
1 ATGTTTTA
13560459 ATGTTTTA
1 ATGTTTTA
13560467 ATGTTTTA
1 ATGTTTTA
13560475 AT
1 AT
13560477 TTGATACTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.62
Consensus pattern (8 bp):
ATGTTTTA
Found at i:13560511 original size:20 final size:20
Alignment explanation
Indices: 13560486--13560525 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
13560476 TTTGATACTG
13560486 TAACTTATCTTTTCTTAATA
1 TAACTTATCTTTTCTTAATA
13560506 TAACTTATCTTTTCTTAATA
1 TAACTTATCTTTTCTTAATA
13560526 CATACATAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.55
Consensus pattern (20 bp):
TAACTTATCTTTTCTTAATA
Found at i:13561996 original size:21 final size:21
Alignment explanation
Indices: 13561942--13561989 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
13561932 GTGGCTTCAG
*
13561942 ACACAGCC-ATGTGGCCATCCC
1 ACAC-GCCTATGTGACCATCCC
13561963 ACACGCCTATGTGACCATCCC
1 ACACGCCTATGTGACCATCCC
13561984 ACACGC
1 ACACGC
13561990 TTGTGTGTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 3 0.12
21 22 0.88
ACGTcount: A:0.25, C:0.44, G:0.17, T:0.15
Consensus pattern (21 bp):
ACACGCCTATGTGACCATCCC
Found at i:13562736 original size:10 final size:10
Alignment explanation
Indices: 13562721--13562748 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
13562711 AGACATGAGT
13562721 AAGCTTACGG
1 AAGCTTACGG
13562731 AAGCTTACGG
1 AAGCTTACGG
13562741 AAGCTTAC
1 AAGCTTAC
13562749 TAAATTCGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.21
Consensus pattern (10 bp):
AAGCTTACGG
Found at i:13564595 original size:46 final size:47
Alignment explanation
Indices: 13564493--13564634 Score: 124
Period size: 46 Copynumber: 2.9 Consensus size: 47
13564483 GTTTTCCCTA
** * * *
13564493 TAAGACCATAATTGGGATATGGCATCGGTGTGATGTGATTATGTGCTTCTGTG
1 TAAGACCATAGCTGGGATATGGCATC---GAG-TGTGA-TATGTG-ATCCGTG
*
13564546 TAAGACCATATCTGGGATATGGCATC-AGTGTGATATGTGATCCGTG
1 TAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGATCCGTG
* * * *
13564592 TAAGACCATGGCTGGGCTATGGCTTCGGTGTGTGATATGTGAT
1 TAAGACCATAGCTGGGATATGGCATC-GAGTGTGATATGTGAT
13564635 TATGTGCAAG
Statistics
Matches: 77, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
46 27 0.35
47 6 0.08
48 19 0.25
49 1 0.01
53 24 0.31
ACGTcount: A:0.23, C:0.13, G:0.31, T:0.33
Consensus pattern (47 bp):
TAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGATCCGTG
Found at i:13580019 original size:18 final size:19
Alignment explanation
Indices: 13579984--13580020 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
13579974 TGTGTTCGGA
13579984 CACACAGGCGTGTAAGAGAC
1 CACACAGGCGTG-AAGAGAC
13580004 CACACAGGCGTG-AGAGA
1 CACACAGGCGTGAAGAGA
13580021 AGCGAACAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
20 12 0.71
ACGTcount: A:0.35, C:0.24, G:0.32, T:0.08
Consensus pattern (19 bp):
CACACAGGCGTGAAGAGAC
Found at i:13582350 original size:18 final size:18
Alignment explanation
Indices: 13582293--13582353 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
13582283 TTGAGTCCAT
* *
13582293 TTATCTTTATGTTTATTA
1 TTATTTTTATTTTTATTA
* *
13582311 TTATTATTATTTTCATTA
1 TTATTTTTATTTTTATTA
13582329 TTATTTTTATTTTTATCT-
1 TTATTTTTATTTTTAT-TA
13582347 TTATTTT
1 TTATTTT
13582354 GTCTTTATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
18 35 0.97
19 1 0.03
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (18 bp):
TTATTTTTATTTTTATTA
Found at i:13582352 original size:12 final size:12
Alignment explanation
Indices: 13582292--13582366 Score: 57
Period size: 12 Copynumber: 6.2 Consensus size: 12
13582282 ATTGAGTCCA
*
13582292 TTTATCTTTATG
1 TTTATCTTTATT
13582304 TTTAT-TATTATT
1 TTTATCT-TTATT
*
13582316 ATTAT-TTTCATT
1 TTTATCTTT-ATT
* *
13582328 ATTATTTTTATT
1 TTTATCTTTATT
13582340 TTTATCTTTA-T
1 TTTATCTTTATT
*
13582351 TTTGTCTTTATAT
1 TTTATCTTTAT-T
13582364 TTT
1 TTT
13582367 GAACTCTATT
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
11 13 0.25
12 33 0.62
13 7 0.13
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.72
Consensus pattern (12 bp):
TTTATCTTTATT
Found at i:13589758 original size:126 final size:126
Alignment explanation
Indices: 13589530--13589789 Score: 297
Period size: 126 Copynumber: 2.1 Consensus size: 126
13589520 AATTTCCTCG
* * * * *
13589530 TCTTCCTCGGTTGTAACTATAACAGTCTTTTCATGGAACAGTTTCTGAGAAGTTACAATCGGTGG
1 TCTTCCTCGGTTGCAACTATAACAGGCTTTTCATCGAACAGTCTCTGAGAAGTTACAATCCGTGG
* ** * * * * *
13589595 TCGAGGAGGCAGTGAATGAAGCGAGCAATCAACAGCTTGACCGCAAGAGACTTTACGTGCA
66 CCGAGGAGGCAACGAAGGAACCGAACAATCAACAGCTTGACCGCAAGAGACTGTACGGGCA
* * * *
13589656 TCTTCCTCGGTTGCAACTCTAACAGGCTTTTCATCGAACAGTCTCTGGGCAGTTACATTCCGT-G
1 TCTTCCTCGGTTGCAACTATAACAGGCTTTTCATCGAACAGTCTCTGAGAAGTTACAATCCGTGG
* * * * * *
13589720 CCATATGAGGCAACGAAGGGACCGAACAATCAAGAGCTTGGCCGCAAGGGACTGTACGGGCA
66 CC-GAGGAGGCAACGAAGGAACCGAACAATCAACAGCTTGACCGCAAGAGACTGTACGGGCA
13589782 TCTTCCTC
1 TCTTCCTC
13589790 ATGAAGCAAC
Statistics
Matches: 110, Mismatches: 23, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
125 2 0.02
126 108 0.98
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.25
Consensus pattern (126 bp):
TCTTCCTCGGTTGCAACTATAACAGGCTTTTCATCGAACAGTCTCTGAGAAGTTACAATCCGTGG
CCGAGGAGGCAACGAAGGAACCGAACAATCAACAGCTTGACCGCAAGAGACTGTACGGGCA
Found at i:13594776 original size:32 final size:35
Alignment explanation
Indices: 13594739--13594821 Score: 127
Period size: 33 Copynumber: 2.4 Consensus size: 35
13594729 GATTTAATTT
13594739 TTTTTAAAAAAATTAATTAAATTA-GGTTT-AGGG
1 TTTTTAAAAAAATTAATTAAATTAGGGTTTAAGGG
13594772 -TTTTAAATAAAATTAATTAAATTAGGGTTTAAGGG
1 TTTTTAAA-AAAATTAATTAAATTAGGGTTTAAGGG
13594807 TTTTTAAAAATAATT
1 TTTTTAAAAA-AATT
13594822 TTGTGTTTAG
Statistics
Matches: 45, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
32 7 0.16
33 16 0.36
34 5 0.11
35 6 0.13
36 11 0.24
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (35 bp):
TTTTTAAAAAAATTAATTAAATTAGGGTTTAAGGG
Found at i:13595125 original size:125 final size:126
Alignment explanation
Indices: 13594903--13595423 Score: 637
Period size: 126 Copynumber: 4.1 Consensus size: 126
13594893 GGTTTTTGTT
* * *
13594903 TTTTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAATATGACTT-TGAAAAAATAGTGAT-
1 TTTTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGA-CATTTCTGAAAAAATAGTG-TC
* * * * *
13594966 AAAAACGCTTCAAGCAGGATGTAATGTCAGCAAAAGTACT-AAAAAAGCTCCCATGTTGACGC
64 AAAAACGCTTCAAGCAGGATGCAATATCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGC
* * * *
13595028 TTTTTTTCTATAGTAGTTTCTGAAAATATAATTTTGAGAAGACATTTCTAAAAAAATAATGTCAA
1 TTTTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGACATTTCTGAAAAAATAGTGTCAA
** * * *
13595093 AAACGCACCAAGCAGGATGCACTATCAGCAAAATTATTGAAAAAAGCTCCCACGAGGACGC
66 AAACGCTTCAAGCAGGATGCAATATCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGC
* *
13595154 TCTTTTTT-TACAGTAGTTCCTAAAAAAATAATTTTGAGAAGACGA-TTCTGAAAAAATAGTGTC
1 T-TTTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGAC-ATTTCTGAAAAAATAGTGTC
* * * * * *
13595217 AAAAACACTTTAAGCAGGATGCACTGTCAGCAAAATTACT-AGAAAAAGCTCCTACGTGGACAC
64 AAAAACGCTTCAAGCAGGATGCAATATCAGCAAAATTACTGA-AAAAAGCTCCCACGTGGACGC
* *
13595280 TTTTTTTCTACAGTAG-TTCTTGAAAAAATAATTTTGATAAAAC-TATTCTGAAAAAATAGTGTC
1 TTTTTTTCTACAGTAGTTTC-TGAAAAAATAATTTTGAGAAGACAT-TTCTGAAAAAATAGTGTC
* *
13595343 AAAAACGCTTTAAGCAGGATGCAATGA-CAGCAAAATTACTGAAAAAAACTCCCACGTGGACGC
64 AAAAACGCTTCAAGCAGGATGCAAT-ATCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGC
*
13595406 TCTTTTTCTACAGTAGTT
1 TTTTTTTCTACAGTAGTT
13595424 CTTGCTCGGC
Statistics
Matches: 340, Mismatches: 43, Indels: 24
0.84 0.11 0.06
Matches are distributed among these distances:
124 4 0.01
125 92 0.27
126 235 0.69
127 9 0.03
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.30
Consensus pattern (126 bp):
TTTTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGACATTTCTGAAAAAATAGTGTCAA
AAACGCTTCAAGCAGGATGCAATATCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGC
Found at i:13595360 original size:252 final size:251
Alignment explanation
Indices: 13594904--13595424 Score: 701
Period size: 252 Copynumber: 2.1 Consensus size: 251
13594894 GTTTTTGTTT
* * * *
13594904 TTTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAATATGACTTTGAAAAAATAGTGATAAA
1 TTTTTT-TACAGTAGTTCCTAAAAAAATAATTTTGAGAAGACGACTTTGAAAAAATAGTGATAAA
* * * * *
13594969 AACGCTTCAAGCAGGATGTAATGTCAGCAAAAGTACTAAAAAAGCTCCCATGTTGACGCTTTTTT
65 AACACTTCAAGCAGGATGCAATGTCAGCAAAAGTACTAAAAAAGCTCCCACGTGGACACTTTTTT
* * *
13595034 TCTATAGTAGTTTCTGAAAATATAATTTTGAGAAGACATTTCTAAAAAAATAATGTCAAAAACGC
130 TCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAAACATTTCTAAAAAAATAATGTCAAAAACGC
* * *
13595099 ACCAAGCAGGATGCACT-ATCAGCAAAATTATTGAAAAAAGCTCCCACGAGGACGCTC
195 ACCAAGCAGGATGCAATGA-CAGCAAAATTACTGAAAAAAACTCCCACGAGGACGCTC
13595156 TTTTTTTACAGTAGTTCCTAAAAAAATAATTTTGAGAAGACGA-TTCTGAAAAAATAGTG-TCAA
1 TTTTTTTACAGTAGTTCCTAAAAAAATAATTTTGAGAAGACGACTT-TGAAAAAATAGTGAT-AA
* * * *
13595219 AAACACTTTAAGCAGGATGCACTGTCAGCAAAATTACTAGAAAAAGCTCCTACGTGGACACTTTT
64 AAACACTTCAAGCAGGATGCAATGTCAGCAAAAGTACTA-AAAAAGCTCCCACGTGGACACTTTT
* * *
13595284 TTTCTACAGTAG-TTCTTGAAAAAATAATTTTGATAAAAC-TATTCTGAAAAAATAGTGTCAAAA
128 TTTCTACAGTAGTTTC-TGAAAAAATAATTTTGAGAAAACAT-TTCTAAAAAAATAATGTCAAAA
*** *
13595347 ACGCTTTAAGCAGGATGCAATGACAGCAAAATTACTGAAAAAAACTCCCACGTGGACGCTC
191 ACGCACCAAGCAGGATGCAATGACAGCAAAATTACTGAAAAAAACTCCCACGAGGACGCTC
*
13595408 TTTTTCTACAGTAGTTC
1 TTTTTTTACAGTAGTTC
13595425 TTGCTCGGCC
Statistics
Matches: 236, Mismatches: 27, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
250 3 0.01
251 86 0.36
252 146 0.62
253 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (251 bp):
TTTTTTTACAGTAGTTCCTAAAAAAATAATTTTGAGAAGACGACTTTGAAAAAATAGTGATAAAA
ACACTTCAAGCAGGATGCAATGTCAGCAAAAGTACTAAAAAAGCTCCCACGTGGACACTTTTTTT
CTACAGTAGTTTCTGAAAAAATAATTTTGAGAAAACATTTCTAAAAAAATAATGTCAAAAACGCA
CCAAGCAGGATGCAATGACAGCAAAATTACTGAAAAAAACTCCCACGAGGACGCTC
Found at i:13600281 original size:50 final size:50
Alignment explanation
Indices: 13600157--13600404 Score: 275
Period size: 49 Copynumber: 4.8 Consensus size: 50
13600147 GATAATAACA
* * ** * *
13600157 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
13600208 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
13600258 TGCCAACGCCATGTCCCAGACATGGTCTTACA-TGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
13600307 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
13600362 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
13600405 TTACCCAAAT
Statistics
Matches: 168, Mismatches: 21, Indels: 11
0.84 0.10 0.05
Matches are distributed among these distances:
49 46 0.27
50 45 0.27
51 33 0.20
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:13600332 original size:99 final size:104
Alignment explanation
Indices: 13600156--13600397 Score: 343
Period size: 99 Copynumber: 2.3 Consensus size: 104
13600146 TGATAATAAC
**
13600156 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACAT-GGATCCTCTCGTGATGGTGCCCATGCCATG
* *
13600221 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
13600258 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGA-CCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGATCCTCTCGTGAT-GGTGCCCATGCCATG
13600320 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
*
13600362 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGG
13600398 GATCTCTTTA
Statistics
Matches: 126, Mismatches: 7, Indels: 11
0.88 0.05 0.08
Matches are distributed among these distances:
98 1 0.01
99 50 0.40
100 3 0.02
101 32 0.25
102 3 0.02
103 1 0.01
104 2 0.02
105 34 0.27
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGATCCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:13600520 original size:13 final size:13
Alignment explanation
Indices: 13600499--13600530 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
13600489 GCTTGGATCA
*
13600499 TCATCAAATAAAT
1 TCATAAAATAAAT
13600512 TCATAAAATAAAT
1 TCATAAAATAAAT
13600525 TCATAA
1 TCATAA
13600531 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:13600777 original size:30 final size:30
Alignment explanation
Indices: 13600742--13600799 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
13600732 CCTCGACTCT
*
13600742 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
13600772 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
13600800 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:13601742 original size:18 final size:18
Alignment explanation
Indices: 13601716--13601759 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
13601706 GACTGAGAAA
* *
13601716 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
13601734 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
13601752 AGGATACA
1 AGGATACA
13601760 CAGATGACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.43, C:0.09, G:0.27, T:0.20
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:13603333 original size:18 final size:19
Alignment explanation
Indices: 13603310--13603348 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
13603300 AAATTAATTT
*
13603310 AAATTACATAA-ATGCAAA
1 AAATTAAATAAGATGCAAA
*
13603328 AAATTAAATAAGATTCAAA
1 AAATTAAATAAGATGCAAA
13603347 AA
1 AA
13603349 TTGAAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.64, C:0.08, G:0.05, T:0.23
Consensus pattern (19 bp):
AAATTAAATAAGATGCAAA
Found at i:13621312 original size:24 final size:23
Alignment explanation
Indices: 13621257--13621311 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 23
13621247 ATTTTTACAT
13621257 ATTTTTTTATTTTTTAAACATACC
1 ATTTTTTTATTTTTTAAACATA-C
13621281 ATTTTTTTAATTTTTTTAAA-ATA-
1 ATTTTTTT-A-TTTTTTAAACATAC
13621304 ATTTTTTT
1 ATTTTTTT
13621312 TCTTAACAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
23 8 0.28
24 8 0.28
25 4 0.14
26 9 0.31
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.65
Consensus pattern (23 bp):
ATTTTTTTATTTTTTAAACATAC
Found at i:13623453 original size:54 final size:54
Alignment explanation
Indices: 13623389--13623493 Score: 210
Period size: 54 Copynumber: 1.9 Consensus size: 54
13623379 TAGAATAATG
13623389 GAATGAAATTGTAATTATTAGAATAGTAATTGTTGGAAAATATGAACGTCAATT
1 GAATGAAATTGTAATTATTAGAATAGTAATTGTTGGAAAATATGAACGTCAATT
13623443 GAATGAAATTGTAATTATTAGAATAGTAATTGTTGGAAAATATGAACGTCA
1 GAATGAAATTGTAATTATTAGAATAGTAATTGTTGGAAAATATGAACGTCA
13623494 TACATGCTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (54 bp):
GAATGAAATTGTAATTATTAGAATAGTAATTGTTGGAAAATATGAACGTCAATT
Found at i:13628030 original size:24 final size:24
Alignment explanation
Indices: 13628003--13628052 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
13627993 ATAACGACAT
13628003 ATACTCAAATGAGATCGGATCTGA
1 ATACTCAAATGAGATCGGATCTGA
13628027 ATACTCAAATGAGATCGGATCTGA
1 ATACTCAAATGAGATCGGATCTGA
13628051 AT
1 AT
13628053 TACCAGTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (24 bp):
ATACTCAAATGAGATCGGATCTGA
Found at i:13630899 original size:18 final size:19
Alignment explanation
Indices: 13630876--13630940 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
13630866 ACACACACCC
* *
13630876 CACCGCT-GTTTCTAATCT
1 CACCGCTAGTATCCAATCT
13630894 CACCGCTAAGTATCCAATCT
1 CACCGCT-AGTATCCAATCT
* *
13630914 CACCGCTACAGTAACTAATCT
1 CACCGCT--AGTATCCAATCT
13630935 CACCGC
1 CACCGC
13630941 CACCGCTGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
18 7 0.18
20 16 0.41
21 16 0.41
ACGTcount: A:0.26, C:0.37, G:0.11, T:0.26
Consensus pattern (19 bp):
CACCGCTAGTATCCAATCT
Found at i:13630933 original size:21 final size:20
Alignment explanation
Indices: 13630887--13630940 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 20
13630877 ACCGCTGTTT
*
13630887 CTAATCTCACCGCTAAGTAT
1 CTAATCTCACCGCTAAGTAA
*
13630907 CCAATCTCACCGCTACAGTAA
1 CTAATCTCACCGCTA-AGTAA
13630928 CTAATCTCACCGC
1 CTAATCTCACCGC
13630941 CACCGCTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.30, C:0.37, G:0.09, T:0.24
Consensus pattern (20 bp):
CTAATCTCACCGCTAAGTAA
Found at i:13640952 original size:15 final size:16
Alignment explanation
Indices: 13640922--13640955 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
13640912 AAATATAGAA
13640922 ATTAAATTCAAAATTT
1 ATTAAATTCAAAATTT
*
13640938 ATTAAATTCAAATTTT
1 ATTAAATTCAAAATTT
13640954 AT
1 AT
13640956 GAAGAGTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTAAATTCAAAATTT
Found at i:13644186 original size:35 final size:34
Alignment explanation
Indices: 13644118--13644289 Score: 227
Period size: 35 Copynumber: 5.0 Consensus size: 34
13644108 TTGGCAAATT
13644118 TATGATACGTAGGTATGGTATTTCCATACTGAGC
1 TATGATACGTAGGTATGGTATTTCCATACTGAGC
*
13644152 TATGATACGTAGGTATGGTATTGTCCATATTGAGC
1 TATGATACGTAGGTATGGTATT-TCCATACTGAGC
* *
13644187 TGTGATACGTAGGTATGGTATTTCCATATTGAGC
1 TATGATACGTAGGTATGGTATTTCCATACTGAGC
* * *
13644221 TATAATACGTAGGTATGGTATTTTCCATACCGAGT
1 TATGATACGTAGGTATGGTA-TTTCCATACTGAGC
* * * *
13644256 TGTGAAACGTAGATATGGTATTAACCATACTGAG
1 TATGATACGTAGGTATGGTATT-TCCATACTGAG
13644290 TTGTGAATCA
Statistics
Matches: 122, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
34 54 0.44
35 68 0.56
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (34 bp):
TATGATACGTAGGTATGGTATTTCCATACTGAGC
Found at i:13644208 original size:69 final size:69
Alignment explanation
Indices: 13644120--13644289 Score: 250
Period size: 69 Copynumber: 2.4 Consensus size: 69
13644110 GGCAAATTTA
* **
13644120 TGATACGTAGGTATGGTATTTCCATACTGAGCTATGATACGTAGGTATGGTATTGTCCATATTGA
1 TGATACGTAGGTATGGTATTTCCATACTGAGCTATAATACGTAGGTATGGTATTGTCCATACCGA
13644185 GCTG
66 GCTG
* *
13644189 TGATACGTAGGTATGGTATTTCCATATTGAGCTATAATACGTAGGTATGGTATTTTCCATACCGA
1 TGATACGTAGGTATGGTATTTCCATACTGAGCTATAATACGTAGGTATGGTATTGTCCATACCGA
*
13644254 GTTG
66 GCTG
* * *
13644258 TGAAACGTAGATATGGTATTAACCATACTGAG
1 TGATACGTAGGTATGGTATT-TCCATACTGAG
13644290 TTGTGAATCA
Statistics
Matches: 90, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
69 81 0.90
70 9 0.10
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (69 bp):
TGATACGTAGGTATGGTATTTCCATACTGAGCTATAATACGTAGGTATGGTATTGTCCATACCGA
GCTG
Found at i:13646937 original size:11 final size:11
Alignment explanation
Indices: 13646914--13646943 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
13646904 ATAAAATATT
13646914 ATAAAACAAATA
1 ATAAAA-AAATA
13646926 ATAAAAAAATA
1 ATAAAAAAATA
13646937 ATAAAAA
1 ATAAAAA
13646944 TAAAGACAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (11 bp):
ATAAAAAAATA
Found at i:13655212 original size:53 final size:52
Alignment explanation
Indices: 13655164--13655332 Score: 157
Period size: 54 Copynumber: 3.2 Consensus size: 52
13655154 TCCAAAAAAA
*
13655164 TTTACTTCCCCCAAACCCTAATTTTTTTTTCTTTTTAATTTCTCCCAAAACT
1 TTTACTTCCCCTAAACCCTAATTTTTTTTTCTTTTTAATTTCTCCCAAAACT
** * *
13655216 TTTACATTCCCCTAAACCCCTCAA-AATTTTTTCCTTTTACTTTCTCCCTAAAACT
1 TTTAC-TTCCCCTAAA-CCCT-AATTTTTTTTTCTTTTTAATTTCTCCC-AAAACT
* * * ** *
13655271 TTTACTTTCCTTAAACCTCT-A-TTTTTTTTCCTTTTGCTTT-TCCTCAAAATT
1 TTTACTTCCCCTAAACC-CTAATTTTTTTTTCTTTTTAATTTCTCC-CAAAACT
13655322 TTTACTTCCCC
1 TTTACTTCCCC
13655333 CAAGCCCCAA
Statistics
Matches: 98, Mismatches: 13, Indels: 13
0.79 0.10 0.10
Matches are distributed among these distances:
51 17 0.17
52 23 0.23
53 11 0.11
54 34 0.35
55 13 0.13
ACGTcount: A:0.21, C:0.30, G:0.01, T:0.49
Consensus pattern (52 bp):
TTTACTTCCCCTAAACCCTAATTTTTTTTTCTTTTTAATTTCTCCCAAAACT
Found at i:13655692 original size:19 final size:19
Alignment explanation
Indices: 13655668--13655705 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
13655658 AAGTTAATAA
*
13655668 CAAATTTGATTACGGTGGG
1 CAAATTTGATTACGATGGG
13655687 CAAATTTGATTACGATGGG
1 CAAATTTGATTACGATGGG
13655706 TGGAAGTGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.32
Consensus pattern (19 bp):
CAAATTTGATTACGATGGG
Found at i:13657106 original size:89 final size:88
Alignment explanation
Indices: 13656942--13657107 Score: 190
Period size: 89 Copynumber: 1.9 Consensus size: 88
13656932 ATACAAGCAT
* * * * * * *
13656942 GCAGTATAACTGCCAGATCAGATGTGCTACGTAGCAAGACTAGCGTATAAGCTGTACTGTGTAAT
1 GCAGTATAACTGCCAGATCAAATATGCTACGTAGCAAGACTAACGTACAAGCGGTACAGTGTAAG
* *
13657007 GTAGTGAACCGCGGTATAGACGC
66 GCAGTAAACCGCGGTATAGACGC
* * *
13657030 GCAGTATAATTGCCAGATCAAATAATGGTACGTAGCATAG-CTAACGTACATGCGGTACAGTGTA
1 GCAGTATAACTGCCAGATCAAAT-ATGCTACGTAGCA-AGACTAACGTACAAGCGGTACAGTGTA
*
13657094 AGGCGGTAAACCGC
64 AGGCAGTAAACCGC
13657108 TATACCATTA
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
88 21 0.33
89 40 0.63
90 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (88 bp):
GCAGTATAACTGCCAGATCAAATATGCTACGTAGCAAGACTAACGTACAAGCGGTACAGTGTAAG
GCAGTAAACCGCGGTATAGACGC
Found at i:13660183 original size:26 final size:24
Alignment explanation
Indices: 13660154--13660202 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
13660144 AATAAAAAAT
*
13660154 TTTAAAAATATAACAAATCAAATATA
1 TTTAAAAACATAA-AAA-CAAATATA
13660180 TTTAAAAACATAAAAACAAATAT
1 TTTAAAAACATAAAAACAAATAT
13660203 TAAAACAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 12 0.55
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (24 bp):
TTTAAAAACATAAAAACAAATATA
Found at i:13660222 original size:21 final size:21
Alignment explanation
Indices: 13660165--13660231 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
13660155 TTAAAAATAT
*
13660165 AACAAAT-CAAAT-ATATTTAA
1 AACAAATAAAAATAATA-TTAA
* *
13660185 AA-ACATAAAAACAAATATTAA
1 AACAAATAAAAA-TAATATTAA
*
13660206 AACAAATAAAAATAATACTAA
1 AACAAATAAAAATAATATTAA
13660227 AACAA
1 AACAA
13660232 TTCTTAAAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
19 3 0.08
20 5 0.14
21 18 0.49
22 11 0.30
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (21 bp):
AACAAATAAAAATAATATTAA
Found at i:13663739 original size:37 final size:37
Alignment explanation
Indices: 13663689--13663802 Score: 135
Period size: 37 Copynumber: 3.1 Consensus size: 37
13663679 ATTCAATCGA
13663689 AACACATCAATCGCTCATAAGAGCTAATCCACCCGAT
1 AACACATCAATCGCTCATAAGAGCTAATCCACCCGAT
* * *
13663726 AACACGTCAATCGCTCATAAGAGCTAGTCCAACCGA-
1 AACACATCAATCGCTCATAAGAGCTAATCCACCCGAT
* * * *
13663762 AACACACCAAAT-TCTCATTAGAGCTAAT-CACCCCAT
1 AACACATC-AATCGCTCATAAGAGCTAATCCACCCGAT
13663798 AACAC
1 AACAC
13663803 GCCAAGTGCT
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
35 5 0.08
36 24 0.37
37 36 0.55
ACGTcount: A:0.39, C:0.32, G:0.11, T:0.18
Consensus pattern (37 bp):
AACACATCAATCGCTCATAAGAGCTAATCCACCCGAT
Found at i:13665586 original size:31 final size:31
Alignment explanation
Indices: 13665548--13665618 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
13665538 GTTTTCATAT
13665548 AACTTGTGAATGCCTATGAATATATAAGTTA
1 AACTTGTGAATGCCTATGAATATATAAGTTA
* *
13665579 AACTTGTGATTGCCTGTGAATATATAAGTTA
1 AACTTGTGAATGCCTATGAATATATAAGTTA
13665610 AACTTGTGA
1 AACTTGTGA
13665619 GTTATTAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (31 bp):
AACTTGTGAATGCCTATGAATATATAAGTTA
Found at i:13668744 original size:22 final size:22
Alignment explanation
Indices: 13668719--13668788 Score: 61
Period size: 25 Copynumber: 3.0 Consensus size: 22
13668709 GTTCAATTGT
13668719 TCCTTTACCTTGAAAATTTCAA
1 TCCTTTACCTTGAAAATTTCAA
*
13668741 TCCTTCCTATTCTTGAAAATTTCAA
1 TCCTT--TA-CCTTGAAAATTTCAA
* **
13668766 GCCTAAACCTT-AAAATTTTCAA
1 TCCTTTACCTTGAAAA-TTTCAA
13668788 T
1 T
13668789 TATCACTAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
21 4 0.11
22 14 0.37
23 1 0.03
24 2 0.05
25 17 0.45
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.40
Consensus pattern (22 bp):
TCCTTTACCTTGAAAATTTCAA
Found at i:13669865 original size:21 final size:21
Alignment explanation
Indices: 13669824--13669867 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
13669814 TACACTATAT
**
13669824 TTTATATTTTTTTACTTAAAG
1 TTTATATTTTTTTACAAAAAG
13669845 TTTA-ATTTTTTTAACAAAAAG
1 TTTATATTTTTTT-ACAAAAAG
13669866 TT
1 TT
13669868 AACATTTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.57
Consensus pattern (21 bp):
TTTATATTTTTTTACAAAAAG
Found at i:13672549 original size:4 final size:4
Alignment explanation
Indices: 13672540--13672581 Score: 57
Period size: 4 Copynumber: 9.8 Consensus size: 4
13672530 ATTTTAATGT
13672540 TTAA TTAA TTAA TTAAA TTAAA TTAA TTGAA TTAA TTAA TTA
1 TTAA TTAA TTAA TT-AA TT-AA TTAA TT-AA TTAA TTAA TTA
13672582 TTTTAATCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 23 0.64
5 13 0.36
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (4 bp):
TTAA
Found at i:13672563 original size:18 final size:18
Alignment explanation
Indices: 13672542--13672578 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
13672532 TTTAATGTTT
13672542 AATTAATT-AATTAAATTA
1 AATTAATTGAATT-AATTA
13672560 AATTAATTGAATTAATTA
1 AATTAATTGAATTAATTA
13672578 A
1 A
13672579 TTATTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
AATTAATTGAATTAATTA
Found at i:13672572 original size:27 final size:29
Alignment explanation
Indices: 13672505--13672581 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 29
13672495 TTACAATATC
*
13672505 TTAAGTT-AATT-TTTAATTAAATTAAATT
1 TTAAGTTGAATTAATTAATTAAATTAAA-T
*
13672533 TTAATGTTTAATTAATTAATTAAATTAAA-
1 TTAA-GTTGAATTAATTAATTAAATTAAAT
13672562 TTAA-TTGAATTAATTAATTA
1 TTAAGTTGAATTAATTAATTA
13672582 TTTTAATCAA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 15 0.34
28 4 0.09
29 7 0.16
30 4 0.09
31 14 0.32
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (29 bp):
TTAAGTTGAATTAATTAATTAAATTAAAT
Found at i:13672575 original size:31 final size:30
Alignment explanation
Indices: 13672517--13672581 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 30
13672507 AAGTTAATTT
*
13672517 TTAATTAAATTAAATTTTAATGTTTAATTAA
1 TTAATTAAATTAAA-TTTAATGATTAATTAA
13672548 TTAATTAAATTAAA-TTAATTGAATTAATTAA
1 TTAATTAAATTAAATTTAA-TG-ATTAATTAA
13672579 TTA
1 TTA
13672582 TTTTAATCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 4 0.13
30 2 0.06
31 25 0.81
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (30 bp):
TTAATTAAATTAAATTTAATGATTAATTAA
Found at i:13672998 original size:27 final size:28
Alignment explanation
Indices: 13672968--13673022 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
13672958 TAAATTTATG
13672968 AATAA-TTTTTTTTAATCTCTAACTGCT
1 AATAATTTTTTTTTAATCTCTAACTGCT
13672995 AATAATTTTTTTTTAATCTCTAACTGCT
1 AATAATTTTTTTTTAATCTCTAACTGCT
13673023 TACTATTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.29, C:0.15, G:0.04, T:0.53
Consensus pattern (28 bp):
AATAATTTTTTTTTAATCTCTAACTGCT
Found at i:13673953 original size:125 final size:119
Alignment explanation
Indices: 13673726--13673956 Score: 270
Period size: 125 Copynumber: 1.9 Consensus size: 119
13673716 TCTTTTAATG
*
13673726 ATTTATGTTCTTTCTTTACCTGGAAAATTGGGTAATTTGAGGTTCTAAGTTCGGCGGTTCTAATG
1 ATTTATGTTCTTTCTTTACCTGGAAAATTGGGTAATTTGAGCTTCTAAGTTCGGCGGTTCTAATG
*
13673791 ATGGTTCTTTTATGGTAGTATGCTATTATTTATGATTTTTATTTTTTTAAGAATA
66 ATGGTTCATTTATGGTAGTA-GCTATTATTTATGATTTTTATTTTTTTAAGAATA
* * ***
13673846 ATTT-TGTTCTTTTTTTTCCTGGAAAATTGGGTAATTTGAGATTCTTCCATTAAGTTCTTTGGTT
1 ATTTATGTTCTTTCTTTACCTGGAAAATTGGGTAATTTGAG---CTT-C--TAAGTTCGGCGGTT
* *
13673910 CTAATGATTGTTCATTTCT-GTCATGTA-CTATTATTTGATGATTTTTA
60 CTAATGATGGTTCATTTATGGT-A-GTAGCTATTATTT-ATGATTTTTA
13673957 CGTTTTCTTT
Statistics
Matches: 93, Mismatches: 9, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
119 34 0.37
120 4 0.04
122 2 0.02
123 1 0.01
124 11 0.12
125 38 0.41
126 3 0.03
ACGTcount: A:0.22, C:0.10, G:0.17, T:0.51
Consensus pattern (119 bp):
ATTTATGTTCTTTCTTTACCTGGAAAATTGGGTAATTTGAGCTTCTAAGTTCGGCGGTTCTAATG
ATGGTTCATTTATGGTAGTAGCTATTATTTATGATTTTTATTTTTTTAAGAATA
Found at i:13688225 original size:13 final size:13
Alignment explanation
Indices: 13688201--13688227 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13688191 GTGGGAGGAA
13688201 AGTTAGGGAGGTT
1 AGTTAGGGAGGTT
13688214 AGTTAGGGAGGTT
1 AGTTAGGGAGGTT
13688227 A
1 A
13688228 TCAGATTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.44, T:0.30
Consensus pattern (13 bp):
AGTTAGGGAGGTT
Found at i:13706171 original size:15 final size:17
Alignment explanation
Indices: 13706152--13706191 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
13706142 TTAAAAAAGC
13706152 TTAAAAAAGAAAAA-TA
1 TTAAAAAAGAAAAATTA
*
13706168 -TAAACAAGAAAAATTA
1 TTAAAAAAGAAAAATTA
13706184 TTAAAAAA
1 TTAAAAAA
13706192 AGTTATAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
15 12 0.60
16 2 0.10
17 6 0.30
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.20
Consensus pattern (17 bp):
TTAAAAAAGAAAAATTA
Found at i:13706216 original size:15 final size:17
Alignment explanation
Indices: 13706188--13706224 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
13706178 AAATTATTAA
*
13706188 AAAAAGTTATAAAG-AT
1 AAAAAGTTAAAAAGTAT
13706204 AAAAA-TTAAAAAGTAT
1 AAAAAGTTAAAAAGTAT
13706220 AAAAA
1 AAAAA
13706225 AAACCCTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.22
Consensus pattern (17 bp):
AAAAAGTTAAAAAGTAT
Found at i:13709273 original size:35 final size:35
Alignment explanation
Indices: 13709234--13709350 Score: 83
Period size: 35 Copynumber: 3.2 Consensus size: 35
13709224 GGATAAACCA
*
13709234 ACGATATTTACACCCAGTGCTAGTCGGGTATACCG
1 ACGATATTTACACCAAGTGCTAGTCGGGTATACCG
** * * * * *
13709269 ACGATAGTAATTGTGAGCCTAGCT-CTAGTTGGATAAACCA
1 ACGATA-T--TT-ACA-CCAAG-TGCTAGTCGGGTATACCG
* *
13709309 ACGATATTTGCACCAAATGCTAGTCGGGTATACCG
1 ACGATATTTACACCAAGTGCTAGTCGGGTATACCG
13709344 ACGATAT
1 ACGATAT
13709351 CTTCGTCTTG
Statistics
Matches: 60, Mismatches: 15, Indels: 14
0.67 0.17 0.16
Matches are distributed among these distances:
34 1 0.02
35 28 0.47
36 2 0.03
37 2 0.03
38 2 0.03
39 2 0.03
40 22 0.37
41 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.26
Consensus pattern (35 bp):
ACGATATTTACACCAAGTGCTAGTCGGGTATACCG
Found at i:13709301 original size:75 final size:75
Alignment explanation
Indices: 13709207--13709349 Score: 250
Period size: 75 Copynumber: 1.9 Consensus size: 75
13709197 GTATTAAATA
* *
13709207 TGAGCCCAGCTCTAGTTGGATAAACCAACGATATTTACACCCAGTGCTAGTCGGGTATACCGACG
1 TGAGCCCAGCTCTAGTTGGATAAACCAACGATATTTACACCAAATGCTAGTCGGGTATACCGACG
13709272 ATAGTAATTG
66 ATAGTAATTG
* *
13709282 TGAGCCTAGCTCTAGTTGGATAAACCAACGATATTTGCACCAAATGCTAGTCGGGTATACCGACG
1 TGAGCCCAGCTCTAGTTGGATAAACCAACGATATTTACACCAAATGCTAGTCGGGTATACCGACG
13709347 ATA
66 ATA
13709350 TCTTCGTCTT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 64 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.25
Consensus pattern (75 bp):
TGAGCCCAGCTCTAGTTGGATAAACCAACGATATTTACACCAAATGCTAGTCGGGTATACCGACG
ATAGTAATTG
Found at i:13709313 original size:40 final size:36
Alignment explanation
Indices: 13709207--13709317 Score: 100
Period size: 35 Copynumber: 3.0 Consensus size: 36
13709197 GTATTAAATA
13709207 TGAGCCCAGCTCTAGTTGGATAAACCAACGATATTT
1 TGAGCCCAGCTCTAGTTGGATAAACCAACGATATTT
** * * * *
13709243 ACA-CCCAG-TGCTAGTCGGGTATACCGACGATAGTAATT
1 TGAGCCCAGCT-CTAGTTGGATAAACCAACGATA-T--TT
*
13709281 GTGAGCCTAGCTCTAGTTGGATAAACCAACGATATTT
1 -TGAGCCCAGCTCTAGTTGGATAAACCAACGATATTT
13709318 GCACCAAATG
Statistics
Matches: 55, Mismatches: 13, Indels: 13
0.68 0.16 0.16
Matches are distributed among these distances:
34 1 0.02
35 23 0.42
36 2 0.04
37 2 0.04
38 2 0.04
39 2 0.04
40 22 0.40
41 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (36 bp):
TGAGCCCAGCTCTAGTTGGATAAACCAACGATATTT
Found at i:13712947 original size:10 final size:10
Alignment explanation
Indices: 13712932--13713017 Score: 50
Period size: 10 Copynumber: 8.1 Consensus size: 10
13712922 GTATAAGAGT
13712932 AATAAATAAA
1 AATAAATAAA
13712942 AATAAATAAA
1 AATAAATAAA
*
13712952 TA-AAATAAA
1 AATAAATAAA
*
13712961 ATTAGTAAAATAGA
1 A--A-T-AAATAAA
13712975 AATAAATAATA
1 AATAAATAA-A
* *
13712986 TAAAAAATAAT
1 -AATAAATAAA
*
13712997 AATACAT-AA
1 AATAAATAAA
13713006 AATAAAATAAA
1 AAT-AAATAAA
13713017 A
1 A
13713018 GGGGGTGGCT
Statistics
Matches: 57, Mismatches: 10, Indels: 17
0.68 0.12 0.20
Matches are distributed among these distances:
9 11 0.19
10 24 0.42
11 6 0.11
12 9 0.16
14 7 0.12
ACGTcount: A:0.73, C:0.01, G:0.02, T:0.23
Consensus pattern (10 bp):
AATAAATAAA
Found at i:13712951 original size:14 final size:14
Alignment explanation
Indices: 13712932--13713016 Score: 61
Period size: 14 Copynumber: 6.1 Consensus size: 14
13712922 GTATAAGAGT
13712932 AATAAATAAAAATA
1 AATAAATAAAAATA
13712946 AATAAAT-AAAATAA
1 AATAAATAAAAAT-A
* * *
13712960 AATTAGTAAAATAGA
1 AATAAATAAAA-ATA
*
13712975 AATAAAT-AATATA
1 AATAAATAAAAATA
*
13712988 AA-AAATAATAATA
1 AATAAATAAAAATA
*
13713001 CATAAA-ATAAAATA
1 AATAAATA-AAAATA
13713015 AA
1 AA
13713017 AGGGGGTGGC
Statistics
Matches: 53, Mismatches: 12, Indels: 12
0.69 0.16 0.16
Matches are distributed among these distances:
12 4 0.08
13 15 0.28
14 24 0.45
15 9 0.17
16 1 0.02
ACGTcount: A:0.73, C:0.01, G:0.02, T:0.24
Consensus pattern (14 bp):
AATAAATAAAAATA
Found at i:13712957 original size:19 final size:19
Alignment explanation
Indices: 13712935--13713016 Score: 63
Period size: 18 Copynumber: 4.7 Consensus size: 19
13712925 TAAGAGTAAT
13712935 AAATAAAAATAAATAAATA
1 AAATAAAAATAAATAAATA
*
13712954 AAAT-AAAAT---T-AGTA
1 AAATAAAAATAAATAAATA
*
13712968 AAATAGAAATAAATAATATA
1 AAATAAAAATAAATAA-ATA
* *
13712988 AAA-AATAAT-AATACATA
1 AAATAAAAATAAATAAATA
13713005 AAAT-AAAATAAA
1 AAATAAAAATAAA
13713017 AGGGGGTGGC
Statistics
Matches: 48, Mismatches: 7, Indels: 17
0.67 0.10 0.24
Matches are distributed among these distances:
14 7 0.15
15 5 0.10
17 10 0.21
18 12 0.25
19 9 0.19
20 5 0.10
ACGTcount: A:0.73, C:0.01, G:0.02, T:0.23
Consensus pattern (19 bp):
AAATAAAAATAAATAAATA
Found at i:13713000 original size:22 final size:22
Alignment explanation
Indices: 13712967--13713012 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
13712957 TAAAATTAGT
*
13712967 AAAATAGAAATAAATAATATAA
1 AAAATAGAAATAAATAAAATAA
*
13712989 AAAATA-ATAATACATAAAATAA
1 AAAATAGA-AATAAATAAAATAA
13713011 AA
1 AA
13713013 TAAAAGGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (22 bp):
AAAATAGAAATAAATAAAATAA
Found at i:13719222 original size:24 final size:24
Alignment explanation
Indices: 13719195--13719246 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
13719185 TTTCTACAAG
* *
13719195 ATTTAGTATTTATTATTATAATAT
1 ATTTAGCATTTATTATCATAATAT
*
13719219 ATTTAGCATTTATTATCATAATTT
1 ATTTAGCATTTATTATCATAATAT
13719243 ATTT
1 ATTT
13719247 GACCTACAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (24 bp):
ATTTAGCATTTATTATCATAATAT
Found at i:13726462 original size:53 final size:53
Alignment explanation
Indices: 13726283--13726489 Score: 189
Period size: 53 Copynumber: 3.8 Consensus size: 53
13726273 ATTAGGGTTT
* * * * * *
13726283 AAGGATACCAAGTAAGACCATGCCAAGGCATTGCATTGGTAAGTTTTACAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAG-TTCATAAGGC
* * * * * * * *
13726337 AAGGAAATCATGCAAGACCATGTCAAGACATGGCATTGATAAACTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTC-ATAAGGC
* * * *
13726392 AAAGATCCCATGTAAGACCATGCCAAGGCATGGCAATGGTGAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
* * * *
13726445 AAGGATACTACGTAAGACCATGTCAAGACATGGAAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
13726490 TAAAAAGGAA
Statistics
Matches: 119, Mismatches: 32, Indels: 5
0.76 0.21 0.03
Matches are distributed among these distances:
53 44 0.37
54 36 0.30
55 39 0.33
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
Found at i:13733798 original size:53 final size:53
Alignment explanation
Indices: 13733616--13733822 Score: 216
Period size: 53 Copynumber: 3.8 Consensus size: 53
13733606 ATTAGGGTTT
* * * * *
13733616 AAGGATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTTTACAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAG-TTCATAAGGC
* * * * * * * *
13733670 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAACTACTATAAGGA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTC-ATAAGGC
* * * *
13733725 AAAGATCCCATGTAAGACCATGCCAAGGCATGGCAATGGTGAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
* *
13733778 AAGGATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
13733823 TAAAAAGAAA
Statistics
Matches: 122, Mismatches: 29, Indels: 5
0.78 0.19 0.03
Matches are distributed among these distances:
53 45 0.37
54 38 0.31
55 39 0.32
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
Found at i:13742100 original size:46 final size:46
Alignment explanation
Indices: 13742048--13742314 Score: 410
Period size: 46 Copynumber: 5.8 Consensus size: 46
13742038 AGTGTGCTCT
*
13742048 CTGATATGGAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
13742094 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGAAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
13742140 CTGATATGAAATGTGTAAGGCCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
13742186 GTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAT
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
13742232 GTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
13742278 ATGACA-GAAAACGAGTAAAACCATAGTTGAAAGATAC
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATAC
13742315 TATGACATCA
Statistics
Matches: 206, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
45 1 0.00
46 205 1.00
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:13743346 original size:6 final size:6
Alignment explanation
Indices: 13743335--13743380 Score: 58
Period size: 6 Copynumber: 7.5 Consensus size: 6
13743325 GTGTTTGAAA
*
13743335 AAAAAG AAAAAG AAAAAG AAAAGAA AAGAAAG AAAAA- AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAA-AG AA-AAAG AAAAAG AAAAAG AAA
13743381 GAAAGAGGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 5 0.14
6 22 0.63
7 6 0.17
8 2 0.06
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:13743350 original size:5 final size:5
Alignment explanation
Indices: 13743331--13743384 Score: 51
Period size: 5 Copynumber: 10.8 Consensus size: 5
13743321 TTGAGTGTTT
*
13743331 GAAAA -AAAA GAAAAA GAAAAA GAAAA GAAAA G-AAA GAAAA -AAAA AAGAAA
1 GAAAA GAAAA G-AAAA G-AAAA GAAAA GAAAA GAAAA GAAAA GAAAA GA-AAA
13743381 GAAA
1 GAAA
13743385 GAGGGGGAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
4 12 0.28
5 16 0.37
6 15 0.35
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:13743366 original size:20 final size:19
Alignment explanation
Indices: 13743332--13743386 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 19
13743322 TGAGTGTTTG
13743332 AAAAAAAAG-AA-AAAGAA
1 AAAAAAAAGAAAGAAAGAA
*
13743349 AAAGAAAAGAAAAGAAAGAA
1 AAAAAAAAG-AAAGAAAGAA
13743369 AAAAAAAAGAAAGAAAGA
1 AAAAAAAAGAAAGAAAGA
13743387 GGGGGAATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.24
19 11 0.33
20 14 0.42
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (19 bp):
AAAAAAAAGAAAGAAAGAA
Found at i:13743384 original size:15 final size:14
Alignment explanation
Indices: 13743331--13743380 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 14
13743321 TTGAGTGTTT
13743331 GAAAAAAAAGAAAAA
1 GAAAAAAAA-AAAAA
13743346 GAAAAAGAAAAGAAAA
1 GAAAAA-AAAA-AAAA
13743362 GAAAGAAAAAAAAAA
1 GAAA-AAAAAAAAAA
13743377 GAAA
1 GAAA
13743381 GAAAGAGGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
15 15 0.47
16 15 0.47
17 2 0.06
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
GAAAAAAAAAAAAA
Found at i:13746971 original size:46 final size:46
Alignment explanation
Indices: 13746919--13747599 Score: 1021
Period size: 46 Copynumber: 14.8 Consensus size: 46
13746909 AGTGTGCTCT
*
13746919 CTGATATGGAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
13746965 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGG-AGAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCA-AC
13747011 CTGATATGAAATGTGTAAG-CCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
13747056 GTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
13747102 GTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* **
13747148 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
13747194 CTGACATGAAATGAGTAAGACCGTGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
13747240 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGG-AGAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCA-AC
13747286 CTGATATGAAATGTGTAATG-CCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAA-GACCATGGTTGAAAGATACCATGGCAAC
*
13747332 GTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
13747378 GTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* **
13747424 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
13747470 CTGACATGAAATGAGTAAGACCGTGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *** **
13747516 ATGACGGGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
13747563 ATGACA-GAAAACGAGTAAAACCATAGTTGAAAGATAC
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATAC
13747600 TATGACATCA
Statistics
Matches: 599, Mismatches: 28, Indels: 16
0.93 0.04 0.02
Matches are distributed among these distances:
45 45 0.08
46 511 0.85
47 43 0.07
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:13749302 original size:29 final size:29
Alignment explanation
Indices: 13749258--13749348 Score: 146
Period size: 29 Copynumber: 3.1 Consensus size: 29
13749248 TTAACAAAGA
*
13749258 AATGCCTCTAAAATAATAACAAAATTAAC
1 AATGCCTTTAAAATAATAACAAAATTAAC
* *
13749287 AATGTCTTTAATATAATAACAAAATTAAC
1 AATGCCTTTAAAATAATAACAAAATTAAC
13749316 AAATGCCTTTAAAATAATAACAAAATTAAC
1 -AATGCCTTTAAAATAATAACAAAATTAAC
13749346 AAT
1 AAT
13749349 AAAATAAGTT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 29 0.52
30 27 0.48
ACGTcount: A:0.55, C:0.13, G:0.03, T:0.29
Consensus pattern (29 bp):
AATGCCTTTAAAATAATAACAAAATTAAC
Found at i:13749333 original size:30 final size:30
Alignment explanation
Indices: 13749257--13749347 Score: 148
Period size: 30 Copynumber: 3.1 Consensus size: 30
13749247 CTTAACAAAG
*
13749257 AAATGCCTCTAAAATAATAACAAAATTAAC
1 AAATGCCTTTAAAATAATAACAAAATTAAC
* *
13749287 -AATGTCTTTAATATAATAACAAAATTAAC
1 AAATGCCTTTAAAATAATAACAAAATTAAC
13749316 AAATGCCTTTAAAATAATAACAAAATTAAC
1 AAATGCCTTTAAAATAATAACAAAATTAAC
13749346 AA
1 AA
13749348 TAAAATAAGT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 26 0.47
30 29 0.53
ACGTcount: A:0.56, C:0.13, G:0.03, T:0.27
Consensus pattern (30 bp):
AAATGCCTTTAAAATAATAACAAAATTAAC
Found at i:13753681 original size:42 final size:42
Alignment explanation
Indices: 13753593--13753682 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 42
13753583 AAATTAGTTT
* ** * *
13753593 CGATGCCATGCCCCAGACAAGGTCTTATACGTGATCTCATAT
1 CGATGCCATGCCCCAAACAAGGTCTTATACGAAATCACATAA
* * *
13753635 CGATGCCATGTCCCAAACATGGTCTTATACGAAATCACTTAA
1 CGATGCCATGCCCCAAACAAGGTCTTATACGAAATCACATAA
13753677 CGATGC
1 CGATGC
13753683 TGAAGCCATA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.26
Consensus pattern (42 bp):
CGATGCCATGCCCCAAACAAGGTCTTATACGAAATCACATAA
Found at i:13757119 original size:11 final size:11
Alignment explanation
Indices: 13757103--13757128 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
13757093 TTTTTCTTGC
13757103 AATTTAATTTT
1 AATTTAATTTT
13757114 AATTTAATTTT
1 AATTTAATTTT
13757125 AATT
1 AATT
13757129 ATTATTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
AATTTAATTTT
Found at i:13762667 original size:21 final size:21
Alignment explanation
Indices: 13762641--13762694 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
13762631 CAGCGGTGGT
*
13762641 GGTGAGATTAGTTACTGTAGC
1 GGTGAGATTAGATACTGTAGC
*
13762662 GGTGAGATTGGATACTGTAGC
1 GGTGAGATTAGATACTGTAGC
13762683 GGTGAGATTAGA
1 GGTGAGATTAGA
13762695 AACAACGGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.26, C:0.07, G:0.37, T:0.30
Consensus pattern (21 bp):
GGTGAGATTAGATACTGTAGC
Found at i:13764745 original size:32 final size:32
Alignment explanation
Indices: 13764706--13764833 Score: 211
Period size: 32 Copynumber: 4.0 Consensus size: 32
13764696 CATAAAAAAT
*
13764706 ATCATACATTAGCTTTACATATAAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
*
13764738 ATCATACATTAGTTTTGCATATAAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
* * *
13764770 ATCATACATTAGGTTCACATATAAAAATGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
13764802 ATCATACATTAGTTTTACATATAAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
13764834 CATAGTTATA
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 87 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (32 bp):
ATCATACATTAGTTTTACATATAAAAAAGTAG
Found at i:13766450 original size:24 final size:27
Alignment explanation
Indices: 13766423--13766484 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 27
13766413 AACAATTTAA
13766423 AATAATTAAAAAGAAATTT-AA-TTT-
1 AATAATTAAAAAGAAATTTAAATTTTC
* *
13766447 AATAA-TCAAAATAAATTTAAATTTTC
1 AATAATTAAAAAGAAATTTAAATTTTC
13766473 AATAATTAAAAA
1 AATAATTAAAAA
13766485 TATTTATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 11 0.35
24 7 0.23
25 3 0.10
26 5 0.16
27 5 0.16
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (27 bp):
AATAATTAAAAAGAAATTTAAATTTTC
Found at i:13769377 original size:25 final size:25
Alignment explanation
Indices: 13769349--13769406 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
13769339 TACAAACTGT
13769349 GAATATGGTAGCAAGAAGAAACAGA
1 GAATATGGTAGCAAGAAGAAACAGA
13769374 GAATATGGTAGCAAGAAGAAACAGA
1 GAATATGGTAGCAAGAAGAAACAGA
13769399 GAATATGG
1 GAATATGG
13769407 GAATGAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.50, C:0.07, G:0.29, T:0.14
Consensus pattern (25 bp):
GAATATGGTAGCAAGAAGAAACAGA
Found at i:13776807 original size:502 final size:504
Alignment explanation
Indices: 13775857--13776831 Score: 1535
Period size: 502 Copynumber: 1.9 Consensus size: 504
13775847 TAAGGAGACA
* * *
13775857 CATGAGATGTGTGCTACATTTGTTGTAGTTCATGCACCTACCTACTTTCCGTTCAAAAAGAATTA
1 CATGAGATGTGTGCTACATTTGCTATAGTTCATGCACCTACCTACTTTCCGTTCAAAAAGAAATA
* * *
13775922 AGCATTTACAAAATCCAAATCATAATTCAAATGTATTCTAGAAATGGTAGAAAAAAATATATTTT
66 AGCACTTACAAAATCCAAATCATAATTCAAATGTATTCCAGAAAGGGTAGAAAAAAATATATTTT
* ** * *
13775987 TTCTGCTTTTTTTTATAAAAATGAGAGGATTTATAATTTAATCCTTATACTTTTAAATCTTTTTA
131 TTCTCCCATTTTTTATAAAAATGAGAGAATTTAAAATTTAATCCTTATACTTTTAAATCTTTTTA
* * * * *
13776052 TTTGGTCTTAAATGTGATTCTCGTAATATCAAAACATTTTCCAACTTATCCTTATGCCTATTAAT
196 TTTGGTCTCAAATGCGATTCTCATAATACCAAAACATTATCCAACTTATCCTTATGCCTATTAAT
* * * *
13776117 TAGTACTAAGACACTCATACTTTGATCAAATTGCACTTTTAGTCCTCAAACTTTACAAATTTTTT
261 TAGTACT-A-ACACTCATACTTTAATAAAATTACACTTTTAGTCCTCAAACTTTACAAATATTTT
* *
13776182 TGGTTTGGTCCTTTAATCACACTTTCAAGTCTAAAATTCTTTTCATTTATTCTCATATCCAAAAT
324 TGGTTTGGTACTTCAATCACACTTTCAAGTCTAAAATTCTTTTCATTTATTCTCATATCCAAAAT
* *
13776247 CACTTTATTTTCATAAGAATTATTTGATTCGAAAAATTTTGCATTTTTCTCGAAAATTCACTGTA
389 CACTTTATTTTCATAAGAATTATTTGATTCGAAAAATTTTGCATTTTTCTCAAAAATTCACTATA
*
13776312 TCCACTATGGAAATAGTGTAACGTGTTTAATTGGAAATTTTGGAGTGTTAT
454 TCCACTATCGAAATAGTGTAACGTGTTTAATTGGAAATTTTGGAGTGTTAT
* * *
13776363 CATGAGATGTGTGCTACCTTTGCTATAGTTCATGCACCTGCCTACTTTCTGTTCAAAAAGAAATA
1 CATGAGATGTGTGCTACATTTGCTATAGTTCATGCACCTACCTACTTTCCGTTCAAAAAGAAATA
* * * * *
13776428 AGCACTTATAAAATCCAAAAATTATAATTCAAATGTATTCCATAAAGGGTAGAGAAAATTATATT
66 AGCACTTACAAAATCC--AAATCATAATTCAAATGTATTCCAGAAAGGGTAGAAAAAAATATATT
13776493 TTTT-TCCCATTTTTTATAAAAATGAGAGAATTTAAAATTTAATCCTTATACTTTTAAATCTTTT
129 TTTTCTCCCATTTTTTATAAAAATGAGAGAATTTAAAATTTAATCCTTATACTTTTAAATCTTTT
* * *
13776557 TATTTGGTCTCAAATGCGATTCTCATAGTGCCAATACATTATCCAACTTATCCTTATGCCTATTA
194 TATTTGGTCTCAAATGCGATTCTCATAATACCAAAACATTATCCAACTTATCCTTATGCCTATTA
*
13776622 ATTAGTACT-A-ACTCATATTTTAATAAAATTACACTTTTAGTCCTCAAACTTTACAAA-ATTTT
259 ATTAGTACTAACACTCATACTTTAATAAAATTACACTTTTAGTCCTCAAACTTTACAAATATTTT
*
13776684 TGGTTTGGTACTTCAATCACACTTTCAATTCTAAAATTCTTTTCATTTATTCTCATATCCAAAAT
324 TGGTTTGGTACTTCAATCACACTTTCAAGTCTAAAATTCTTTTCATTTATTCTCATATCCAAAAT
13776749 CACTTTATTTTCATAAGAATTATTTGATTCGAAAAATTTTGCATTTTTCTCAAAAATTCACTATA
389 CACTTTATTTTCATAAGAATTATTTGATTCGAAAAATTTTGCATTTTTCTCAAAAATTCACTATA
*
13776814 TCCATTATCGAAATAGTG
454 TCCACTATCGAAATAGTG
13776832 CAAAGCATTT
Statistics
Matches: 428, Mismatches: 39, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
502 145 0.34
503 43 0.10
504 1 0.00
506 73 0.17
507 121 0.28
508 45 0.11
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (504 bp):
CATGAGATGTGTGCTACATTTGCTATAGTTCATGCACCTACCTACTTTCCGTTCAAAAAGAAATA
AGCACTTACAAAATCCAAATCATAATTCAAATGTATTCCAGAAAGGGTAGAAAAAAATATATTTT
TTCTCCCATTTTTTATAAAAATGAGAGAATTTAAAATTTAATCCTTATACTTTTAAATCTTTTTA
TTTGGTCTCAAATGCGATTCTCATAATACCAAAACATTATCCAACTTATCCTTATGCCTATTAAT
TAGTACTAACACTCATACTTTAATAAAATTACACTTTTAGTCCTCAAACTTTACAAATATTTTTG
GTTTGGTACTTCAATCACACTTTCAAGTCTAAAATTCTTTTCATTTATTCTCATATCCAAAATCA
CTTTATTTTCATAAGAATTATTTGATTCGAAAAATTTTGCATTTTTCTCAAAAATTCACTATATC
CACTATCGAAATAGTGTAACGTGTTTAATTGGAAATTTTGGAGTGTTAT
Found at i:13780568 original size:61 final size:63
Alignment explanation
Indices: 13780493--13780641 Score: 168
Period size: 60 Copynumber: 2.5 Consensus size: 63
13780483 CTATTCAGAA
* *
13780493 ATCAGAGT-TAACTGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCC-CTTAC-AGT
1 ATCAGAGTAT-ACTGGGCCTTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAGT
* * * *
13780554 ATCAGAGTATACTGGGCC-TAGCCCATGTCAGTATCAATTTGGGCCGTAGCCCTATTACAAGT
1 ATCAGAGTATACTGGGCCTTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAGT
* *
13780616 -TGAGA-TATATTGGGCCTT-GCCCATAT
1 ATCAGAGTATACTGGGCCTTAGCCCATAT
13780642 TAACACAGTT
Statistics
Matches: 75, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
60 46 0.61
61 25 0.33
62 4 0.05
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (63 bp):
ATCAGAGTATACTGGGCCTTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAGT
Found at i:13781337 original size:16 final size:15
Alignment explanation
Indices: 13781316--13781346 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
13781306 CGAAATGTCA
13781316 GCTTTTCGGCATTTTG
1 GCTTTTCGGC-TTTTG
13781332 GCTTTTCGGCTTTTG
1 GCTTTTCGGCTTTTG
13781347 CCGATCTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.03, C:0.19, G:0.26, T:0.52
Consensus pattern (15 bp):
GCTTTTCGGCTTTTG
Found at i:13783653 original size:44 final size:44
Alignment explanation
Indices: 13783590--13783678 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
13783580 TGGTTAGAAG
13783590 ATAAACAAATTAAAAAGATGAATATTTATCAAATTCTAAAACTT
1 ATAAACAAATTAAAAAGATGAATATTTATCAAATTCTAAAACTT
13783634 ATAAACAAATTAAAAAGATGAATATTTATCAAATTCTAAAACTT
1 ATAAACAAATTAAAAAGATGAATATTTATCAAATTCTAAAACTT
13783678 A
1 A
13783679 CTTACGTAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.55, C:0.09, G:0.04, T:0.31
Consensus pattern (44 bp):
ATAAACAAATTAAAAAGATGAATATTTATCAAATTCTAAAACTT
Found at i:13783667 original size:24 final size:24
Alignment explanation
Indices: 13783595--13783668 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
13783585 AGAAGATAAA
13783595 CAAATTAAAAAGATGAATATTTAT
1 CAAATTAAAAAGATGAATATTTAT
* * * *
13783619 CAAATTCTAAAA-CT---TA-TAAA
1 CAAATT-AAAAAGATGAATATTTAT
13783639 CAAATTAAAAAGATGAATATTTAT
1 CAAATTAAAAAGATGAATATTTAT
13783663 CAAATT
1 CAAATT
13783669 CTAAAACTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 12
0.64 0.14 0.21
Matches are distributed among these distances:
19 4 0.11
20 9 0.25
21 2 0.06
23 2 0.06
24 15 0.42
25 4 0.11
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.32
Consensus pattern (24 bp):
CAAATTAAAAAGATGAATATTTAT
Found at i:13786118 original size:13 final size:13
Alignment explanation
Indices: 13786100--13786124 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13786090 TCATGTGGAA
13786100 ATGATTGCAAACC
1 ATGATTGCAAACC
13786113 ATGATTGCAAAC
1 ATGATTGCAAAC
13786125 GATTGCATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (13 bp):
ATGATTGCAAACC
Found at i:13791326 original size:19 final size:18
Alignment explanation
Indices: 13791282--13791329 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
13791272 TATTTCTTTC
*
13791282 GTTGGGTTTGAAGTTTTA
1 GTTGGATTTGAAGTTTTA
* * *
13791300 TTTAGATTTGCAGTTTTTA
1 GTTGGATTTGAAG-TTTTA
13791319 GTTGGATTTGA
1 GTTGGATTTGA
13791330 TGTTATAGGA
Statistics
Matches: 22, Mismatches: 7, Indels: 1
0.73 0.23 0.03
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.19, C:0.02, G:0.27, T:0.52
Consensus pattern (18 bp):
GTTGGATTTGAAGTTTTA
Found at i:13796189 original size:56 final size:56
Alignment explanation
Indices: 13796103--13796208 Score: 203
Period size: 56 Copynumber: 1.9 Consensus size: 56
13796093 ATTGATTTAT
13796103 TTTTGAATATTTTTGTAAAAATTATTTTTATATTGTTTCATTTAATAAATAGGTTC
1 TTTTGAATATTTTTGTAAAAATTATTTTTATATTGTTTCATTTAATAAATAGGTTC
*
13796159 TTTTGAATATTTTTGTAAAACTTATTTTTATATTGTTTCATTTAATAAAT
1 TTTTGAATATTTTTGTAAAAATTATTTTTATATTGTTTCATTTAATAAAT
13796209 TAGAAGTTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.57
Consensus pattern (56 bp):
TTTTGAATATTTTTGTAAAAATTATTTTTATATTGTTTCATTTAATAAATAGGTTC
Found at i:13799501 original size:43 final size:43
Alignment explanation
Indices: 13799454--13799536 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
13799444 TTCAAACTGA
*
13799454 TTCGAGAATCGATTAAGAAGGTTGGTTTAGGGTTAGAAATTGT
1 TTCGAGAATCGATTAAGAAGGTTGGTTTAAGGTTAGAAATTGT
*
13799497 TTCGAGAATCGATTAAGAAGGTTTGTTTAAGGTTAGAAAT
1 TTCGAGAATCGATTAAGAAGGTTGGTTTAAGGTTAGAAAT
13799537 CGATTTGATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.35
Consensus pattern (43 bp):
TTCGAGAATCGATTAAGAAGGTTGGTTTAAGGTTAGAAATTGT
Found at i:13799796 original size:12 final size:12
Alignment explanation
Indices: 13799774--13799808 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
13799764 GGATTCTTTC
*
13799774 GATTTCAATTTT
1 GATTTTAATTTT
*
13799786 GATTTTGATTTT
1 GATTTTAATTTT
13799798 GATTTTAATTT
1 GATTTTAATTT
13799809 AGGGATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.23, C:0.03, G:0.11, T:0.63
Consensus pattern (12 bp):
GATTTTAATTTT
Found at i:13800343 original size:21 final size:21
Alignment explanation
Indices: 13800318--13800359 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
13800308 ACATGGATGA
*
13800318 TACAGATGTAGGTGAACTGTG
1 TACAGAAGTAGGTGAACTGTG
13800339 TACAGAAGTAGGTGAACTGTG
1 TACAGAAGTAGGTGAACTGTG
13800360 CGATAGTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.33, T:0.26
Consensus pattern (21 bp):
TACAGAAGTAGGTGAACTGTG
Found at i:13802063 original size:75 final size:75
Alignment explanation
Indices: 13801940--13802106 Score: 246
Period size: 75 Copynumber: 2.2 Consensus size: 75
13801930 TTAGTGAGTG
* * * *
13801940 TTTTTTAATATGCATGCAATGTTTTTTAATATGTCTGTGTATGATTGTTGGTGGGGTTGGTCA-T
1 TTTTTTAATATGCATGCAATGTTTTTTAATATATCTGTGTATGATTGTTGGCGAGGATGGT-ATT
*
13802004 ATGTTGTTGAC
65 ATATTGTTGAC
*
13802015 TTTTTTAATATGCATGCAATGTTTTTTAATTTATCTGTGTATGATTGTTGGCGAGGATGGTATTA
1 TTTTTTAATATGCATGCAATGTTTTTTAATATATCTGTGTATGATTGTTGGCGAGGATGGTATTA
13802080 TATTGTTGAC
66 TATTGTTGAC
*
13802090 TATTTTTAATACGCATG
1 T-TTTTTAATATGCATG
13802107 AATTGACTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
74 1 0.01
75 68 0.82
76 14 0.17
ACGTcount: A:0.22, C:0.07, G:0.22, T:0.49
Consensus pattern (75 bp):
TTTTTTAATATGCATGCAATGTTTTTTAATATATCTGTGTATGATTGTTGGCGAGGATGGTATTA
TATTGTTGAC
Found at i:13802222 original size:28 final size:25
Alignment explanation
Indices: 13802168--13802233 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 25
13802158 CACATGTTGT
13802168 TGACTATTTTTTAATAAGCATGCAG
1 TGACTATTTTTTAATAAGCATGCAG
* *
13802193 TGATTATTTTTTAATAATATGCATGTAG
1 TGACTATTTTTTAAT-A-A-GCATGCAG
*
13802221 TGACTAATTTTTA
1 TGACTATTTTTTA
13802234 GGTGTGTGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
25 14 0.41
26 1 0.03
27 1 0.03
28 18 0.53
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.47
Consensus pattern (25 bp):
TGACTATTTTTTAATAAGCATGCAG
Found at i:13802246 original size:6 final size:6
Alignment explanation
Indices: 13802239--13802380 Score: 123
Period size: 6 Copynumber: 24.2 Consensus size: 6
13802229 TTTTAGGTGT
* * *
13802239 GTGTGT GTGTGC ATGTGC GTGTGC GTGTGC GTGTGC GTGCGC GTG-GC
1 GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC
* * *
13802286 GTGCGC GTGTGC GTGTGC --GTGC GTGTGC GCGTGC GCGTGC GTGTGCAC
1 GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTG--C
* * * * * *
13802334 GTGCGC GTGTGC GCGTGC GCGT-- GTGCGC GTGCGC GTGTGC GCGTGC
1 GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC
13802380 G
1 G
13802381 CGTGTGCGCA
Statistics
Matches: 115, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
4 6 0.05
5 5 0.04
6 99 0.86
8 5 0.04
ACGTcount: A:0.01, C:0.23, G:0.49, T:0.26
Consensus pattern (6 bp):
GTGTGC
Found at i:13802317 original size:8 final size:8
Alignment explanation
Indices: 13802286--13802389 Score: 89
Period size: 8 Copynumber: 13.8 Consensus size: 8
13802276 TGCGCGTGGC
13802286 GTGCGCGT
1 GTGCGCGT
*
13802294 GTGCGTGT
1 GTGCGCGT
* *
13802302 GCGTGCGT
1 GTGCGCGT
13802310 GTGCGCGT
1 GTGCGCGT
*
13802318 GCGCGTGCGT
1 GTGC--GCGT
*
13802328 GTGCAC--
1 GTGCGCGT
13802334 GTGCGCGT
1 GTGCGCGT
13802342 GTGCGC--
1 GTGCGCGT
13802348 GTGCGCGT
1 GTGCGCGT
13802356 GTGCGC--
1 GTGCGCGT
13802362 GTGCGCGT
1 GTGCGCGT
13802370 GTGCGC--
1 GTGCGCGT
13802376 GTGCGCGT
1 GTGCGCGT
13802384 GTGCGC
1 GTGCGC
13802390 ATGCGTGCGT
Statistics
Matches: 76, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
6 23 0.30
8 46 0.61
10 7 0.09
ACGTcount: A:0.01, C:0.27, G:0.49, T:0.23
Consensus pattern (8 bp):
GTGCGCGT
Found at i:13802323 original size:14 final size:14
Alignment explanation
Indices: 13802255--13802394 Score: 147
Period size: 14 Copynumber: 9.5 Consensus size: 14
13802245 GTGTGCATGT
*
13802255 GCGTGTGCGTGTGC
1 GCGTGCGCGTGTGC
* *
13802269 GTGTGCGTGCGCGTG-
1 GCGTGC--GCGTGTGC
13802284 GCGTGCGCGTGTGC
1 GCGTGCGCGTGTGC
*
13802298 GTGTGCGTGCGTGTGC
1 GCGTGC--GCGTGTGC
13802314 GCGTGCGCGTGCGTGTGC
1 GCGT--GC--GCGTGTGC
*
13802332 ACGTGCGCGTGTGC
1 GCGTGCGCGTGTGC
13802346 GCGTGCGCGTGTGC
1 GCGTGCGCGTGTGC
13802360 GCGTGCGCGTGTGC
1 GCGTGCGCGTGTGC
13802374 GCGTGCGCGTGTGC
1 GCGTGCGCGTGTGC
*
13802388 GCATGCG
1 GCGTGCG
13802395 TGCGTGTGTG
Statistics
Matches: 109, Mismatches: 10, Indels: 14
0.82 0.08 0.11
Matches are distributed among these distances:
13 6 0.06
14 64 0.59
15 5 0.05
16 19 0.17
18 15 0.14
ACGTcount: A:0.01, C:0.26, G:0.49, T:0.24
Consensus pattern (14 bp):
GCGTGCGCGTGTGC
Found at i:13802381 original size:6 final size:6
Alignment explanation
Indices: 13802255--13802384 Score: 127
Period size: 6 Copynumber: 20.8 Consensus size: 6
13802245 GTGTGCATGT
* * * * *
13802255 GCGTGT GCGTGT GCGTGT GCGTGC GCGTG- GCGTGC GCGTGT GCGTGT
1 GCGTGC GCGTGC GCGTGC GCGTGC GCGTGC GCGTGC GCGTGC GCGTGC
* * *
13802302 GCGTGC GTGTGC GCGTGC GCGTGC GTGTGC ACGTGC GCGTGTGC GCGTGC
1 GCGTGC GCGTGC GCGTGC GCGTGC GCGTGC GCGTGC GC--GTGC GCGTGC
13802352 GCGTGTGC GCGTGC GCGTGTGC GCGTGC GCGTG
1 GC--GTGC GCGTGC GC--GTGC GCGTGC GCGTG
13802385 TGCGCATGCG
Statistics
Matches: 108, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
5 5 0.05
6 85 0.79
8 18 0.17
ACGTcount: A:0.01, C:0.25, G:0.50, T:0.24
Consensus pattern (6 bp):
GCGTGC
Found at i:13807211 original size:148 final size:146
Alignment explanation
Indices: 13806953--13807231 Score: 434
Period size: 148 Copynumber: 1.9 Consensus size: 146
13806943 GATTTTTTTT
***
13806953 AAAAGAGAAAGTTTAGATTTTTAAAATAAAAATATATTTTATAGTCATATTAAAGGAAATTTTTA
1 AAAAGAGAAAGTTTAGATTTTTAAAATAAAAATATATTTTATAGTCATATTAAAGGAAAAGCTTA
* * *
13807018 AAATTTTAAAATAAAGTTTTGATCTTTTTCAACTATTTTGAAATAAAACTTTGATTTTTAAGAAA
66 AAATTTTAAAACAAAGTTTTAATCTTTTTCAACTATTTCGAAATAAAACTTTGATTTTTAAGAAA
13807083 ATAGTGTTTTTTTAAA
131 ATAGTGTTTTTTTAAA
* *
13807099 AAAAGAGAAAGTTTAGATTTTTTAAAATAAAAATATGTCTTT-TAGTCATTTTAAAGGAAAAGCT
1 AAAAGAGAAAGTTTAGA-TTTTTAAAATAAAAATATAT-TTTATAGTCATATTAAAGGAAAAGCT
* *
13807163 TAAATTTTTTAAAACAAAGTTTTAATCTTTTTCAACTATTTCGAAATAAAGCTTTGATTTTTAAG
64 TAAA-ATTTTAAAACAAAGTTTTAATCTTTTTCAACTATTTCGAAATAAAACTTTGATTTTTAAG
13807228 AAAA
128 AAAA
13807232 ATAATAATTT
Statistics
Matches: 120, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
146 17 0.14
147 41 0.34
148 62 0.52
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.42
Consensus pattern (146 bp):
AAAAGAGAAAGTTTAGATTTTTAAAATAAAAATATATTTTATAGTCATATTAAAGGAAAAGCTTA
AAATTTTAAAACAAAGTTTTAATCTTTTTCAACTATTTCGAAATAAAACTTTGATTTTTAAGAAA
ATAGTGTTTTTTTAAA
Found at i:13810133 original size:39 final size:39
Alignment explanation
Indices: 13810050--13810136 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
13810040 GGACTTTAGC
* * *
13810050 CCGGACATATTTCCAGCACGTAGCCTGCGGACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCTTAAGT
13810089 CCGGATATAATTCCAGCACATAGCCTGCGGACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCTTAAGT
13810128 CCGGATATA
1 CCGGATATA
13810137 CATCACTGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATAGCCTGCGGACCTTAAGT
Found at i:13812234 original size:18 final size:20
Alignment explanation
Indices: 13812199--13812236 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
13812189 TCTATTATCC
*
13812199 TTTTTTATTTTACTTAAATT
1 TTTTTTATTTTACATAAATT
13812219 TTTTTTA-TTT-CATAAATT
1 TTTTTTATTTTACATAAATT
13812237 AAACCATTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 3 0.18
20 7 0.41
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTTTATTTTACATAAATT
Found at i:13813845 original size:13 final size:13
Alignment explanation
Indices: 13813827--13813853 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13813817 TGACAAATCC
13813827 AAATAATTTTCTA
1 AAATAATTTTCTA
13813840 AAATAATTTTCTA
1 AAATAATTTTCTA
13813853 A
1 A
13813854 CTTTTGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATTTTCTA
Found at i:13822031 original size:42 final size:42
Alignment explanation
Indices: 13821972--13822269 Score: 349
Period size: 42 Copynumber: 7.3 Consensus size: 42
13821962 AAAGAAAGCA
*
13821972 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTATTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * ** * *
13822014 TTCATTGCATTTAGAGGCTCAGGCATAGAAGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
*
13822056 TTTATTGCATTTAGAGGCCCAA--GTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * *
13822096 TTCATTGCA--TAAAGG-CCAGGTGTGGAGATCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
13822135 TTCATTGCA--TAGAGGCCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* ** * *
13822175 TTCATTGCATTTTGAGGCCCAAGCATAGAGATCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * * * * *
13822217 TTTAATGCATTTAAAGGTCCAGGTGTGGAGCTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
13822259 TTCATTGCATT
1 TTCATTGCATT
13822270 GTATATGAAT
Statistics
Matches: 214, Mismatches: 37, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
37 3 0.01
38 5 0.02
39 31 0.14
40 54 0.25
42 121 0.57
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
Found at i:13822157 original size:161 final size:163
Alignment explanation
Indices: 13821972--13822268 Score: 465
Period size: 161 Copynumber: 1.8 Consensus size: 163
13821962 AAAGAAAGCA
* * *
13821972 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTATTTTTCATTGCATTTAGAGGCTCAGG
1 TTCATTGCA-TTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAAG
* * *
13822037 CATAGA-AGTCCATTTACTTTTTATTGCATTTAGAGGCCCA-AGTGGAGGTCCATTTACTTTTCA
65 CATAGAGA-TCCATTTACTTTTTAATGCATTTAAAGGCCCAGAGTGGAGCTCCATTTACTTTTCA
13822100 TTGCATAAAGGCCAGGTGTGGAGATCCATTTACTT
129 TTGCATAAAGGCCAGGTGTGGAGATCCATTTACTT
*
13822135 TTCATTGCA-TAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATTGCATTTTGAGGCCCAAGC
1 TTCATTGCATTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAAGC
* *
13822199 ATAGAGATCCATTTACTTTTTAATGCATTTAAAGGTCCAGGTGTGGAGCTCCATTTACTTTTCAT
66 ATAGAGATCCATTTACTTTTTAATGCATTTAAAGGCCCA-GAGTGGAGCTCCATTTACTTTTCAT
13822264 TGCAT
130 TGCAT
13822269 TGTATATGAA
Statistics
Matches: 122, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
161 85 0.70
162 1 0.01
163 36 0.30
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (163 bp):
TTCATTGCATTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAAGC
ATAGAGATCCATTTACTTTTTAATGCATTTAAAGGCCCAGAGTGGAGCTCCATTTACTTTTCATT
GCATAAAGGCCAGGTGTGGAGATCCATTTACTT
Found at i:13822263 original size:84 final size:84
Alignment explanation
Indices: 13821975--13822269 Score: 399
Period size: 84 Copynumber: 3.6 Consensus size: 84
13821965 GAAAGCATTC
* *
13821975 ATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTATTTTTCATTGCATTTAGAGGCTCAGGCAT
1 ATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGGCAT
13822040 AGA-AGTCCATTTACTTTTT
66 AGAGA-TCCATTTACTTTTT
* **
13822059 ATTGCATTTAGAGGCCCAA--GTGGAGGTCCATTTACTTTTCATTGCA--TAAAGG-CCAGGTGT
1 ATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGGCAT
* *
13822119 GGAGATCCATTTACTTTTC
66 AGAGATCCATTTACTTTTT
* *
13822138 ATTGCA--TAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATTGCATTTTGAGGCCCAAGCAT
1 ATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGGCAT
13822201 AGAGATCCATTTACTTTTT
66 AGAGATCCATTTACTTTTT
* * * * *
13822220 AATGCATTTAAAGGTCCAGGTGTGGAGCTCCATTTACTTTTCATTGCATT
1 ATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATTGCATT
13822270 GTATATGAAT
Statistics
Matches: 184, Mismatches: 19, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
77 11 0.06
79 53 0.29
80 6 0.03
81 4 0.02
82 53 0.29
84 57 0.31
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.36
Consensus pattern (84 bp):
ATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGGCAT
AGAGATCCATTTACTTTTT
Found at i:13827861 original size:35 final size:35
Alignment explanation
Indices: 13827810--13827876 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
13827800 GTTTTTAGGG
*
13827810 TTAGGGTTTTGCTAAAATAAGTTAGGGTTTAGTAT
1 TTAGGGTTTTGCTAAAACAAGTTAGGGTTTAGTAT
* *
13827845 TTAGGTTTTTGTTAAAACAAGTTAGGGTTTAG
1 TTAGGGTTTTGCTAAAACAAGTTAGGGTTTAG
13827877 AGTTTTAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.28, C:0.03, G:0.25, T:0.43
Consensus pattern (35 bp):
TTAGGGTTTTGCTAAAACAAGTTAGGGTTTAGTAT
Found at i:13828152 original size:30 final size:31
Alignment explanation
Indices: 13827968--13828158 Score: 117
Period size: 34 Copynumber: 6.1 Consensus size: 31
13827958 ATAATTTAAG
* *
13827968 TTAGGGTTTTAAATAAATTAGGGCTTA-GGTT
1 TTAGGGTTTTAAATAAATTA-AGATTAGGGTT
* *
13827999 TTATGGTTTTAAATAGATTAAGTAAATTAGGGTT
1 TTAGGGTTTTAAATAAATTAAG---ATTAGGGTT
* **
13828033 CTAGAATTTTAAATAAATTAA-ATTAGGGTT
1 TTAGGGTTTTAAATAAATTAAGATTAGGGTT
* ** **
13828063 GTA-GG-TTTAGGGTTTATTAA-ATTAGGG-T
1 TTAGGGTTTTA-AATAAATTAAGATTAGGGTT
** *
13828091 TTATGCTTTTTAAATAGATTAAGTAAATTAGGGTT
1 TTA-GGGTTTTAAATAAATTAAG---ATTAGGGTT
13828126 TTAGGGTTTTAAATAAATTAAG-TTAGGGTT
1 TTAGGGTTTTAAATAAATTAAGATTAGGGTT
13828156 TTA
1 TTA
13828159 AATAAATTAA
Statistics
Matches: 121, Mismatches: 26, Indels: 27
0.70 0.15 0.16
Matches are distributed among these distances:
28 7 0.06
29 13 0.11
30 29 0.24
31 22 0.18
33 3 0.02
34 43 0.36
35 4 0.03
ACGTcount: A:0.34, C:0.02, G:0.21, T:0.43
Consensus pattern (31 bp):
TTAGGGTTTTAAATAAATTAAGATTAGGGTT
Found at i:13828154 original size:22 final size:22
Alignment explanation
Indices: 13828126--13828179 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
13828116 AATTAGGGTT
*
13828126 TTAGGGTTTTAAATAAATTAAG
1 TTAGGGTTTTAAATAAATTAAA
13828148 TTAGGGTTTTAAATAAATTAAA
1 TTAGGGTTTTAAATAAATTAAA
13828170 TTAGGGTTTT
1 TTAGGGTTTT
13828180 GGATTTAGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (22 bp):
TTAGGGTTTTAAATAAATTAAA
Found at i:13828244 original size:110 final size:108
Alignment explanation
Indices: 13828064--13828364 Score: 417
Period size: 110 Copynumber: 2.8 Consensus size: 108
13828054 ATTAGGGTTG
* ** * *
13828064 TAGG-TTTAGGGTTTATTAAATTAGGGTTTATGCTTTTTAAATAGATTAAGTAAATTAGGGTTTT
1 TAGGTTTTAGGATTTAGGAAATTAGGGTTTATGTTTTTTAAATAGATTAAGTAAATTAGGGTTCT
* *
13828128 AGGGTTTTAAATAAATTAAGTTAGGGTTTTAAATAAATTAAAT
66 AGGGTTTTAAATAAATTAAGTTAGGGTTTAAAATAAACTAAAT
* *
13828171 TAGGGTTTT-GGATTTAGGGAATTAGGGCTTATGTTTTTTTAAAATAGATTAAGTAAATTAGGGT
1 TA-GGTTTTAGGATTTAGGAAATTAGGGTTTATG-TTTTTT-AAATAGATTAAGTAAATTAGGGT
* *
13828235 TCTAAGGTTTTAAATAAATTAAGTTAGGGTTTAAAATAAACTACAT
63 TCTAGGGTTTTAAATAAATTAAGTTAGGGTTTAAAATAAACTAAAT
* ** * *
13828281 TAGGTTTTAGGGTTTATTAAATTAGAGTTTATGTTTTTTAAATAGATTAAATAAATTAGGGTTCT
1 TAGGTTTTAGGATTTAGGAAATTAGGGTTTATGTTTTTTAAATAGATTAAGTAAATTAGGGTTCT
13828346 AGGGTTTTAAATAAATTAA
66 AGGGTTTTAAATAAATTAA
13828365 AATAGGGATT
Statistics
Matches: 170, Mismatches: 19, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
107 2 0.01
108 64 0.38
109 20 0.12
110 84 0.49
ACGTcount: A:0.36, C:0.02, G:0.20, T:0.43
Consensus pattern (108 bp):
TAGGTTTTAGGATTTAGGAAATTAGGGTTTATGTTTTTTAAATAGATTAAGTAAATTAGGGTTCT
AGGGTTTTAAATAAATTAAGTTAGGGTTTAAAATAAACTAAAT
Found at i:13828289 original size:22 final size:22
Alignment explanation
Indices: 13828239--13828289 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
13828229 TAGGGTTCTA
*
13828239 AGGTTTT-AAATAAATTAAGTT
1 AGGTTTTAAAATAAACTAAGTT
*
13828260 AGGGTTTAAAATAAACTACA-TT
1 AGGTTTTAAAATAAACTA-AGTT
13828282 AGGTTTTA
1 AGGTTTTA
13828290 GGGTTTATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 6 0.24
22 18 0.72
23 1 0.04
ACGTcount: A:0.41, C:0.04, G:0.16, T:0.39
Consensus pattern (22 bp):
AGGTTTTAAAATAAACTAAGTT
Found at i:13828338 original size:34 final size:34
Alignment explanation
Indices: 13828298--13828365 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
13828288 TAGGGTTTAT
** *
13828298 TAAATTAGAGTT-TATGTTTTTTAAATAGATTAAA
1 TAAATTAGAGTTCTA-GGGTTTTAAATAAATTAAA
*
13828332 TAAATTAGGGTTCTAGGGTTTTAAATAAATTAAA
1 TAAATTAGAGTTCTAGGGTTTTAAATAAATTAAA
13828366 ATAGGGATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 27 0.93
35 2 0.07
ACGTcount: A:0.41, C:0.01, G:0.15, T:0.43
Consensus pattern (34 bp):
TAAATTAGAGTTCTAGGGTTTTAAATAAATTAAA
Found at i:13828390 original size:28 final size:29
Alignment explanation
Indices: 13828326--13828404 Score: 97
Period size: 28 Copynumber: 2.7 Consensus size: 29
13828316 TTTTAAATAG
* *
13828326 ATTAAATAAATTAGGGTTCTAGGGTTTTAA
1 ATTAATTAAATTAGGGTT-TAGGGTTTAAA
* * *
13828356 ATAAATTAAAATAGGGATTAGGG-TTAAA
1 ATTAATTAAATTAGGGTTTAGGGTTTAAA
13828384 ATTAATTAAATTAGGGTTTAG
1 ATTAATTAAATTAGGGTTTAG
13828405 TTTTTTTAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
28 22 0.54
29 5 0.12
30 14 0.34
ACGTcount: A:0.42, C:0.01, G:0.20, T:0.37
Consensus pattern (29 bp):
ATTAATTAAATTAGGGTTTAGGGTTTAAA
Found at i:13828782 original size:125 final size:126
Alignment explanation
Indices: 13828457--13828834 Score: 537
Period size: 126 Copynumber: 3.0 Consensus size: 126
13828447 CTATTTTTAC
* *
13828457 CCTGAAAAAATAATTTTGAGAAGACATTTCTGAACAAATAGTGTTAAAAACGCTTCAAGCAGGAT
1 CCTGAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGAT
* * * * * *
13828522 GCAATGTCATTAAAAATATAGACAAAAGCTCCCACGCGAACGCTCTTTTGCTATAGTAGTT
66 GCAATGTCAGTAAAAATATAGAAAAAAGCTCCCACGTGGACGCTCTTTTACTACAGTAGTT
*
13828583 CCTGAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAAATGCATT-AAGCAGGA
1 CCTGAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAAACGC-TTCAAGCAGGA
*
13828647 TGCAATGTCAGTAAAAATATAGAAAAAAGCTCCCACGTGGACACTCTTTTACTACAGTAGTT
65 TGCAATGTCAGTAAAAATATAGAAAAAAGCTCCCACGTGGACGCTCTTTTACTACAGTAGTT
* * * * *
13828709 CCTG-AAAAATAATTCTAAGAAGACGTTTCTGAACAAATAGTATCAAAAACGCTTCAAGTAAGAT
1 CCTGAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGAT
* * * * *
13828773 GCAATGTCAGT-AAAATTTCTGAAAAAAGCTCCCATGTGGATGCTCTTTTTCTACAGTAGTT
66 GCAATGTCAGTAAAAATAT-AGAAAAAAGCTCCCACGTGGACGCTCTTTTACTACAGTAGTT
13828834 C
1 C
13828835 AAGCTTGGCC
Statistics
Matches: 227, Mismatches: 22, Indels: 7
0.89 0.09 0.03
Matches are distributed among these distances:
124 8 0.04
125 100 0.44
126 117 0.52
127 2 0.01
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.28
Consensus pattern (126 bp):
CCTGAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGAT
GCAATGTCAGTAAAAATATAGAAAAAAGCTCCCACGTGGACGCTCTTTTACTACAGTAGTT
Found at i:13829020 original size:9 final size:9
Alignment explanation
Indices: 13829003--13829037 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
13828993 CGTCGCCAAG
*
13829003 TAGATTTTA
1 TAGAATTTA
13829012 TAGAATTTA
1 TAGAATTTA
13829021 TAGAATTTA
1 TAGAATTTA
13829030 TAGAATTT
1 TAGAATTT
13829038 CGTAAAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (9 bp):
TAGAATTTA
Found at i:13831753 original size:27 final size:28
Alignment explanation
Indices: 13831716--13831881 Score: 143
Period size: 27 Copynumber: 6.1 Consensus size: 28
13831706 AGCAGGGCTG
*
13831716 CCAGA-ACAGATA-ATGTGACAGAGTCA
1 CCAGATACAGATATATGTGACAGAGCCA
* *
13831742 CCAGATACAGATA-ATCGTGGCAGGGCCA
1 CCAGATACAGATATAT-GTGACAGAGCCA
*
13831770 CCAGA-ACAGATATATGTGGCAGAGCCA
1 CCAGATACAGATATATGTGACAGAGCCA
*
13831797 CCAGAT-CAGATATTTGTGGA-AGAGCCA
1 CCAGATACAGATATATGT-GACAGAGCCA
* **
13831824 CCAGAT-CAGATATTTGTGGTAGAGCCA
1 CCAGATACAGATATATGTGACAGAGCCA
* * *
13831851 CCAGAT-CAAATA-ATTGTGGCATAGCCA
1 CCAGATACAGATATA-TGTGACAGAGCCA
13831878 CCAG
1 CCAG
13831882 GACGCTTCCT
Statistics
Matches: 122, Mismatches: 11, Indels: 13
0.84 0.08 0.09
Matches are distributed among these distances:
26 6 0.05
27 99 0.81
28 17 0.14
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.19
Consensus pattern (28 bp):
CCAGATACAGATATATGTGACAGAGCCA
Found at i:13831774 original size:54 final size:54
Alignment explanation
Indices: 13831716--13831881 Score: 217
Period size: 54 Copynumber: 3.1 Consensus size: 54
13831706 AGCAGGGCTG
* * * *
13831716 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGGGCCA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCAGAGCCA
* *
13831770 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGAAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCAGAGCCA
* * * * *
13831824 CCAGATCAGATATTTGTGGTAGAGCCACCAGATCAAATAATTGTGGCATAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCAGAGCCA
13831878 CCAG
1 CCAG
13831882 GACGCTTCCT
Statistics
Matches: 98, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
54 80 0.82
55 18 0.18
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.19
Consensus pattern (54 bp):
CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCAGAGCCA
Found at i:13833628 original size:26 final size:26
Alignment explanation
Indices: 13833500--13833628 Score: 204
Period size: 26 Copynumber: 5.0 Consensus size: 26
13833490 CATGAAATTC
* *
13833500 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTA
* * *
13833526 TTATCATGAAACATTTATCTAACCCA
1 TTATCATGGAACATTTACCTAACCTA
*
13833552 TTATCATGGAACATTGACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
13833578 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
13833604 TTATCATGGAACATTTACCTAACCT
1 TTATCATGGAACATTTACCTAACCT
13833629 GAACATTTAC
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 97 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.33
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCTA
Found at i:13833634 original size:17 final size:17
Alignment explanation
Indices: 13833612--13833645 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
13833602 TATTATCATG
13833612 GAACATTTACCTAACCT
1 GAACATTTACCTAACCT
13833629 GAACATTTACCTAACCT
1 GAACATTTACCTAACCT
13833646 ATTATCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.06, T:0.29
Consensus pattern (17 bp):
GAACATTTACCTAACCT
Found at i:13844262 original size:23 final size:22
Alignment explanation
Indices: 13844213--13844266 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
13844203 TGTTTGATTA
13844213 TAAA-ATA-TTTAAATTAGTTT
1 TAAATATATTTTAAATTAGTTT
13844233 TAAAATATATTTTAAATTAGTGTAT
1 T-AAATATATTTTAAATTAGT-T-T
13844258 T-AATATATT
1 TAAATATATT
13844267 AAAATAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
20 1 0.03
21 3 0.10
22 3 0.10
23 19 0.66
24 1 0.03
25 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (22 bp):
TAAATATATTTTAAATTAGTTT
Found at i:13846860 original size:38 final size:38
Alignment explanation
Indices: 13846809--13846881 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
13846799 TTAAATGGCT
13846809 TAATTGCTAACATGTCTTTAGATTAATTGTCATTTAAG
1 TAATTGCTAACATGTCTTTAGATTAATTGTCATTTAAG
13846847 TAATTGCTAACATGTCTTTAGATTAATTGTCATTT
1 TAATTGCTAACATGTCTTTAGATTAATTGTCATTT
13846882 CAGGCATTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.47
Consensus pattern (38 bp):
TAATTGCTAACATGTCTTTAGATTAATTGTCATTTAAG
Found at i:13848895 original size:15 final size:15
Alignment explanation
Indices: 13848875--13848922 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
13848865 CTATTTTAAG
13848875 TTTATTTTAATTTTA
1 TTTATTTTAATTTTA
*
13848890 TTTATTTTTA-TTTA
1 TTTATTTTAATTTTA
13848904 TTATTATTTTAGATTTTA
1 -T-TTATTTTA-ATTTTA
13848922 T
1 T
13848923 ATTAATTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 4 0.15
15 10 0.37
16 7 0.26
17 2 0.07
18 4 0.15
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (15 bp):
TTTATTTTAATTTTA
Found at i:13849828 original size:18 final size:19
Alignment explanation
Indices: 13849805--13849844 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
13849795 TTCCTTTAAA
13849805 TTATTTCAT-TATTTA-TTT
1 TTATTTCATCT-TTTACTTT
13849823 TTATTTCATCTTTTACTTT
1 TTATTTCATCTTTTACTTT
13849842 TTA
1 TTA
13849845 CCTTTTACGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (19 bp):
TTATTTCATCTTTTACTTT
Found at i:13851347 original size:27 final size:27
Alignment explanation
Indices: 13851309--13851363 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
13851299 TTCATGCGCA
13851309 GGTTAAGTATCATTTGATTTGTATGTC
1 GGTTAAGTATCATTTGATTTGTATGTC
13851336 GGTTAAGTATCATTTGATTTGTATGTC
1 GGTTAAGTATCATTTGATTTGTATGTC
13851363 G
1 G
13851364 ATTCAGCATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.22, C:0.07, G:0.24, T:0.47
Consensus pattern (27 bp):
GGTTAAGTATCATTTGATTTGTATGTC
Found at i:13857753 original size:18 final size:18
Alignment explanation
Indices: 13857732--13857766 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13857722 ATTTTCCTGT
13857732 TAACATAAAACACCTAAA
1 TAACATAAAACACCTAAA
* *
13857750 TAACTTAAAATACCTAA
1 TAACATAAAACACCTAA
13857767 TAATTATCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.20, G:0.00, T:0.23
Consensus pattern (18 bp):
TAACATAAAACACCTAAA
Found at i:13857858 original size:11 final size:11
Alignment explanation
Indices: 13857785--13857863 Score: 56
Period size: 11 Copynumber: 7.2 Consensus size: 11
13857775 AAAAATTTAG
13857785 AATAAAATAAT
1 AATAAAATAAT
13857796 AA-AAAATAAT
1 AATAAAATAAT
* ** *
13857806 AA-GAGCTGAT
1 AATAAAATAAT
13857816 AAATAAAAT-AT
1 -AATAAAATAAT
**
13857827 AATAAAAATTTGT
1 AAT-AAAA-TAAT
13857840 AATAAAATAAT
1 AATAAAATAAT
13857851 AATAAAATAAT
1 AATAAAATAAT
13857862 AA
1 AA
13857864 GAGCTCTTAT
Statistics
Matches: 53, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
10 17 0.32
11 25 0.47
12 7 0.13
13 4 0.08
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.27
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:13865280 original size:62 final size:62
Alignment explanation
Indices: 13865131--13865354 Score: 225
Period size: 62 Copynumber: 3.6 Consensus size: 62
13865121 TGCAGGGTTT
* * *
13865131 ACACGGCCCGGGACAC-GAACGTGTGGCCAAGCCGTGTAACTCACTATTTGTGCTTAAAAACC
1 ACACGGCCAGGGACACAG-GCGTGTGCCCAAGCCGTGTAACTCACTATTTGTGCTTAAAAACC
* * * * * * * *
13865193 ACGCAGCCAGGGGCCCGGGCATGTGCCCAAGCAGTGTAACTCACTATTTGCGCTTAAAAACC
1 ACACGGCCAGGGACACAGGCGTGTGCCCAAGCCGTGTAACTCACTATTTGTGCTTAAAAACC
* * * * * * * *
13865255 ACACGGCCAGGGACACAGGCGTGTGCGCAGGCCGTATAATTGACTGTTTGTGCTTAAAGATC
1 ACACGGCCAGGGACACAGGCGTGTGCCCAAGCCGTGTAACTCACTATTTGTGCTTAAAAACC
* * *
13865317 ACACGGCCAAGGTACACAGGTGTGTACCCAAGCCGTGT
1 ACACGGCC-AGGGACACAGGCGTGTGCCCAAGCCGTGT
13865355 GACAAGAGGT
Statistics
Matches: 128, Mismatches: 32, Indels: 3
0.79 0.20 0.02
Matches are distributed among these distances:
62 104 0.81
63 24 0.19
ACGTcount: A:0.26, C:0.28, G:0.27, T:0.19
Consensus pattern (62 bp):
ACACGGCCAGGGACACAGGCGTGTGCCCAAGCCGTGTAACTCACTATTTGTGCTTAAAAACC
Done.