Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 39 of 226
Found at i:16737934 original size:23 final size:23
Alignment explanation
Indices: 16737882--16737964 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
16737872 TCTGATTAGT
*
16737882 ATACGATACAT-AAGTGCCTG-A
1 ATACGACACATAAAGTGCCTGAA
*
16737903 A-ACGACACACAAAGTGCCTGAA
1 ATACGACACATAAAGTGCCTGAA
*
16737925 ATACGACACATAAAGTGCCTAAA
1 ATACGACACATAAAGTGCCTGAA
*
16737948 ATATGACACATAAAGTG
1 ATACGACACATAAAGTG
16737965 TTTGATCGGC
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
20 7 0.13
21 10 0.19
22 2 0.04
23 35 0.65
ACGTcount: A:0.45, C:0.20, G:0.17, T:0.18
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAA
Found at i:16738142 original size:17 final size:17
Alignment explanation
Indices: 16738122--16738154 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16738112 TCATATTTTT
*
16738122 CATTTGATTCAATTTCA
1 CATTTCATTCAATTTCA
16738139 CATTTCATTCAATTTC
1 CATTTCATTCAATTTC
16738155 GATAAGCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.21, G:0.03, T:0.48
Consensus pattern (17 bp):
CATTTCATTCAATTTCA
Found at i:16739443 original size:33 final size:33
Alignment explanation
Indices: 16739406--16739549 Score: 105
Period size: 33 Copynumber: 4.3 Consensus size: 33
16739396 ATAATCCAGT
*
16739406 TATGGTGTTATCATCAAAATGCCATAGCCCATC
1 TATGGTCTTATCATCAAAATGCCATAGCCCATC
* * * * *
16739439 TATGGTCTTAT-ATATAAACACTGCCATGGTCTAAC
1 TATGGTCTTATCAT-CAAA-A-TGCCATAGCCCATC
* * * * *
16739474 CATGGTCTTA-CGTTCATAGTGCCATAACCCAGT-
1 TATGGTCTTATC-ATCAAAATGCCATAGCCCA-TC
* *
16739507 TATGGTCTTATCATCAGAATGCCATAGCCCAGC
1 TATGGTCTTATCATCAAAATGCCATAGCCCATC
16739540 TATGGTCTTA
1 TATGGTCTTA
16739550 CATATAAACA
Statistics
Matches: 81, Mismatches: 22, Indels: 16
0.68 0.18 0.13
Matches are distributed among these distances:
32 2 0.02
33 55 0.68
34 2 0.02
35 21 0.26
36 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.32
Consensus pattern (33 bp):
TATGGTCTTATCATCAAAATGCCATAGCCCATC
Found at i:16739568 original size:101 final size:101
Alignment explanation
Indices: 16739380--16739619 Score: 356
Period size: 101 Copynumber: 2.4 Consensus size: 101
16739370 AATTAATCCT
* * * * *
16739380 TTACATTCGTAGTGCCATAATCCAGTTATGGTGTTATCATCAAAATGCCATAGCCCATCTATGGT
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAAAATGCCATAGCCCAGCTATGGT
* *
16739445 CTTATATATAAACACTGCCATGG-TCTAACCATGGTC
66 CTTACATATAAACACCGCCATGGTTC-AACCATGGTC
*
16739481 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTATGGT
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAAAATGCCATAGCCCAGCTATGGT
* *
16739546 CTTACATATAAACACCGTCATGGTTCAATCATGGTC
66 CTTACATATAAACACCGCCATGGTTCAACCATGGTC
* *
16739582 TTACGTTCATAGTGTCATAACCTAGTTATGGTCTTATC
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATC
16739620 CGTCAATTTA
Statistics
Matches: 126, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
101 124 0.98
102 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (101 bp):
TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAAAATGCCATAGCCCAGCTATGGT
CTTACATATAAACACCGCCATGGTTCAACCATGGTC
Found at i:16744081 original size:58 final size:58
Alignment explanation
Indices: 16743991--16744109 Score: 202
Period size: 58 Copynumber: 2.1 Consensus size: 58
16743981 AATAGGGGTT
* *
16743991 GAGTACTAGTAATAGAAAAAAGGAGGCTAATCGAATCAGGAAATGCTTAACCGAAAAA
1 GAGTACCAGAAATAGAAAAAAGGAGGCTAATCGAATCAGGAAATGCTTAACCGAAAAA
* *
16744049 GAGTACCAGAAATAGCAGAAAGGAGGCTAATCGAATCAGGAAATGCTTAACCGAAAAA
1 GAGTACCAGAAATAGAAAAAAGGAGGCTAATCGAATCAGGAAATGCTTAACCGAAAAA
16744107 GAG
1 GAG
16744110 AGGCGATTGA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.47, C:0.13, G:0.24, T:0.15
Consensus pattern (58 bp):
GAGTACCAGAAATAGAAAAAAGGAGGCTAATCGAATCAGGAAATGCTTAACCGAAAAA
Found at i:16749935 original size:101 final size:101
Alignment explanation
Indices: 16749755--16749945 Score: 256
Period size: 101 Copynumber: 1.9 Consensus size: 101
16749745 GAATTGATGG
* * * * * * * * *
16749755 ATAAGACCATGGTTGGACCATGGCAATGTTTAAATGTACGGCCATAGTTGGGCTATGGCATTTTA
1 ATAAGACCATGGTTGGACCATGACAATATATAAATGTAAGACCATAGCTGAGCTATGACATTCTA
*
16749820 ATGAAAAGATCATAACTAAGTTATGGCACCTTGAGC
66 ATGAAAAGACCATAACTAAGTTATGGCACCTTGAGC
*
16749856 ATAAGACCATGGTTGGACCATGACAATATATATATGTAAGACCATAGCTGAGCTATGACATTCTA
1 ATAAGACCATGGTTGGACCATGACAATATATAAATGTAAGACCATAGCTGAGCTATGACATTCTA
* * *
16749921 ATGATAAGACCATAATTAGGTTATG
66 ATGAAAAGACCATAACTAAGTTATG
16749946 ACACTACAAA
Statistics
Matches: 76, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
101 76 1.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (101 bp):
ATAAGACCATGGTTGGACCATGACAATATATAAATGTAAGACCATAGCTGAGCTATGACATTCTA
ATGAAAAGACCATAACTAAGTTATGGCACCTTGAGC
Found at i:16749962 original size:101 final size:101
Alignment explanation
Indices: 16749755--16749967 Score: 232
Period size: 101 Copynumber: 2.1 Consensus size: 101
16749745 GAATTGATGG
* * * * * * * * *
16749755 ATAAGACCATGGTTGGACCATGGCAATGTTTAAATGTACGGCCATAGTTGGGCTATGGCATTTTA
1 ATAAGACCATGGTTGGACCATGACAATATATAAATGTAAGACCATAGCTGAGCTATGACATTCTA
* * ** *
16749820 ATGAAAAGATCATAACTAAGTTATGGCACCTTGAGC
66 ATGAAAAGACCATAACTAAGTTATGACACCTACAGA
*
16749856 ATAAGACCATGGTTGGACCATGACAATATATATATGTAAGACCATAGCTGAGCTATGACATTCTA
1 ATAAGACCATGGTTGGACCATGACAATATATAAATGTAAGACCATAGCTGAGCTATGACATTCTA
* * *
16749921 ATGATAAGACCATAATTAGGTTATGACA-CTACA-A
66 ATGAAAAGACCATAACTAAGTTATGACACCTACAGA
16749955 ATGTAAGACCATG
1 A--TAAGACCATG
16749968 ACAGGGACAT
Statistics
Matches: 92, Mismatches: 18, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
99 1 0.01
100 3 0.03
101 88 0.96
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.28
Consensus pattern (101 bp):
ATAAGACCATGGTTGGACCATGACAATATATAAATGTAAGACCATAGCTGAGCTATGACATTCTA
ATGAAAAGACCATAACTAAGTTATGACACCTACAGA
Found at i:16762486 original size:28 final size:26
Alignment explanation
Indices: 16762427--16762496 Score: 68
Period size: 28 Copynumber: 2.5 Consensus size: 26
16762417 ATTTATTAAT
*
16762427 TATTTATAATGTTAATCATTTAAACAA
1 TATTTATAAT-TTAATAATTTAAACAA
* *
16762454 GATTTATTAATTTAATAATTTAAAACTA
1 TATTTA-TAATTTAATAATTT-AAACAA
*
16762482 TATTTACAAATTTAA
1 TATTTA-TAATTTAA
16762497 AAGATAATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
27 14 0.40
28 21 0.60
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (26 bp):
TATTTATAATTTAATAATTTAAACAA
Found at i:16765633 original size:64 final size:64
Alignment explanation
Indices: 16765532--16765660 Score: 231
Period size: 64 Copynumber: 2.0 Consensus size: 64
16765522 GGGCGGTGTA
* *
16765532 TACTCCAACTGATCTAATAGTCACTCTATTGTTTCTAGGCAATTCTCAGCAATTTCGGGTTCTG
1 TACTCCAACTGATCTAATAGTCACTCTACTGTTTCTAGGCAATACTCAGCAATTTCGGGTTCTG
*
16765596 TACTCTAACTGATCTAATAGTCACTCTACTGTTTCTAGGCAATACTCAGCAATTTCGGGTTCTG
1 TACTCCAACTGATCTAATAGTCACTCTACTGTTTCTAGGCAATACTCAGCAATTTCGGGTTCTG
16765660 T
1 T
16765661 GCCTTTCATG
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.37
Consensus pattern (64 bp):
TACTCCAACTGATCTAATAGTCACTCTACTGTTTCTAGGCAATACTCAGCAATTTCGGGTTCTG
Found at i:16775720 original size:5 final size:5
Alignment explanation
Indices: 16775704--16775735 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
16775694 TGCACCATAG
*
16775704 AACAT AATAT AACAT AACAT AACAT AACAT AA
1 AACAT AACAT AACAT AACAT AACAT AACAT AA
16775736 AGTAGCTCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.62, C:0.16, G:0.00, T:0.22
Consensus pattern (5 bp):
AACAT
Found at i:16776975 original size:7 final size:7
Alignment explanation
Indices: 16776963--16776987 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
16776953 AATCAATATA
16776963 ACATAAT
1 ACATAAT
16776970 ACATAAT
1 ACATAAT
16776977 ACATAAT
1 ACATAAT
16776984 ACAT
1 ACAT
16776988 TTATTTAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (7 bp):
ACATAAT
Found at i:16777878 original size:13 final size:13
Alignment explanation
Indices: 16777860--16777886 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16777850 TAAGCTTTTG
16777860 CAGCTTAGTAAGT
1 CAGCTTAGTAAGT
16777873 CAGCTTAGTAAGT
1 CAGCTTAGTAAGT
16777886 C
1 C
16777887 GTAAACAAAC
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:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (13 bp):
CAGCTTAGTAAGT
Found at i:16784527 original size:22 final size:22
Alignment explanation
Indices: 16784494--16784558 Score: 94
Period size: 22 Copynumber: 3.0 Consensus size: 22
16784484 CTCCAATTAT
*
16784494 TAGCACATTAGTGCTCTCTGTA
1 TAGCACTTTAGTGCTCTCTGTA
* * *
16784516 TAGTACTTTAGTGTTCTTTGTA
1 TAGCACTTTAGTGCTCTCTGTA
16784538 TAGCACTTTAGTGCTCTCTGT
1 TAGCACTTTAGTGCTCTCTGT
16784559 TTAATAGTGC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (22 bp):
TAGCACTTTAGTGCTCTCTGTA
Found at i:16788277 original size:22 final size:21
Alignment explanation
Indices: 16788242--16788282 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
16788232 ACGACGGATA
16788242 CGGGTTAGAGGTGTTACAAAC
1 CGGGTTAGAGGTGTTACAAAC
*
16788263 CGGGTATAGGGGTGTTACAA
1 CGGGT-TAGAGGTGTTACAA
16788283 CGCCATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.27, C:0.12, G:0.37, T:0.24
Consensus pattern (21 bp):
CGGGTTAGAGGTGTTACAAAC
Found at i:16792416 original size:50 final size:50
Alignment explanation
Indices: 16792350--16792642 Score: 406
Period size: 50 Copynumber: 5.8 Consensus size: 50
16792340 ATTTGGGTAA
* *
16792350 AGAGGTCCCATATAAGACCATGTCTGGGACATGACATTGGCACAGAGATG
1 AGAGGTCCCATATAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
16792400 AGAGGTCACATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATATAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
16792450 ATAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
1 AGAGGTCCCATATAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
16792500 AGAGGTCCCATATAAGACCATGTCTGAGACATGGCGTTGGCACTGAGATG
1 AGAGGTCCCATATAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*** * *
16792550 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATATAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
16792600 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATATAAGACCATGTCTGGGACATGGCATTGGCA
16792643 TGTTATGATC
Statistics
Matches: 213, Mismatches: 29, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
50 179 0.84
51 34 0.16
ACGTcount: A:0.28, C:0.22, G:0.30, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATATAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:16795326 original size:26 final size:27
Alignment explanation
Indices: 16795297--16795360 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
16795287 AACTAGGTCT
16795297 AACTATAAATTTTTCTAAA-T-TCACCC
1 AACTATAAATTTTT-TAAATTATCACCC
*
16795323 AACTATGAATTTTTTAAATTAGTCACCC
1 AACTATAAATTTTTTAAATTA-TCACCC
*
16795351 AATTATAAAT
1 AACTATAAAT
16795361 ATACTTTGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 4 0.12
26 14 0.44
28 14 0.44
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.39
Consensus pattern (27 bp):
AACTATAAATTTTTTAAATTATCACCC
Found at i:16813783 original size:2 final size:2
Alignment explanation
Indices: 16813776--16813804 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
16813766 TAATATCTCC
16813776 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16813805 TGGTTAGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16814537 original size:21 final size:22
Alignment explanation
Indices: 16814490--16814537 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
16814480 GCTTTAATGG
* * *
16814490 TTTTTTTTTTGTGTTAATTTTA
1 TTTTTTTTTAGTGTAAATTTGA
*
16814512 CTTTTTTTTAGT-TAAATTTGA
1 TTTTTTTTTAGTGTAAATTTGA
16814533 TTTTT
1 TTTTT
16814538 AAATTTTTAA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.17, C:0.02, G:0.08, T:0.73
Consensus pattern (22 bp):
TTTTTTTTTAGTGTAAATTTGA
Found at i:16814696 original size:17 final size:19
Alignment explanation
Indices: 16814663--16814699 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
16814653 ATGCTAATTT
16814663 AAATTTATAAAATATTAAA
1 AAATTTATAAAATATTAAA
16814682 AAATTTA-AAAA-ATTAAA
1 AAATTTATAAAATATTAAA
16814699 A
1 A
16814700 TTAAGTATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 4 0.22
19 7 0.39
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AAATTTATAAAATATTAAA
Found at i:16817095 original size:2 final size:2
Alignment explanation
Indices: 16817088--16817113 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16817078 ATTTCTCATG
16817088 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
16817114 GGTTGATAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16822819 original size:18 final size:19
Alignment explanation
Indices: 16822792--16822830 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
16822782 TTTGGATTCT
* *
16822792 TTTTATAAA-TATTTTGAA
1 TTTTAAAAATTATTTAGAA
16822810 TTTTAAAAATTATTTAGAA
1 TTTTAAAAATTATTTAGAA
16822829 TT
1 TT
16822831 ATTTTGTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TTTTAAAAATTATTTAGAA
Found at i:16826812 original size:13 final size:13
Alignment explanation
Indices: 16826794--16826819 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16826784 TTTTATTTGT
16826794 TTATTCCCACCGG
1 TTATTCCCACCGG
16826807 TTATTCCCACCGG
1 TTATTCCCACCGG
16826820 CCGAATGTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.38, G:0.15, T:0.31
Consensus pattern (13 bp):
TTATTCCCACCGG
Found at i:16827423 original size:22 final size:21
Alignment explanation
Indices: 16827392--16827432 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
16827382 CATGGCTTGC
*
16827392 ATTTGGATGTGTTCTTATTTAA
1 ATTTGAATGTGTTC-TATTTAA
16827414 ATTTGAATGTGTTCTATTT
1 ATTTGAATGTGTTCTATTT
16827433 TGACATGGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.22, C:0.05, G:0.17, T:0.56
Consensus pattern (21 bp):
ATTTGAATGTGTTCTATTTAA
Found at i:16829228 original size:2 final size:2
Alignment explanation
Indices: 16829221--16829246 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16829211 TTAGATACAA
16829221 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
16829247 TATGCTCGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16829763 original size:41 final size:41
Alignment explanation
Indices: 16829718--16829991 Score: 374
Period size: 41 Copynumber: 6.7 Consensus size: 41
16829708 GGTTTTAAAA
* *
16829718 CCTAGCAGATTAAGTGCCGGTGAACTGAATCAGGCTATAAG
1 CCTAGCAGACTAAGTGCCGGTGATCTGAATCAGGCTATAAG
*
16829759 CCTAGCA-AGCTAAGTGCCGGTGATTTGAATCAGGCTATAAG
1 CCTAGCAGA-CTAAGTGCCGGTGATCTGAATCAGGCTATAAG
*
16829800 CCTAGCA-AGCTAAGTGCCGGTGATTTGAATCAGGCTATAAG
1 CCTAGCAGA-CTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* *
16829841 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGACTATAAG
1 CCTAGCAGACTAAGTGCCGGTGATCTGAATCAGGCTATAAG
*
16829882 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
1 CCTAGCAGACTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* * * *
16829923 CCTAGCAGGCTAAGTGTCGGTGATCTAAATCAGGCTTTAAG
1 CCTAGCAGACTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* *
16829964 CCTAACA-AGCTAAGTGCCAGTGAATCTG
1 CCTAGCAGA-CTAAGTGCCGGTG-ATCTG
16829992 TTTAAATTAA
Statistics
Matches: 214, Mismatches: 15, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
40 1 0.00
41 209 0.98
42 4 0.02
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (41 bp):
CCTAGCAGACTAAGTGCCGGTGATCTGAATCAGGCTATAAG
Found at i:16829855 original size:82 final size:82
Alignment explanation
Indices: 16829728--16829991 Score: 420
Period size: 82 Copynumber: 3.2 Consensus size: 82
16829718 CCTAGCAGAT
* * *
16829728 TAAGTGCCGGTGAACTGAATCAGGCTATAAGCCTAGCAAGCTAAGTGCCGGTGATTTGAATCAGG
1 TAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGG
16829793 CTATAAGCCTAGCAAGC
66 CTATAAGCCTAGCAAGC
* *
16829810 TAAGTGCCGGTGATTTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGA
1 TAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGG
*
16829875 CTATAAGCCTAGCAGGC
66 CTATAAGCCTAGCAAGC
* *
16829892 TAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGTCGGTGATCTAAATCAGG
1 TAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGG
* *
16829957 CTTTAAGCCTAACAAGC
66 CTATAAGCCTAGCAAGC
*
16829974 TAAGTGCCAGTGAATCTG
1 TAAGTGCCGGTG-ATCTG
16829992 TTTAAATTAA
Statistics
Matches: 167, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
82 162 0.97
83 5 0.03
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.23
Consensus pattern (82 bp):
TAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGG
CTATAAGCCTAGCAAGC
Found at i:16829937 original size:123 final size:123
Alignment explanation
Indices: 16829718--16829991 Score: 413
Period size: 123 Copynumber: 2.2 Consensus size: 123
16829708 GGTTTTAAAA
** * *
16829718 CCTAGCAGATTAAGTGCCGGTGAACTGAATCAGGCTATAAGCCTAGCAAGCTAAGTGCCGGTGAT
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGACTATAAGCCTAGCAAGCTAAGTGCCGGTGAT
* * *
16829783 TTGAATCAGGCTATAAGCCTAGCAAGCTAAGTGCCGGTGATTTGAATCAGGCTATAAG
66 CTGAATCAGGCTATAAGCCTAGCAAGCTAAGTGCCGGTGATCTAAATCAGGCTATAAG
*
16829841 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGACTATAAGCCTAGCAGGCTAAGTGCCGGTGAT
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGACTATAAGCCTAGCAAGCTAAGTGCCGGTGAT
* * *
16829906 CTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGTCGGTGATCTAAATCAGGCTTTAAG
66 CTGAATCAGGCTATAAGCCTAGCAAGCTAAGTGCCGGTGATCTAAATCAGGCTATAAG
* * *
16829964 CCTAACAAGCTAAGTGCCAGTGAATCTG
1 CCTAGCAGGCTAAGTGCCGGTG-ATCTG
16829992 TTTAAATTAA
Statistics
Matches: 136, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
123 131 0.96
124 5 0.04
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (123 bp):
CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGACTATAAGCCTAGCAAGCTAAGTGCCGGTGAT
CTGAATCAGGCTATAAGCCTAGCAAGCTAAGTGCCGGTGATCTAAATCAGGCTATAAG
Found at i:16832454 original size:12 final size:12
Alignment explanation
Indices: 16832437--16832463 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
16832427 AGAAAATTTT
16832437 AACAATATGATA
1 AACAATATGATA
16832449 AACAATATGATA
1 AACAATATGATA
16832461 AAC
1 AAC
16832464 CTTGTATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.11, G:0.07, T:0.22
Consensus pattern (12 bp):
AACAATATGATA
Found at i:16834801 original size:49 final size:49
Alignment explanation
Indices: 16834744--16834847 Score: 145
Period size: 49 Copynumber: 2.1 Consensus size: 49
16834734 TCATGTGTTA
* * ** *
16834744 TAATTTTATACAGTGTTGAGTTTTTTATTCATGATATTGAACTCAATTT
1 TAATTTTATAAAGTGTTCACCTTTTTATTCATGATATTAAACTCAATTT
* *
16834793 TAATTTTATAAAGTGTTCCCCTTTTTATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTTATTCATGATATTAAACTCAATTT
16834842 TAATTT
1 TAATTT
16834848 ATTTTTTTTC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.30, C:0.10, G:0.09, T:0.52
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTTATTCATGATATTAAACTCAATTT
Found at i:16836411 original size:39 final size:43
Alignment explanation
Indices: 16836362--16836461 Score: 109
Period size: 44 Copynumber: 2.3 Consensus size: 43
16836352 TCCTTATGCT
* *
16836362 ATTACACCTCTATTC-T-ATTCAACCAAACACAAGAA-TA-CC
1 ATTACGCCTCTATTCATCATTCAACCAAACAAAAGAATTATCC
*
16836401 ATTACGCCTCTATTCCATTCCATTCAACCAAACAAAAGAATTATCT
1 ATTACGCCTCTATT-CA-T-CATTCAACCAAACAAAAGAATTATCC
*
16836447 ATTACGCATCTATTC
1 ATTACGCCTCTATTC
16836462 CATTACACTT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
39 13 0.26
40 1 0.02
42 1 0.02
44 18 0.36
45 3 0.06
46 14 0.28
ACGTcount: A:0.37, C:0.29, G:0.04, T:0.30
Consensus pattern (43 bp):
ATTACGCCTCTATTCATCATTCAACCAAACAAAAGAATTATCC
Found at i:16836428 original size:44 final size:46
Alignment explanation
Indices: 16836373--16836465 Score: 136
Period size: 44 Copynumber: 2.1 Consensus size: 46
16836363 TTACACCTCT
* * *
16836373 ATTCTATTCAACCAAACACAAGAA-TA-CCATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTATCCATTACGCATCTATTCC
*
16836417 ATTCCATTCAACCAAACAAAAGAATTATCTATTACGCATCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTATCCATTACGCATCTATTCC
16836463 ATT
1 ATT
16836466 ACACTTATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 22 0.51
45 2 0.05
46 19 0.44
ACGTcount: A:0.38, C:0.28, G:0.04, T:0.30
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAAAAGAATTATCCATTACGCATCTATTCC
Found at i:16837422 original size:21 final size:21
Alignment explanation
Indices: 16837376--16837422 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
16837366 GGTTTTCTAG
16837376 GATTTTTTATTTTAGTGTTTA
1 GATTTTTTATTTTAGTGTTTA
* *
16837397 CATTTTTTAATTTTA-TTTTTA
1 GATTTTTT-ATTTTAGTGTTTA
16837418 GATTT
1 GATTT
16837423 AAAATTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.21, C:0.02, G:0.09, T:0.68
Consensus pattern (21 bp):
GATTTTTTATTTTAGTGTTTA
Found at i:16839899 original size:11 final size:11
Alignment explanation
Indices: 16839882--16839919 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
16839872 TTTTTAATCA
16839882 AATATATATTT
1 AATATATATTT
* *
16839893 TATATATATTA
1 AATATATATTT
16839904 AATATATATTT
1 AATATATATTT
16839915 AATAT
1 AATAT
16839920 GGTTCGGGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATATATATTT
Found at i:16840090 original size:25 final size:25
Alignment explanation
Indices: 16840056--16840105 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
16840046 ATCACCTCTA
*
16840056 GTGAGAGCCAAGTATCGGGAAGCTC
1 GTGAGAGCCAAATATCGGGAAGCTC
*
16840081 GTGAGAGCCAAATATCGGGACGCTC
1 GTGAGAGCCAAATATCGGGAAGCTC
16840106 ATAAAAACTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.28, C:0.22, G:0.34, T:0.16
Consensus pattern (25 bp):
GTGAGAGCCAAATATCGGGAAGCTC
Found at i:16847943 original size:19 final size:20
Alignment explanation
Indices: 16847904--16847944 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
16847894 AATAAAAATG
*
16847904 ATTAAATGTAAATTAACTTA
1 ATTAAATGTAAATTAAATTA
*
16847924 ATTAAA-GTAGATTAAATTA
1 ATTAAATGTAAATTAAATTA
16847943 AT
1 AT
16847945 CTTAATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.39
Consensus pattern (20 bp):
ATTAAATGTAAATTAAATTA
Found at i:16871439 original size:23 final size:23
Alignment explanation
Indices: 16871389--16871433 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
16871379 AAATTAATTA
16871389 TGTAATATCCCGAAAATTACTAC
1 TGTAATATCCCGAAAATTACTAC
16871412 TGTAATATCCCGAAAATTACTA
1 TGTAATATCCCGAAAATTACTA
16871434 TAGTAAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (23 bp):
TGTAATATCCCGAAAATTACTAC
Found at i:16873320 original size:46 final size:46
Alignment explanation
Indices: 16873253--16873346 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 46
16873243 ACAATGCTAT
16873253 AACTCAGTATGGTTTCATTCACTGAAACACCATACCTAATTTTCAC
1 AACTCAGTATGGTTTCATTCACTGAAACACCATACCTAATTTTCAC
*
16873299 AACTCAGTATGGTTTTC-TTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGG-TTTCATTCACTGAAACACCATACCTAATTTTCAC
16873345 AA
1 AA
16873347 TTTGCCATGG
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 42 0.91
47 4 0.09
ACGTcount: A:0.32, C:0.27, G:0.09, T:0.33
Consensus pattern (46 bp):
AACTCAGTATGGTTTCATTCACTGAAACACCATACCTAATTTTCAC
Found at i:16876714 original size:24 final size:25
Alignment explanation
Indices: 16876682--16876733 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
16876672 TGATCGAGAT
* *
16876682 GCTCCGAAGAGCA-TTTAACGGGAA
1 GCTCCGAAGAACACTATAACGGGAA
*
16876706 GCTCGGAAGAACACTATAACGGGAA
1 GCTCCGAAGAACACTATAACGGGAA
16876731 GCT
1 GCT
16876734 TGAAAAGGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.35, C:0.21, G:0.29, T:0.15
Consensus pattern (25 bp):
GCTCCGAAGAACACTATAACGGGAA
Found at i:16877623 original size:46 final size:46
Alignment explanation
Indices: 16877524--16877731 Score: 323
Period size: 46 Copynumber: 4.6 Consensus size: 46
16877514 TACTTATGAT
* *
16877524 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGACTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATACTAC
* *
16877567 CACTTATCACTTTGTCACTTGATCAGATAAGTGTATCTAAAACTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATACTAC
* * *
16877613 CACTTATCACTATATCACTTGATCAGATAAGTGTAGCTAATGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATACTAC
*
16877659 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATACTAC
16877705 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
16877732 AGTACTCAAA
Statistics
Matches: 152, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
43 10 0.07
44 5 0.03
45 19 0.12
46 118 0.78
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATACTAC
Found at i:16881887 original size:17 final size:17
Alignment explanation
Indices: 16881867--16881904 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
16881857 AATAATTTAA
16881867 AATATA-AACATTAATAT
1 AATATACAA-ATTAATAT
*
16881884 AATATACAAATTATTAT
1 AATATACAAATTAATAT
16881901 AATA
1 AATA
16881905 AATAATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (17 bp):
AATATACAAATTAATAT
Found at i:16882785 original size:16 final size:15
Alignment explanation
Indices: 16882760--16882790 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
16882750 AATTATTAAA
16882760 ATAATAATTATAATT
1 ATAATAATTATAATT
16882775 ATAAGTAATTATAATT
1 ATAA-TAATTATAATT
16882791 CTTTGCATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (15 bp):
ATAATAATTATAATT
Found at i:16883189 original size:20 final size:19
Alignment explanation
Indices: 16883144--16883192 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
16883134 ATTTAGTTAA
16883144 AATT-AATATAAATAATTT
1 AATTAAATATAAATAATTT
* *
16883162 ATAATAAATACTAAGTAATTT
1 A-ATTAAATA-TAAATAATTT
16883183 AATTAAATAT
1 AATTAAATAT
16883193 TTAGTAGATC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 1 0.04
19 3 0.12
20 11 0.44
21 10 0.40
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (19 bp):
AATTAAATATAAATAATTT
Found at i:16883191 original size:24 final size:23
Alignment explanation
Indices: 16883131--16883191 Score: 56
Period size: 24 Copynumber: 2.7 Consensus size: 23
16883121 TAAATAATTT
* *
16883131 GTAATTTAGTTAAAATTAATATAA
1 GTAATTTAATT-AAATAAATATAA
*
16883155 ATAATTT-A-T-AATAAATACTAA
1 GTAATTTAATTAAATAAATA-TAA
16883176 GTAATTTAATTAAATA
1 GTAATTTAATTAAATA
16883192 TTTAGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
20 7 0.24
21 9 0.31
22 2 0.07
23 1 0.03
24 10 0.34
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (23 bp):
GTAATTTAATTAAATAAATATAA
Found at i:16883198 original size:20 final size:21
Alignment explanation
Indices: 16883148--16883191 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
16883138 AGTTAAAATT
*
16883148 AATA-TAAATAATTTATAATA
1 AATACTAAGTAATTTATAATA
*
16883168 AATACTAAGTAATTTA-ATTA
1 AATACTAAGTAATTTATAATA
16883188 AATA
1 AATA
16883192 TTTAGTAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
AATACTAAGTAATTTATAATA
Found at i:16890656 original size:25 final size:26
Alignment explanation
Indices: 16890622--16890670 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
16890612 AGTGGTAGTC
*
16890622 TCTAGGCATA-TTTGTGAAAAGGAAT
1 TCTAGGCATATTTTGCGAAAAGGAAT
16890647 TCTAGGCATATTTTGCGAAAAGGA
1 TCTAGGCATATTTTGCGAAAAGGA
16890671 GTAAGTGTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (26 bp):
TCTAGGCATATTTTGCGAAAAGGAAT
Found at i:16896518 original size:34 final size:34
Alignment explanation
Indices: 16896462--16896526 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
16896452 GATAGAATGA
* *
16896462 AAAATAAAATATAGTTCTTGACAGATAAGACAAC
1 AAAATAAAATATAGTCCATGACAGATAAGACAAC
* * *
16896496 AAAATGAAATGTAGTCCATGACAGGTAAGAC
1 AAAATAAAATATAGTCCATGACAGATAAGAC
16896527 TTTAATGATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.49, C:0.12, G:0.17, T:0.22
Consensus pattern (34 bp):
AAAATAAAATATAGTCCATGACAGATAAGACAAC
Found at i:16907073 original size:100 final size:100
Alignment explanation
Indices: 16906900--16907101 Score: 404
Period size: 100 Copynumber: 2.0 Consensus size: 100
16906890 TCCCGTAGTT
16906900 ATAAAATTTAGGTTTGTCCATCAGTAACTAGTATCTCTTATTGTGCTTTGTGTTTACCAATTATG
1 ATAAAATTTAGGTTTGTCCATCAGTAACTAGTATCTCTTATTGTGCTTTGTGTTTACCAATTATG
16906965 AATTAGTCTTTACCTGGTTCTCCTGTAATTATGCC
66 AATTAGTCTTTACCTGGTTCTCCTGTAATTATGCC
16907000 ATAAAATTTAGGTTTGTCCATCAGTAACTAGTATCTCTTATTGTGCTTTGTGTTTACCAATTATG
1 ATAAAATTTAGGTTTGTCCATCAGTAACTAGTATCTCTTATTGTGCTTTGTGTTTACCAATTATG
16907065 AATTAGTCTTTACCTGGTTCTCCTGTAATTATGCC
66 AATTAGTCTTTACCTGGTTCTCCTGTAATTATGCC
16907100 AT
1 AT
16907102 TGGTTTGATT
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 102 1.00
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.44
Consensus pattern (100 bp):
ATAAAATTTAGGTTTGTCCATCAGTAACTAGTATCTCTTATTGTGCTTTGTGTTTACCAATTATG
AATTAGTCTTTACCTGGTTCTCCTGTAATTATGCC
Found at i:16913306 original size:21 final size:21
Alignment explanation
Indices: 16913261--16913301 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
16913251 CACGACCAAC
16913261 AAATATATTAATATATAAACA
1 AAATATATTAATATATAAACA
*
16913282 AAATATAATTATTATATAAA
1 AAATAT-ATTAATATATAAA
16913302 TAAATTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
AAATATATTAATATATAAACA
Found at i:16917314 original size:17 final size:18
Alignment explanation
Indices: 16917294--16917328 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
16917284 TTTATTAATT
*
16917294 TTAAAATTTTAAA-AAAA
1 TTAAAATATTAAATAAAA
16917311 TTAAAATATTAAATAAAA
1 TTAAAATATTAAATAAAA
16917329 AAAATTCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TTAAAATATTAAATAAAA
Found at i:16928899 original size:43 final size:43
Alignment explanation
Indices: 16928851--16928932 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 43
16928841 TTAACCACGT
** * * *
16928851 TAAGGTTAAATTTTCATATTTATTCAAAATAATCACATTCTGA
1 TAAGGTTAAATTCCCACATTTATTAAAAAGAATCACATTCTGA
*
16928894 TAAGGTTAACTTCCCACATTTATTAAAAAGAATCACATT
1 TAAGGTTAAATTCCCACATTTATTAAAAAGAATCACATT
16928933 TTCTTATGTG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (43 bp):
TAAGGTTAAATTCCCACATTTATTAAAAAGAATCACATTCTGA
Found at i:16933138 original size:41 final size:41
Alignment explanation
Indices: 16932983--16933139 Score: 208
Period size: 41 Copynumber: 3.8 Consensus size: 41
16932973 TTGTATATAA
** * *
16932983 CACCGGCATAAAGCCTGCTAGGCACCAAG-CTCGATACATTT
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCT-GATATAATT
* * *
16933024 CACCGGCACAAAGCCTGCTAGACATAAAGTCTGATATAATT
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATT
*
16933065 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGACATAATT
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATT
* *
16933106 CACCAGCATAAAGCCTGCTAGGCATAACGCCTGA
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGA
16933140 ACTTACAAAA
Statistics
Matches: 103, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
41 101 0.98
42 2 0.02
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19
Consensus pattern (41 bp):
CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATT
Found at i:16937713 original size:43 final size:42
Alignment explanation
Indices: 16937666--16937797 Score: 113
Period size: 42 Copynumber: 3.1 Consensus size: 42
16937656 GGTTGAAGGC
* *
16937666 TGAACAGAAGCACATAAGTGCTAAACAGAAACCCCATAAGGGT
1 TGAACAGAAGCACATAAGAGCTAAAC-GAAAACCCATAAGGGT
* * * *
16937709 TGAACGGAAGCTCATACGAGCTGAACGAAAACCCATAAGGGT
1 TGAACAGAAGCACATAAGAGCTAAACGAAAACCCATAAGGGT
* * * * * * * *
16937751 TAAACTGAAGCTCAAAAGAGTTGAACGGAAA-CCATTAGGGT
1 TGAACAGAAGCACATAAGAGCTAAACGAAAACCCATAAGGGT
*
16937792 TAAACA
1 TGAACA
16937798 AAAACTCATA
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
41 14 0.19
42 40 0.53
43 21 0.28
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.16
Consensus pattern (42 bp):
TGAACAGAAGCACATAAGAGCTAAACGAAAACCCATAAGGGT
Found at i:16937761 original size:42 final size:42
Alignment explanation
Indices: 16937693--16937796 Score: 129
Period size: 42 Copynumber: 2.5 Consensus size: 42
16937683 GTGCTAAACA
* * * *
16937693 GAAACCCCATAAGGGTTGAACGGAAGCTCATACGAGCTGAAC
1 GAAAACCCATAAGGGTTAAACGGAAGCTCAAAAGAGCTGAAC
* *
16937735 GAAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGTTGAAC
1 GAAAACCCATAAGGGTTAAACGGAAGCTCAAAAGAGCTGAAC
* *
16937777 GGAAA-CCATTAGGGTTAAAC
1 GAAAACCCATAAGGGTTAAAC
16937797 AAAAACTCAT
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
41 14 0.26
42 40 0.74
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.16
Consensus pattern (42 bp):
GAAAACCCATAAGGGTTAAACGGAAGCTCAAAAGAGCTGAAC
Found at i:16937813 original size:41 final size:42
Alignment explanation
Indices: 16937693--16937813 Score: 109
Period size: 42 Copynumber: 2.9 Consensus size: 42
16937683 GTGCTAAACA
* * ** * * *
16937693 GAAACCCCATAAGGGTTGAACGGAAGCTCATACGAGCTGAAC
1 GAAAACCCATAAGGGTTAAACAAAAACTCATAAGAGTTGAAC
** * *
16937735 GAAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGTTGAAC
1 GAAAACCCATAAGGGTTAAACAAAAACTCATAAGAGTTGAAC
* * *
16937777 GGAAA-CCATTAGGGTTAAACAAAAACTCATATGAGTT
1 GAAAACCCATAAGGGTTAAACAAAAACTCATAAGAGTT
16937814 AACAGAAGCT
Statistics
Matches: 66, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
41 26 0.39
42 40 0.61
ACGTcount: A:0.41, C:0.18, G:0.22, T:0.18
Consensus pattern (42 bp):
GAAAACCCATAAGGGTTAAACAAAAACTCATAAGAGTTGAAC
Found at i:16940721 original size:46 final size:46
Alignment explanation
Indices: 16940617--16940886 Score: 219
Period size: 46 Copynumber: 5.6 Consensus size: 46
16940607 TACGTATGAT
* *
16940617 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
16940660 CACTTACCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*** *
16940706 CACTTATCACTTTGTCACCACTT-ATCACTTG-TTCCTGATCAGATAAGTGTAGCTA-
1 CACTTATCACTTTGT---CACTTGATCA---GATAAGTG-T-AGCTAA----AGCTAC
* * *
16940761 AAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAACTAC
1 CA-CT--TA----TCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
16940814 CACTTATCACTTTGTCATTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
16940860 CACTTATCACTTTGTCTCTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
16940887 AGTACTCAAA
Statistics
Matches: 181, Mismatches: 21, Indels: 47
0.73 0.08 0.19
Matches are distributed among these distances:
43 9 0.05
44 5 0.03
45 20 0.11
46 83 0.46
48 4 0.02
49 5 0.03
50 4 0.02
51 2 0.01
52 11 0.06
53 1 0.01
55 1 0.01
56 12 0.07
57 2 0.01
58 4 0.02
59 5 0.03
60 4 0.02
62 9 0.05
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:16940805 original size:108 final size:107
Alignment explanation
Indices: 16940617--16940830 Score: 383
Period size: 108 Copynumber: 2.0 Consensus size: 107
16940607 TACGTATGAT
*
16940617 CACTTATCACTTGTCCCTGATCAGATAAGTGTAGCTAGGCTACCACTTACCACTTTGTCACTTGA
1 CACTTATCACTTGTCCCTGATCAGATAAGTGTAGCTAAGCTACCACTTACCACTTTGTCACTTGA
*
16940682 TCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCAC
66 TCAGATAAGTGTAGCTAAAACTACCACTTATCACTTTGTCAC
* *
16940724 CACTTATCACTTGTTCCTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTG
1 CACTTATCACTTGTCCCTGATCAGATAAGTGTAGCT-AAGCTACCACTTACCACTTTGTCACTTG
16940789 ATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTTGTCA
65 ATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTTGTCA
16940831 TTTGATCAGA
Statistics
Matches: 102, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
107 35 0.34
108 67 0.66
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.33
Consensus pattern (107 bp):
CACTTATCACTTGTCCCTGATCAGATAAGTGTAGCTAAGCTACCACTTACCACTTTGTCACTTGA
TCAGATAAGTGTAGCTAAAACTACCACTTATCACTTTGTCAC
Found at i:16946686 original size:21 final size:20
Alignment explanation
Indices: 16946662--16946706 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
16946652 GTTCAATTAA
* *
16946662 TAAATTTTTAAAAATTTCGAT
1 TAAAATTTT-AAAATTTCAAT
16946683 TAAAAATTTTAAAATTTCAAT
1 T-AAAATTTTAAAATTTCAAT
16946704 TAA
1 TAA
16946707 TAATAATTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
20 2 0.10
21 12 0.57
22 7 0.33
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (20 bp):
TAAAATTTTAAAATTTCAAT
Found at i:16949237 original size:19 final size:20
Alignment explanation
Indices: 16949201--16949240 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
16949191 GATTAATGGG
16949201 AAAAAAAGAAAACAATAATA
1 AAAAAAAGAAAACAATAATA
16949221 AAAAGAAAG-AAAC-ATAATA
1 AAAA-AAAGAAAACAATAATA
16949240 A
1 A
16949241 CAATAACCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 8 0.42
21 4 0.21
ACGTcount: A:0.78, C:0.05, G:0.07, T:0.10
Consensus pattern (20 bp):
AAAAAAAGAAAACAATAATA
Found at i:16961960 original size:3 final size:3
Alignment explanation
Indices: 16961954--16961981 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
16961944 GTGTAGGCAA
16961954 TGG TGG TGG TGG TGG TGG TGG TGG TGG T
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG T
16961982 TTTGGCAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.64, T:0.36
Consensus pattern (3 bp):
TGG
Found at i:16961961 original size:45 final size:45
Alignment explanation
Indices: 16961912--16962058 Score: 150
Period size: 45 Copynumber: 3.1 Consensus size: 45
16961902 GTGCAGGCAA
16961912 TGGTGGTGGTGGTGGTTTTGGCAGGGGGGGAGGTGTAGGCAATGGTGGTGGTGG
1 TGGTGGTGGTGGTGGTTTTGGCAGGGGGGGAGGTGTAGGCAA---------TGG
16961966 TGGTGGTGGTGGTGGTTTTGGCAGGGGGGGAGGTGTAGGCAATGG
1 TGGTGGTGGTGGTGGTTTTGGCAGGGGGGGAGGTGTAGGCAATGG
** * * * * *
16962011 TGGTCTTGGTGGAGGCTTCGGCAGAGGGGGAGGTATAGGCAATGG
1 TGGTGGTGGTGGTGGTTTTGGCAGGGGGGGAGGTGTAGGCAATGG
16962056 TGG
1 TGG
16962059 AACCGGGGCT
Statistics
Matches: 86, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
45 44 0.51
54 42 0.49
ACGTcount: A:0.12, C:0.06, G:0.56, T:0.26
Consensus pattern (45 bp):
TGGTGGTGGTGGTGGTTTTGGCAGGGGGGGAGGTGTAGGCAATGG
Found at i:16961991 original size:54 final size:54
Alignment explanation
Indices: 16961912--16962014 Score: 206
Period size: 54 Copynumber: 1.9 Consensus size: 54
16961902 GTGCAGGCAA
16961912 TGGTGGTGGTGGTGGTTTTGGCAGGGGGGGAGGTGTAGGCAATGGTGGTGGTGG
1 TGGTGGTGGTGGTGGTTTTGGCAGGGGGGGAGGTGTAGGCAATGGTGGTGGTGG
16961966 TGGTGGTGGTGGTGGTTTTGGCAGGGGGGGAGGTGTAGGCAATGGTGGT
1 TGGTGGTGGTGGTGGTTTTGGCAGGGGGGGAGGTGTAGGCAATGGTGGT
16962015 CTTGGTGGAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.10, C:0.04, G:0.58, T:0.28
Consensus pattern (54 bp):
TGGTGGTGGTGGTGGTTTTGGCAGGGGGGGAGGTGTAGGCAATGGTGGTGGTGG
Found at i:16970150 original size:57 final size:58
Alignment explanation
Indices: 16970052--16970170 Score: 213
Period size: 57 Copynumber: 2.1 Consensus size: 58
16970042 AAATCAATGT
*
16970052 ATTTAATTTGATTTTAGGTTGGTATATTATTTAAATTGCACAATTCAATTTGGATTTG
1 ATTTAATTTGATTTTAGGTTGGTATATTATTTAAATCGCACAATTCAATTTGGATTTG
*
16970110 ATTT-ATTTGATTTTAGGTTGGTGTATTATTTAAATCGCACAATTCAATTTGGATTTG
1 ATTTAATTTGATTTTAGGTTGGTATATTATTTAAATCGCACAATTCAATTTGGATTTG
16970167 ATTT
1 ATTT
16970171 TTTCACATGG
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
57 55 0.93
58 4 0.07
ACGTcount: A:0.28, C:0.06, G:0.16, T:0.50
Consensus pattern (58 bp):
ATTTAATTTGATTTTAGGTTGGTATATTATTTAAATCGCACAATTCAATTTGGATTTG
Found at i:16978613 original size:20 final size:21
Alignment explanation
Indices: 16978583--16978631 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
16978573 TATATAAAAA
*
16978583 TATTATTGTAATAA-TATAATT
1 TATT-TTGTAAAAAGTATAATT
*
16978604 TATTTTGTAAAAAGTATGATT
1 TATTTTGTAAAAAGTATAATT
16978625 T-TTTTGT
1 TATTTTGT
16978632 CATTTTCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (21 bp):
TATTTTGTAAAAAGTATAATT
Found at i:16982225 original size:23 final size:24
Alignment explanation
Indices: 16982191--16982249 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 24
16982181 CTCACTTGAA
*
16982191 CTTCCCGATTACAT-CTCTTATGAG
1 CTTCCC-ATTACATACTCATATGAG
*
16982215 CTTCCTATTACATGACTCATATGAG
1 CTTCCCATTACAT-ACTCATATGAG
16982240 CTTCCCATTA
1 CTTCCCATTA
16982250 TATGGATCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.23
24 5 0.17
25 18 0.60
ACGTcount: A:0.24, C:0.29, G:0.10, T:0.37
Consensus pattern (24 bp):
CTTCCCATTACATACTCATATGAG
Found at i:16996618 original size:21 final size:21
Alignment explanation
Indices: 16996589--16996763 Score: 233
Period size: 21 Copynumber: 8.3 Consensus size: 21
16996579 GTGTTTTACT
* * *
16996589 TTCTATTCAACTCTTTCGAGC
1 TTCTGTTCAGCTCTTACGAGC
* ** *
16996610 TTCTGTTCAACTCTTATAAGT
1 TTCTGTTCAGCTCTTACGAGC
* * * *
16996631 TTCTGTTCAACTTTTATGAGT
1 TTCTGTTCAGCTCTTACGAGC
16996652 TTCTGTTCAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTACGAGC
16996673 TTCTGTTCAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTACGAGC
16996694 TTCTGTTCAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTACGAGC
16996715 TTCTGTTCAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTACGAGC
*
16996736 TTCTGTTCAGCTCTTATGAGC
1 TTCTGTTCAGCTCTTACGAGC
*
16996757 TTTTGTT
1 TTCTGTT
16996764 AACAATGTAC
Statistics
Matches: 141, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 141 1.00
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTACGAGC
Found at i:17003051 original size:22 final size:22
Alignment explanation
Indices: 17003023--17003098 Score: 107
Period size: 22 Copynumber: 3.5 Consensus size: 22
17003013 TGGCGTGAAA
17003023 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
17003045 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
* * * **
17003067 CATGAGGGTTTAGTTCGTTAAA
1 CATGAGAGCTTAGTACGTTAGC
17003089 CATGAGAGCT
1 CATGAGAGCT
17003099 GGTGTTTGAT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.29
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:17006394 original size:6 final size:6
Alignment explanation
Indices: 17006383--17006417 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
17006373 TGTTGAGGTC
17006383 GGTGCT GGTGCT GGTGCT GGTGCT GGTGCT GGTGC
1 GGTGCT GGTGCT GGTGCT GGTGCT GGTGCT GGTGC
17006418 AGGCGGTGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.17, G:0.51, T:0.31
Consensus pattern (6 bp):
GGTGCT
Found at i:17006427 original size:18 final size:18
Alignment explanation
Indices: 17006386--17006428 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
17006376 TGAGGTCGGT
* *
17006386 GCTGGTGCTGGTGCTGGT
1 GCTGGTGCTGGTGCAGGC
17006404 GCTGGTGCTGGTGCAGGC
1 GCTGGTGCTGGTGCAGGC
*
17006422 GGTGGTG
1 GCTGGTG
17006429 AGGCGGTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.02, C:0.16, G:0.53, T:0.28
Consensus pattern (18 bp):
GCTGGTGCTGGTGCAGGC
Found at i:17015492 original size:2 final size:2
Alignment explanation
Indices: 17015485--17015511 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17015475 CCCTCCTTTT
17015485 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
17015512 TTCTTCTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:17024107 original size:46 final size:46
Alignment explanation
Indices: 17024040--17024212 Score: 274
Period size: 46 Copynumber: 3.8 Consensus size: 46
17024030 TGGAATGTAG
17024040 GTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAAGTAA
1 GTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAAGTAA
* * *
17024086 GTATGATATTTCAGTAAAGAAAACCATACTGAGTTGTGAGAAGTAG
1 GTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAAGTAA
* * * *
17024132 GTATGGTATTTCAGTAACGAAAATCATACTGTGTTGTGAAAAGTAT
1 GTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAAGTAA
*
17024178 GTATGGTATTTCAGTGAAGAAAACCATACTGAGTT
1 GTATGGTATTTCAGTAAAGAAAACCATACTGAGTT
17024213 ATAGCATTGT
Statistics
Matches: 114, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 114 1.00
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.31
Consensus pattern (46 bp):
GTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAAGTAA
Found at i:17025794 original size:2 final size:2
Alignment explanation
Indices: 17025789--17025831 Score: 52
Period size: 2 Copynumber: 20.5 Consensus size: 2
17025779 TTTTTTTTTG
17025789 TA TA TA TA TA TA TA TCA TA TA TA T- TGA TA TA TA TCA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA T-A TA TA TA T-A TA TA TA
17025831 T
1 T
17025832 TGACTTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
1 1 0.03
2 31 0.84
3 5 0.14
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:17025818 original size:19 final size:19
Alignment explanation
Indices: 17025796--17025834 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
17025786 TTGTATATAT
17025796 ATATATATCATATATATTG
1 ATATATATCATATATATTG
17025815 ATATATATCATATATATTG
1 ATATATATCATATATATTG
17025834 A
1 A
17025835 CTTTTTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (19 bp):
ATATATATCATATATATTG
Found at i:17040390 original size:4 final size:4
Alignment explanation
Indices: 17040383--17040409 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
17040373 CCCTCCCTGT
17040383 CTGA CTGA CTGA CTGA CTGA CTGA CTG
1 CTGA CTGA CTGA CTGA CTGA CTGA CTG
17040410 TCTCTGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.26
Consensus pattern (4 bp):
CTGA
Found at i:17058717 original size:30 final size:29
Alignment explanation
Indices: 17058681--17058737 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
17058671 TGATTTTAAT
* *
17058681 TCAGTCACTCAACTTTAGAAAAATGACAAA
1 TCAGTCACT-AACATTACAAAAATGACAAA
*
17058711 TCAGTCACTAACATTACAAAGATGACA
1 TCAGTCACTAACATTACAAAAATGACA
17058738 GAAAGTTGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.46, C:0.21, G:0.11, T:0.23
Consensus pattern (29 bp):
TCAGTCACTAACATTACAAAAATGACAAA
Found at i:17064497 original size:32 final size:32
Alignment explanation
Indices: 17064428--17064497 Score: 92
Period size: 31 Copynumber: 2.2 Consensus size: 32
17064418 ATGTTTGAAA
* *
17064428 TGTT-ACATTTTAGTCACTTATGTTATTGTGT
1 TGTTAACATTTTAGTCACTGATGTTAATGTGT
17064459 TG-TAACATTTTAGTCACTGAGTGTTAAT-TGT
1 TGTTAACATTTTAGTCACTGA-TGTTAATGTGT
17064490 TGTTAACA
1 TGTTAACA
17064498 GTGTAACGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 1 0.03
31 22 0.65
32 11 0.32
ACGTcount: A:0.24, C:0.10, G:0.17, T:0.49
Consensus pattern (32 bp):
TGTTAACATTTTAGTCACTGATGTTAATGTGT
Found at i:17064646 original size:19 final size:19
Alignment explanation
Indices: 17064611--17064653 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
17064601 CTTTTTTTTA
*
17064611 TTTTTTTTTGTACTTTC-T
1 TTTTTTTTTCTACTTTCAT
*
17064629 TTTTTTTTCTCTATTTTCAT
1 TTTTTTTT-TCTACTTTCAT
17064649 TTTTT
1 TTTTT
17064654 CTCTATGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.38
19 7 0.33
20 6 0.29
ACGTcount: A:0.07, C:0.12, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTTTTTTCTACTTTCAT
Found at i:17074901 original size:21 final size:21
Alignment explanation
Indices: 17074875--17074946 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
17074865 GCTCGTAAGC
17074875 TGAACAGAAACTCTTAAGAGT
1 TGAACAGAAACTCTTAAGAGT
* * * *
17074896 TGAACAGAAGCTCATAATAGC
1 TGAACAGAAACTCTTAAGAGT
17074917 TGAACAGAAACTCTTAAGAGT
1 TGAACAGAAACTCTTAAGAGT
*
17074938 TGAATAGAA
1 TGAACAGAA
17074947 GCTCATAGCT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.22
Consensus pattern (21 bp):
TGAACAGAAACTCTTAAGAGT
Found at i:17074924 original size:42 final size:41
Alignment explanation
Indices: 17074858--17074953 Score: 158
Period size: 42 Copynumber: 2.3 Consensus size: 41
17074848 GTACATCGTT
*
17074858 AACAGAAGCTCGT-AAGCTGAACAGAAACTCTTAAGAGTTG
1 AACAGAAGCTCATAAAGCTGAACAGAAACTCTTAAGAGTTG
17074898 AACAGAAGCTCATAATAGCTGAACAGAAACTCTTAAGAGTTG
1 AACAGAAGCTCATAA-AGCTGAACAGAAACTCTTAAGAGTTG
*
17074940 AATAGAAGCTCATA
1 AACAGAAGCTCATA
17074954 GCTAAACGGA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
40 12 0.23
41 1 0.02
42 39 0.75
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.21
Consensus pattern (41 bp):
AACAGAAGCTCATAAAGCTGAACAGAAACTCTTAAGAGTTG
Found at i:17075022 original size:21 final size:21
Alignment explanation
Indices: 17074998--17075080 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
17074988 TGAACGAAAA
*
17074998 CTCATAAGAGTTTAACAGAAG
1 CTCATAAGAGTTAAACAGAAG
* * *
17075019 CTCA-ATAGAGTTGAACGGAAA
1 CTCATA-AGAGTTAAACAGAAG
**
17075040 CTCATTTGAGTTAAACAGAAG
1 CTCATAAGAGTTAAACAGAAG
* *
17075061 CTCGTAAGAGCTAAACAGAA
1 CTCATAAGAGTTAAACAGAA
17075081 AGTAAAACAC
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
20 1 0.02
21 47 0.98
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (21 bp):
CTCATAAGAGTTAAACAGAAG
Found at i:17075051 original size:42 final size:42
Alignment explanation
Indices: 17074983--17075063 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
17074973 TAAACTCGTA
*
17074983 AGAGCTGAACGAAAACTCATAAGAGTTTAACAGAAGCTCAAT
1 AGAGCTGAACGAAAACTCATAAGAGTTAAACAGAAGCTCAAT
* * **
17075025 AGAGTTGAACGGAAACTCATTTGAGTTAAACAGAAGCTC
1 AGAGCTGAACGAAAACTCATAAGAGTTAAACAGAAGCTC
17075064 GTAAGAGCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (42 bp):
AGAGCTGAACGAAAACTCATAAGAGTTAAACAGAAGCTCAAT
Found at i:17077934 original size:17 final size:16
Alignment explanation
Indices: 17077910--17077945 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
17077900 TTCAATATTA
*
17077910 GTTTTAGTTTATTTTT
1 GTTTTAGTTCATTTTT
17077926 GTTTCTAGTTCATTTTT
1 GTTT-TAGTTCATTTTT
17077943 GTT
1 GTT
17077946 AATTGTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.11, C:0.06, G:0.14, T:0.69
Consensus pattern (16 bp):
GTTTTAGTTCATTTTT
Found at i:17080391 original size:2 final size:2
Alignment explanation
Indices: 17080384--17080413 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17080374 CTGAATATTC
17080384 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17080414 TCCTCCTCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17080512 original size:9 final size:9
Alignment explanation
Indices: 17080498--17080526 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
17080488 AATTTACTTG
17080498 TTCAGAATT
1 TTCAGAATT
17080507 TTCAGAATT
1 TTCAGAATT
17080516 TTCAGAATT
1 TTCAGAATT
17080525 TT
1 TT
17080527 TGGTTCAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (9 bp):
TTCAGAATT
Found at i:17083311 original size:20 final size:20
Alignment explanation
Indices: 17083286--17083325 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
17083276 AACATTTTCC
*
17083286 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
17083306 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
17083326 TTATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:17083340 original size:34 final size:35
Alignment explanation
Indices: 17083274--17083340 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
17083264 CAAACACCAG
17083274 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
17083309 AAAACATTTTCCAG-AAATTATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
17083341 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 16 0.53
35 14 0.47
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:17092733 original size:73 final size:71
Alignment explanation
Indices: 17092642--17092777 Score: 236
Period size: 73 Copynumber: 1.9 Consensus size: 71
17092632 ACCAAAAACT
* *
17092642 AAAGACAACATTTTAAGTCAAAAGAAAGGTTTGGCTTAGAGATCAAAAATCAAAATAAATATAAC
1 AAAGAAAACATTTTAAGTCAAAA-AAAGGTTTGACTTAGAGAT-AAAAATCAAAATAAATATAAC
17092707 TGCCAAAA
64 TGCCAAAA
17092715 AAAGAAAACATTTTAAGTCAAAAAAAGGTTTGACTTAGAGATAAAAATCAAAATAAATATAAC
1 AAAGAAAACATTTTAAGTCAAAAAAAGGTTTGACTTAGAGATAAAAATCAAAATAAATATAAC
17092778 ACTGAAGATA
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
71 21 0.34
72 18 0.30
73 22 0.36
ACGTcount: A:0.54, C:0.10, G:0.12, T:0.23
Consensus pattern (71 bp):
AAAGAAAACATTTTAAGTCAAAAAAAGGTTTGACTTAGAGATAAAAATCAAAATAAATATAACTG
CCAAAA
Found at i:17126356 original size:51 final size:51
Alignment explanation
Indices: 17126300--17126407 Score: 139
Period size: 51 Copynumber: 2.1 Consensus size: 51
17126290 TCATTTTCAA
* *
17126300 TTTCATTTTGGAGAAAACC-ATATTCATTTTCAAATAATT-CCATTTCTCCAT
1 TTTCATTTTGGAG-AAACCGATAATCATTTCCAAAT-ATTACCATTTCTCCAT
* *
17126351 TTTCATTTTGGAGAAACCGATAATCATTTCCAAATGTTACCCATTTCTTCAT
1 TTTCATTTTGGAGAAACCGATAATCATTTCCAAATATTA-CCATTTCTCCAT
17126403 TTTCA
1 TTTCA
17126408 CCATTTCTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
50 7 0.14
51 27 0.54
52 16 0.32
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (51 bp):
TTTCATTTTGGAGAAACCGATAATCATTTCCAAATATTACCATTTCTCCAT
Found at i:17129388 original size:20 final size:21
Alignment explanation
Indices: 17129363--17129401 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
17129353 CTGACTTCTA
*
17129363 CTTT-AAAAATTAATTTGGCT
1 CTTTAAAAAAATAATTTGGCT
17129383 CTTTAAAAAAATAATTTGG
1 CTTTAAAAAAATAATTTGG
17129402 ATTTTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (21 bp):
CTTTAAAAAAATAATTTGGCT
Found at i:17129408 original size:21 final size:21
Alignment explanation
Indices: 17129363--17129409 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
17129353 CTGACTTCTA
* *
17129363 CTTT-AAAAATTAATTTGGCT
1 CTTTAAAAAAATAATTTGGAT
17129383 CTTTAAAAAAATAATTTGGAT
1 CTTTAAAAAAATAATTTGGAT
*
17129404 TTTTAA
1 CTTTAA
17129410 TTTATCAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (21 bp):
CTTTAAAAAAATAATTTGGAT
Found at i:17141293 original size:16 final size:15
Alignment explanation
Indices: 17141244--17141295 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
17141234 GAAAATTTAT
*
17141244 ATTTTCCATCTTTCT
1 ATTTTCCATCTTTCA
* *
17141259 ATATTTCTATCCCTTCA
1 AT-TTTCCAT-CTTTCA
17141276 ATTTTCCATCTTTCCA
1 ATTTTCCATCTTT-CA
17141292 ATTT
1 ATTT
17141296 CCTTTCCACC
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
15 5 0.17
16 18 0.62
17 6 0.21
ACGTcount: A:0.19, C:0.27, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTTTCCATCTTTCA
Found at i:17156271 original size:41 final size:40
Alignment explanation
Indices: 17156170--17156274 Score: 101
Period size: 41 Copynumber: 2.6 Consensus size: 40
17156160 AGTTCGAAGC
*
17156170 AATAGTTGACACCCAGTGTCTCATCG-ACAAAGCCGAAGAA
1 AATAG-TGACACCCAGTGTCTCATCGAACAAACCCGAAGAA
** ** *
17156210 AAT--TGGTACCCAGTACCTCATCGAATC-TACCCGAAGAA
1 AATAGTGACACCCAGTGTCTCATCGAA-CAAACCCGAAGAA
17156248 ATATAGTGACACCCAGTGTCTCATCGA
1 A-ATAGTGACACCCAGTGTCTCATCGA
17156275 CTCGAGGTCG
Statistics
Matches: 50, Mismatches: 10, Indels: 9
0.72 0.14 0.13
Matches are distributed among these distances:
37 16 0.32
38 11 0.22
39 3 0.06
40 3 0.06
41 17 0.34
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (40 bp):
AATAGTGACACCCAGTGTCTCATCGAACAAACCCGAAGAA
Found at i:17159545 original size:33 final size:33
Alignment explanation
Indices: 17159508--17159650 Score: 117
Period size: 33 Copynumber: 4.3 Consensus size: 33
17159498 TGGTCCAACC
*
17159508 ATGGTCTTACGTTCATAGTGCCATAACCCAGTT
1 ATGGTCTTACGTTCATAGTGCCATAACCCAGCT
** * *
17159541 ATGGTCTTATC-ACCAGAATGCCATAACCCAGCT
1 ATGGTCTTA-CGTTCATAGTGCCATAACCCAGCT
* * * * *** * *
17159574 ATGGTCTTACATATAAACACTGCCATGGTCCAACC
1 ATGGTCTTACGT-T-CATAGTGCCATAACCCAGCT
*
17159609 ATGGTCTTACGTTCATAGTGCCATAACCCAGTT
1 ATGGTCTTACGTTCATAGTGCCATAACCCAGCT
17159642 ATGGTCTTA
1 ATGGTCTTA
17159651 TCCGTCAATT
Statistics
Matches: 81, Mismatches: 25, Indels: 8
0.71 0.22 0.07
Matches are distributed among these distances:
32 1 0.01
33 55 0.68
34 2 0.02
35 23 0.28
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (33 bp):
ATGGTCTTACGTTCATAGTGCCATAACCCAGCT
Found at i:17159597 original size:101 final size:101
Alignment explanation
Indices: 17159413--17159652 Score: 401
Period size: 101 Copynumber: 2.4 Consensus size: 101
17159403 AATTCATCCT
* * * *
17159413 TTACATTCGTAGTGCCATAACCCAGTTATGGTCTTTTCATCAGAATGCCATAGACCAACTATGAT
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCACCAGAATGCCATAGACCAACTATGAT
*
17159478 CTTACATATAACCACTGCCATGGTCCAACCATGGTC
66 CTTACATATAAACACTGCCATGGTCCAACCATGGTC
* *
17159514 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCACCAGAATGCCATA-ACCCAGCTATGG
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCACCAGAATGCCATAGA-CCAACTATGA
17159578 TCTTACATATAAACACTGCCATGGTCCAACCATGGTC
65 TCTTACATATAAACACTGCCATGGTCCAACCATGGTC
17159615 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATC
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATC
17159653 CGTCAATTCA
Statistics
Matches: 131, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
100 1 0.01
101 130 0.99
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (101 bp):
TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCACCAGAATGCCATAGACCAACTATGAT
CTTACATATAAACACTGCCATGGTCCAACCATGGTC
Found at i:17161891 original size:22 final size:22
Alignment explanation
Indices: 17161846--17161891 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
17161836 TAATATAGAC
* *
17161846 TTAATAGATGCAGGAAAATATT
1 TTAATAGATGAAAGAAAATATT
17161868 TTAATAGATGAAAAGAAAAT-TT
1 TTAATAGATG-AAAGAAAATATT
17161890 TT
1 TT
17161892 GAACTACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.48, C:0.02, G:0.15, T:0.35
Consensus pattern (22 bp):
TTAATAGATGAAAGAAAATATT
Found at i:17166876 original size:21 final size:22
Alignment explanation
Indices: 17166852--17166907 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
17166842 AATATTTTTC
*
17166852 TCATAAAATTTATTTAAAAA-A
1 TCATAAAAATTATTTAAAAATA
17166873 TCATAAAAAATTA-TTAAAAATA
1 TCAT-AAAAATTATTTAAAAATA
17166895 T-ATAAAAATTATT
1 TCATAAAAATTATT
17166908 AAATATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 8 0.26
21 14 0.45
22 9 0.29
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.38
Consensus pattern (22 bp):
TCATAAAAATTATTTAAAAATA
Found at i:17166893 original size:20 final size:20
Alignment explanation
Indices: 17166854--17166910 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
17166844 TATTTTTCTC
*
17166854 ATAAAATTTATTTAAAAA-AT
1 ATAAAAATTA-TTAAAAATAT
17166874 CATAAAAAATTATTAAAAATAT
1 -AT-AAAAATTATTAAAAATAT
17166896 ATAAAAATTATTAAA
1 ATAAAAATTATTAAA
17166911 TATTTTAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
20 13 0.39
21 11 0.33
22 9 0.27
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAAAAATTATTAAAAATAT
Found at i:17166910 original size:10 final size:10
Alignment explanation
Indices: 17166868--17166920 Score: 56
Period size: 10 Copynumber: 5.4 Consensus size: 10
17166858 AATTTATTTA
* *
17166868 AAAAATCATA
1 AAAAATTATT
17166878 AAAAATTATT
1 AAAAATTATT
17166888 AAAAA-TATAT
1 AAAAATTAT-T
17166898 AAAAATTATT
1 AAAAATTATT
*
17166908 AAATATT-TT
1 AAAAATTATT
17166917 AAAA
1 AAAA
17166921 TATGAAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
9 8 0.22
10 26 0.70
11 3 0.08
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (10 bp):
AAAAATTATT
Found at i:17167049 original size:20 final size:20
Alignment explanation
Indices: 17167024--17167098 Score: 62
Period size: 20 Copynumber: 3.7 Consensus size: 20
17167014 ACATGTCTAT
17167024 AAAAATCATAAAAATTATAA
1 AAAAATCATAAAAATTATAA
* * *
17167044 AAAAATTATTAAAATTGGT-A
1 AAAAATCATAAAAATT-ATAA
* * * *
17167064 TAAACTTATACAAATTATAAA
1 AAAAATCATAAAAATTAT-AA
17167085 AAAAATCATAAAAA
1 AAAAATCATAAAAA
17167099 CTTGAAGTGG
Statistics
Matches: 40, Mismatches: 12, Indels: 5
0.70 0.21 0.09
Matches are distributed among these distances:
19 1 0.03
20 27 0.68
21 12 0.30
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (20 bp):
AAAAATCATAAAAATTATAA
Found at i:17167226 original size:8 final size:8
Alignment explanation
Indices: 17167213--17167255 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
17167203 TGAACCAATT
17167213 TTTTTTAA
1 TTTTTTAA
17167221 TTTTTTAA
1 TTTTTTAA
17167229 TTTTTTAA
1 TTTTTTAA
*
17167237 TATTTTAA
1 TTTTTTAA
* *
17167245 TATTTTGA
1 TTTTTTAA
17167253 TTT
1 TTT
17167256 ATTATGTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (8 bp):
TTTTTTAA
Found at i:17167622 original size:19 final size:18
Alignment explanation
Indices: 17167557--17167622 Score: 55
Period size: 17 Copynumber: 3.6 Consensus size: 18
17167547 AGTTTATATC
*
17167557 AATTTAAATATTTTTAT-
1 AATTTAAATATTTTTTTA
*
17167574 AATGTTACAT-TTTTTTTA
1 AAT-TTAAATATTTTTTTA
*
17167592 AGAATTACAATATGTTTTTTA
1 A-ATTTA-AATAT-TTTTTTA
17167613 AATTTAAATA
1 AATTTAAATA
17167623 AGTTTTATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
17 9 0.24
18 9 0.24
19 7 0.18
20 5 0.13
21 8 0.21
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (18 bp):
AATTTAAATATTTTTTTA
Found at i:17167627 original size:19 final size:20
Alignment explanation
Indices: 17167585--17167638 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
17167575 ATGTTACATT
* *
17167585 TTTTTTAAGAATTACAATATG
1 TTTTTTAA-ATTTACAATAAG
17167606 TTTTTTAAATTTA-AATAAG
1 TTTTTTAAATTTACAATAAG
*
17167625 TTTTATTAATTTTA
1 TTTT-TTAAATTTA
17167639 TATTTTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 9 0.31
20 12 0.41
21 8 0.28
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (20 bp):
TTTTTTAAATTTACAATAAG
Found at i:17167645 original size:34 final size:35
Alignment explanation
Indices: 17167606--17167685 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 35
17167596 TTACAATATG
* *
17167606 TTTTTTAAATTTA-AATAAGTTTTATTAATTTTATA
1 TTTTTTAAATTTATAAGAAGTTTTA-AAATTTTATA
* *
17167641 TTTTTTATAATTTATTAGAATTTTTAAAATTTTAT-
1 TTTTTTA-AATTTATAAGAAGTTTTAAAATTTTATA
17167676 TTTTTTAAAT
1 TTTTTTAAAT
17167686 ATTTTAAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
34 3 0.08
35 14 0.36
36 14 0.36
37 8 0.21
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (35 bp):
TTTTTTAAATTTATAAGAAGTTTTAAAATTTTATA
Found at i:17167651 original size:17 final size:17
Alignment explanation
Indices: 17167625--17167682 Score: 55
Period size: 19 Copynumber: 3.3 Consensus size: 17
17167615 TTTAAATAAG
17167625 TTTTATTAATTTTATATT
1 TTTTA-TAATTTTATATT
* *
17167643 TTTTATAATTTATTAGAAT
1 TTTTATAA-TT-TTATATT
*
17167662 TTTTAAAATTTTAT-TT
1 TTTTATAATTTTATATT
17167678 TTTTA
1 TTTTA
17167683 AATATTTTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
16 6 0.18
17 6 0.18
18 9 0.27
19 12 0.36
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTTATAATTTTATATT
Found at i:17167700 original size:34 final size:36
Alignment explanation
Indices: 17167632--17167708 Score: 99
Period size: 35 Copynumber: 2.2 Consensus size: 36
17167622 AAGTTTTATT
17167632 AATTTTATATTTTTTATAATTTATTAGAATTTTTAA
1 AATTTTATATTTTTTATAATTTATTAGAATTTTTAA
17167668 AATTTTAT-TTTTTTA-AATATT-TTA-AATATTTTAA
1 AATTTTATATTTTTTATAAT-TTATTAGAAT-TTTTAA
17167702 ATATTTT
1 A-ATTTT
17167709 TGATGATATT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
33 3 0.08
34 13 0.34
35 14 0.37
36 8 0.21
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (36 bp):
AATTTTATATTTTTTATAATTTATTAGAATTTTTAA
Found at i:17185604 original size:23 final size:23
Alignment explanation
Indices: 17185578--17185674 Score: 158
Period size: 23 Copynumber: 4.2 Consensus size: 23
17185568 TGTTATATTT
17185578 CAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATAA
* **
17185601 CAGTGGTAGCTTCAGCTACATTT
1 CAGTGGTAGCTTCGGCTACATAA
17185624 CAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATAA
*
17185647 CAGTGGTAGCTTCGGCTACATAT
1 CAGTGGTAGCTTCGGCTACATAA
17185670 CAGTG
1 CAGTG
17185675 TTGCACTTAT
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 67 1.00
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.29
Consensus pattern (23 bp):
CAGTGGTAGCTTCGGCTACATAA
Found at i:17185627 original size:46 final size:46
Alignment explanation
Indices: 17185574--17185674 Score: 184
Period size: 46 Copynumber: 2.2 Consensus size: 46
17185564 CCAGTGTTAT
17185574 ATTTCAGTGGTAGCTTCGGCTACATAACAGTGGTAGCTTCAGCTAC
1 ATTTCAGTGGTAGCTTCGGCTACATAACAGTGGTAGCTTCAGCTAC
*
17185620 ATTTCAGTGGTAGCTTCGGCTACATAACAGTGGTAGCTTCGGCTAC
1 ATTTCAGTGGTAGCTTCGGCTACATAACAGTGGTAGCTTCAGCTAC
*
17185666 ATATCAGTG
1 ATTTCAGTG
17185675 TTGCACTTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 53 1.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.31
Consensus pattern (46 bp):
ATTTCAGTGGTAGCTTCGGCTACATAACAGTGGTAGCTTCAGCTAC
Found at i:17187056 original size:55 final size:55
Alignment explanation
Indices: 17186972--17187082 Score: 186
Period size: 55 Copynumber: 2.0 Consensus size: 55
17186962 CGTTTAACCC
* * *
17186972 TAATGGGTTTTAGTTCAACTCTTTTGAGCTTCGGTTTAACCCTTATGGGTTTCCG
1 TAATGAGTTTCAGTTCAACTCTTTTGAGCTTCAGTTTAACCCTTATGGGTTTCCG
*
17187027 TAATGAGTTTCAGTTCAGCTCTTTTGAGCTTCAGTTTAACCCTTATGGGTTTCCG
1 TAATGAGTTTCAGTTCAACTCTTTTGAGCTTCAGTTTAACCCTTATGGGTTTCCG
17187082 T
1 T
17187083 TCAGCTCTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (55 bp):
TAATGAGTTTCAGTTCAACTCTTTTGAGCTTCAGTTTAACCCTTATGGGTTTCCG
Found at i:17187059 original size:21 final size:21
Alignment explanation
Indices: 17187029--17187115 Score: 75
Period size: 21 Copynumber: 4.1 Consensus size: 21
17187019 GGTTTCCGTA
*
17187029 ATGAGTTTCAGTTCAGCTCTT
1 ATGAGCTTCAGTTCAGCTCTT
* * * *
17187050 TTGAGCTTCAGTTTAACCCTT
1 ATGAGCTTCAGTTCAGCTCTT
* * *
17187071 ATGGGTTTCCGTTCAGCTCTT
1 ATGAGCTTCAGTTCAGCTCTT
* * *
17187092 ATGAGCTTCTGTTCAACCCTT
1 ATGAGCTTCAGTTCAGCTCTT
17187113 ATG
1 ATG
17187116 GGTTTCCGTT
Statistics
Matches: 49, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.41
Consensus pattern (21 bp):
ATGAGCTTCAGTTCAGCTCTT
Found at i:17187097 original size:42 final size:42
Alignment explanation
Indices: 17187033--17187125 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 42
17187023 TCCGTAATGA
* * *
17187033 GTTTCAGTTCAGCTCTTTTGAGCTTCAGTTTAACCCTTATGG
1 GTTTCCGTTCAGCTCTTATGAGCTTCAGTTCAACCCTTATGG
*
17187075 GTTTCCGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGG
1 GTTTCCGTTCAGCTCTTATGAGCTTCAGTTCAACCCTTATGG
17187117 GTTTCCGTT
1 GTTTCCGTT
17187126 TAGCACTTGT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (42 bp):
GTTTCCGTTCAGCTCTTATGAGCTTCAGTTCAACCCTTATGG
Found at i:17187142 original size:42 final size:42
Alignment explanation
Indices: 17187033--17187145 Score: 145
Period size: 42 Copynumber: 2.7 Consensus size: 42
17187023 TCCGTAATGA
* * * * *
17187033 GTTTCAGTTCAGCTCTTTTGAGCTTCAGTTTAACCCTTATGG
1 GTTTCCGTTCAGCACTTATGAGCTTCTGTTCAACCCTTATGG
*
17187075 GTTTCCGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGG
1 GTTTCCGTTCAGCACTTATGAGCTTCTGTTCAACCCTTATGG
* * *
17187117 GTTTCCGTTTAGCACTTGTGTGCTTCTGT
1 GTTTCCGTTCAGCACTTATGAGCTTCTGT
17187146 GTAGCCTTCG
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.43
Consensus pattern (42 bp):
GTTTCCGTTCAGCACTTATGAGCTTCTGTTCAACCCTTATGG
Found at i:17188809 original size:29 final size:30
Alignment explanation
Indices: 17188756--17188812 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
17188746 TCCGAGCCTT
17188756 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGTAAAAGTTTA
* *
17188786 GGGGCAAAATTGTAATTTTG-AAAAGTT
1 GGGGCAAAAATGTAATTATGTAAAAGTT
17188813 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.32
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGTAAAAGTTTA
Found at i:17189043 original size:13 final size:13
Alignment explanation
Indices: 17189025--17189056 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
17189015 TTTCCAGCAA
17189025 TTATGAATTTATT
1 TTATGAATTTATT
17189038 TTATGAATTTATT
1 TTATGAATTTATT
*
17189051 TGATGA
1 TTATGA
17189057 TGATCCAAGC
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:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:17193781 original size:21 final size:22
Alignment explanation
Indices: 17193748--17193789 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
17193738 TATTTTTGAA
* *
17193748 ATTTTTATATTTTTTAATTTTG
1 ATTTTGATATTTTATAATTTTG
17193770 ATTTTGAT-TTTTATAATTTT
1 ATTTTGATATTTTATAATTTT
17193790 TGAATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (22 bp):
ATTTTGATATTTTATAATTTTG
Found at i:17193804 original size:28 final size:27
Alignment explanation
Indices: 17193748--17193804 Score: 62
Period size: 28 Copynumber: 2.0 Consensus size: 27
17193738 TATTTTTGAA
* *
17193748 ATTTTTATATTTTTTAATTTTGATTTTG
1 ATTTTTATATTTTTGAATTTT-ATATTG
17193776 ATTTTTATAATTTTTGAATTATT-TATTG
1 ATTTTTAT-ATTTTTGAATT-TTATATTG
17193804 A
1 A
17193805 CGTGACAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
28 13 0.52
29 10 0.40
30 2 0.08
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (27 bp):
ATTTTTATATTTTTGAATTTTATATTG
Found at i:17196773 original size:5 final size:5
Alignment explanation
Indices: 17196765--17196790 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
17196755 AAGATGAAAT
17196765 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
17196791 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:17197645 original size:30 final size:31
Alignment explanation
Indices: 17197604--17197664 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
17197594 GGGTTGGGAG
* *
17197604 GGGAGAGGAGTAAAAGTTTTGGGGGGAAAGT
1 GGGAGAGGAGTAAAAGTTTTGAGGGAAAAGT
17197635 GGGA-AGGAGTAAAAGTTTTGAGGGAAAAGT
1 GGGAGAGGAGTAAAAGTTTTGAGGGAAAAGT
17197665 AAAAAGGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.36, C:0.00, G:0.44, T:0.20
Consensus pattern (31 bp):
GGGAGAGGAGTAAAAGTTTTGAGGGAAAAGT
Found at i:17198272 original size:14 final size:15
Alignment explanation
Indices: 17198214--17198274 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 15
17198204 ATAACTTAAG
*
17198214 TTCATCATTTAATTT
1 TTCAACATTTAATTT
** *
17198229 TTCAGTATTTATTTT
1 TTCAACATTTAATTT
*
17198244 TTCAGACACTT-ATTT
1 TTCA-ACATTTAATTT
17198259 TT-AACATTTAATTT
1 TTCAACATTTAATTT
17198273 TT
1 TT
17198275 TACTTATTCA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
13 5 0.14
14 7 0.19
15 21 0.58
16 3 0.08
ACGTcount: A:0.26, C:0.11, G:0.03, T:0.59
Consensus pattern (15 bp):
TTCAACATTTAATTT
Found at i:17202284 original size:22 final size:24
Alignment explanation
Indices: 17202242--17202285 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
17202232 TAACTAAGCT
17202242 TACTTACTTTTCTAACTTAATTCA
1 TACTTACTTTTCTAACTTAATTCA
17202266 TACTT-CTTTTCT-ACTTAATT
1 TACTTACTTTTCTAACTTAATT
17202286 TCTTGTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (24 bp):
TACTTACTTTTCTAACTTAATTCA
Found at i:17202680 original size:13 final size:13
Alignment explanation
Indices: 17202662--17202694 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
17202652 CTTTCTCTGT
17202662 TTCTTTTATGTTC
1 TTCTTTTATGTTC
17202675 TTCTTTTATGTTC
1 TTCTTTTATGTTC
17202688 TTCTTTT
1 TTCTTTT
17202695 GTTTCTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.06, C:0.15, G:0.06, T:0.73
Consensus pattern (13 bp):
TTCTTTTATGTTC
Found at i:17202916 original size:5 final size:5
Alignment explanation
Indices: 17202897--17202967 Score: 71
Period size: 5 Copynumber: 14.6 Consensus size: 5
17202887 TTAGTTTATT
*
17202897 TAATA T-ATAA TAATA TAATA TAATA TAAT- TAATA TTATA TAATA TATTATA
1 TAATA TAAT-A TAATA TAATA TAATA TAATA TAATA TAATA TAATA TA--ATA
17202948 TAATA -AA-A TAATA T-ATA TAA
1 TAATA TAATA TAATA TAATA TAA
17202968 AACATAAAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 16
0.76 0.03 0.22
Matches are distributed among these distances:
3 1 0.02
4 14 0.25
5 34 0.61
6 2 0.04
7 5 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TAATA
Done.