Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 129 of 204
Found at i:39415278 original size:45 final size:45
Alignment explanation
Indices: 39415228--39415313 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
39415218 TCATTGACCA
* * *
39415228 AGTATAAATAATTAATGATAAATAATATGTAAATTAGTTAAATTT
1 AGTATAAATAATTAATAACAAATAATATGTAAATTAATTAAATTT
*
39415273 AGTATAAATAATTAATAACAAATACTATGTAAATTAATTAA
1 AGTATAAATAATTAATAACAAATAATATGTAAATTAATTAA
39415314 CTAAAGAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.37
Consensus pattern (45 bp):
AGTATAAATAATTAATAACAAATAATATGTAAATTAATTAAATTT
Found at i:39417134 original size:6 final size:6
Alignment explanation
Indices: 39417123--39417156 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
39417113 GTTTCCCAAA
*
39417123 AAATGG AAATGG AAATGG AAATGG AAATGA AAAT
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAAT
39417157 ATGAAATGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.26, T:0.18
Consensus pattern (6 bp):
AAATGG
Found at i:39421552 original size:26 final size:25
Alignment explanation
Indices: 39421523--39421596 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 25
39421513 GTCACTTTAA
39421523 TATTAAATTAATATAATATTTAATCT
1 TATTAAATTAATATAATATTT-ATCT
* * *
39421549 TATTAAAATAATAAAATGTTTATCT
1 TATTAAATTAATATAATATTTATCT
*
39421574 TACATTAAAATTAATTTAATATT
1 T--ATT-AAATTAATATAATATT
39421597 AAGATAATCA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
25 5 0.13
26 18 0.47
27 3 0.08
28 12 0.32
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (25 bp):
TATTAAATTAATATAATATTTATCT
Found at i:39424615 original size:51 final size:51
Alignment explanation
Indices: 39424451--39424601 Score: 212
Period size: 51 Copynumber: 3.0 Consensus size: 51
39424441 TGGTTATGGA
* * *
39424451 CACATGTGTAGTACTAAGTGCAGGTTACTATGTGTACCGGATAGCTTTGGT
1 CACATGTGTGGTACTAAGTGCAGGCTACTATGTGTACCGGATAGCATTGGT
* * * * * *
39424502 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGTATTGGT
1 CACATGTGTGGTACTAAGTGCAGGCTACTATGTGTACCGGATAGCATTGGT
*
39424553 CACATGTGTGGTACTAAGTGTAGGCTACTATGTGTACCGGATAGCATTG
1 CACATGTGTGGTACTAAGTGCAGGCTACTATGTGTACCGGATAGCATTG
39424602 ATCATAAGGG
Statistics
Matches: 86, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 86 1.00
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.32
Consensus pattern (51 bp):
CACATGTGTGGTACTAAGTGCAGGCTACTATGTGTACCGGATAGCATTGGT
Found at i:39429550 original size:21 final size:21
Alignment explanation
Indices: 39429526--39429569 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
39429516 GAATCTTTAG
*
39429526 TATTTATTGTATCATTT-TATT
1 TATTTAAT-TATCATTTCTATT
*
39429547 TATTTAATTATCCTTTCTATT
1 TATTTAATTATCATTTCTATT
39429568 TA
1 TA
39429570 ACTAGTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (21 bp):
TATTTAATTATCATTTCTATT
Found at i:39433979 original size:29 final size:27
Alignment explanation
Indices: 39433915--39433979 Score: 67
Period size: 29 Copynumber: 2.3 Consensus size: 27
39433905 TTGACAAGAA
* * *
39433915 ATAATAATATATAAAATTTTAAAATAT
1 ATAATAATACATAAAATTTTAAAAAAG
* *
39433942 ATAAAAATACATAACTATTTTAAAAAAAG
1 ATAATAATACATAA-AATTTT-AAAAAAG
39433971 ATAATAATA
1 ATAATAATA
39433980 AAATTAAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
27 12 0.40
28 5 0.17
29 13 0.43
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.34
Consensus pattern (27 bp):
ATAATAATACATAAAATTTTAAAAAAG
Found at i:39434211 original size:17 final size:17
Alignment explanation
Indices: 39434191--39434229 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
39434181 ATTTTAAAAA
**
39434191 ATATTTGAGTATTTTAT
1 ATATTTGAACATTTTAT
*
39434208 ATATTTTAACATTTTAT
1 ATATTTGAACATTTTAT
39434225 ATATT
1 ATATT
39434230 ATTTCTTGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (17 bp):
ATATTTGAACATTTTAT
Found at i:39435372 original size:15 final size:15
Alignment explanation
Indices: 39435349--39435378 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39435339 GTAAGGATGT
39435349 GAACACACCATGTGC
1 GAACACACCATGTGC
*
39435364 GAACCCACCATGTGC
1 GAACACACCATGTGC
39435379 CAGCCCCTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.37, G:0.20, T:0.13
Consensus pattern (15 bp):
GAACACACCATGTGC
Found at i:39438064 original size:6 final size:6
Alignment explanation
Indices: 39438048--39438093 Score: 58
Period size: 6 Copynumber: 7.5 Consensus size: 6
39438038 TAGGTTTCCA
*
39438048 AAAATG GAAATG AAAAT- ATAAATG AAAATG AAAATG AAAATTG AAA
1 AAAATG AAAATG AAAATG A-AAATG AAAATG AAAATG AAAA-TG AAA
39438094 CTTACAATCC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
5 1 0.03
6 28 0.80
7 6 0.17
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (6 bp):
AAAATG
Found at i:39438281 original size:27 final size:27
Alignment explanation
Indices: 39438234--39438298 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
39438224 GTGAAATTTC
* **
39438234 TCAAAATTTTA-CCGGGAGTAAAATTG
1 TCAAAATTTTATCAGGGAGTAAAATCA
*
39438260 TCAAAATTTTATCAGGGGGTAAAATCA
1 TCAAAATTTTATCAGGGAGTAAAATCA
39438287 TCAAAATTTTAT
1 TCAAAATTTTAT
39438299 TGAAGCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 11 0.32
27 23 0.68
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (27 bp):
TCAAAATTTTATCAGGGAGTAAAATCA
Found at i:39440497 original size:12 final size:11
Alignment explanation
Indices: 39440480--39440543 Score: 56
Period size: 12 Copynumber: 5.5 Consensus size: 11
39440470 CAAGTGAATT
39440480 AATTCACAAACG
1 AATTCA-AAACG
* **
39440492 AATTCAGAATT
1 AATTCAAAACG
39440503 AATTCATAAACG
1 AATTCA-AAACG
**
39440515 AATTCAAAATT
1 AATTCAAAACG
39440526 AATTCACAAACG
1 AATTCA-AAACG
39440538 AATTCA
1 AATTCA
39440544 GAATTAATTC
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
11 17 0.43
12 23 0.57
ACGTcount: A:0.50, C:0.17, G:0.06, T:0.27
Consensus pattern (11 bp):
AATTCAAAACG
Found at i:39440505 original size:23 final size:23
Alignment explanation
Indices: 39440475--39440554 Score: 142
Period size: 23 Copynumber: 3.5 Consensus size: 23
39440465 CATCACAAGT
39440475 GAATTAATTCACAAACGAATTCA
1 GAATTAATTCACAAACGAATTCA
*
39440498 GAATTAATTCATAAACGAATTCA
1 GAATTAATTCACAAACGAATTCA
*
39440521 AAATTAATTCACAAACGAATTCA
1 GAATTAATTCACAAACGAATTCA
39440544 GAATTAATTCA
1 GAATTAATTCA
39440555 TCTTGGGTCC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.29
Consensus pattern (23 bp):
GAATTAATTCACAAACGAATTCA
Found at i:39440508 original size:11 final size:11
Alignment explanation
Indices: 39440476--39440554 Score: 59
Period size: 11 Copynumber: 6.9 Consensus size: 11
39440466 ATCACAAGTG
39440476 AATTAATTCACA
1 AATTAATTCA-A
** *
39440488 AACGAATTCAG
1 AATTAATTCAA
39440499 AATTAATTCATA
1 AATTAATTCA-A
**
39440511 AACGAATTCAA
1 AATTAATTCAA
39440522 AATTAATTCACA
1 AATTAATTCA-A
** *
39440534 AACGAATTCAG
1 AATTAATTCAA
39440545 AATTAATTCA
1 AATTAATTCA
39440555 TCTTGGGTCC
Statistics
Matches: 50, Mismatches: 15, Indels: 5
0.71 0.21 0.07
Matches are distributed among these distances:
11 25 0.50
12 25 0.50
ACGTcount: A:0.49, C:0.15, G:0.06, T:0.29
Consensus pattern (11 bp):
AATTAATTCAA
Found at i:39443320 original size:10 final size:10
Alignment explanation
Indices: 39443305--39443330 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
39443295 AGTAAATGAG
39443305 TAAAACAGAA
1 TAAAACAGAA
39443315 TAAAACAGAA
1 TAAAACAGAA
39443325 TAAAAC
1 TAAAAC
39443331 CGTCTAACGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.69, C:0.12, G:0.08, T:0.12
Consensus pattern (10 bp):
TAAAACAGAA
Found at i:39443984 original size:27 final size:27
Alignment explanation
Indices: 39443956--39444377 Score: 461
Period size: 27 Copynumber: 15.6 Consensus size: 27
39443946 TACCCTATGG
* *
39443956 GGGTATTTTAGTAATTTTACCCATCGG
1 GGGTATTTTGGTAATTTTACCCATCGA
* * * *
39443983 GGAGTATTTCGGTAATTTTACCCTTTGT
1 GG-GTATTTTGGTAATTTTACCCATCGA
* *
39444011 GGGTATCTTGGTAATTTTACCCATCAA
1 GGGTATTTTGGTAATTTTACCCATCGA
** *
39444038 GGGTATTTCAGTAAATTTACCCATC-A
1 GGGTATTTTGGTAATTTTACCCATCGA
* * * *
39444064 GGGGTATTTCGATAATTTTACCCGTCAA
1 -GGGTATTTTGGTAATTTTACCCATCGA
* *
39444092 GGGTATTTCGGTAATTTAACCCATCGA
1 GGGTATTTTGGTAATTTTACCCATCGA
* * *
39444119 GGGTATTTCGGTAGTTTTATCCATCGA
1 GGGTATTTTGGTAATTTTACCCATCGA
* * * *
39444146 AGGTATTTCGGTAATTATACCCATTGA
1 GGGTATTTTGGTAATTTTACCCATCGA
* * *
39444173 GGATATTTCGATAATTTTACCCATCGA
1 GGGTATTTTGGTAATTTTACCCATCGA
*
39444200 GGGTATTTTGGTAATTTTACCCGTCGA
1 GGGTATTTTGGTAATTTTACCCATCGA
* *
39444227 -GGTATTTTGATAATTTTACCCATCTA
1 GGGTATTTTGGTAATTTTACCCATCGA
39444253 GGGTATTTTGGTAATTTTACCCATCGA
1 GGGTATTTTGGTAATTTTACCCATCGA
* * *
39444280 GAGTATTTCGGTAGTTTTACCCATCGA
1 GGGTATTTTGGTAATTTTACCCATCGA
* * **
39444307 GGGTATTTCGATAATTTTACTTATCGA
1 GGGTATTTTGGTAATTTTACCCATCGA
*
39444334 GGGTATTTCGGTAATTTTACCCATCGA
1 GGGTATTTTGGTAATTTTACCCATCGA
*
39444361 GGGTATTTTGATAATTT
1 GGGTATTTTGGTAATTT
39444378 AGGCCCATTA
Statistics
Matches: 333, Mismatches: 58, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
26 24 0.07
27 286 0.86
28 23 0.07
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACCCATCGA
Found at i:39445411 original size:13 final size:14
Alignment explanation
Indices: 39445378--39445420 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 14
39445368 TTCCCAAATT
*
39445378 CTCTCCTAAAATCA
1 CTCTCCTTAAATCA
39445392 CT-T-CTTAAATC-
1 CTCTCCTTAAATCA
39445403 CTCTCCTTAAATCA
1 CTCTCCTTAAATCA
39445417 CTCT
1 CTCT
39445421 TTTGACCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
11 2 0.08
12 8 0.32
13 9 0.36
14 6 0.24
ACGTcount: A:0.28, C:0.35, G:0.00, T:0.37
Consensus pattern (14 bp):
CTCTCCTTAAATCA
Found at i:39445568 original size:25 final size:25
Alignment explanation
Indices: 39445531--39445584 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
39445521 TGAACCTCTG
*
39445531 ACCTCCTTACCACACCTGTGACGCC
1 ACCTCATTACCACACCTGTGACGCC
* *
39445556 ACCTCATTGCCACACCTGTGTCGCC
1 ACCTCATTACCACACCTGTGACGCC
39445581 ACCT
1 ACCT
39445585 TGCCAATACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.19, C:0.46, G:0.13, T:0.22
Consensus pattern (25 bp):
ACCTCATTACCACACCTGTGACGCC
Found at i:39448723 original size:27 final size:27
Alignment explanation
Indices: 39448692--39449466 Score: 930
Period size: 27 Copynumber: 28.7 Consensus size: 27
39448682 TTTACCGTAT
* *
39448692 GAGGGTATTTCGGTAATTTTAACCATC
1 GAGGGTATTTCGATAATTTTACCCATC
* ** * * *
39448719 AAGGGTATTTTAAAAATTTTACCCTTT
1 GAGGGTATTTCGATAATTTTACCCATC
39448746 GAGGGTATTTCGATAATTTTACCCATC
1 GAGGGTATTTCGATAATTTTACCCATC
* * * *
39448773 AAGGGTATTTTGGA-AAATTTACCCTTC
1 GAGGGTA-TTTCGATAATTTTACCCATC
* * * *
39448800 GGGGGTATTTCGGTAGTTTTACCCATT
1 GAGGGTATTTCGATAATTTTACCCATC
* * *
39448827 GAGAGTATTTCGATAATTTTACCCTTT
1 GAGGGTATTTCGATAATTTTACCCATC
* * *
39448854 AAGGGTATTTTGGTAATTTTACCCATC
1 GAGGGTATTTCGATAATTTTACCCATC
* *
39448881 GGGGGTATTTCGGTAATTTTACCCATC
1 GAGGGTATTTCGATAATTTTACCCATC
* **
39448908 -ATGGGTATTTTGGA-AATTTTACCTTTC
1 GA-GGGTA-TTTCGATAATTTTACCCATC
* *
39448935 GGGGGGTATTTCAATAATTTTACCCATC
1 -GAGGGTATTTCGATAATTTTACCCATC
* * *
39448963 GGGGGTATGTCAATAATTTTACCCATC
1 GAGGGTATTTCGATAATTTTACCCATC
*
39448990 G-GAGGTATTTCAATAATTTTACCCATC
1 GAG-GGTATTTCGATAATTTTACCCATC
* *
39449017 GGGGGTATTTCGTTAATTTTACCCATC
1 GAGGGTATTTCGATAATTTTACCCATC
*
39449044 GAGGGTATTTCAATAATTTTACCCATC
1 GAGGGTATTTCGATAATTTTACCCATC
*
39449071 GAGGGTATTTCAATAATTTTACCCATC
1 GAGGGTATTTCGATAATTTTACCCATC
* * *
39449098 GAGGTTATTTTGGTAATTTTACCCATC
1 GAGGGTATTTCGATAATTTTACCCATC
* *
39449125 GAGGGTATTTTGGTAATTTTACCCATC
1 GAGGGTATTTCGATAATTTTACCCATC
* * *
39449152 GAGGGTATTTTGGTAGTTTTACCCATC
1 GAGGGTATTTCGATAATTTTACCCATC
*
39449179 GAGGGTATTTCGATAGTTTTACCCATC
1 GAGGGTATTTCGATAATTTTACCCATC
*
39449206 GAGGGTATTTCGATAGTTTTA-CCATC
1 GAGGGTATTTCGATAATTTTACCCATC
*
39449232 GAGGGTATTTCGATAATTTTACCCATT
1 GAGGGTATTTCGATAATTTTACCCATC
39449259 GAGGGTATTTCGATAATTTTACCCATC
1 GAGGGTATTTCGATAATTTTACCCATC
*
39449286 GAGGGTATTTCGATAATTTTACACATC
1 GAGGGTATTTCGATAATTTTACCCATC
* * * *
39449313 GAAGGTATTTCGGTAATTTTATCCATT
1 GAGGGTATTTCGATAATTTTACCCATC
*
39449340 GAGTGTATTTCGATAATTTTACCCATC
1 GAGGGTATTTCGATAATTTTACCCATC
39449367 GAGGGTATTTCGATAATTTTACCCATC
1 GAGGGTATTTCGATAATTTTACCCATC
*
39449394 GAGGGTATTTCGATAATTTTACACATC
1 GAGGGTATTTCGATAATTTTACCCATC
* * * *
39449421 GAAGGTATTTCGGTAATTTTATCCATT
1 GAGGGTATTTCGATAATTTTACCCATC
*
39449448 GAGTGTATTTCGATAATTT
1 GAGGGTATTTCGATAATTT
39449467 AGGCCCATTA
Statistics
Matches: 649, Mismatches: 89, Indels: 20
0.86 0.12 0.03
Matches are distributed among these distances:
26 30 0.05
27 593 0.91
28 26 0.04
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (27 bp):
GAGGGTATTTCGATAATTTTACCCATC
Found at i:39450164 original size:10 final size:10
Alignment explanation
Indices: 39450145--39450176 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
39450135 GGAAGATTTC
*
39450145 GATAGAAGAG
1 GATAGGAGAG
39450155 GATAGGAGAG
1 GATAGGAGAG
39450165 GATAGGAGAG
1 GATAGGAGAG
39450175 GA
1 GA
39450177 AAGAAGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.47, T:0.09
Consensus pattern (10 bp):
GATAGGAGAG
Found at i:39450669 original size:25 final size:25
Alignment explanation
Indices: 39450632--39450685 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
39450622 TGAAGCTCTA
39450632 ACCTCCTTACCACACCTGTGACGCC
1 ACCTCCTTACCACACCTGTGACGCC
* *
39450657 ACCTCCTTGCCACACCTGTGTCGCC
1 ACCTCCTTACCACACCTGTGACGCC
39450682 ACCT
1 ACCT
39450686 TGCCACTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.17, C:0.48, G:0.13, T:0.22
Consensus pattern (25 bp):
ACCTCCTTACCACACCTGTGACGCC
Found at i:39450689 original size:22 final size:23
Alignment explanation
Indices: 39450636--39450691 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 23
39450626 GCTCTAACCT
*
39450636 CCTTACCACACCTGTGACGCCACC
1 CCTTGCCACACCTGTGACGCCA-C
*
39450660 TCCTTGCCACACCTGTGTCGCCA-
1 -CCTTGCCACACCTGTGACGCCAC
39450683 CCTTGCCAC
1 CCTTGCCAC
39450692 TACACCACAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 9 0.31
25 20 0.69
ACGTcount: A:0.16, C:0.48, G:0.14, T:0.21
Consensus pattern (23 bp):
CCTTGCCACACCTGTGACGCCAC
Found at i:39469291 original size:13 final size:13
Alignment explanation
Indices: 39469273--39469297 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39469263 GTCTTAAGTG
39469273 TTGAGTTGAATCA
1 TTGAGTTGAATCA
39469286 TTGAGTTGAATC
1 TTGAGTTGAATC
39469298 CATTATATTG
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:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (13 bp):
TTGAGTTGAATCA
Found at i:39474841 original size:42 final size:42
Alignment explanation
Indices: 39474793--39474884 Score: 175
Period size: 42 Copynumber: 2.2 Consensus size: 42
39474783 GAATGCCCAA
*
39474793 ACGGCCTGAGACACGGGCATTTGTCTCAGCCATGTGAGTCAC
1 ACGGCCTGAGACACGAGCATTTGTCTCAGCCATGTGAGTCAC
39474835 ACGGCCTGAGACACGAGCATTTGTCTCAGCCATGTGAGTCAC
1 ACGGCCTGAGACACGAGCATTTGTCTCAGCCATGTGAGTCAC
39474877 ACGGCCTG
1 ACGGCCTG
39474885 GCCACAGGGC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.22, C:0.29, G:0.28, T:0.21
Consensus pattern (42 bp):
ACGGCCTGAGACACGAGCATTTGTCTCAGCCATGTGAGTCAC
Found at i:39477375 original size:33 final size:33
Alignment explanation
Indices: 39477333--39477409 Score: 154
Period size: 33 Copynumber: 2.3 Consensus size: 33
39477323 GGGTAAAATA
39477333 GTCATTTTACCCTTTAGGGGTATTTTGGTCATG
1 GTCATTTTACCCTTTAGGGGTATTTTGGTCATG
39477366 GTCATTTTACCCTTTAGGGGTATTTTGGTCATG
1 GTCATTTTACCCTTTAGGGGTATTTTGGTCATG
39477399 GTCATTTTACC
1 GTCATTTTACC
39477410 TATTTTGGGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.16, C:0.17, G:0.22, T:0.45
Consensus pattern (33 bp):
GTCATTTTACCCTTTAGGGGTATTTTGGTCATG
Found at i:39483801 original size:198 final size:198
Alignment explanation
Indices: 39483463--39483858 Score: 792
Period size: 198 Copynumber: 2.0 Consensus size: 198
39483453 AGTTATGGTG
39483463 TGATCATGATTTTAAGCATGATAAATACAAATTGGTCATAATTTAGATGGAATTTGATATAGCTT
1 TGATCATGATTTTAAGCATGATAAATACAAATTGGTCATAATTTAGATGGAATTTGATATAGCTT
39483528 GTTCATGGTTGGATGATTTGGAATCATGAGTGTGTGTTATGTGTTAAATTACAGGTTTGTTTGGT
66 GTTCATGGTTGGATGATTTGGAATCATGAGTGTGTGTTATGTGTTAAATTACAGGTTTGTTTGGT
39483593 GCCTTAAAACACCATTTGAGTAATTTAAGATGTGGGCATGTAATGGGTATTTTGCCATTTTTGCA
131 GCCTTAAAACACCATTTGAGTAATTTAAGATGTGGGCATGTAATGGGTATTTTGCCATTTTTGCA
39483658 CTA
196 CTA
39483661 TGATCATGATTTTAAGCATGATAAATACAAATTGGTCATAATTTAGATGGAATTTGATATAGCTT
1 TGATCATGATTTTAAGCATGATAAATACAAATTGGTCATAATTTAGATGGAATTTGATATAGCTT
39483726 GTTCATGGTTGGATGATTTGGAATCATGAGTGTGTGTTATGTGTTAAATTACAGGTTTGTTTGGT
66 GTTCATGGTTGGATGATTTGGAATCATGAGTGTGTGTTATGTGTTAAATTACAGGTTTGTTTGGT
39483791 GCCTTAAAACACCATTTGAGTAATTTAAGATGTGGGCATGTAATGGGTATTTTGCCATTTTTGCA
131 GCCTTAAAACACCATTTGAGTAATTTAAGATGTGGGCATGTAATGGGTATTTTGCCATTTTTGCA
39483856 CTA
196 CTA
39483859 AGGTATCGAT
Statistics
Matches: 198, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
198 198 1.00
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.40
Consensus pattern (198 bp):
TGATCATGATTTTAAGCATGATAAATACAAATTGGTCATAATTTAGATGGAATTTGATATAGCTT
GTTCATGGTTGGATGATTTGGAATCATGAGTGTGTGTTATGTGTTAAATTACAGGTTTGTTTGGT
GCCTTAAAACACCATTTGAGTAATTTAAGATGTGGGCATGTAATGGGTATTTTGCCATTTTTGCA
CTA
Found at i:39498459 original size:2 final size:2
Alignment explanation
Indices: 39498452--39498494 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
39498442 TTATCAAAAT
39498452 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39498494 T
1 T
39498495 GAAATTGATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39499123 original size:16 final size:15
Alignment explanation
Indices: 39499102--39499162 Score: 68
Period size: 15 Copynumber: 3.8 Consensus size: 15
39499092 TTATAGGCCT
39499102 TTTATATATTTTTAA
1 TTTATATATTTTTAA
39499117 TTGTATATATTTTTATAAA
1 TT-TATATA-TTTT-T-AA
* *
39499136 TTTATAAATTTTTAT
1 TTTATATATTTTTAA
39499151 TTTATATATTTT
1 TTTATATATTTT
39499163 AAAATATTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
15 14 0.36
16 7 0.18
17 8 0.21
18 6 0.15
19 4 0.10
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (15 bp):
TTTATATATTTTTAA
Found at i:39499125 original size:18 final size:17
Alignment explanation
Indices: 39499104--39499162 Score: 56
Period size: 18 Copynumber: 3.6 Consensus size: 17
39499094 ATAGGCCTTT
39499104 TATATATTTTTAATTGTA
1 TATATATTTTTAATT-TA
39499122 TATAT-TTTTATAAATTTA
1 TATATATTTT-T-AATTTA
39499140 TA-A-ATTTTT-ATTT-
1 TATATATTTTTAATTTA
39499153 TATATATTTT
1 TATATATTTT
39499163 AAAATATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
13 2 0.06
14 5 0.14
15 5 0.14
16 1 0.03
17 9 0.25
18 10 0.28
19 4 0.11
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
TATATATTTTTAATTTA
Found at i:39501610 original size:15 final size:15
Alignment explanation
Indices: 39501590--39501619 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39501580 TTTATTACTC
*
39501590 TTTTGAATTATTTAA
1 TTTTGAATGATTTAA
39501605 TTTTGAATGATTTAA
1 TTTTGAATGATTTAA
39501620 AAAATATTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (15 bp):
TTTTGAATGATTTAA
Found at i:39502832 original size:45 final size:44
Alignment explanation
Indices: 39502765--39502852 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 44
39502755 ATGTTTTTAA
*
39502765 TTTCCCACTTAAACTCTAATTAGTGTAGGTTATTTTAATATTAG
1 TTTCCCACTTAAACTCTAATTAGTGTAAGTTATTTTAATATTAG
39502809 TTTCCCACTTAAAACTCTAATTAGTGTAAGTTATTTTAATATTA
1 TTTCCCACTT-AAACTCTAATTAGTGTAAGTTATTTTAATATTA
39502853 TTTGACCTGC
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
44 10 0.24
45 32 0.76
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (44 bp):
TTTCCCACTTAAACTCTAATTAGTGTAAGTTATTTTAATATTAG
Found at i:39504689 original size:59 final size:56
Alignment explanation
Indices: 39504535--39504694 Score: 205
Period size: 56 Copynumber: 2.8 Consensus size: 56
39504525 GCCTGGTGAG
39504535 AATTTTCCTAAGTCAGCCTAGCTCTTAAAAGATGAGAATTCTCCTATGTCAGCTTA
1 AATTTTCCTAAGTCAGCCTAGCTCTTAAAAGATGAGAATTCTCCTATGTCAGCTTA
* *** * *
39504591 AGTCAGCCTAAGTTAGCCTAGCTCTTAAAAGATGAGAATTCTCCTATTTCTTTA-CTTCA
1 AATTTTCCTAAGTCAGCCTAGCTCTTAAAAGATGAGAATTCTCCTATGTC---AGCTT-A
* *
39504650 AATTTTCCTAAGTCAACCTAGCTCTCAAAAGATGAGAATTCTCCT
1 AATTTTCCTAAGTCAGCCTAGCTCTTAAAAGATGAGAATTCTCCT
39504695 GAAAATTCTT
Statistics
Matches: 87, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
56 44 0.51
58 3 0.03
59 40 0.46
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.34
Consensus pattern (56 bp):
AATTTTCCTAAGTCAGCCTAGCTCTTAAAAGATGAGAATTCTCCTATGTCAGCTTA
Found at i:39507534 original size:31 final size:31
Alignment explanation
Indices: 39507499--39507561 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
39507489 CCTCACATAA
39507499 TATGATGTTTTGCTTATGAAAATTAATAAGT
1 TATGATGTTTTGCTTATGAAAATTAATAAGT
39507530 TATGATGTTTTGCTTATGAAAATTAATAAGT
1 TATGATGTTTTGCTTATGAAAATTAATAAGT
39507561 T
1 T
39507562 GATTGAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.03, G:0.16, T:0.46
Consensus pattern (31 bp):
TATGATGTTTTGCTTATGAAAATTAATAAGT
Found at i:39514653 original size:282 final size:282
Alignment explanation
Indices: 39514149--39515520 Score: 1839
Period size: 282 Copynumber: 4.9 Consensus size: 282
39514139 ATGAAGGCGA
** * *
39514149 AGACTAATGCAGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTTATTTGTCTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
* * * * *
39514214 CAACTTCATGAAGGAGTCGACATTGAGGAAGCAACTGTTCTGAGTATGATCGAGAAACCGCCAGA
66 CAACTTCATGAAGGAGTCGACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
* *
39514279 TCATGGAGGTAACAAATCAAAATTACCTGTT-TTCGAGGCAAGGTCTCTGGAGGATATACATAAA
131 TCATGGAGATAACAAATCAAAATTACCTGTTGTT-GAGGCAAGATCTCTGGAGGATATACATAAA
* *
39514343 GCTGTTCGACAACTTCCGGAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAAGAATGA
195 GCTGTTCAACAACTTCCGGAATCTAATCCAGCTGAGCTGCCACATTCTTCAGGCTCAAAGAATGA
*
39514408 ATCATCAAAAGATACGAAAACTG
260 ATCATCAAAAGATACGAAGACTG
* *
39514431 AGACTAATCTGGTGCTGCCTA-TTCTTGAAGCAAGATCAGCCGAAGATATTGATTTGGCTTTTAA
1 AGACTAATGTGGTGCTGCC-AGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAA
* * *
39514495 GCAACTTCATGAAGGAGTCGACATTGAGGAAGTAATTGTTCCAAGTATGATCGAGAAACTGACAG
65 GCAACTTCATGAAGGAGTCGACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAG
* *
39514560 ATCATGGAGATAACAAATCAAAATTACCTATTGTTGAGGCAAGGTCTCTGGAGGATATACATAAA
130 ATCATGGAGATAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGAGGATATACATAAA
* * * *
39514625 GCTGTTCGACAACTTCCGGAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTTAAGGAATGA
195 GCTGTTCAACAACTTCCGGAATCTAATCCAGCTGAGCTGCCACATTCTTCAGGCTCAAAGAATGA
* * *
39514690 ATCATCAACAGATATGAATACTG
260 ATCATCAAAAGATACGAAGACTG
* * *
39514713 AGACTAATGTGGTGCTTCCAGTTCTTGAAACAAGGTCAGCAGAAGATATTGATTTGGCTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
* **
39514778 CAACTTCATGAAGGAGTCAATGTTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
66 CAACTTCATGAAGGAGTCGACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
* * * * *
39514843 TCTTGGAGATAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGAGGATTTAGACAAAT
131 TCATGGAGATAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGAGGATATACATAAAG
* * * * * ** **
39514908 CTATTCAACAACTTGCGAAACCTAATCCAGCAT-A--TTCTTCAGGC-TCAGGCTCAAAGAATGA
196 CTGTTCAACAACTTCCGGAATCTAATCCAGC-TGAGCTGCCACATTCTTCAGGCTCAAAGAATGA
* *
39514969 ATCATCAAAAGATGCGAAGACCG
260 ATCATCAAAAGATACGAAGACTG
*
39514992 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCCGAAGATATTGATTTGGCTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
* *
39515057 CAACTTCATGACGGAGTGGACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
66 CAACTTCATGAAGGAGTCGACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
* * * * * *
39515122 CCATGGAGATAACAAATCAAAATTACGTGTTGTCGAGGCAAGATCTCTGGAGGACATAGACAAAG
131 TCATGGAGATAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGAGGATATACATAAAG
* * ** *
39515187 CTATTCAACAACTTCCGAAATCTAATCCAGCTGAGCTGCCACATTCTTCAGTTTCAAGGAATGAA
196 CTGTTCAACAACTTCCGGAATCTAATCCAGCTGAGCTGCCACATTCTTCAGGCTCAAAGAATGAA
* *
39515252 CCATCAAAAGATATGAAGACTG
261 TCATCAAAAGATACGAAGACTG
39515274 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
* ** * * *
39515339 CAACTGCATGAAGGAG-CTGATGTTGAGGAAGTAATTGTTCCAAGTATGATTGTGGAAC--CACA
66 CAACTTCATGAAGGAGTC-GACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGC-CA
* *** * *
39515401 GGATGACACAGATAACAAATCAAAATTACCTGTTGTGGAGGCAAGATCTCTGAAGGA-ATTACAT
129 -GATCATGGAGATAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGAGGATA-TACAT
* * ** * *
39515465 AATGCTGTCCAACAA-GGCCTGGAATCTGATCCAGCTAAGCTGCCACATTCTTCAGG
192 AAAGCTGTTCAACAACTTCC-GGAATCTAATCCAGCTGAGCTGCCACATTCTTCAGG
39515521 TGTAAACAAT
Statistics
Matches: 964, Mismatches: 113, Indels: 26
0.87 0.10 0.02
Matches are distributed among these distances:
278 1 0.00
279 242 0.25
280 5 0.01
281 11 0.01
282 701 0.73
283 4 0.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.26
Consensus pattern (282 bp):
AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
CAACTTCATGAAGGAGTCGACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
TCATGGAGATAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGAGGATATACATAAAG
CTGTTCAACAACTTCCGGAATCTAATCCAGCTGAGCTGCCACATTCTTCAGGCTCAAAGAATGAA
TCATCAAAAGATACGAAGACTG
Found at i:39515200 original size:561 final size:562
Alignment explanation
Indices: 39514134--39515457 Score: 1874
Period size: 561 Copynumber: 2.4 Consensus size: 562
39514124 TTGTTACAGG
* **
39514134 AAGATATGAAGGC-GAAGACTAATGCAGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATAT
1 AAGATATGAAGACTG-AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATAT
* * ** * * *
39514198 TTATTTGTCTTTTAAGCAACTTCATGAAGGAGTCGACATTGAGGAAGCAACTGTTCTGAGTATGA
65 TGATTTGGCTTTTAAGCAACTTCATGAAGGAGTCGATGTTGAGGAAGTAATTGTTCCGAGTATGA
* * *
39514263 TCGAGAAACCGCCAGATCATGGAGGTAACAAATCAAAATTACCTGTT-TTCGAGGCAAGGTCTCT
130 TTGAGAAA-CGCCAGATCATGGAGATAACAAATCAAAATTACCTGTTGTT-GAGGCAAGATCTCT
* * * * * **
39514327 GGAGGATATACATAAAGCTGTTCGACAACTTCCGGAATCTAATCCAGCTGAGCCGCCACATTCTT
193 GGAGGATATACACAAAGCTATTCAACAACTTCCGAAACCTAATCCAGCTGA-CCGCCACAGGCTT
*
39514392 CAGGCTCAAAGAATGAATCATCAAAAGATACGAAAACTGAGACTAATCTGGTGCTGCCTATTCTT
257 CAGGCTCAAAGAATGAATCATCAAAAGATACGAAAACCGAGACTAATCTGGTGCTGCCTATTCTT
39514457 GAAGCAAGATCAGCCGAAGATATTGATTTGGCTTTTAAGCAACTTCATGAAGGAGTCGACATTGA
322 GAAGCAAGATCAGCCGAAGATATTGATTTGGCTTTTAAGCAACTTCATGAAGGAGTCGACATTGA
*
39514522 GGAAGTAATTGTTCCAAGTATGATCGAGAAACTGACAGATCATGGAGATAACAAATCAAAATTAC
387 GGAAGTAATTGTTCCAAGTATGATCGAGAAACTGACAGACCATGGAGATAACAAATCAAAATTAC
* * * * * * *
39514587 CTATTGTTGAGGCAAGGTCTCTGGAGGATATACATAAAGCTGTTCGACAACTTCCGGAATCTAAT
452 CTATTGTCGAGGCAAGATCTCTGGAGGACATACACAAAGCTATTCAACAACTTCCGAAATCTAAT
*
39514652 CCAGCTGAGCCGCCACATTCTTCAGGCTT-AAGGAATGAATCATCAA
517 CCAGCTGAGCCGCCACATTCTTCA-GCTTCAAGGAATGAACCATCAA
* * * * *
39514698 CAGATATGAATACTGAGACTAATGTGGTGCTTCCAGTTCTTGAAACAAGGTCAGCAGAAGATATT
1 AAGATATGAAGACTGAGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATT
*
39514763 GATTTGGCTTTTAAGCAACTTCATGAAGGAGTCAATGTTGAGGAAGTAATTGTTCCGAGTATGAT
66 GATTTGGCTTTTAAGCAACTTCATGAAGGAGTCGATGTTGAGGAAGTAATTGTTCCGAGTATGAT
*
39514828 TGAGAAACTGCCAGATCTTGGAGATAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGG
131 TGAGAAAC-GCCAGATCATGGAGATAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGG
* * * * ** **
39514893 AGGATTTAGACAAATCTATTCAACAACTTGCGAAACCTAATCCAGCAT-A-TTCTTCAGGC-TCA
195 AGGATATACACAAAGCTATTCAACAACTTCCGAAACCTAATCCAGC-TGACCGCCACAGGCTTCA
* * *
39514955 GGCTCAAAGAATGAATCATCAAAAGATGCGAAGACCGAGACTAATGTGGTGCTGCC-AGTTCTTG
259 GGCTCAAAGAATGAATCATCAAAAGATACGAAAACCGAGACTAATCTGGTGCTGCCTA-TTCTTG
* *
39515019 AAGCAAGATCAGCCGAAGATATTGATTTGGCTTTTAAGCAACTTCATGACGGAGTGGACATTGAG
323 AAGCAAGATCAGCCGAAGATATTGATTTGGCTTTTAAGCAACTTCATGAAGGAGTCGACATTGAG
* * * *
39515084 GAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGACCATGGAGATAACAAATCAAAATTACG
388 GAAGTAATTGTTCCAAGTATGATCGAGAAACTGACAGACCATGGAGATAACAAATCAAAATTACC
* *
39515149 TGTTGTCGAGGCAAGATCTCTGGAGGACATAGACAAAGCTATTCAACAACTTCCGAAATCTAATC
453 TATTGTCGAGGCAAGATCTCTGGAGGACATACACAAAGCTATTCAACAACTTCCGAAATCTAATC
* *
39515214 CAGCTGAGCTGCCACATTCTTCAGTTTCAAGGAATGAACCATCAA
518 CAGCTGAGCCGCCACATTCTTCAGCTTCAAGGAATGAACCATCAA
39515259 AAGATATGAAGACTGAGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATT
1 AAGATATGAAGACTGAGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATT
* *
39515324 GATTTGGCTTTTAAGCAACTGCATGAAGGAG-CTGATGTTGAGGAAGTAATTGTTCCAAGTATGA
66 GATTTGGCTTTTAAGCAACTTCATGAAGGAGTC-GATGTTGAGGAAGTAATTGTTCCGAGTATGA
* * * *** *
39515388 TTGTGGAAC-CACAGGATGACACAGATAACAAATCAAAATTACCTGTTGTGGAGGCAAGATCTCT
130 TTGAGAAACGC-CA-GATCATGGAGATAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCT
*
39515452 GAAGGA
193 GGAGGA
39515458 ATTACATAAT
Statistics
Matches: 676, Mismatches: 75, Indels: 21
0.88 0.10 0.03
Matches are distributed among these distances:
559 1 0.00
560 7 0.01
561 453 0.67
562 4 0.01
563 1 0.00
564 206 0.30
565 4 0.01
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.26
Consensus pattern (562 bp):
AAGATATGAAGACTGAGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATT
GATTTGGCTTTTAAGCAACTTCATGAAGGAGTCGATGTTGAGGAAGTAATTGTTCCGAGTATGAT
TGAGAAACGCCAGATCATGGAGATAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGA
GGATATACACAAAGCTATTCAACAACTTCCGAAACCTAATCCAGCTGACCGCCACAGGCTTCAGG
CTCAAAGAATGAATCATCAAAAGATACGAAAACCGAGACTAATCTGGTGCTGCCTATTCTTGAAG
CAAGATCAGCCGAAGATATTGATTTGGCTTTTAAGCAACTTCATGAAGGAGTCGACATTGAGGAA
GTAATTGTTCCAAGTATGATCGAGAAACTGACAGACCATGGAGATAACAAATCAAAATTACCTAT
TGTCGAGGCAAGATCTCTGGAGGACATACACAAAGCTATTCAACAACTTCCGAAATCTAATCCAG
CTGAGCCGCCACATTCTTCAGCTTCAAGGAATGAACCATCAA
Found at i:39518033 original size:5 final size:5
Alignment explanation
Indices: 39518023--39518063 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
39518013 AATTTTAAAA
* *
39518023 TATTT TATTT TATTT TATTT TA--T TATTT CAGTT TATTT TAT
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TAT
39518064 AATATTTAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
3 3 0.10
5 27 0.90
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (5 bp):
TATTT
Found at i:39518050 original size:18 final size:18
Alignment explanation
Indices: 39518036--39518076 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
39518026 TTTATTTTAT
39518036 TTTATTTTATTATTTCAG
1 TTTATTTTATTATTTCAG
39518054 TTTATTTTATAATATTT-AG
1 TTTATTTTAT--TATTTCAG
39518073 TTTA
1 TTTA
39518077 AAGTATTAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.48
19 6 0.29
20 5 0.24
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (18 bp):
TTTATTTTATTATTTCAG
Found at i:39522305 original size:31 final size:31
Alignment explanation
Indices: 39522270--39522335 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
39522260 AACAAACTAG
*
39522270 TGACTTAAATAAAAAATTTTGAATAGCTCAA
1 TGACTTAAATAAAAAATTTCGAATAGCTCAA
* * * *
39522301 TGACTTAAATGAAAACTTTCGAATAGTTCAG
1 TGACTTAAATAAAAAATTTCGAATAGCTCAA
39522332 TGAC
1 TGAC
39522336 CAAAACAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (31 bp):
TGACTTAAATAAAAAATTTCGAATAGCTCAA
Found at i:39524175 original size:25 final size:27
Alignment explanation
Indices: 39524132--39524186 Score: 96
Period size: 25 Copynumber: 2.1 Consensus size: 27
39524122 TCACTTTGAG
39524132 TTAATAAAATTCTCTTTAAGTTTTCTT
1 TTAATAAAATTCTCTTTAAGTTTTCTT
39524159 TTAA-AAAATTCTC-TTAAGTTTTCTT
1 TTAATAAAATTCTCTTTAAGTTTTCTT
39524184 TTA
1 TTA
39524187 GAAGAGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 15 0.54
26 9 0.32
27 4 0.14
ACGTcount: A:0.31, C:0.11, G:0.04, T:0.55
Consensus pattern (27 bp):
TTAATAAAATTCTCTTTAAGTTTTCTT
Found at i:39532242 original size:267 final size:267
Alignment explanation
Indices: 39531763--39532287 Score: 755
Period size: 267 Copynumber: 2.0 Consensus size: 267
39531753 ATGATGTTGC
* * * * *
39531763 AAAGATTGAAGTCACAACGGGGAATCTTATTACCTTGGCGTTGTAGCAGAGCAGATTGAAGTCAC
1 AAAGATTGAAGCCACAACGGCGAATCTTATTACCCTGGCATTGTAGCAGAGCAGATTGAAGCCAC
* *
39531828 GACAGCGAATCTAATCTCCCTGGCGTTAAGGCTTGGATTAGCTAAAGTGGAGCGGATTAAAGCTG
66 GACAGCGAATCTAATCTCCCTGGCGTTAAGGCTTGGATTAGATAAAGTAGAGCGGATTAAAGCTG
* * * * *
39531893 TGGGCAGTGAATCCTATCTCTTTGACATTACACTGGAGAATATTAAAGCCACAACGGCAAATCTT
131 TGGGCAGCGAACCCTATCTCATTGACATTACACTGGAGAAGATTAAAGCCACAACGACAAATCTT
* *
39531958 ACTCCCCTGGCGGTGTAGTGGAACAAATTGAAGCTACGACGGTGAATCTCGTTTCCCTAACATGG
196 ACTCCCCTGGCGGTGTAGTGGAACAAATTGAAGCTACGACGGCGAATCTCATTTCCCTAACATGG
39532023 CAATTTA
261 CAATTTA
* *
39532030 AAAGATTGAAGCCACAACGGCGAATCTTATTTCCCTGGCATTGTAGCGGAGCAGATTGAAGCCAC
1 AAAGATTGAAGCCACAACGGCGAATCTTATTACCCTGGCATTGTAGCAGAGCAGATTGAAGCCAC
* * *
39532095 GACGGCGAATCTTATCTCCCTGGCGTTAAGGCTTGGATTAGATGAAA-TAGAGCGGATTGAAGCT
66 GACAGCGAATCTAATCTCCCTGGCGTTAAGGCTTGGATTAGAT-AAAGTAGAGCGGATTAAAGCT
* * * * ** *
39532159 GTGGGTAGCGAACCCTATCTCATTGGCATTACAGTGGAGCAGATTAAAGCTGCAACGACGAATCT
130 GTGGGCAGCGAACCCTATCTCATTGACATTACACTGGAGAAGATTAAAGCCACAACGACAAATCT
* * ** *
39532224 TACTTCCCTGGTGGTGTAGTGGAACTGATTGAAGCTACGACGGCGAATCTTATTTCCCTAACAT
195 TACTCCCCTGGCGGTGTAGTGGAACAAATTGAAGCTACGACGGCGAATCTCATTTCCCTAACAT
39532288 TGCGATTAAA
Statistics
Matches: 226, Mismatches: 31, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
267 223 0.99
268 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.26
Consensus pattern (267 bp):
AAAGATTGAAGCCACAACGGCGAATCTTATTACCCTGGCATTGTAGCAGAGCAGATTGAAGCCAC
GACAGCGAATCTAATCTCCCTGGCGTTAAGGCTTGGATTAGATAAAGTAGAGCGGATTAAAGCTG
TGGGCAGCGAACCCTATCTCATTGACATTACACTGGAGAAGATTAAAGCCACAACGACAAATCTT
ACTCCCCTGGCGGTGTAGTGGAACAAATTGAAGCTACGACGGCGAATCTCATTTCCCTAACATGG
CAATTTA
Found at i:39532549 original size:45 final size:45
Alignment explanation
Indices: 39532485--39532607 Score: 174
Period size: 45 Copynumber: 2.7 Consensus size: 45
39532475 GAGTAAGTAG
* *
39532485 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCCCAAGAAAGCGA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCAA
* * *
39532530 GTCTTATTTCCCTGAAGTTGCAGTGGAGGAGACTCAAGAAAGCAA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCAA
* * *
39532575 GTCTTATCCCCCTGAAATTGCAGTGGGGCAGAC
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC
39532608 TAAATAAACA
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 68 1.00
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.23
Consensus pattern (45 bp):
GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCAA
Found at i:39532608 original size:45 final size:45
Alignment explanation
Indices: 39532485--39532644 Score: 171
Period size: 45 Copynumber: 3.6 Consensus size: 45
39532475 GAGTAAGTAG
* * * *
39532485 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCCCAAGAAAGCGA
1 GTCTTATCTCCCTGAAGTTGCAGTGGGGCAGACTCAAGAAAGCAA
*
39532530 GTCTTATTTCCCTGAAGTTGCAGTGGAGG-AGACTCAAGAAAGCAA
1 GTCTTATCTCCCTGAAGTTGCAGTGG-GGCAGACTCAAGAAAGCAA
* * * *
39532575 GTCTTATCCCCCTGAAATTGCAGTGGGGCAGACTAAATAAA-CAA
1 GTCTTATCTCCCTGAAGTTGCAGTGGGGCAGACTCAAGAAAGCAA
* * * * *
39532619 ATCCTATCTTCCTAAAGTTGTAGTGG
1 GTCTTATCTCCCTGAAGTTGCAGTGG
39532645 AGTGGATTAG
Statistics
Matches: 96, Mismatches: 17, Indels: 5
0.81 0.14 0.04
Matches are distributed among these distances:
44 24 0.25
45 71 0.74
46 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.25
Consensus pattern (45 bp):
GTCTTATCTCCCTGAAGTTGCAGTGGGGCAGACTCAAGAAAGCAA
Found at i:39537090 original size:33 final size:33
Alignment explanation
Indices: 39537048--39537116 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
39537038 CGATACACGT
39537048 AGTAGCCTTCACATAGTACTACACACGTGATCA
1 AGTAGCCTTCACATAGTACTACACACGTGATCA
39537081 AGTAGCCTTCACATAGTACTACACACGTGATCA
1 AGTAGCCTTCACATAGTACTACACACGTGATCA
39537114 AGT
1 AGT
39537117 TTTACGGTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (33 bp):
AGTAGCCTTCACATAGTACTACACACGTGATCA
Found at i:39537206 original size:51 final size:51
Alignment explanation
Indices: 39537081--39537363 Score: 290
Period size: 51 Copynumber: 5.6 Consensus size: 51
39537071 CACGTGATCA
* * *
39537081 AGTAGCCTTCACATAGTACTACACACGTGATC-AAG-TTTTACGGTTCACAA
1 AGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTT-CGGTACACAT
*
39537131 AGTAGCCTTCACATAGTACTACACACATGACCAAAGCTTTTCGGTACACAT
1 AGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTTCGGTACACAT
* * * * * *
39537182 AGTAGCCTTCACTTAGTACTACACATGTGACC--ATCATTTATCGATTCACGT
1 AGTAGCCTTCACATAGTACTACACACGTGACCAAAGC-TTT-TCGGTACACAT
* * *
39537233 AGTAGCCTTTACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACAT
1 AGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTTCGGTACACAT
* * * * * *
39537284 TGTAGCCTTCACTTAGTACTACACATGTGACCATTA--TTTATCGATACACGT
1 AGTAGCCTTCACATAGTACTACACACGTGACCA-AAGCTTT-TCGGTACACAT
* *
39537335 GGTAGCCTTCACACAGTACTACACACGTG
1 AGTAGCCTTCACATAGTACTACACACGTG
39537364 TTCATCGATA
Statistics
Matches: 192, Mismatches: 33, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
49 2 0.01
50 35 0.18
51 146 0.76
52 7 0.04
53 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (51 bp):
AGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTTCGGTACACAT
Found at i:39537256 original size:102 final size:102
Alignment explanation
Indices: 39537081--39537360 Score: 400
Period size: 102 Copynumber: 2.8 Consensus size: 102
39537071 CACGTGATCA
* * * *** * ** *
39537081 AGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA-CGGTTCACAAAGTAGCCTTCACAT
1 AGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCCTTCACAC
*
39537145 AGTACTACACACATGACCAAAGCTTTTCGGTACACAT
66 AGTACTACACACATGACCAAAGCTTCTCGGTACACAT
*
39537182 AGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCCTTTACAC
1 AGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCCTTCACAC
*
39537247 AGTACTACACACGTGACCAAAGCTTCTCGGTACACAT
66 AGTACTACACACATGACCAAAGCTTCTCGGTACACAT
* * * *
39537284 TGTAGCCTTCACTTAGTACTACACATGTGACCATTATTTATCGATACACGTGGTAGCCTTCACAC
1 AGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCCTTCACAC
39537349 AGTACTACACAC
66 AGTACTACACAC
39537361 GTGTTCATCG
Statistics
Matches: 160, Mismatches: 18, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
101 34 0.21
102 126 0.79
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (102 bp):
AGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCCTTCACAC
AGTACTACACACATGACCAAAGCTTCTCGGTACACAT
Found at i:39537358 original size:153 final size:151
Alignment explanation
Indices: 39537081--39537359 Score: 355
Period size: 153 Copynumber: 1.8 Consensus size: 151
39537071 CACGTGATCA
* * * *
39537081 AGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTTCACAAAGTAGCCTTCACATA
1 AGTAGCCTTCACACAGTACTACACACGTGACCAAGTTCTACGGTACACAAAGTAGCCTTCACATA
* **
39537146 GTACTACACACATGACCAAAGCTTTTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTG
66 GTACTACACACATGACCAAA-CTTTTCGATACACATAGTAGCCTTCACACAGTACTACACATGTG
39537211 ACCATCATTTATCGATTCACGT
130 ACCATCATTTATCGATTCACGT
* ** *
39537233 AGTAGCCTTTACACAGTACTACACACGTGACCAAAGCTTCT-CGGTACACATTGTAGCCTTCACT
1 AGTAGCCTTCACACAGTACTACACACGTGACC-AAG-TTCTACGGTACACAAAGTAGCCTTCACA
** * * *
39537297 TAGTACTACACATGTGACCATTA-TTTATCGATACACGTGGTAGCCTTCACACAGTACTACACA
64 TAGTACTACACACATGACCA-AACTTT-TCGATACACATAGTAGCCTTCACACAGTACTACACA
39537360 CGTGTTCATC
Statistics
Matches: 107, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
152 32 0.30
153 71 0.66
154 4 0.04
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (151 bp):
AGTAGCCTTCACACAGTACTACACACGTGACCAAGTTCTACGGTACACAAAGTAGCCTTCACATA
GTACTACACACATGACCAAACTTTTCGATACACATAGTAGCCTTCACACAGTACTACACATGTGA
CCATCATTTATCGATTCACGT
Found at i:39545635 original size:18 final size:19
Alignment explanation
Indices: 39545602--39545640 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
39545592 TAAATAGTTT
39545602 GAGTTATTCAAGTTAA-TC
1 GAGTTATTCAAGTTAACTC
39545620 GAGTTATTC-AGATTAACTC
1 GAGTTATTCAAG-TTAACTC
39545639 GA
1 GA
39545641 ATAAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.11
18 13 0.68
19 4 0.21
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (19 bp):
GAGTTATTCAAGTTAACTC
Found at i:39548190 original size:25 final size:25
Alignment explanation
Indices: 39548157--39548211 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
39548147 ATTTTTATAA
39548157 TTTTTGTCGGTTTGATACTTATTTT
1 TTTTTGTCGGTTTGATACTTATTTT
39548182 TTTTTGTCGGTTTGATACTTATTTT
1 TTTTTGTCGGTTTGATACTTATTTT
39548207 TTTTT
1 TTTTT
39548212 AGCTAATTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.11, C:0.07, G:0.15, T:0.67
Consensus pattern (25 bp):
TTTTTGTCGGTTTGATACTTATTTT
Found at i:39548597 original size:23 final size:23
Alignment explanation
Indices: 39548554--39548603 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
39548544 CAAATTTAGT
**
39548554 TAAAAAAATAAATGTTAAAGTGA
1 TAAAAAAATAAACATTAAAGTGA
*
39548577 TAAAAAATATAAACATT-AAGTGT
1 TAAAAAA-ATAAACATTAAAGTGA
39548600 TAAA
1 TAAA
39548604 TTTATCTCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.60, C:0.02, G:0.10, T:0.28
Consensus pattern (23 bp):
TAAAAAAATAAACATTAAAGTGA
Found at i:39549388 original size:19 final size:19
Alignment explanation
Indices: 39549300--39549397 Score: 55
Period size: 19 Copynumber: 5.3 Consensus size: 19
39549290 TGACTAGTCA
*
39549300 AAAAAGTATTAAAAA-TATAA
1 AAAAA-TATTAAAAATTAT-T
*
39549320 AAAAATATTTAGAAATTA-T
1 AAAAATA-TTAAAAATTATT
* * * *
39549339 AGAAATTTTTATAAATT-CT
1 A-AAAATATTAAAAATTATT
39549358 AAAAA-A-TAAAAATTATT
1 AAAAATATTAAAAATTATT
*
39549375 AAAAATATTAAAAAAT-TT
1 AAAAATATTAAAAATTATT
39549393 AAAAA
1 AAAAA
39549398 ATAATTTAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 16
0.70 0.11 0.18
Matches are distributed among these distances:
16 7 0.11
17 6 0.10
18 11 0.18
19 20 0.33
20 15 0.25
21 2 0.03
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (19 bp):
AAAAATATTAAAAATTATT
Found at i:39565351 original size:28 final size:26
Alignment explanation
Indices: 39565282--39565356 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 26
39565272 AATTGGCAAC
*
39565282 AGTTAGGACATAATAAAAACATGTTT
1 AGTTAGGACATATTAAAAACATGTTT
* *
39565308 AGTCTAGGACAAATTAATAACATGTATT
1 AGT-TAGGACATATTAAAAACATGT-TT
*
39565336 AGGTTATGACATATTAAAAAC
1 A-GTTAGGACATATTAAAAAC
39565357 TATATTAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 3 0.08
27 18 0.45
28 17 0.43
29 2 0.05
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.31
Consensus pattern (26 bp):
AGTTAGGACATATTAAAAACATGTTT
Found at i:39565373 original size:27 final size:29
Alignment explanation
Indices: 39565343--39565403 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
39565333 ATTAGGTTAT
*
39565343 GACATATTAAAAAC-T-ATATTAAAATAA
1 GACATATTAAAAACTTAATAATAAAATAA
* * *
39565370 GACACATTAAACACTTAATAATAAAATCA
1 GACATATTAAAAACTTAATAATAAAATAA
39565399 GACAT
1 GACAT
39565404 TTATTTTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 12 0.44
28 1 0.04
29 14 0.52
ACGTcount: A:0.56, C:0.13, G:0.05, T:0.26
Consensus pattern (29 bp):
GACATATTAAAAACTTAATAATAAAATAA
Found at i:39571023 original size:7 final size:8
Alignment explanation
Indices: 39571003--39571034 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
39570993 CTAAAGCATA
39571003 AAAAAAGAG
1 AAAAAA-AG
39571012 AAAAAAAG
1 AAAAAAAG
39571020 AAAAAAAG
1 AAAAAAAG
39571028 AAAAAAA
1 AAAAAAA
39571035 AATAATTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.74
9 6 0.26
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:39571036 original size:18 final size:18
Alignment explanation
Indices: 39571002--39571036 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
39570992 CCTAAAGCAT
*
39571002 AAAAAAAGAGAAAAAAAG
1 AAAAAAAGAAAAAAAAAG
39571020 AAAAAAAGAAAAAAAAA
1 AAAAAAAGAAAAAAAAA
39571037 TAATTTGGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (18 bp):
AAAAAAAGAAAAAAAAAG
Found at i:39572137 original size:12 final size:12
Alignment explanation
Indices: 39572120--39572144 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39572110 GGTGTTCATT
39572120 CGGTTAACCGAC
1 CGGTTAACCGAC
39572132 CGGTTAACCGAC
1 CGGTTAACCGAC
39572144 C
1 C
39572145 CGAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:39572318 original size:9 final size:9
Alignment explanation
Indices: 39572304--39572389 Score: 111
Period size: 9 Copynumber: 9.4 Consensus size: 9
39572294 TTTGGTTAAA
39572304 AATTACCCG
1 AATTACCCG
39572313 AATTACCCG
1 AATTACCCG
*
39572322 AATTAACCG
1 AATTACCCG
39572331 AATTACCCG
1 AATTACCCG
*
39572340 AATTAACCG
1 AATTACCCG
*
39572349 AATTAACCG
1 AATTACCCG
39572358 AATTA-CCG
1 AATTACCCG
*
39572366 AAAAATACCCG
1 --AATTACCCG
39572377 AATTACCCG
1 AATTACCCG
39572386 AATT
1 AATT
39572390 TTTTTATTTT
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
8 3 0.04
9 59 0.86
10 4 0.06
11 3 0.04
ACGTcount: A:0.41, C:0.27, G:0.10, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:39575899 original size:28 final size:29
Alignment explanation
Indices: 39575868--39575929 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 29
39575858 ATTAGGTTAT
* *
39575868 GACATATTAAAAACTT-GTATTAAAATAA
1 GACATATTAAAAACTTAATAATAAAATAA
* * *
39575896 GACACATTAAACACTTAATAATAAAATCA
1 GACATATTAAAAACTTAATAATAAAATAA
39575925 GACAT
1 GACAT
39575930 TTATTTTATT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
28 14 0.52
29 13 0.48
ACGTcount: A:0.53, C:0.13, G:0.06, T:0.27
Consensus pattern (29 bp):
GACATATTAAAAACTTAATAATAAAATAA
Found at i:39585140 original size:27 final size:27
Alignment explanation
Indices: 39585102--39585164 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
39585092 GTTGAACCAA
*
39585102 TGTTTACTGTCTAGGTGGACTACTCC-G
1 TGTTTACTGTCTAGGAGGACTAC-CCTG
* *
39585129 TGTTTACTGTCTTGGAGGACTACCCTT
1 TGTTTACTGTCTAGGAGGACTACCCTG
39585156 TGTTTACTG
1 TGTTTACTG
39585165 AATTCGAGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
26 2 0.06
27 30 0.94
ACGTcount: A:0.14, C:0.21, G:0.24, T:0.41
Consensus pattern (27 bp):
TGTTTACTGTCTAGGAGGACTACCCTG
Found at i:39585667 original size:38 final size:38
Alignment explanation
Indices: 39585620--39585700 Score: 146
Period size: 38 Copynumber: 2.2 Consensus size: 38
39585610 TATAATTTTT
39585620 AAAAG-ATTAAATCAAAATTTTATATTTTTAGGGGGGA
1 AAAAGTATTAAATCAAAATTTTATATTTTTAGGGGGGA
*
39585657 GAAAGTATTAAATCAAAATTTTATATTTTTAGGGGGGA
1 AAAAGTATTAAATCAAAATTTTATATTTTTAGGGGGGA
39585695 AAAAGT
1 AAAAGT
39585701 GTAATTTTAC
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
37 4 0.10
38 37 0.90
ACGTcount: A:0.43, C:0.02, G:0.20, T:0.35
Consensus pattern (38 bp):
AAAAGTATTAAATCAAAATTTTATATTTTTAGGGGGGA
Found at i:39586979 original size:6 final size:6
Alignment explanation
Indices: 39586968--39586996 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
39586958 AAATTATAAT
39586968 ATATTA ATATTA ATATTA ATATTA ATATT
1 ATATTA ATATTA ATATTA ATATTA ATATT
39586997 CAAACCATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
ATATTA
Found at i:39587421 original size:25 final size:24
Alignment explanation
Indices: 39587393--39587444 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 24
39587383 AAAAAAAAGA
39587393 TATTTAATTGA-TATGCTTTAATTTT
1 TATTTAATTGAGTAT-CTTT-ATTTT
*
39587418 TATTTAATTTAGTATCTTTATTTT
1 TATTTAATTGAGTATCTTTATTTT
39587442 TAT
1 TAT
39587445 AATATTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 8 0.32
25 14 0.56
26 3 0.12
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.63
Consensus pattern (24 bp):
TATTTAATTGAGTATCTTTATTTT
Found at i:39597194 original size:30 final size:30
Alignment explanation
Indices: 39597158--39597219 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
39597148 TGAATTATTT
* * *
39597158 TTAAAAATTTGGTTACTCTTTTTGTAAATA
1 TTAAAAATTAGATGACTCTTTTTGTAAATA
*
39597188 TTAAAAATTAGATGCCTCTTTTTGTAAATA
1 TTAAAAATTAGATGACTCTTTTTGTAAATA
39597218 TT
1 TT
39597220 TTTAAAAAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.34, C:0.08, G:0.10, T:0.48
Consensus pattern (30 bp):
TTAAAAATTAGATGACTCTTTTTGTAAATA
Found at i:39603321 original size:14 final size:14
Alignment explanation
Indices: 39603302--39603328 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39603292 GTAGTCCAGT
39603302 TGAACTGAACCGAG
1 TGAACTGAACCGAG
39603316 TGAACTGAACCGA
1 TGAACTGAACCGA
39603329 CCAAGAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (14 bp):
TGAACTGAACCGAG
Found at i:39607139 original size:47 final size:48
Alignment explanation
Indices: 39607087--39607181 Score: 122
Period size: 49 Copynumber: 2.0 Consensus size: 48
39607077 ATGCCTAAAT
* * *
39607087 TATTTAAGCAACT-A-AAAATTCACAAGAACTTAATTAATTAAACTAAG
1 TATTTAAGCAACTAAGAAAATT-AAAACAACTGAATTAATTAAACTAAG
*
39607134 TATTTAAGCAAGTAAAGAAAATTAAAACAACTGAATTAATTAAACTAA
1 TATTTAAGCAACT-AAGAAAATTAAAACAACTGAATTAATTAAACTAA
39607182 ACATATTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
47 12 0.29
49 23 0.56
50 6 0.15
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.28
Consensus pattern (48 bp):
TATTTAAGCAACTAAGAAAATTAAAACAACTGAATTAATTAAACTAAG
Found at i:39610156 original size:12 final size:11
Alignment explanation
Indices: 39610140--39610181 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
39610130 TCTTTTCTTT
39610140 TTATTTTTTTC
1 TTATTTTTTTC
39610151 TCTATTTTTTTC
1 T-TATTTTTTTC
*
39610163 TTATTCTTATTC
1 TTATT-TTTTTC
39610175 TT-TTTTT
1 TTATTTTT
39610182 ATAGTCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 2 0.07
11 7 0.26
12 18 0.67
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.79
Consensus pattern (11 bp):
TTATTTTTTTC
Found at i:39610183 original size:11 final size:10
Alignment explanation
Indices: 39610118--39610181 Score: 56
Period size: 10 Copynumber: 6.1 Consensus size: 10
39610108 CAACTTTTCC
*
39610118 TTTCTTTGTT
1 TTTCTTTTTT
39610128 TTTCTTTTCTT
1 TTTCTTTT-TT
*
39610139 TTTATTTTTT
1 TTTCTTTTTT
* *
39610149 TCTCTATTTT
1 TTTCTTTTTT
39610159 TTTCTTATTCTT
1 TTTCTT-TT-TT
*
39610171 ATTCTTTTTT
1 TTTCTTTTTT
39610181 T
1 T
39610182 ATAGTCTTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
10 22 0.52
11 13 0.31
12 7 0.17
ACGTcount: A:0.06, C:0.12, G:0.02, T:0.80
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:39619297 original size:19 final size:19
Alignment explanation
Indices: 39619275--39619312 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
39619265 TCAATCATCC
39619275 CTCATCGCATCA-TCTCTCA
1 CTCAT-GCATCATTCTCTCA
*
39619294 CTCATTCATCATTCTCTCA
1 CTCATGCATCATTCTCTCA
39619313 ACTCTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.21, C:0.39, G:0.03, T:0.37
Consensus pattern (19 bp):
CTCATGCATCATTCTCTCA
Found at i:39625652 original size:21 final size:21
Alignment explanation
Indices: 39625626--39625667 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
39625616 AGGGTATGTT
*
39625626 GCGACATCCTCAACCTGTGTC
1 GCGACACCCTCAACCTGTGTC
* *
39625647 GCGACACCCTTAGCCTGTGTC
1 GCGACACCCTCAACCTGTGTC
39625668 ATGACATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.38, G:0.21, T:0.24
Consensus pattern (21 bp):
GCGACACCCTCAACCTGTGTC
Found at i:39642715 original size:26 final size:27
Alignment explanation
Indices: 39642650--39642951 Score: 291
Period size: 27 Copynumber: 11.3 Consensus size: 27
39642640 GGTATAACAG
39642650 TCATTTTA-CCTAT-GGGGTATTTC-A
1 TCATTTTACCCTATGGGGGTATTTCGA
* *
39642674 GT-ACTCTTACCATATGGGGGTATTTCGA
1 -TCA-TTTTACCCTATGGGGGTATTTCGA
* * *
39642702 TCA-CTCACCCTATGGGGGTATTTCGGT
1 TCATTTTACCCTATGGGGGTATTTC-GA
39642729 TC-TTTTACCCTATGGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGA
39642755 TC-TTTTACCCTATGGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGA
* *
39642781 TCATTTTATCCAATGGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGA
*
39642808 TCATTTTACTCTATGGGGGTATTTC-A
1 TCATTTTACCCTATGGGGGTATTTCGA
* *
39642834 GTCATTTTACCCTATGGGGGTATTTTGG
1 -TCATTTTACCCTATGGGGGTATTTCGA
* * * *
39642862 TCATTTTATCCTATAGAGGTATTT-TA
1 TCATTTTACCCTATGGGGGTATTTCGA
* *
39642888 GTCATTTTACCTTATGGGGGTATTT-TA
1 -TCATTTTACCCTATGGGGGTATTTCGA
* ** * *
39642915 GTCATTTTACTCTATAAGGGTATTTTGG
1 -TCATTTTACCCTATGGGGGTATTTCGA
39642943 TCATTTTAC
1 TCATTTTAC
39642952 ATATTTTGGG
Statistics
Matches: 234, Mismatches: 31, Indels: 22
0.82 0.11 0.08
Matches are distributed among these distances:
24 1 0.00
25 5 0.02
26 53 0.23
27 173 0.74
28 2 0.01
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.43
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTCGA
Found at i:39642883 original size:81 final size:80
Alignment explanation
Indices: 39642650--39642950 Score: 328
Period size: 81 Copynumber: 3.8 Consensus size: 80
39642640 GGTATAACAG
* * * * *
39642650 TCATTTTACCTAT-GGGGTATTTCAGT-ACTCTTACCATATGGGGGTATTTCGATCA-CTCACCC
1 TCATTTTACCTATGGGGGTATTTCAGTCA-TTTTACCCTATGGGGGTATTTCGATCATTTTATCC
*
39642712 TATGGGGGTATTTCGGT
65 TATGGGGGTATTTC-GA
39642729 TC-TTTTACCCTATGGGGGTATTTC-GATC-TTTTACCCTATGGGGGTATTTCGATCATTTTATC
1 TCATTTTA-CCTATGGGGGTATTTCAG-TCATTTTACCCTATGGGGGTATTTCGATCATTTTATC
*
39642791 CAATGGGGGTATTTCGA
64 CTATGGGGGTATTTCGA
* *
39642808 TCATTTTACTCTATGGGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTTGGTCATTTTATCC
1 TCATTTTAC-CTATGGGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCGATCATTTTATCC
* * *
39642873 TATAGAGGTATTT-TA
65 TATGGGGGTATTTCGA
* * ** * *
39642888 GTCATTTTACCTTATGGGGGTATTTTAGTCATTTTACTCTATAAGGGTATTTTGGTCATTTTA
1 -TCATTTTACC-TATGGGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCGATCATTTTA
39642951 CATATTTTGG
Statistics
Matches: 194, Mismatches: 17, Indels: 20
0.84 0.07 0.09
Matches are distributed among these distances:
78 5 0.03
79 37 0.19
80 52 0.27
81 100 0.52
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (80 bp):
TCATTTTACCTATGGGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCGATCATTTTATCCT
ATGGGGGTATTTCGA
Found at i:39645303 original size:29 final size:31
Alignment explanation
Indices: 39645250--39645308 Score: 86
Period size: 29 Copynumber: 1.9 Consensus size: 31
39645240 GATGTCAGTC
*
39645250 ATGCAGTGAACAGTATGTAATATCATTAATTG
1 ATGCAGTGAACAGTA-GCAATATCATTAATTG
39645282 ATGCAGT-AACAGTA-CAATATCATTAAT
1 ATGCAGTGAACAGTAGCAATATCATTAAT
39645309 CAGTGCAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 12 0.46
31 7 0.27
32 7 0.27
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (31 bp):
ATGCAGTGAACAGTAGCAATATCATTAATTG
Found at i:39645808 original size:54 final size:53
Alignment explanation
Indices: 39645711--39645962 Score: 283
Period size: 54 Copynumber: 4.7 Consensus size: 53
39645701 GGTATAACAG
* * * * *
39645711 TCATTTTACCCTATGGGGTATTTCGATCATCTTAACCTATGGGGGTATTTCAA
1 TCATTTTACCCTATAGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCAA
* * * *
39645764 TCATCTTACCCTATAGGGATATTTCGGTCATTTTATCCTATGGGGGTATTTCAG
1 TCATTTTACCCTATAGGG-TATTTTGGTCATTTTACCCTATGGGGGTATTTCAA
*
39645818 TCATTTTACTCC-ATAAGGGTATTTTGGT-ATTTTTACCCTATGGGGGTATTTCGA
1 TCATTTTAC-CCTAT-AGGGTATTTTGGTCA-TTTTACCCTATGGGGGTATTTCAA
* * * * **
39645872 TTATTTTACCCTATGGGGGTATTTTGGTCATTTTACCCTATGGAGTTATTTCGT
1 TCATTTTACCCTAT-AGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCAA
*
39645926 TCATTTTACCCTATAAGGGTATTTTGGCCATTTTACC
1 TCATTTTACCCTAT-AGGGTATTTTGGTCATTTTACC
39645963 TATTTTGGGG
Statistics
Matches: 172, Mismatches: 21, Indels: 11
0.84 0.10 0.05
Matches are distributed among these distances:
53 19 0.11
54 146 0.85
55 7 0.04
ACGTcount: A:0.20, C:0.17, G:0.19, T:0.43
Consensus pattern (53 bp):
TCATTTTACCCTATAGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCAA
Found at i:39645957 original size:27 final size:27
Alignment explanation
Indices: 39645710--39645962 Score: 237
Period size: 27 Copynumber: 9.4 Consensus size: 27
39645700 GGGTATAACA
39645710 GTCATTTTACCCTATG-GGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * * * *
39645736 ATCATCTTAACCTATGGGGGTATTTCA
1 GTCATTTTACCCTATGAGGGTATTTCG
* *
39645763 ATCATCTTACCCTAT-AGGGATATTTCG
1 GTCATTTTACCCTATGAGGG-TATTTCG
* * *
39645790 GTCATTTTATCCTATGGGGGTATTTCA
1 GTCATTTTACCCTATGAGGGTATTTCG
* *
39645817 GTCATTTTACTCC-ATAAGGGTATTTTG
1 GTCATTTTAC-CCTATGAGGGTATTTCG
*
39645844 GT-ATTTTTACCCTATGGGGGTATTTCG
1 GTCA-TTTTACCCTATGAGGGTATTTCG
* * * *
39645871 ATTATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGAGGGTATTTCG
*
39645898 GTCATTTTACCCTATG-GAGTTATTTCG
1 GTCATTTTACCCTATGAG-GGTATTTCG
* * *
39645925 TTCATTTTACCCTATAAGGGTATTTTG
1 GTCATTTTACCCTATGAGGGTATTTCG
*
39645952 GCCATTTTACC
1 GTCATTTTACC
39645963 TATTTTGGGG
Statistics
Matches: 186, Mismatches: 32, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
26 20 0.11
27 159 0.85
28 7 0.04
ACGTcount: A:0.20, C:0.17, G:0.19, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTATGAGGGTATTTCG
Found at i:39647665 original size:50 final size:50
Alignment explanation
Indices: 39647550--39647742 Score: 253
Period size: 50 Copynumber: 3.8 Consensus size: 50
39647540 GATAATAACA
* * ** *
39647550 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* *
39647601 TGCCCATGCCATGTCCTAGACATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
39647651 TGCCAACGCCATGTCAC-AGATATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTC-CTAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
39647701 TGCCAATGTCATGTCCTAGACATGGTCTAACATGAGACCTCT
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCT
39647743 TTACCCAAAT
Statistics
Matches: 124, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
49 1 0.01
50 89 0.72
51 34 0.27
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:39647725 original size:100 final size:101
Alignment explanation
Indices: 39647550--39647742 Score: 280
Period size: 100 Copynumber: 1.9 Consensus size: 101
39647540 GATAATAACA
* ** *
39647550 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGGTGCCCATGCCATGT
1 TGCCAAAGCCATGTCACAGACATGGTCTTACATGGGATCCTCTCATATCGGTGCCAATGCCATGT
* *
39647615 CCTAGACATGGTCTTACAGGGGACCTCTCATCTCGG
66 CCTAGACATGGTCTAACAGGAGACCTCTCATCTCGG
* * * *
39647651 TGCCAACGCCATGTCACAGATATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCAATGTCATGT
1 TGCCAAAGCCATGTCACAGACATGGTCTTACATGGGATCCTCTCATATCGGTGCCAATGCCATGT
*
39647715 CCTAGACATGGTCTAACATGAGACCTCT
66 CCTAGACATGGTCTAACAGGAGACCTCT
39647743 TTACCCAAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
100 47 0.58
101 34 0.42
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.27
Consensus pattern (101 bp):
TGCCAAAGCCATGTCACAGACATGGTCTTACATGGGATCCTCTCATATCGGTGCCAATGCCATGT
CCTAGACATGGTCTAACAGGAGACCTCTCATCTCGG
Found at i:39651522 original size:18 final size:18
Alignment explanation
Indices: 39651499--39651534 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
39651489 ATAAAATAAA
39651499 ATAATTTTGAAGTCTCTT
1 ATAATTTTGAAGTCTCTT
39651517 ATAATTTTGAAGTCTCTT
1 ATAATTTTGAAGTCTCTT
39651535 TTAAAACAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (18 bp):
ATAATTTTGAAGTCTCTT
Found at i:39652179 original size:121 final size:121
Alignment explanation
Indices: 39652038--39652261 Score: 344
Period size: 121 Copynumber: 1.9 Consensus size: 121
39652028 ATCTCAACAT
*
39652038 AACTTTTCTTTTTTTAGTTCTCTAGTCATATG-GTGATTGAAACCATTGCATATCTCCATACTTT
1 AACTTTTCTTTTTTTAGTTCTCTACTCATATGCG-GATTGAAACCATTGCATATCTCCATACTTT
* * * * *
39652102 GAAGATTGTAGTATATTTGGGTCATCAGAATGTCATATTTCATTATAATGAATAAAA
65 GAAGATTGCAGTAGATTTGAGACATCAAAATGTCATATTTCATTATAATGAATAAAA
* *
39652159 AACTTTTCTTCTTTTT-GTTCTCTACTCATATGCGGATTGAAACCATTGCATGTCTCCATGCTTT
1 AACTTTTCTT-TTTTTAGTTCTCTACTCATATGCGGATTGAAACCATTGCATATCTCCATACTTT
39652223 GAAGATTGCAGTAGATTTGAGACATCAAAATGTCATATT
65 GAAGATTGCAGTAGATTTGAGACATCAAAATGTCATATT
39652262 AGAAGAAGAT
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
121 87 0.94
122 6 0.06
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.41
Consensus pattern (121 bp):
AACTTTTCTTTTTTTAGTTCTCTACTCATATGCGGATTGAAACCATTGCATATCTCCATACTTTG
AAGATTGCAGTAGATTTGAGACATCAAAATGTCATATTTCATTATAATGAATAAAA
Found at i:39657947 original size:16 final size:16
Alignment explanation
Indices: 39657926--39657956 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
39657916 AAATCAGAAT
39657926 CAAATTATTCATTTTG
1 CAAATTATTCATTTTG
39657942 CAAATTATTCATTTT
1 CAAATTATTCATTTT
39657957 AGCTCCTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.13, G:0.03, T:0.52
Consensus pattern (16 bp):
CAAATTATTCATTTTG
Found at i:39660956 original size:73 final size:73
Alignment explanation
Indices: 39660837--39660986 Score: 266
Period size: 73 Copynumber: 2.1 Consensus size: 73
39660827 ACAAGTCCTA
*
39660837 TGTCGCGACACCTTAGTGCTTGTATGGTGACATCAAAGGTAGTATGCAAGGTTTAGGGGTAGCTT
1 TGTCGCGACACATTAGTGCTTGTATGGTGACATCAAAGGTAGTATGCAAGGTTTAGGGGTAGCTT
39660902 CAAGGGTG
66 CAAGGGTG
39660910 TGTCGCGACACATTAGTGCATT-TATGGTGACATCAAAGGTAGTATGCAAGGTTTAGGGGTAGCT
1 TGTCGCGACACATTAGTGC-TTGTATGGTGACATCAAAGGTAGTATGCAAGGTTTAGGGGTAGCT
*
39660974 TTAAGGGTG
65 TCAAGGGTG
39660983 TGTC
1 TGTC
39660987 ATGACATCCC
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
73 72 0.97
74 2 0.03
ACGTcount: A:0.24, C:0.14, G:0.32, T:0.30
Consensus pattern (73 bp):
TGTCGCGACACATTAGTGCTTGTATGGTGACATCAAAGGTAGTATGCAAGGTTTAGGGGTAGCTT
CAAGGGTG
Found at i:39669463 original size:50 final size:50
Alignment explanation
Indices: 39669401--39669636 Score: 301
Period size: 50 Copynumber: 4.7 Consensus size: 50
39669391 ATTTGGGTAA
* * * * *
39669401 AGAGGTCTCATGTAAGACCATGTATAGGACATGGTGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
* * * * *
39669451 AGATGTCTCATGTAAGATCATGTTTGGGACATGGCGTTGCCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
*
39669501 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
** * * *
39669551 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCAATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
**
39669601 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
39669637 TTCGGCATGT
Statistics
Matches: 162, Mismatches: 23, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 133 0.82
51 29 0.18
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
Found at i:39691641 original size:15 final size:15
Alignment explanation
Indices: 39691621--39691650 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39691611 CCAGGCCCAT
39691621 TAAAACCAAATAAAA
1 TAAAACCAAATAAAA
*
39691636 TAAAACCAGATAAAA
1 TAAAACCAAATAAAA
39691651 ATGAACAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.13, G:0.03, T:0.13
Consensus pattern (15 bp):
TAAAACCAAATAAAA
Found at i:39692003 original size:13 final size:13
Alignment explanation
Indices: 39691985--39692019 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
39691975 AAATAACAGC
* *
39691985 AAAAATAATAGAG
1 AAAAATAAAAAAG
39691998 AAAAATAAAAAAG
1 AAAAATAAAAAAG
39692011 AAAAATAAA
1 AAAAATAAA
39692020 TATTTTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (13 bp):
AAAAATAAAAAAG
Found at i:39700500 original size:16 final size:15
Alignment explanation
Indices: 39700473--39700506 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
39700463 ATAACTAGTA
*
39700473 TATAATTATATTTAT
1 TATAATTATATTAAT
39700488 TATAATATATATTAAT
1 TATAAT-TATATTAAT
39700504 TAT
1 TAT
39700507 TATCAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATAATTATATTAAT
Found at i:39702166 original size:12 final size:12
Alignment explanation
Indices: 39702149--39702183 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
39702139 TGAGGATCCT
39702149 GAAAAAGAAGAA
1 GAAAAAGAAGAA
39702161 GAAAAAGAAGAA
1 GAAAAAGAAGAA
*
39702173 GAACAAGAAGA
1 GAAAAAGAAGA
39702184 TCCCATAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.71, C:0.03, G:0.26, T:0.00
Consensus pattern (12 bp):
GAAAAAGAAGAA
Found at i:39703953 original size:165 final size:165
Alignment explanation
Indices: 39703753--39704082 Score: 624
Period size: 165 Copynumber: 2.0 Consensus size: 165
39703743 GATTGAGGCA
39703753 CCAGTGTTGATTCAACCAGAGTCCAGGAAGGAGTATGTGGTCTAGGGGGATGCATCGTATATGAG
1 CCAGTGTTGATTCAACCAGAGTCCAGGAAGGAGTATGTGGTCTAGGGGGATGCATCGTATATGAG
39703818 ACTTAGTGATGTGCTGATGAAAAAGGGCAATGTGGTAGCTTATGCTTCGAGACAGTTGAAGCCAC
66 ACTTAGTGATGTGCTGATGAAAAAGGGCAATGTGGTAGCTTATGCTTCGAGACAGTTGAAGCCAC
39703883 ATGAGTGTAATTACTCGACCCATGATTTTGGAGTT
131 ATGAGTGTAATTACTCGACCCATGATTTTGGAGTT
**
39703918 CCAGTGTTGATTCAACCAGAGTCTGGGAAGGAGTATGTGGTCTAGGGGGATGCATCGTATATGAG
1 CCAGTGTTGATTCAACCAGAGTCCAGGAAGGAGTATGTGGTCTAGGGGGATGCATCGTATATGAG
*
39703983 ACTTAGTTATGTGCTGATGAAAAAGGGCAATGTGGTAGCTTATGCTTCGAGACAGTTGAAGCCAC
66 ACTTAGTGATGTGCTGATGAAAAAGGGCAATGTGGTAGCTTATGCTTCGAGACAGTTGAAGCCAC
*
39704048 ATGAGTGTAATTACTTGACCCATGATTTTGGAGTT
131 ATGAGTGTAATTACTCGACCCATGATTTTGGAGTT
39704083 AGTTGTAGTA
Statistics
Matches: 161, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
165 161 1.00
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.29
Consensus pattern (165 bp):
CCAGTGTTGATTCAACCAGAGTCCAGGAAGGAGTATGTGGTCTAGGGGGATGCATCGTATATGAG
ACTTAGTGATGTGCTGATGAAAAAGGGCAATGTGGTAGCTTATGCTTCGAGACAGTTGAAGCCAC
ATGAGTGTAATTACTCGACCCATGATTTTGGAGTT
Found at i:39712506 original size:44 final size:46
Alignment explanation
Indices: 39712450--39712537 Score: 119
Period size: 44 Copynumber: 2.0 Consensus size: 46
39712440 TACAACATCT
*
39712450 ATTTCATCCAACCAAAC-ACAAGAA-TACT-ATTACAACTTTATTTC
1 ATTTCATCCAACCAAACAAC-AGAATTACTAATTACAACTCTATTTC
* *
39712494 ATTTCATTCAACCAAACAACTGAATTACTAATTACAACTCTATT
1 ATTTCATCCAACCAAACAACAGAATTACTAATTACAACTCTATT
39712538 CTATTACAGC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
44 19 0.50
45 6 0.16
46 13 0.34
ACGTcount: A:0.41, C:0.24, G:0.02, T:0.33
Consensus pattern (46 bp):
ATTTCATCCAACCAAACAACAGAATTACTAATTACAACTCTATTTC
Found at i:39712545 original size:16 final size:16
Alignment explanation
Indices: 39712524--39712554 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39712514 TGAATTACTA
39712524 ATTACAACTCTATTCT
1 ATTACAACTCTATTCT
*
39712540 ATTACAGCTCTATTC
1 ATTACAACTCTATTC
39712555 CATTCTCCCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.26, G:0.03, T:0.42
Consensus pattern (16 bp):
ATTACAACTCTATTCT
Found at i:39719399 original size:12 final size:12
Alignment explanation
Indices: 39719382--39719406 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39719372 CATTTTTTTT
39719382 TTATTAAAAATA
1 TTATTAAAAATA
39719394 TTATTAAAAATA
1 TTATTAAAAATA
39719406 T
1 T
39719407 GAAATTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TTATTAAAAATA
Found at i:39724298 original size:23 final size:23
Alignment explanation
Indices: 39724272--39724350 Score: 113
Period size: 23 Copynumber: 3.3 Consensus size: 23
39724262 GACCGAAATT
39724272 AAATATATTTGATTAAAAATAAAA
1 AAATATATTTGATTAAAAAT-AAA
*
39724296 AATATATATTTGATTAAAAATAAT
1 AA-ATATATTTGATTAAAAATAAA
* *
39724320 ATATATATTTGATTAAAAATTAA
1 AAATATATTTGATTAAAAATAAA
39724343 AAATATAT
1 AAATATAT
39724351 AATTCGAGCC
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
23 26 0.53
24 5 0.10
25 18 0.37
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (23 bp):
AAATATATTTGATTAAAAATAAA
Found at i:39724306 original size:25 final size:24
Alignment explanation
Indices: 39724274--39724351 Score: 122
Period size: 25 Copynumber: 3.2 Consensus size: 24
39724264 CCGAAATTAA
39724274 ATATATTTGATTAAAAATAAAAAAT
1 ATATATTTGATTAAAAAT-AAAAAT
*
39724299 ATATATTTGATTAAAAAT-AATAT
1 ATATATTTGATTAAAAATAAAAAT
39724322 ATATATTTGATTAAAAATTAAAAAT
1 ATATATTTGATTAAAAA-TAAAAAT
39724347 ATATA
1 ATATA
39724352 ATTCGAGCCA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
23 21 0.43
24 1 0.02
25 27 0.55
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (24 bp):
ATATATTTGATTAAAAATAAAAAT
Found at i:39726229 original size:18 final size:20
Alignment explanation
Indices: 39726208--39726248 Score: 50
Period size: 18 Copynumber: 2.1 Consensus size: 20
39726198 GAAAATTTTA
39726208 TTTTAATATTTT-TA-ATAT
1 TTTTAATATTTTATATATAT
* *
39726226 TTTTGATGTTTTATATATAT
1 TTTTAATATTTTATATATAT
39726246 TTT
1 TTT
39726249 AAAAAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
18 10 0.53
19 2 0.11
20 7 0.37
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTAATATTTTATATATAT
Found at i:39730389 original size:20 final size:20
Alignment explanation
Indices: 39730341--39730389 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
39730331 ATCTTCTTTC
* *
39730341 ATCCTTCATTTTATTTTTTT
1 ATCCTTCAGTTTATTTTCTT
*
39730361 ATCCCTCAGTTTATTTTCTT
1 ATCCTTCAGTTTATTTTCTT
*
39730381 ATCTTTCAG
1 ATCCTTCAG
39730390 CTAATTGATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.16, C:0.20, G:0.04, T:0.59
Consensus pattern (20 bp):
ATCCTTCAGTTTATTTTCTT
Found at i:39732826 original size:18 final size:18
Alignment explanation
Indices: 39732803--39732837 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39732793 CAAAAACATG
*
39732803 AAGCATCAAAATGGTTTC
1 AAGCATCAAAATAGTTTC
*
39732821 AAGCATGAAAATAGTTT
1 AAGCATCAAAATAGTTT
39732838 GGCACATCGT
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:0.43, C:0.11, G:0.17, T:0.29
Consensus pattern (18 bp):
AAGCATCAAAATAGTTTC
Found at i:39738369 original size:16 final size:16
Alignment explanation
Indices: 39738348--39738378 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
39738338 TTTTATTTAA
39738348 ATTTAAATAATTTTTC
1 ATTTAAATAATTTTTC
39738364 ATTTAAATAATTTTT
1 ATTTAAATAATTTTT
39738379 TATATGTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTAAATAATTTTTC
Found at i:39744609 original size:27 final size:27
Alignment explanation
Indices: 39744576--39744971 Score: 443
Period size: 27 Copynumber: 14.7 Consensus size: 27
39744566 GTAATGGGCC
*
39744576 TAAAATTACTGAAATACCCACGATGGG
1 TAAAATTACTGAAATACCCTCGATGGG
39744603 TAAAATTACTGAAATACCCTCGATGGG
1 TAAAATTACTGAAATACCCTCGATGGG
**
39744630 TAAAATTACCAAAATACCCTCGATGGG
1 TAAAATTACTGAAATACCCTCGATGGG
* *
39744657 TAAAATTA-TCGAAATACACTCGATGGA
1 TAAAATTACT-GAAATACCCTCGATGGG
* *
39744684 TAAAATTACTGAAATACCC-CTAAAGGG
1 TAAAATTACTGAAATACCCTC-GATGGG
**
39744711 TAAAATTACCAAAATACCC-CTGATGGG
1 TAAAATTACTGAAATACCCTC-GATGGG
* **
39744738 TAAAATTACTGAAATACCTTTTATGGG
1 TAAAATTACTGAAATACCCTCGATGGG
*
39744765 TAAAATTA-TCGAAATACCCTCAATGGG
1 TAAAATTACT-GAAATACCCTCGATGGG
* *
39744792 TAAAATTACTGAAATACCCTCCATAGG
1 TAAAATTACTGAAATACCCTCGATGGG
* * *
39744819 TAAAATTATTAAAATAGCCTCGATGGG
1 TAAAATTACTGAAATACCCTCGATGGG
39744846 TAAAATTACTGAAATACCC-CTGAT-GG
1 TAAAATTACTGAAATACCCTC-GATGGG
39744872 TAAAATTA-TCGAAATACCC-CTGATGGG
1 TAAAATTACT-GAAATACCCTC-GATGGG
39744899 TAAAATTA-TCGAAATACCCTCGATGGG
1 TAAAATTACT-GAAATACCCTCGATGGG
* *
39744926 TAAAATTATTGAAATA-CCTCTGATAGG
1 TAAAATTACTGAAATACCCTC-GATGGG
* *
39744953 TAAAATTACCGTAATACCC
1 TAAAATTACTGAAATACCC
39744972 CTGTTAGGGT
Statistics
Matches: 319, Mismatches: 37, Indels: 25
0.84 0.10 0.07
Matches are distributed among these distances:
25 1 0.00
26 31 0.10
27 281 0.88
28 6 0.02
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (27 bp):
TAAAATTACTGAAATACCCTCGATGGG
Found at i:39745194 original size:27 final size:25
Alignment explanation
Indices: 39745120--39745201 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 25
39745110 CTGTTTCTAC
39745120 TGGCTTTGCCACACACATACTGATACTGG
1 TGGCTTTG-C-CACA-ATACTG-TACTGG
* *
39745149 TGGCTCTGCCATAACTACTGTTACTGG
1 TGGCTTTGCCACAA-TACTG-TACTGG
39745176 TGGCTTTGCCACATATACTGTACTGG
1 TGGCTTTGCCACA-ATACTGTACTGG
39745202 AAGCTCTGCT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
26 7 0.15
27 30 0.65
28 2 0.04
29 7 0.15
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.32
Consensus pattern (25 bp):
TGGCTTTGCCACAATACTGTACTGG
Found at i:39747284 original size:24 final size:25
Alignment explanation
Indices: 39747235--39747284 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
39747225 AATAACAGCG
*
39747235 AGCTCATGCGAGCTAAGAATCGGTA
1 AGCTCATACGAGCTAAGAATCGGTA
*
39747260 AGCTCATACGAGCTGA-AATCGGTA
1 AGCTCATACGAGCTAAGAATCGGTA
39747284 A
1 A
39747285 CCCTAATGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.20
Consensus pattern (25 bp):
AGCTCATACGAGCTAAGAATCGGTA
Found at i:39750513 original size:27 final size:27
Alignment explanation
Indices: 39750483--39750541 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
39750473 TTTCATCTCC
* *
39750483 TAGGGGTATAACAGTCATTTTACTCTA
1 TAGGGGTATAACAGCCATTTTACCCTA
**
39750510 TAGGGGTATTTCAGCCATTTTACCCTA
1 TAGGGGTATAACAGCCATTTTACCCTA
39750537 T-GGGG
1 TAGGGG
39750542 ATATTTTGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.36
Consensus pattern (27 bp):
TAGGGGTATAACAGCCATTTTACCCTA
Found at i:39750546 original size:27 final size:26
Alignment explanation
Indices: 39750496--39750695 Score: 195
Period size: 27 Copynumber: 7.4 Consensus size: 26
39750486 GGGTATAACA
* *
39750496 GTCATTTTACTCTATAGGGGTATTTCA
1 GTCATTTTACCCTAT-GGGGTATTTCG
* *
39750523 GCCATTTTACCCTATGGGGATATTTTG
1 GTCATTTTACCCTATGGGG-TATTTCG
* * *
39750550 GTTATTTTACCCAATGGAGGTAGTTCG
1 GTCATTTTACCCTATGG-GGTATTTCG
* *
39750577 GTCAGTTCACCCTATGGGAGTATTTCG
1 GTCATTTTACCCTATGGG-GTATTTCG
* *
39750604 GTCATTTTACCCTATGAGGTTATTTTG
1 GTCATTTTACCCTATG-GGGTATTTCG
*
39750631 GTCATTTTATCCTATGGGGGTATTTCG
1 GTCATTTTACCCTAT-GGGGTATTTCG
* *
39750658 GTCATTTTACCCTAAGGGGGTATGGT-G
1 GTCATTTTACCCT-ATGGGGTAT-TTCG
39750685 GTCATTTTACC
1 GTCATTTTACC
39750696 TATTTTGGGG
Statistics
Matches: 142, Mismatches: 24, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
26 5 0.04
27 130 0.92
28 7 0.05
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.41
Consensus pattern (26 bp):
GTCATTTTACCCTATGGGGTATTTCG
Found at i:39750658 original size:81 final size:80
Alignment explanation
Indices: 39750507--39750695 Score: 218
Period size: 81 Copynumber: 2.3 Consensus size: 80
39750497 TCATTTTACT
* * * *
39750507 CTATAGGGGTATTTCAGCCATTTTACCCTATGGGGATATTTTGGTTATTTTACCCAATGGAGGTA
1 CTAT-GGGGTATTTCGGTCATTTTACCCTATGAGGATATTTTGGTCATTTTACCCAATGGAGGTA
39750572 GTTCGGTCAGTTCACC
65 GTTCGGTCAGTTCACC
* * * *
39750588 CTATGGGAGTATTTCGGTCATTTTACCCTATGAGGTTATTTTGGTCATTTTATCCTATGGGGGTA
1 CTATGGG-GTATTTCGGTCATTTTACCCTATGAGGATATTTTGGTCATTTTACCCAATGGAGGTA
* * *
39750653 TTTCGGTCATTTTACC
65 GTTCGGTCAGTTCACC
* *
39750669 CTAAGGGGGTATGGT-GGTCATTTTACC
1 CT-ATGGGGTAT-TTCGGTCATTTTACC
39750696 TATTTTGGGG
Statistics
Matches: 92, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
80 3 0.03
81 84 0.91
82 5 0.05
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.40
Consensus pattern (80 bp):
CTATGGGGTATTTCGGTCATTTTACCCTATGAGGATATTTTGGTCATTTTACCCAATGGAGGTAG
TTCGGTCAGTTCACC
Found at i:39753685 original size:31 final size:30
Alignment explanation
Indices: 39753632--39753692 Score: 70
Period size: 31 Copynumber: 2.0 Consensus size: 30
39753622 GATATCAGTC
***
39753632 ATGCAGTGAACAATATGTAATATCATTAATCA
1 ATGCAGTGAACAATACAAAATAT--TTAATCA
39753664 ATGCAGT-AACAATACAAAATATTTAATCA
1 ATGCAGTGAACAATACAAAATATTTAATCA
39753693 GTACAGATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
29 7 0.27
31 12 0.46
32 7 0.27
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.30
Consensus pattern (30 bp):
ATGCAGTGAACAATACAAAATATTTAATCA
Found at i:39754110 original size:27 final size:27
Alignment explanation
Indices: 39754058--39754141 Score: 75
Period size: 27 Copynumber: 3.1 Consensus size: 27
39754048 GCATAAGACC
*
39754058 ATAACAGTCATTTCATCTCCTA--GGGGT
1 ATAACAGTCATTTTA-CT-CTATGGGGGT
39754085 ATAACAGTCATTTTACTCTATGGGGGGT
1 ATAACAGTCATTTTACTCTAT-GGGGGT
** *
39754113 ATTTC-GATCATTTTACCCTATGGGGGT
1 ATAACAG-TCATTTTACTCTATGGGGGT
39754140 AT
1 AT
39754142 TTTGGTTATT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
25 3 0.06
26 2 0.04
27 23 0.47
28 21 0.43
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (27 bp):
ATAACAGTCATTTTACTCTATGGGGGT
Found at i:39754152 original size:27 final size:27
Alignment explanation
Indices: 39754091--39754233 Score: 187
Period size: 27 Copynumber: 5.3 Consensus size: 27
39754081 GGGTATAACA
*
39754091 GTCATTTTACTCTATGGGGGGTATTTCG
1 GTCATTTTACCCTAT-GGGGGTATTTCG
* *
39754119 ATCATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
39754146 GTTATTTTACCCTATGGGGTTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
39754173 GTAATTTTACCCTATGTGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
39754200 GTCATTTTACCCAATGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
39754227 GTCATTT
1 GTCATTT
39754234 CCCTATTTTA
Statistics
Matches: 101, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
27 88 0.87
28 13 0.13
ACGTcount: A:0.17, C:0.15, G:0.23, T:0.45
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:39762130 original size:25 final size:25
Alignment explanation
Indices: 39762097--39762151 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
39762087 CAAGGTAAAA
*
39762097 GAGTATGTGATTACAATCATCTCAT
1 GAGTTTGTGATTACAATCATCTCAT
39762122 GAGTTTGTGATTACAATCATCTCAT
1 GAGTTTGTGATTACAATCATCTCAT
39762147 GAGTT
1 GAGTT
39762152 GTGTAAGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (25 bp):
GAGTTTGTGATTACAATCATCTCAT
Found at i:39762721 original size:24 final size:24
Alignment explanation
Indices: 39762673--39762719 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
39762663 ATTGGTCATA
*
39762673 GAGAGAATTGAGGAGGGATATTTG
1 GAGAGAATTGAGGAGGAATATTTG
*
39762697 GAGAGATTTGAGGAGAGAATATT
1 GAGAGAATTGAGGAG-GAATATT
39762720 GGGATTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.38, T:0.26
Consensus pattern (24 bp):
GAGAGAATTGAGGAGGAATATTTG
Found at i:39763574 original size:52 final size:52
Alignment explanation
Indices: 39763496--39763643 Score: 269
Period size: 52 Copynumber: 2.8 Consensus size: 52
39763486 CCCACGAATC
*
39763496 ATGGGCGATAGACTGTGGAGGCTTCCATGAGCATTTTCATGGGCGATAGACT
1 ATGGGTGATAGACTGTGGAGGCTTCCATGAGCATTTTCATGGGCGATAGACT
39763548 ATGGGTGATAGACTGTGGAGGCTTCCATGAGCATTTTCATGGGCGATAGACT
1 ATGGGTGATAGACTGTGGAGGCTTCCATGAGCATTTTCATGGGCGATAGACT
* *
39763600 GTGGGTGATAGACTGTGGAGGCTTACATGAGCATTTTCATGGGC
1 ATGGGTGATAGACTGTGGAGGCTTCCATGAGCATTTTCATGGGC
39763644 TTAAGTCGTA
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 93 1.00
ACGTcount: A:0.22, C:0.16, G:0.34, T:0.28
Consensus pattern (52 bp):
ATGGGTGATAGACTGTGGAGGCTTCCATGAGCATTTTCATGGGCGATAGACT
Found at i:39763609 original size:14 final size:14
Alignment explanation
Indices: 39763587--39763617 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
39763577 AGCATTTTCA
39763587 TGGGCGATAGACTG
1 TGGGCGATAGACTG
*
39763601 TGGGTGATAGACTG
1 TGGGCGATAGACTG
39763615 TGG
1 TGG
39763618 AGGCTTACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.10, G:0.45, T:0.26
Consensus pattern (14 bp):
TGGGCGATAGACTG
Found at i:39764075 original size:80 final size:81
Alignment explanation
Indices: 39763935--39764105 Score: 254
Period size: 80 Copynumber: 2.1 Consensus size: 81
39763925 GCCCCTATTA
* *
39763935 GGTAAAATGATCGAAATACCCCTATAGGGTAAAATGACCAAAATATCCCCACAAGATAAAATGAT
1 GGTAAAATGATCGAAATACCCCTATAGGGTAAAATGACCAAAATACCCCCACAAGATAAAATGAC
39764000 TGAAATACCCCCATAG
66 TGAAATACCCCCATAG
* * * * * * *
39764016 GGTAAAATGATTGAGATACCTC-ATAGGGTAAAATGACCTAAATACCCCCATAGGGTAAAATGAC
1 GGTAAAATGATCGAAATACCCCTATAGGGTAAAATGACCAAAATACCCCCACAAGATAAAATGAC
39764080 TGAAATACCCCCATAG
66 TGAAATACCCCCATAG
39764096 GGTAAAATGA
1 GGTAAAATGA
39764106 CTGTTATACC
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
80 62 0.77
81 19 0.23
ACGTcount: A:0.43, C:0.19, G:0.18, T:0.20
Consensus pattern (81 bp):
GGTAAAATGATCGAAATACCCCTATAGGGTAAAATGACCAAAATACCCCCACAAGATAAAATGAC
TGAAATACCCCCATAG
Found at i:39764106 original size:27 final size:27
Alignment explanation
Indices: 39763935--39764117 Score: 210
Period size: 27 Copynumber: 6.8 Consensus size: 27
39763925 GCCCCTATTA
*
39763935 GGTAAAATGA-TCGAAATACCCCTATAG
1 GGTAAAATGACT-GAAATACCCCCATAG
** * * *
39763962 GGTAAAATGACCAAAATATCCCCACAA
1 GGTAAAATGACTGAAATACCCCCATAG
* *
39763989 GATAAAATGATTGAAATACCCCCATAG
1 GGTAAAATGACTGAAATACCCCCATAG
* * *
39764016 GGTAAAATGATTGAGATA-CCTCATAG
1 GGTAAAATGACTGAAATACCCCCATAG
39764042 GGTAAAATGACCT-AAATACCCCCATAG
1 GGTAAAATGA-CTGAAATACCCCCATAG
39764069 GGTAAAATGACTGAAATACCCCCATAG
1 GGTAAAATGACTGAAATACCCCCATAG
**
39764096 GGTAAAATGACTGTTATACCCC
1 GGTAAAATGACTGAAATACCCC
39764118 TAGGAGATGA
Statistics
Matches: 131, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
26 23 0.18
27 108 0.82
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.21
Consensus pattern (27 bp):
GGTAAAATGACTGAAATACCCCCATAG
Found at i:39769481 original size:57 final size:57
Alignment explanation
Indices: 39769420--39769532 Score: 217
Period size: 57 Copynumber: 2.0 Consensus size: 57
39769410 AGTTTTACCT
39769420 AACACTAGCATATTTAAATCATAAAACCGTATAAAAACAAAATTTAAACCAAAATCC
1 AACACTAGCATATTTAAATCATAAAACCGTATAAAAACAAAATTTAAACCAAAATCC
*
39769477 AACACTAGCATATTTAAATCATAAAACCGTATAAAAACCAAATTTAAACCAAAATC
1 AACACTAGCATATTTAAATCATAAAACCGTATAAAAACAAAATTTAAACCAAAATC
39769533 TATAAAGGCC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.54, C:0.19, G:0.04, T:0.23
Consensus pattern (57 bp):
AACACTAGCATATTTAAATCATAAAACCGTATAAAAACAAAATTTAAACCAAAATCC
Found at i:39773634 original size:26 final size:26
Alignment explanation
Indices: 39773605--39773662 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
39773595 CCAATATCTA
*
39773605 AGCAAAGTTGCCAGTAATAGTATTGC
1 AGCAAAGCTGCCAGTAATAGTATTGC
*
39773631 AGCAAAGCTGCCAGTAATAGTATTGT
1 AGCAAAGCTGCCAGTAATAGTATTGC
39773657 AGCAAA
1 AGCAAA
39773663 ACTGTCAGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (26 bp):
AGCAAAGCTGCCAGTAATAGTATTGC
Found at i:39773678 original size:26 final size:25
Alignment explanation
Indices: 39773616--39773702 Score: 81
Period size: 26 Copynumber: 3.5 Consensus size: 25
39773606 GCAAAGTTGC
* * *
39773616 CAGTAATAGTATTGCAGCAAAGCTG
1 CAGTAACAGTATTGTAGCAAAACTG
*
39773641 CCAGTAATAGTATTGTAGCAAAACTG
1 -CAGTAACAGTATTGTAGCAAAACTG
*
39773667 TCAGCAACAGTA---TAGCAAAACTG
1 -CAGTAACAGTATTGTAGCAAAACTG
39773690 CTAGTAACAGTAT
1 C-AGTAACAGTAT
39773703 GCTTCCTCCA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.02
23 20 0.38
26 32 0.60
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (25 bp):
CAGTAACAGTATTGTAGCAAAACTG
Found at i:39773686 original size:23 final size:23
Alignment explanation
Indices: 39773656--39773702 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
39773646 AATAGTATTG
39773656 TAGCAAAACTG-TCAGCAACAGTA
1 TAGCAAAACTGCT-AGCAACAGTA
*
39773679 TAGCAAAACTGCTAGTAACAGTA
1 TAGCAAAACTGCTAGCAACAGTA
39773702 T
1 T
39773703 GCTTCCTCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (23 bp):
TAGCAAAACTGCTAGCAACAGTA
Found at i:39773886 original size:27 final size:27
Alignment explanation
Indices: 39773856--39774023 Score: 115
Period size: 27 Copynumber: 6.3 Consensus size: 27
39773846 CCATCCTCTA
39773856 GGGGTATAAT-AGCCATTTTACCCTATG
1 GGGGTAT-ATCAGCCATTTTACCCTATG
* * *
39773883 GGGGTATTTCGGTCATTTTACCCTATG
1 GGGGTATATCAGCCATTTTACCCTATG
* * * ** *
39773910 AGGGTATTTCGGTTATTTTACCCTATA
1 GGGGTATATCAGCCATTTTACCCTATG
* * * *
39773937 AGGGTATTTCTGTCATTTTACCCTATG
1 GGGGTATATCAGCCATTTTACCCTATG
* ** *
39773964 GGGGTATTTTGGTCATTTTACCCTATG
1 GGGGTATATCAGCCATTTTACCCTATG
* * * * *
39773991 AGAGTATTTCAGTCATTTTACCTTA-G
1 GGGGTATATCAGCCATTTTACCCTATG
39774017 GGGGTAT
1 GGGGTAT
39774024 TTCGATCATT
Statistics
Matches: 121, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
26 7 0.06
27 114 0.94
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (27 bp):
GGGGTATATCAGCCATTTTACCCTATG
Found at i:39773928 original size:54 final size:54
Alignment explanation
Indices: 39773869--39774034 Score: 235
Period size: 54 Copynumber: 3.1 Consensus size: 54
39773859 GTATAATAGC
* * *
39773869 CATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCGGT
1 CATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCGGT
* * * *
39773923 TATTTTACCCTATAAGGGTATTTCTGTCATTTTACCCTATGGGGGTATTTTGGT
1 CATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCGGT
* * *
39773977 CATTTTACCCTATGAGAGTATTTCAGTCATTTTACCTTA-GGGGGTATTTCGAT
1 CATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCGGT
39774030 CATTT
1 CATTT
39774035 ATTGACCTCT
Statistics
Matches: 99, Mismatches: 13, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
53 17 0.17
54 82 0.83
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.43
Consensus pattern (54 bp):
CATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCGGT
Found at i:39777252 original size:31 final size:32
Alignment explanation
Indices: 39777206--39777277 Score: 119
Period size: 31 Copynumber: 2.3 Consensus size: 32
39777196 AGCTGAGCTG
*
39777206 AAATAATCACAGGAAAAGTAGAGGTGTCACCT
1 AAATAAACACAGGAAAAGTAGAGGTGTCACCT
*
39777238 AAATAAACA-AGGAAAGGTAGAGGTGTCACCT
1 AAATAAACACAGGAAAAGTAGAGGTGTCACCT
39777269 AAATAAACA
1 AAATAAACA
39777278 TACTTTAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 30 0.79
32 8 0.21
ACGTcount: A:0.49, C:0.14, G:0.21, T:0.17
Consensus pattern (32 bp):
AAATAAACACAGGAAAAGTAGAGGTGTCACCT
Found at i:39798236 original size:46 final size:46
Alignment explanation
Indices: 39798169--39798377 Score: 190
Period size: 46 Copynumber: 4.5 Consensus size: 46
39798159 GTTCTTACCT
*
39798169 AGGTTCCTAGCTCCTGCATATGTTGCAGAATGGAGAA-ATCAAATTC
1 AGGTTCCCAGCTCCTGCATATGTTGCAGAATGGAGAATAT-AAATTC
* * ** * * *
39798215 AGGTTCCCAGTTCCTGTATATGTTGTGGACTTGAGAATATAGATTC
1 AGGTTCCCAGCTCCTGCATATGTTGCAGAATGGAGAATATAAATTC
* * * * * ** *
39798261 AAGTTCCCAGCTCCTGGATATCTTGCAGACTAGAGAATATAGGTTT
1 AGGTTCCCAGCTCCTGCATATGTTGCAGAATGGAGAATATAAATTC
* *
39798307 AGGTTCCCAACTCCTGCATATGTTGC-GAATTGGAGAATA-AAAGTTT
1 AGGTTCCCAGCTCCTGCATATGTTGCAGAA-TGGAGAATATAAA-TTC
* *
39798353 AGGTTCCCAGCTCTTGCAAATGTTG
1 AGGTTCCCAGCTCCTGCATATGTTG
39798378 TAGGCTGGGG
Statistics
Matches: 132, Mismatches: 28, Indels: 6
0.80 0.17 0.04
Matches are distributed among these distances:
45 3 0.02
46 127 0.96
47 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (46 bp):
AGGTTCCCAGCTCCTGCATATGTTGCAGAATGGAGAATATAAATTC
Found at i:39801803 original size:16 final size:16
Alignment explanation
Indices: 39801782--39801814 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
39801772 GAGATAGTCT
39801782 ACGGGAAGCCCACATC
1 ACGGGAAGCCCACATC
39801798 ACGGGAAGCCCACATC
1 ACGGGAAGCCCACATC
39801814 A
1 A
39801815 GCATTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.36, G:0.24, T:0.06
Consensus pattern (16 bp):
ACGGGAAGCCCACATC
Found at i:39808865 original size:23 final size:22
Alignment explanation
Indices: 39808826--39808877 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
39808816 TAATTTTGAA
*
39808826 AAAAAATATTAAAAATATTATTT
1 AAAAAATATCAAAAATA-TATTT
*
39808849 AAAAAAT-TCAAAGAATATCTTT
1 AAAAAATATCAAA-AATATATTT
39808871 AAAAAAT
1 AAAAAAT
39808878 CTGAAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 15 0.58
23 11 0.42
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAAAATATCAAAAATATATTT
Found at i:39809566 original size:18 final size:17
Alignment explanation
Indices: 39809542--39809588 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
39809532 ACCGGTCACC
39809542 TTAAAAAAATATTAATT
1 TTAAAAAAATATTAATT
*
39809559 TGTAAAAATATA-TAATT
1 T-TAAAAAAATATTAATT
*
39809576 TTAAAAAAGTATT
1 TTAAAAAAATATT
39809589 TTGTTTATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 8 0.32
17 8 0.32
18 9 0.36
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (17 bp):
TTAAAAAAATATTAATT
Found at i:39809567 original size:16 final size:16
Alignment explanation
Indices: 39809546--39809582 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
39809536 GTCACCTTAA
39809546 AAAAATAT-TAATTTGT
1 AAAAATATATAATTT-T
39809562 AAAAATATATAATTTT
1 AAAAATATATAATTTT
39809578 AAAAA
1 AAAAA
39809583 AGTATTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
AAAAATATATAATTTT
Done.