Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 5 of 297
Found at i:1485933 original size:54 final size:54
Alignment explanation
Indices: 1485868--1486101 Score: 342
Period size: 54 Copynumber: 4.3 Consensus size: 54
1485858 TTAGTTTACC
* * *
1485868 AAATTACCAAAATACCCTTGGTTTATAAAATCACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCTTAGTTTATAAAATTACCAAAATACCCTTGGTTTGTA
* * *
1485922 AAATTACCAAAATACCTTTGGTTTACAAAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCTTAGTTTATAAAATTACCAAAATACCCTTGGTTTGTA
*
1485976 AAATTACTAAAATACCCTTAGTTTATAAAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCTTAGTTTATAAAATTACCAAAATACCCTTGGTTTGTA
* * * * *
1486030 AAATTATCAAAATACCCTTAGTTTGTAAAATTACCAAAATACCATTGATTTGTG
1 AAATTACCAAAATACCCTTAGTTTATAAAATTACCAAAATACCCTTGGTTTGTA
**
1486084 AAATTACTGAAATACCCT
1 AAATTACCAAAATACCCT
1486102 CGACCTGTAA
Statistics
Matches: 163, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 163 1.00
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (54 bp):
AAATTACCAAAATACCCTTAGTTTATAAAATTACCAAAATACCCTTGGTTTGTA
Found at i:1486693 original size:27 final size:27
Alignment explanation
Indices: 1486193--1486683 Score: 750
Period size: 27 Copynumber: 18.2 Consensus size: 27
1486183 CGATTTACAA
*
1486193 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
1486220 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
1486247 AATTATC-AAAGTACCCCTGTAGGGTAG
1 AATTACCGAAA-TACCCCTGTAGGGTAG
* *
1486274 AATTACCGAAATACCCCTATAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
1486301 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
1486328 AATTATCGAAATATCCCTGTAGGATAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
1486355 AATTACCAAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
1486382 AATTACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
1486409 AATTACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
1486436 AATTACTGAAATACCCTTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
1486463 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
1486490 AATTACCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
1486517 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
1486544 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
1486571 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
**
1486598 AATTATTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
1486625 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
1486652 AATTACTAAAATACCCCTGTAGGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
1486679 AATTA
1 AATTA
1486684 TTGAGATACC
Statistics
Matches: 425, Mismatches: 37, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
26 3 0.01
27 419 0.99
28 3 0.01
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:1487193 original size:22 final size:22
Alignment explanation
Indices: 1487138--1487202 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
1487128 TTAAAGCCTT
*
1487138 CTGATTATGGCTCTGTGTCAAC
1 CTGATTATGGCTCTGTGCCAAC
*
1487160 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
* * *
1487182 CTGATTACGGCTGTGTACCAA
1 CTGATTATGGCTCTGTGCCAA
1487203 ACGTATTTGC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.31
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:1487391 original size:27 final size:27
Alignment explanation
Indices: 1487361--1487462 Score: 127
Period size: 27 Copynumber: 3.8 Consensus size: 27
1487351 ATTCTGTTAA
* *
1487361 GTGGCTTTGCCACATTATCTGTTTCTG
1 GTGGCTCTGCCACAATATCTGTTTCTG
*
1487388 GTGGCTATGCCACAAATATCTG-TTCTG
1 GTGGCTCTGCCAC-AATATCTGTTTCTG
1487415 GTGGCTCTGCCACAATATCTGTATT-TG
1 GTGGCTCTGCCACAATATCTGT-TTCTG
* *
1487442 GTGACTCTGTCACAATATCTG
1 GTGGCTCTGCCACAATATCTG
1487463 ATAACTGAGC
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
26 8 0.12
27 50 0.75
28 9 0.13
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.37
Consensus pattern (27 bp):
GTGGCTCTGCCACAATATCTGTTTCTG
Found at i:1487637 original size:6 final size:6
Alignment explanation
Indices: 1487599--1487681 Score: 64
Period size: 6 Copynumber: 13.3 Consensus size: 6
1487589 TTGCATTCAC
* *
1487599 ATTCTG ATTTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTG ATTCTG
1 ATTCTG A-TTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
*
1487649 -TCACCTG ATTCTG ATTCTG ATTCT- AGTTCTG AT
1 AT--TCTG ATTCTG ATTCTG ATTCTG A-TTCTG AT
1487682 AATGTTTCTT
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
5 4 0.06
6 44 0.71
7 12 0.19
8 2 0.03
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:1487679 original size:31 final size:31
Alignment explanation
Indices: 1487599--1487672 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
1487589 TTGCATTCAC
* *
1487599 ATTCTGATTTTTGATTCTGTTACCTGATACTG
1 ATTCTGA-TTCTGATTCTGTCACCTGATACTG
*
1487631 ATTCTGATTCTGATTCTGTCACCTGATTCTG
1 ATTCTGATTCTGATTCTGTCACCTGATACTG
1487662 ATTCTGATTCT
1 ATTCTGATTCT
1487673 AGTTCTGATA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 32 0.82
32 7 0.18
ACGTcount: A:0.18, C:0.19, G:0.15, T:0.49
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTCACCTGATACTG
Found at i:1490568 original size:56 final size:54
Alignment explanation
Indices: 1490477--1490582 Score: 131
Period size: 56 Copynumber: 1.9 Consensus size: 54
1490467 GGGGTAAAGC
* **
1490477 AAAGGGAAAAAAATTTGGGGGTTTGGAGGAAGTAAAAGTTTTGGGAAAAAATTT
1 AAAGGAAAAAAAATTTGGGGCCTTGGAGGAAGTAAAAGTTTTGGGAAAAAATTT
* ** *
1490531 AAAGGAAAAAAAAGTTTTGGGGCCTTGGGGGAAGTAAATTTTTTGGGGAAAA
1 AAAGGAAAAAAAA--TTTGGGGCCTTGGAGGAAGTAAAAGTTTTGGGAAAAA
1490583 GTAAAAGGGT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
54 12 0.28
56 31 0.72
ACGTcount: A:0.41, C:0.02, G:0.32, T:0.25
Consensus pattern (54 bp):
AAAGGAAAAAAAATTTGGGGCCTTGGAGGAAGTAAAAGTTTTGGGAAAAAATTT
Found at i:1492480 original size:16 final size:17
Alignment explanation
Indices: 1492459--1492494 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
1492449 CATTTGGAGG
1492459 CTTTCTTCTT-CTTTTT
1 CTTTCTTCTTGCTTTTT
1492475 CTTTCTTCTTGCTTTTT
1 CTTTCTTCTTGCTTTTT
1492492 CTT
1 CTT
1492495 GAAATCTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.00, C:0.25, G:0.03, T:0.72
Consensus pattern (17 bp):
CTTTCTTCTTGCTTTTT
Found at i:1494071 original size:18 final size:19
Alignment explanation
Indices: 1494030--1494074 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
1494020 GTTAAAAAGG
1494030 TTATTTTT-ATTTTGATTC
1 TTATTTTTCATTTTGATTC
* *
1494048 TCATTTTTCATTTTTATT-
1 TTATTTTTCATTTTGATTC
1494066 TTATTTTTC
1 TTATTTTTC
1494075 TTTAACTAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.73
Consensus pattern (19 bp):
TTATTTTTCATTTTGATTC
Found at i:1494563 original size:21 final size:21
Alignment explanation
Indices: 1494537--1494578 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1494527 CCATATGGCT
1494537 GTGTCCCTTGGGCACACGGGC
1 GTGTCCCTTGGGCACACGGGC
1494558 GTGTCCCTTGGGCACACGGGC
1 GTGTCCCTTGGGCACACGGGC
1494579 ACGTGAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.10, C:0.33, G:0.38, T:0.19
Consensus pattern (21 bp):
GTGTCCCTTGGGCACACGGGC
Found at i:1497880 original size:50 final size:50
Alignment explanation
Indices: 1497652--1497943 Score: 239
Period size: 50 Copynumber: 5.8 Consensus size: 50
1497642 GTAACCAAAG
* *
1497652 CTATCTGGTACGCATAGTAGCCTGA-ACTTAGTACTACACATGTGACC-AA
1 CTATCTGGTACACATAGTAGCCT-ACACTTAGTACTACACACGTGACCTAA
* * * * * *
1497701 CAATCTGGTACACGTAGTAGCTTGCACTTGGTACTACACACATGACCTAA
1 CTATCTGGTACACATAGTAGCCTACACTTAGTACTACACACGTGACCTAA
* * * ** * *
1497751 CCATCTGATACACGTAGTAGCCTGTACTTAGTACTACACACATGA-TTGAA
1 CTATCTGGTACACATAGTAGCCTACACTTAGTACTACACACGTGACCT-AA
* * * * * * * * *
1497801 GTTGTCGGGTACGCATAATAGCCTGCACTTAGTACTGCACATGCGACCTAA
1 -CTATCTGGTACACATAGTAGCCTACACTTAGTACTACACACGTGACCTAA
*
1497852 CTATCTGGTACACATAGTAGCCTACACTTAGTACTACAGACGTGACCTAAAA
1 CTATCTGGTACACATAGTAGCCTACACTTAGTACTACACACGTGACCT--AA
* *** * *
1497904 CCATCTTAAATACATAGTAGCCTACACATAGTACTACACA
1 CTATCTGGTACACATAGTAGCCTACACTTAGTACTACACA
1497944 TGTGTTCTCA
Statistics
Matches: 191, Mismatches: 45, Indels: 11
0.77 0.18 0.04
Matches are distributed among these distances:
49 39 0.20
50 82 0.43
51 34 0.18
52 36 0.19
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (50 bp):
CTATCTGGTACACATAGTAGCCTACACTTAGTACTACACACGTGACCTAA
Found at i:1497943 original size:151 final size:149
Alignment explanation
Indices: 1497658--1497945 Score: 371
Period size: 151 Copynumber: 1.9 Consensus size: 149
1497648 AAAGCTATCT
* * * *
1497658 GGTACGCATAGTAGCCTGAACTTAGTACTACACATGTGACCAACAATCTGGTACACGTAGTAGCT
1 GGTACGCATAATAGCCTGAACTTAGTACTACACATGCGACCAACAATCTGGTACACATAGTAGCC
* * * * ** *
1497723 TGCACTTGGTACTACACACATGACCTAACCATCTGATACACGTAGTAGCCTGTACTTAGTACTAC
66 TACACTTAGTACTACACACATGACCTAACCATCTGAAACACATAGTAGCCTACACATAGTACTA-
1497788 ACACATGATTGAAGTTGTCG
130 ACACATGATTGAAGTTGTCG
* * *
1497808 GGTACGCATAATAGCCTGCACTTAGTACTGCACATGCGACCTAACTATCTGGTACACATAGTAGC
1 GGTACGCATAATAGCCTGAACTTAGTACTACACATGCGACC-AACAATCTGGTACACATAGTAGC
* * * *
1497873 CTACACTTAGTACTACAGACGTGACCTAAAACCATCTTAAATACATAGTAGCCTACACATAGTAC
65 CTACACTTAGTACTACACACATGACCT--AACCATCTGAAACACATAGTAGCCTACACATAGTAC
1497938 T-ACACATG
128 TAACACATG
1497946 TGTTCTCACA
Statistics
Matches: 117, Mismatches: 18, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
150 37 0.32
151 50 0.43
153 30 0.26
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (149 bp):
GGTACGCATAATAGCCTGAACTTAGTACTACACATGCGACCAACAATCTGGTACACATAGTAGCC
TACACTTAGTACTACACACATGACCTAACCATCTGAAACACATAGTAGCCTACACATAGTACTAA
CACATGATTGAAGTTGTCG
Found at i:1504322 original size:20 final size:20
Alignment explanation
Indices: 1504294--1504337 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1504284 ACCAAATTTG
*
1504294 CAACTTACCATAATCTTTCA
1 CAACATACCATAATCTTTCA
*
1504314 CAACATACCATAGTCTTTCA
1 CAACATACCATAATCTTTCA
1504334 CAAC
1 CAAC
1504338 TTAAACCACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.02, T:0.30
Consensus pattern (20 bp):
CAACATACCATAATCTTTCA
Found at i:1504510 original size:41 final size:43
Alignment explanation
Indices: 1504402--1504518 Score: 139
Period size: 41 Copynumber: 2.8 Consensus size: 43
1504392 ATACCAATGA
* ** *
1504402 CATATCCCAAATATGGTCTTACATGGGATCTCATGTCAATGGC
1 CATATCCCAAATATGGTCTTACACGAAATCTCATATCAATGGC
* * **
1504445 AATAGCCCAGCTATGGTCTTACACGAAATCTCATATC-AT-GC
1 CATATCCCAAATATGGTCTTACACGAAATCTCATATCAATGGC
*
1504486 CATATCCCAAATATGGTCTTACACGTAATCTCA
1 CATATCCCAAATATGGTCTTACACGAAATCTCA
1504519 ACTAACCCTA
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
41 30 0.49
42 2 0.03
43 29 0.48
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.29
Consensus pattern (43 bp):
CATATCCCAAATATGGTCTTACACGAAATCTCATATCAATGGC
Found at i:1520727 original size:46 final size:46
Alignment explanation
Indices: 1520677--1520852 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
1520667 TGATTGAGCA
1520677 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
1520723 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* **
1520768 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACA
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
1520816 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1520853 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 64 0.58
47 28 0.25
48 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:1520833 original size:93 final size:93
Alignment explanation
Indices: 1520674--1520845 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
1520664 GGATGATTGA
***
1520674 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
1520739 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
1520767 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
1520832 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
1520846 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:1523284 original size:41 final size:41
Alignment explanation
Indices: 1523235--1523320 Score: 165
Period size: 41 Copynumber: 2.1 Consensus size: 41
1523225 TCGGCAGCCA
1523235 GTGT-AGGGAACTCGAGATTTGTTAAACCTGAGTGCCAGCG
1 GTGTGAGGGAACTCGAGATTTGTTAAACCTGAGTGCCAGCG
1523275 GTGTGAGGGAACTCGAGATTTGTTAAACCTGAGTGCCAGCG
1 GTGTGAGGGAACTCGAGATTTGTTAAACCTGAGTGCCAGCG
1523316 GTGTG
1 GTGTG
1523321 GTAGAAATCA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 4 0.09
41 41 0.91
ACGTcount: A:0.23, C:0.16, G:0.35, T:0.26
Consensus pattern (41 bp):
GTGTGAGGGAACTCGAGATTTGTTAAACCTGAGTGCCAGCG
Found at i:1527433 original size:67 final size:67
Alignment explanation
Indices: 1527325--1527460 Score: 263
Period size: 67 Copynumber: 2.0 Consensus size: 67
1527315 GGTCATTTAG
*
1527325 TTATTAAAATGACTTAAAAACAAAATTAAAAGCCAATTTTTGTCCATCTTCTTCATTAGGCCGAA
1 TTATTAAAATGAATTAAAAACAAAATTAAAAGCCAATTTTTGTCCATCTTCTTCATTAGGCCGAA
1527390 AT
66 AT
1527392 TTATTAAAATGAATTAAAAACAAAATTAAAAGCCAATTTTTGTCCATCTTCTTCATTAGGCCGAA
1 TTATTAAAATGAATTAAAAACAAAATTAAAAGCCAATTTTTGTCCATCTTCTTCATTAGGCCGAA
1527457 AT
66 AT
1527459 TT
1 TT
1527461 CAAGGGTTCT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.35
Consensus pattern (67 bp):
TTATTAAAATGAATTAAAAACAAAATTAAAAGCCAATTTTTGTCCATCTTCTTCATTAGGCCGAA
AT
Found at i:1528387 original size:46 final size:46
Alignment explanation
Indices: 1528337--1528512 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
1528327 TGATTGAGCA
1528337 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
1528383 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
1528428 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
1528476 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1528513 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 5 0.05
46 61 0.55
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:1528493 original size:93 final size:93
Alignment explanation
Indices: 1528334--1528505 Score: 310
Period size: 93 Copynumber: 1.8 Consensus size: 93
1528324 GGATGATTGA
*
1528334 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
1528399 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
1528427 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
1528491 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
1528506 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:1532560 original size:37 final size:35
Alignment explanation
Indices: 1532509--1532619 Score: 111
Period size: 37 Copynumber: 3.0 Consensus size: 35
1532499 ATTCCAAAAA
*
1532509 TAATATTATTTTAATAGTTTAATATTAAATTTAATT
1 TAATATTATCTTAATAGTTTAATATT-AATTTAATT
*
1532545 TAATACTTATCTTAATAGTATT-TTATTAATTTAATAT
1 TAATA-TTATCTTAATAGT-TTAATATTAATTTAAT-T
1532582 TAAAATGATTATCTTAATA-TTTAAT-TTAATTTAGATT
1 T--AAT-ATTATCTTAATAGTTTAATATTAATTTA-ATT
1532619 T
1 T
1532620 TATCTACAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 15
0.78 0.04 0.18
Matches are distributed among these distances:
36 13 0.20
37 30 0.47
38 6 0.09
39 14 0.22
40 1 0.02
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.54
Consensus pattern (35 bp):
TAATATTATCTTAATAGTTTAATATTAATTTAATT
Found at i:1537916 original size:26 final size:26
Alignment explanation
Indices: 1537880--1537939 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
1537870 GAAGCTCCGG
1537880 AGAGCCATTAATCAGGAAGCTCACAA
1 AGAGCCATTAATCAGGAAGCTCACAA
* * *
1537906 AGAGCCTTTAATTAGGAAGCTCACGA
1 AGAGCCATTAATCAGGAAGCTCACAA
1537932 AGAGCCAT
1 AGAGCCAT
1537940 ATATAGGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (26 bp):
AGAGCCATTAATCAGGAAGCTCACAA
Found at i:1539091 original size:46 final size:47
Alignment explanation
Indices: 1539035--1539156 Score: 138
Period size: 50 Copynumber: 2.6 Consensus size: 47
1539025 GGGTTGACAG
* *
1539035 GACAGAAATGAGTCATGTAAGTCCATATCAG-ATATATGGCTTTGGA
1 GACAGGAATGAGTCATGTAAGTCCATATCAGAATATATGGCATTGGA
* * *
1539081 GACAGGAATGAGCCATGTAAGCCCATATTAGATATATATATGGCATTGGA
1 GACAGGAATGAGTCATGTAAGTCCATATCAG--A-ATATATGGCATTGGA
* * *
1539131 GATAGGAATAATTCATGTAAGTCCAT
1 GACAGGAATGAGTCATGTAAGTCCAT
1539157 GTTGAAGACA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
46 27 0.44
50 35 0.56
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (47 bp):
GACAGGAATGAGTCATGTAAGTCCATATCAGAATATATGGCATTGGA
Found at i:1547861 original size:21 final size:20
Alignment explanation
Indices: 1547837--1547877 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1547827 TTTTTTAAAA
1547837 ATTTTATGAACTTTTTATTTT
1 ATTTTATGAA-TTTTTATTTT
* *
1547858 ATTTTTTTAATTTTTATTTT
1 ATTTTATGAATTTTTATTTT
1547878 TGAATATGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (20 bp):
ATTTTATGAATTTTTATTTT
Found at i:1551162 original size:46 final size:47
Alignment explanation
Indices: 1551092--1551213 Score: 142
Period size: 46 Copynumber: 2.6 Consensus size: 47
1551082 ATCTTCATAT
* * * *
1551092 ATCGATGCCATAGCCCGGCTATGGTCTTACACAAATCA-CATATCTCAC
1 ATCGATGCCATATCCCAGATATGGTCTTACAC-AAT-AGCATATATCAC
* *
1551140 -T-GATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCAC
1 ATCGATGCCATATCCCAGATATGGTCTTACACAATAGCATATATCAC
*
1551185 ATCGATGCCATATCCCAAATATGGTCTTA
1 ATCGATGCCATATCCCAGATATGGTCTTA
1551214 TACGGAAATC
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
44 1 0.02
45 11 0.17
46 26 0.41
47 26 0.41
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (47 bp):
ATCGATGCCATATCCCAGATATGGTCTTACACAATAGCATATATCAC
Found at i:1551195 original size:47 final size:48
Alignment explanation
Indices: 1551092--1551225 Score: 150
Period size: 47 Copynumber: 2.8 Consensus size: 48
1551082 ATCTTCATAT
* * * * *
1551092 ATCGATGCCATAGCCCGGCTATGGTCTTACACAAATCACATATCTCAC
1 ATCGATGCCATATCCCAGATATGGTCTTATACAAATCACATATATCAC
*
1551140 -T-GATGCCATATCCCAGATATGGTCTTATAC-AGT-AGCATATATCAC
1 ATCGATGCCATATCCCAGATATGGTCTTATACAAATCA-CATATATCAC
*
1551185 ATCGATGCCATATCCCAAATATGGTCTTATACGGAAATCAC
1 ATCGATGCCATATCCCAGATATGGTCTTATAC--AAATCAC
1551226 TTGTCACTTG
Statistics
Matches: 71, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
44 1 0.01
45 11 0.15
46 26 0.37
47 29 0.41
50 3 0.04
51 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (48 bp):
ATCGATGCCATATCCCAGATATGGTCTTATACAAATCACATATATCAC
Found at i:1551277 original size:31 final size:31
Alignment explanation
Indices: 1551242--1551422 Score: 231
Period size: 31 Copynumber: 5.8 Consensus size: 31
1551232 CTTGTCACTT
*
1551242 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* * * *
1551273 GTAGCCGGAGCTATCATTTTTTCACTAATCAG
1 GTAGCCGAAGCTACCA-CTTTTCACTGATCAG
*
1551305 GTAGCCGGAGCTACCACTTTTCACT-ATTCAG
1 GTAGCCGAAGCTACCACTTTTCACTGA-TCAG
*
1551336 GTAACCTGAA-CTACCACTTTTCACTGATCAG
1 GTAGCC-GAAGCTACCACTTTTCACTGATCAG
* *
1551367 GTAGCAGAAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
1551398 GTAGCTGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
1551423 TGTCATTTGT
Statistics
Matches: 131, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
30 4 0.03
31 97 0.74
32 30 0.23
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.29
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:1551508 original size:50 final size:51
Alignment explanation
Indices: 1551398--1551526 Score: 181
Period size: 50 Copynumber: 2.5 Consensus size: 51
1551388 CACTGATCAG
* * *
1551398 GTAGCTGAAGCTACCACTTTTCACTTGTCATTTGTCATTGATCAAATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAAATAAGT
* *
1551449 GTAGCCGAAGCTATCACTTATCACTT-TCACTTT-TCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCA-TTTGTCATTGATCAAATAAGT
*
1551499 GTAGTCGAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
1551527 TGCCATGGTC
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
50 43 0.61
51 27 0.39
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAAATAAGT
Found at i:1552564 original size:9 final size:9
Alignment explanation
Indices: 1552550--1552575 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1552540 CCCAAATTTC
1552550 ACAATTCAT
1 ACAATTCAT
1552559 ACAATTCAT
1 ACAATTCAT
1552568 ACAATTCA
1 ACAATTCA
1552576 GTCCTTGCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (9 bp):
ACAATTCAT
Found at i:1557350 original size:47 final size:45
Alignment explanation
Indices: 1557193--1557556 Score: 242
Period size: 47 Copynumber: 7.8 Consensus size: 45
1557183 GGGATATATT
* * *
1557193 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGC-TCTTATATATGCAT
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCATC---TCTGTG-AG
** * *
1557243 GCTAATGCATGTCCCAGACATGTCTTACACTAGCACAACTCT-T-A-
1 GCCGATGCATGTCCCAGACATGTCTTACACT-G-GCATCTCTGTGAG
* *
1557287 GCTGATGCATGTCCCAGACACGTCTTACACTGGCTATCTCTGTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGC-ATCTCTGT-GAG
* * *
1557334 GCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTCT-AA
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCA-TC-TCTGTGAG
* * * *
1557380 GCCGATGCCATGTCCCATACGTGGTATTACACTGGCTAT-TATAGT-ATG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGC-ATCTCT-GTGA-G
* * * *
1557428 GCTGATGCATGTGCCAGACATGTCTTACACTAGCACTCGTCTG-GAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCA-TC-TCTGTGAG
* * *
1557474 GCCGATGCCATGTCCCAGACATGGTCTTACATTGGC-TCTCATAATGTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCATCTC-T-GTGAG
*
1557522 GCCGAAGCATGTCCCAGACATGTCTTACACTGGCA
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCA
1557557 CACAAATCAC
Statistics
Matches: 251, Mismatches: 38, Indels: 53
0.73 0.11 0.15
Matches are distributed among these distances:
42 1 0.00
43 6 0.02
44 30 0.12
45 4 0.02
46 45 0.18
47 88 0.35
48 54 0.22
49 16 0.06
50 6 0.02
51 1 0.00
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (45 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCATCTCTGTGAG
Found at i:1557454 original size:94 final size:94
Alignment explanation
Indices: 1557193--1557557 Score: 411
Period size: 94 Copynumber: 3.9 Consensus size: 94
1557183 GGGATATATT
* **
1557193 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTTATA-TATGCATGCTAATGCATGTCC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATTATAGTATG---GCCGATGCATGTCC
* *
1557257 CAGACATGTCTTACACTAGCA--CAACTCTTA
63 CAGACATGTCTTACACTAGCACTCATCTCTAA
* * *
1557287 GCTGATG-CATGTCCCAGACA-CGTCTTACACTGGCTATCTCT-GTCGA-GGCCGATGCATGTCC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTAT-TATAGT--ATGGCCGATGCATGTCC
1557348 CAGACATGTCTTACACTAGCACTCATCTCTAA
63 CAGACATGTCTTACACTAGCACTCATCTCTAA
* * * * *
1557380 GCCGATGCCATGTCCCATACGTGGTATTACACTGGCTATTATAGTATGGCTGATGCATGTGCCAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATTATAGTATGGCCGATGCATGTCCCAG
* ** *
1557445 ACATGTCTTACACTAGCACTCGTCTGGAT
66 ACATGTCTTACACTAGCACTCATCTCTAA
* * * * * *
1557474 GCCGATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCATAATGTGGCCGAAGCATGTCCCAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATTATAGTATGGCCGATGCATGTCCCAG
*
1557539 ACATGTCTTACACTGGCAC
66 ACATGTCTTACACTAGCAC
1557558 ACAAATCACC
Statistics
Matches: 229, Mismatches: 32, Indels: 20
0.81 0.11 0.07
Matches are distributed among these distances:
91 33 0.14
92 15 0.07
93 30 0.13
94 133 0.58
95 18 0.08
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (94 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATTATAGTATGGCCGATGCATGTCCCAG
ACATGTCTTACACTAGCACTCATCTCTAA
Found at i:1564946 original size:47 final size:44
Alignment explanation
Indices: 1564836--1565145 Score: 240
Period size: 47 Copynumber: 6.7 Consensus size: 44
1564826 TACGCGTGCT
* *
1564836 GATGCATGTCCCAGACATGTCTTACACTAGCACAACTCT-TA-GCC
1 GATGCATGTCCCAGACATGTCTTACACT-G-GCATCTCTGTAGGCC
1564880 GATGCATGTCCCAGACATGTCTTACACTGGCTATCTCTGTCGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGC-ATCTCTGT--AGGCC
*
1564927 GATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTCTGTA--CC
1 GATGCATGTCCCAGACATGTCTTACACT-G---GCATCTCTGTAGGCC
* * *
1564973 GATGCCATGTCCCAGACATAGTCTTACACTGGCTAT-TATACTATGGCT
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGC-ATCTCT-GTA-GGCC
* * * *
1565021 GATGCATGTGCCAGACATGTCTTACACTAGC-CCT-TGGTTGGATGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCATCTCT-G-T--AGGCC
*
1565067 GATGCCATGTCCCAGACATGGTCTTACACTGGC-TCTCATAATATGGCC
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCATCTC-T-GTA-GGCC
* *
1565115 GAAGCATGTCCCAGGCATGTCTTACACTGGC
1 GATGCATGTCCCAGACATGTCTTACACTGGC
1565146 GCACAAATCA
Statistics
Matches: 219, Mismatches: 22, Indels: 48
0.76 0.08 0.17
Matches are distributed among these distances:
42 1 0.00
43 6 0.03
44 33 0.15
45 6 0.03
46 38 0.17
47 87 0.40
48 37 0.17
49 1 0.00
50 9 0.04
51 1 0.00
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (44 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCATCTCTGTAGGCC
Found at i:1565039 original size:141 final size:140
Alignment explanation
Indices: 1564784--1565145 Score: 348
Period size: 141 Copynumber: 2.6 Consensus size: 140
1564774 GGATATATTA
* * * * * *
1564784 CCGATGCCATGCCCCAAACATGGTCTTACACTGGCTCTCAT-ATACGCGTG-CTGATGCATGTCC
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATAATA----TGACCGAAGCATGTCC
* * * * * *
1564847 CAGACATGTCTTACACTAGC-A-CA-ACTCTTAGCCGATGCATGTCCCAGACATGTCTTACACTG
62 CAGACATGTCTTACACTGGCTATTATACT-ATGGCTGATGCATGTCCCAGACATGTCTTACACTA
*
1564909 GCTATCTCT-G-TCGAGG
126 GC--CCT-TGGTTCGAGG
* * *
1564925 CCGATG-CATGTCCCAGACAT-GTCTTACACTAGCACTCAT-CTCTGTACCGATGCCATGTCCCA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATAATATG-ACCGAAG-CATGTCCCA
*
1564987 GACATAGTCTTACACTGGCTATTATACTATGGCTGATGCATGTGCCAGACATGTCTTACACTAGC
64 GACAT-GTCTTACACTGGCTATTATACTATGGCTGATGCATGTCCCAGACATGTCTTACACTAGC
* *
1565052 CCTTGGTTGGATG
128 CCTTGGTTCGAGG
* * * *
1565065 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATATGGCCGAAGCATGTCCCAGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATAATATGACCGAAGCATGTCCCAGA
1565130 CATGTCTTACACTGGC
66 CATGTCTTACACTGGC
1565146 GCACAAATCA
Statistics
Matches: 185, Mismatches: 24, Indels: 25
0.79 0.10 0.11
Matches are distributed among these distances:
135 2 0.01
137 5 0.03
138 15 0.08
139 33 0.18
140 36 0.19
141 66 0.36
142 25 0.14
143 3 0.02
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (140 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATAATATGACCGAAGCATGTCCCAGA
CATGTCTTACACTGGCTATTATACTATGGCTGATGCATGTCCCAGACATGTCTTACACTAGCCCT
TGGTTCGAGG
Found at i:1565040 original size:94 final size:94
Alignment explanation
Indices: 1564782--1565142 Score: 400
Period size: 94 Copynumber: 3.9 Consensus size: 94
1564772 TGGGATATAT
* * * ** *
1564782 TACCGATGCCATGCCCCAAACATGGTCTTACACTGGCTCTCATATAC-GCGTGCTGATGCATGTC
1 TACCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATC-TATACTATG-GCCGATGCATGTC
*
1564846 CCAGACATGTCTTACACTAGCA-CAACTCT-
64 CCAGACATGTCTTACACTAGCACCATCTCTG
* * *
1564875 TAGCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTATCTCTGTCGA-GGCCGATGCATGTC
1 TA-CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCTAT-ACTATGGCCGATGCATGTC
1564937 CCAGACATGTCTTACACTAGCACTCATCTCTG
64 CCAGACATGTCTTACACTAGCAC-CATCTCTG
* * *
1564969 TACCGATGCCATGTCCCAGACATAGTCTTACACTGGCTAT-TATACTATGGCTGATGCATGTGCC
1 TACCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCTATACTATGGCCGATGCATGTCCC
* *
1565033 AGACATGTCTTACACTAGC-CCTTGGT-TGG
66 AGACATGTCTTACACTAGCACCAT-CTCT-G
* * * *
1565062 ATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC-ATAATATGGCCGAAGCATGTCC
1 -TACCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCTATACTATGGCCGATGCATGTCC
*
1565126 CAGGCATGTCTTACACT
65 CAGACATGTCTTACACT
1565143 GGCGCACAAA
Statistics
Matches: 232, Mismatches: 23, Indels: 25
0.83 0.08 0.09
Matches are distributed among these distances:
91 36 0.16
92 21 0.09
93 31 0.13
94 128 0.55
95 16 0.07
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (94 bp):
TACCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCTATACTATGGCCGATGCATGTCCC
AGACATGTCTTACACTAGCACCATCTCTG
Found at i:1575876 original size:7 final size:7
Alignment explanation
Indices: 1575864--1575889 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1575854 ATATGTAAGT
1575864 TTATATA
1 TTATATA
1575871 TTATATA
1 TTATATA
1575878 TTATATA
1 TTATATA
1575885 TTATA
1 TTATA
1575890 ATAATTAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TTATATA
Found at i:1579712 original size:26 final size:26
Alignment explanation
Indices: 1579683--1579790 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
1579673 TGGTACAAAT
1579683 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
1579709 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
1579735 TGATAATTGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
1579761 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
1579787 TGAT
1 TGAT
1579791 GGGCATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.32, C:0.07, G:0.23, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:1581494 original size:32 final size:27
Alignment explanation
Indices: 1581412--1581494 Score: 116
Period size: 27 Copynumber: 3.1 Consensus size: 27
1581402 AGGAAGCGTC
*
1581412 CTGGTGGCTATGCCACA-ATTATCTGAT
1 CTGGTGGCTCTGCCACATA-TATCTGAT
*
1581439 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACATATATCTGAT
1581466 CTGGTGGCTCTGCCACA-ATATCTGTAT
1 CTGGTGGCTCTGCCACATATATCTG-AT
1581493 CT
1 CT
1581495 AGTGACTTCG
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
26 7 0.14
27 43 0.84
28 1 0.02
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACATATATCTGAT
Found at i:1582135 original size:47 final size:47
Alignment explanation
Indices: 1582082--1582175 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
1582072 ACACGAAAAC
1582082 AGGCAAAGCTTCCGCAATGAAGATATTTTCCAAAATTAATCACTTTT
1 AGGCAAAGCTTCCGCAATGAAGATATTTTCCAAAATTAATCACTTTT
*
1582129 AGGCAAAGCTTTCGCAATGAAGATATTTTCCAAAATTAATCACTTTT
1 AGGCAAAGCTTCCGCAATGAAGATATTTTCCAAAATTAATCACTTTT
1582176 CCTAAAAAGG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (47 bp):
AGGCAAAGCTTCCGCAATGAAGATATTTTCCAAAATTAATCACTTTT
Found at i:1583042 original size:12 final size:12
Alignment explanation
Indices: 1583025--1583055 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1583015 ACTCGGGGAA
1583025 GAGGCCGTGGTC
1 GAGGCCGTGGTC
1583037 GAGGCCGTGGTC
1 GAGGCCGTGGTC
1583049 GAGGCCG
1 GAGGCCG
1583056 AGGTAGTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.10, C:0.26, G:0.52, T:0.13
Consensus pattern (12 bp):
GAGGCCGTGGTC
Found at i:1587890 original size:26 final size:26
Alignment explanation
Indices: 1587837--1587945 Score: 173
Period size: 26 Copynumber: 4.2 Consensus size: 26
1587827 TGGTACAAAT
1587837 TGATAATGGGTTAGGTAAAATGTTCCA
1 TGATAATGGGTTAGGT-AAATGTTCCA
* *
1587864 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
1587890 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
1587916 TGATAATGGTTTAGGTAAATGTTCTA
1 TGATAATGGGTTAGGTAAATGTTCCA
1587942 TGAT
1 TGAT
1587946 GGGCATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
26 61 0.80
27 15 0.20
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:1589607 original size:27 final size:26
Alignment explanation
Indices: 1589567--1589678 Score: 143
Period size: 27 Copynumber: 4.2 Consensus size: 26
1589557 AGGAAGCGTC
*
1589567 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
1589594 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
1589621 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* * *
1589649 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
1589675 CTGG
1 CTGG
1589679 CAGCCATGCT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 7 0.09
27 52 0.68
28 17 0.22
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:1589671 original size:54 final size:54
Alignment explanation
Indices: 1589567--1589678 Score: 172
Period size: 54 Copynumber: 2.1 Consensus size: 54
1589557 AGGAAGCGTC
*
1589567 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * *
1589621 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
1589675 CTGG
1 CTGG
1589679 CAGCCATGCT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
54 35 0.66
55 18 0.34
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:1591263 original size:51 final size:50
Alignment explanation
Indices: 1591077--1591321 Score: 282
Period size: 49 Copynumber: 4.9 Consensus size: 50
1591067 TAGCCGAAGC
* * *
1591077 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACA-
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACC-ACAT
* * *
1591127 -ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTCAC
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCACAT
* ** *
1591176 CATCTAATACACATAGTAGCCTGCACTTAGTACTACACACGTGATCACAGT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCACA-T
* * * * * *
1591227 TTTCGGGTACGCATAGTAGCCTGCACTTAGAACTACACATGAGACCA-AT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCACAT
*
1591276 TAT-TCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC
1 TATCT-GGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACC
1591322 TCACAATAGT
Statistics
Matches: 163, Mismatches: 28, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
48 2 0.01
49 80 0.49
50 44 0.27
51 37 0.23
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (50 bp):
TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCACAT
Found at i:1598327 original size:40 final size:40
Alignment explanation
Indices: 1598205--1598344 Score: 115
Period size: 40 Copynumber: 3.5 Consensus size: 40
1598195 GACTTCGAGT
* * * * *
1598205 CGATGAGACACTGGGTGTCAATTTACTACTTCAGATCAATT
1 CGATGAGACACTGGGTGTCAAATTATTACTTCAAAT-TATC
* * * **
1598246 CGATGAGGCACTGGGTGTC-AA-T-TTACTTCGATTTAGG
1 CGATGAGACACTGGGTGTCAAATTATTACTTCAAATTATC
* *
1598283 CGATGAGACATTGAGTGTCAAATTATTACTTCAAATTATC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCAAATTATC
* * *
1598323 CGATGAGGCATTGGGTGCCAAA
1 CGATGAGACACTGGGTGTCAAA
1598345 CTGGTGTGTT
Statistics
Matches: 77, Mismatches: 19, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
37 17 0.22
38 9 0.12
39 2 0.03
40 31 0.40
41 18 0.23
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.31
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAAATTATTACTTCAAATTATC
Found at i:1601823 original size:5 final size:5
Alignment explanation
Indices: 1601805--1601836 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
1601795 GGATTCGGTT
1601805 TTTTC TTCTTC TTTTC TTTTC TTTTC TTTTC T
1 TTTTC TT-TTC TTTTC TTTTC TTTTC TTTTC T
1601837 CTTCATCTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:1601833 original size:15 final size:16
Alignment explanation
Indices: 1601805--1601860 Score: 62
Period size: 15 Copynumber: 3.6 Consensus size: 16
1601795 GGATTCGGTT
1601805 TTTTCTTCTTCTTTTC
1 TTTTCTTCTTCTTTTC
1601821 TTTTCTT-TTCTTTTC
1 TTTTCTTCTTCTTTTC
* * *
1601836 TCTTCATCTAC-TTTC
1 TTTTCTTCTTCTTTTC
*
1601851 TCTTCTTCTT
1 TTTTCTTCTT
1601861 TTCCCCCATA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 25 0.74
16 9 0.26
ACGTcount: A:0.04, C:0.27, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTCTTCTTCTTTTC
Found at i:1607859 original size:40 final size:40
Alignment explanation
Indices: 1607799--1607982 Score: 239
Period size: 40 Copynumber: 4.6 Consensus size: 40
1607789 TATTCGAATG
*
1607799 ATATCCGGGCTAAG-TCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
* * *
1607839 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAG-TGACT
* * *
1607879 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
*
1607919 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
*
1607959 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
1607983 CTTGTGCGAG
Statistics
Matches: 126, Mismatches: 13, Indels: 10
0.85 0.09 0.07
Matches are distributed among these distances:
39 1 0.01
40 122 0.97
41 3 0.02
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
Found at i:1607932 original size:80 final size:80
Alignment explanation
Indices: 1607799--1607982 Score: 264
Period size: 80 Copynumber: 2.3 Consensus size: 80
1607789 TATTCGAATG
* * *
1607799 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGAT-CCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAG-TCCCGAAGGC
* *
1607863 ATTTGTGCGAGTTG-CT
65 ATTTATGCGAG-TGACC
* *
1607879 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATATCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAGTCCCGAAGGCA
*
1607944 TTTATGCTAGTGACC
66 TTTATGCGAGTGACC
1607959 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
1607983 CTTGTGCGAG
Statistics
Matches: 94, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
79 3 0.03
80 91 0.97
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAGTCCCGAAGGCA
TTTATGCGAGTGACC
Found at i:1613403 original size:37 final size:37
Alignment explanation
Indices: 1613353--1613431 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
1613343 TTATTACGAA
* *
1613353 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
1613390 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
1613427 GTCTT
1 GTCTT
1613432 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:1613628 original size:47 final size:47
Alignment explanation
Indices: 1613550--1614654 Score: 2012
Period size: 47 Copynumber: 23.5 Consensus size: 47
1613540 CCCTTCGGGA
* * * * * * * *
1613550 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
1613597 CATGTCACATATATACACTTTCACATTCATCACATCGACCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
1613644 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
1613691 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
1613738 CTTATCACATATATACACTCTCACATTCATCACATCGGCTATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
1613785 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1613832 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1613879 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1613926 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1613973 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1614020 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1614067 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1614114 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1614161 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1614208 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1614255 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1614302 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1614349 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1614396 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1614443 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1614490 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1614537 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1614584 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
1614631 CTTATCACACAGATACACTTTCAC
1 CTTATTACATATATACACTTTCAC
1614655 GTATGGGTTT
Statistics
Matches: 1033, Mismatches: 25, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 1033 1.00
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:1621123 original size:40 final size:40
Alignment explanation
Indices: 1621068--1621325 Score: 423
Period size: 40 Copynumber: 6.5 Consensus size: 40
1621058 CGGATGATAA
* *
1621068 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
1621108 CCGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1621148 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1621188 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
1621228 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
1621268 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
1621308 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
1621326 TACTTGGTTT
Statistics
Matches: 208, Mismatches: 8, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
39 17 0.08
40 190 0.91
41 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:1624664 original size:57 final size:58
Alignment explanation
Indices: 1624554--1624691 Score: 154
Period size: 57 Copynumber: 2.4 Consensus size: 58
1624544 ATTTTACAGC
* * * * * *
1624554 AGGATTACCAGTCTAGGCTAAATCCTATCTATAGCATATGCTCTAGAGAGCTTA-ATT
1 AGGATTACCCGTCCAGGCTAAATCCAATCTATAACATAAGCTCAAGAGAGCTTACATT
* * * *
1624611 TGGATTACCCGTCCAGGCTAAATCCAATTTATAACCTAAGCTCAAGAGGGCTTACATT
1 AGGATTACCCGTCCAGGCTAAATCCAATCTATAACATAAGCTCAAGAGAGCTTACATT
*
1624669 AGAATTACCCGTCC-GAGCTAAAT
1 AGGATTACCCGTCCAG-GCTAAAT
1624692 TCTATCTGCA
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
57 45 0.67
58 22 0.33
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.28
Consensus pattern (58 bp):
AGGATTACCCGTCCAGGCTAAATCCAATCTATAACATAAGCTCAAGAGAGCTTACATT
Found at i:1628753 original size:51 final size:50
Alignment explanation
Indices: 1628672--1628774 Score: 161
Period size: 51 Copynumber: 2.0 Consensus size: 50
1628662 AACTGACTCT
* *
1628672 TTCCCTCGGGGCCTACAACTGAAACCGAAAGACCATGGAGCAACAGATTA
1 TTCCCTCAGGGCCTACAACTAAAACCGAAAGACCATGGAGCAACAGATTA
* *
1628722 TNTCCCTCAGGGCCTACAACTAAAACTGAAAGACCATGGAGTAACAGATTA
1 T-TCCCTCAGGGCCTACAACTAAAACCGAAAGACCATGGAGCAACAGATTA
1628773 TT
1 TT
1628775 ACACCAAGTG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
50 2 0.04
51 46 0.96
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.19
Consensus pattern (50 bp):
TTCCCTCAGGGCCTACAACTAAAACCGAAAGACCATGGAGCAACAGATTA
Found at i:1632292 original size:47 final size:47
Alignment explanation
Indices: 1632238--1632431 Score: 289
Period size: 47 Copynumber: 4.1 Consensus size: 47
1632228 TTAGGATTTT
** *
1632238 ATGTGATGAATGTGAATGTGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1632285 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
1632332 ATGTGATGAATGTGAGCACGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * *
1632379 ATGTGGTGAATATGAACATGCATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1632426 ATGTGA
1 ATGTGA
1632432 AAAATGTATG
Statistics
Matches: 132, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 132 1.00
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:1632338 original size:22 final size:22
Alignment explanation
Indices: 1632267--1632338 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
1632257 GCATATATGA
1632267 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
* * *
1632289 GATGAATG-TGAACAT-GCATATATGT
1 GAT-AAGGCCG-A-ATGGC-CA-ATGT
1632314 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
1632336 GAT
1 GAT
1632339 GAATGTGAGC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 11 0.30
23 9 0.24
24 9 0.24
25 8 0.22
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (22 bp):
GATAAGGCCGAATGGCCAATGT
Found at i:1632559 original size:50 final size:49
Alignment explanation
Indices: 1632401--1632585 Score: 270
Period size: 48 Copynumber: 3.8 Consensus size: 49
1632391 TGAACATGCA
*
1632401 TATATGTGGTAAAGCCGAATGGCTAATGTGAAAA-ATGTATGAGAAATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAAATATGTATGAGATATG
*
1632449 TATATGTAGTAAAGCCGAATGGCTAATGTG-AAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAAATATGTATGAGATATG
* * *
1632497 CATATGTGGTAAAGCTGAATGG-TCAATGTGAAATATATATATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCT-AATGTGAAA-ATATGTATGAGATATG
*
1632547 TATATGTGGTAAAGCCGAATGGCTAGTGTG-AAATATGTA
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAAATATGTA
1632586 GGCAATGTGC
Statistics
Matches: 122, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
47 4 0.03
48 73 0.60
49 4 0.03
50 40 0.33
51 1 0.01
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.30
Consensus pattern (49 bp):
TATATGTGGTAAAGCCGAATGGCTAATGTGAAAATATGTATGAGATATG
Found at i:1632559 original size:98 final size:96
Alignment explanation
Indices: 1632402--1632585 Score: 289
Period size: 98 Copynumber: 1.9 Consensus size: 96
1632392 GAACATGCAT
*
1632402 ATATGTGGTAAAGCCGAATGGCTAATGTGAAAAATGTATGAGAAATGTATATGTAGTAAAGCCGA
1 ATATGTGGTAAAGCCGAATGGCTAATGTGAAAAATATATGAGAAATGTATATGTAGTAAAGCCGA
1632467 ATGGCTAATGTGAAATATGTATGAGATATGC
66 ATGGCTAATGTGAAATATGTATGAGATATGC
* * *
1632498 ATATGTGGTAAAGCTGAATGG-TCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGC
1 ATATGTGGTAAAGCCGAATGGCT-AATGTGAAA-A-ATATATGAGAAATGTATATGTAGTAAAGC
*
1632562 CGAATGGCTAGTGTGAAATATGTA
63 CGAATGGCTAATGTGAAATATGTA
1632586 GGCAATGTGC
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
95 1 0.01
96 29 0.36
97 1 0.01
98 49 0.61
ACGTcount: A:0.38, C:0.07, G:0.26, T:0.30
Consensus pattern (96 bp):
ATATGTGGTAAAGCCGAATGGCTAATGTGAAAAATATATGAGAAATGTATATGTAGTAAAGCCGA
ATGGCTAATGTGAAATATGTATGAGATATGC
Found at i:1632839 original size:37 final size:37
Alignment explanation
Indices: 1632731--1632839 Score: 173
Period size: 37 Copynumber: 2.9 Consensus size: 37
1632721 GGAAATATAT
* *
1632731 TCCGGGTAAGACCCGATGACTACATGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
*
1632768 TCCGGGTAAGACTCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
1632805 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
1632840 CGTCTGAGCT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:1639530 original size:7 final size:7
Alignment explanation
Indices: 1639518--1639547 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
1639508 ACCACAGCAA
1639518 TCAAATC
1 TCAAATC
1639525 TCAAATC
1 TCAAATC
1639532 TCAAATC
1 TCAAATC
1639539 TCAAATC
1 TCAAATC
1639546 TC
1 TC
1639548 CTACCCACCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.40, C:0.30, G:0.00, T:0.30
Consensus pattern (7 bp):
TCAAATC
Found at i:1640637 original size:14 final size:16
Alignment explanation
Indices: 1640607--1640638 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1640597 TAAAACCAAG
1640607 ATATCAAAAAATGAAA
1 ATATCAAAAAATGAAA
1640623 ATAT-AAAAAAT-AAA
1 ATATCAAAAAATGAAA
1640637 AT
1 AT
1640639 TTAATTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 7 0.44
16 4 0.25
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.22
Consensus pattern (16 bp):
ATATCAAAAAATGAAA
Found at i:1655662 original size:40 final size:39
Alignment explanation
Indices: 1655618--1655722 Score: 122
Period size: 39 Copynumber: 2.6 Consensus size: 39
1655608 AGTGACCATA
*
1655618 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGACTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
* *
1655658 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGACTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
1655696 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGACTAAG-CCCGAAGGCATTTG
1655723 AACGAGTAGC
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
38 2 0.03
39 32 0.55
40 24 0.41
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGACTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:1655679 original size:39 final size:40
Alignment explanation
Indices: 1655578--1655741 Score: 169
Period size: 40 Copynumber: 4.1 Consensus size: 40
1655568 TTGAATGATG
* *
1655578 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTATA
*
1655618 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-A
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTATA
*
1655657 TTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATA
* * **
1655697 ACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATA-CTATA
1655737 TCCGG
1 TCCGG
1655742 TTAAATTCCG
Statistics
Matches: 106, Mismatches: 10, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
39 36 0.34
40 59 0.56
41 10 0.09
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATA
Found at i:1655741 original size:79 final size:80
Alignment explanation
Indices: 1655578--1655728 Score: 191
Period size: 79 Copynumber: 1.9 Consensus size: 80
1655568 TTGAATGATG
*
1655578 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
**
1655643 GTGCGAGATACTAAT
66 GAACGAGATACTAAT
* * * * *
1655658 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCAT
1655720 TTGAACGAG
64 TTGAACGAG
1655729 TAGCTATATC
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
78 1 0.02
79 42 0.69
80 18 0.30
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
GAACGAGATACTAAT
Found at i:1661333 original size:50 final size:50
Alignment explanation
Indices: 1661215--1661489 Score: 268
Period size: 50 Copynumber: 5.5 Consensus size: 50
1661205 CTGTTACGCA
* * * *
1661215 TAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAAT-TCAGT-CATG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTGA-TACACG
* * *
1661264 TAGTAGCCTGCACTTAGTACTGCACGCGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTGATACACG
* * * * * * * *
1661314 TAATAGCCTGCACTTAGTACTACACACGTGATCGAAGCTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAA-CAATCTGATACACG
** * * *
1661365 TAGTAGCCCCCACTTAGTACTACACATGTAACCTAACAATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTGATACACG
* * *
1661415 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAA-AACTGTCTTAAACACA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAA---TCTGATACACG
*
1661467 TAGTAGCCTGCACATAGTACTAC
1 TAGTAGCCTGCACTTAGTACTAC
1661490 GCATGTGTTC
Statistics
Matches: 183, Mismatches: 37, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
49 38 0.21
50 78 0.43
51 38 0.21
52 29 0.16
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTGATACACG
Found at i:1661399 original size:101 final size:101
Alignment explanation
Indices: 1661264--1661445 Score: 283
Period size: 101 Copynumber: 1.8 Consensus size: 101
1661254 TTCAGTCATG
** * * * *
1661264 TAGTAGCCTGCACTTAGTACTGCACGCGTGACCTAACCATCTGATACACGTAATAGCCTGCACTT
1 TAGTAGCCCCCACTTAGTACTACACACGTAACCTAACAATCTGATACACGTAATAGCCTGCACTT
1661329 AGTACTACACACGTGATCGAAGCTATCGGGTACGCA
66 AGTACTACACACGTGATCGAAGCTATCGGGTACGCA
* * *
1661365 TAGTAGCCCCCACTTAGTACTACACATGTAACCTAACAATCTGGTACACGTAGTAGCCTGCACTT
1 TAGTAGCCCCCACTTAGTACTACACACGTAACCTAACAATCTGATACACGTAATAGCCTGCACTT
1661430 AGTACTACACACGTGA
66 AGTACTACACACGTGA
1661446 CCTAAAACTG
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
101 72 1.00
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (101 bp):
TAGTAGCCCCCACTTAGTACTACACACGTAACCTAACAATCTGATACACGTAATAGCCTGCACTT
AGTACTACACACGTGATCGAAGCTATCGGGTACGCA
Found at i:1669774 original size:27 final size:27
Alignment explanation
Indices: 1669744--1669834 Score: 121
Period size: 27 Copynumber: 3.4 Consensus size: 27
1669734 TTAGAATTTT
1669744 CCACAAAGGCTATT-TTTTCAGAGTTCG
1 CCACAAAGGCTATTATTTT-AGAGTTCG
*
1669771 CCACAAAGGCTATTATTTTATAGTTCG
1 CCACAAAGGCTATTATTTTAGAGTTCG
* * * *
1669798 CTACAAAGGCTGTTCTTTTAGAGTTCA
1 CCACAAAGGCTATTATTTTAGAGTTCG
1669825 CCACAAAGGC
1 CCACAAAGGC
1669835 CATTCCTTGT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
27 52 0.93
28 4 0.07
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.32
Consensus pattern (27 bp):
CCACAAAGGCTATTATTTTAGAGTTCG
Found at i:1672729 original size:2 final size:2
Alignment explanation
Indices: 1672722--1672746 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1672712 TCAAAACAAA
1672722 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
1672747 ATGATTCACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1673156 original size:20 final size:21
Alignment explanation
Indices: 1673122--1673161 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1673112 ACACACCAAC
1673122 TATATATATACAAAA-AATTG
1 TATATATATACAAAAGAATTG
* *
1673142 TATATATTTATAAAAGAATT
1 TATATATATACAAAAGAATT
1673162 TATTCATCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (21 bp):
TATATATATACAAAAGAATTG
Found at i:1675499 original size:22 final size:22
Alignment explanation
Indices: 1675446--1675504 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
1675436 TATGGATTGG
* *
1675446 TTTTTTAAATAATCATAGAAAA
1 TTTTTTAAAAAATTATAGAAAA
*** *
1675468 TTTAAAAAAAAATTATAGCAAA
1 TTTTTTAAAAAATTATAGAAAA
1675490 TTTTTT-AAAAATTAT
1 TTTTTTAAAAAATTAT
1675505 TGAGAATTAT
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
21 9 0.32
22 19 0.68
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (22 bp):
TTTTTTAAAAAATTATAGAAAA
Found at i:1675522 original size:31 final size:30
Alignment explanation
Indices: 1675478--1675535 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
1675468 TTTAAAAAAA
*
1675478 AATTATAGCAAATTTTTTAAAAATTATTGAG
1 AATTATAGCAAA-TTATTAAAAATTATTGAG
*
1675509 AATTATAAG-AAATTATTAATAATTATT
1 AATTAT-AGCAAATTATTAAAAATTATT
1675536 TTTTAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 13 0.54
31 9 0.38
32 2 0.08
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (30 bp):
AATTATAGCAAATTATTAAAAATTATTGAG
Found at i:1684271 original size:12 final size:13
Alignment explanation
Indices: 1684233--1684271 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
1684223 AAATATTTGA
1684233 CTTGTTCTTAATT
1 CTTGTTCTTAATT
*
1684246 ATGTGTTCTTAATT
1 CT-TGTTCTTAATT
1684260 CTTGTT-TTAATT
1 CTTGTTCTTAATT
1684272 TTCCAGGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 6 0.26
13 5 0.22
14 12 0.52
ACGTcount: A:0.18, C:0.10, G:0.10, T:0.62
Consensus pattern (13 bp):
CTTGTTCTTAATT
Found at i:1688458 original size:12 final size:12
Alignment explanation
Indices: 1688429--1688461 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1688419 TATAGTGAAT
1688429 ACAATAATAA-G
1 ACAATAATAATG
1688440 A-AATAATAATG
1 ACAATAATAATG
1688451 ACAATAATAAT
1 ACAATAATAAT
1688462 AAAAATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 8 0.40
11 3 0.15
12 9 0.45
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.24
Consensus pattern (12 bp):
ACAATAATAATG
Found at i:1690445 original size:94 final size:94
Alignment explanation
Indices: 1690283--1690900 Score: 623
Period size: 94 Copynumber: 6.6 Consensus size: 94
1690273 TAGTATCATG
* * * * * * * * * **
1690283 GCTTCATCTTGCTCCATTGCAA-TTTAAAGAAATAAGATTTGTTGTTGTAGTTTCATTTCAACTT
1 GCTTCATCTTGCTCCACTACAACTTTAAGGAGATAAGATTTGCTATGGTAGCTTCATTCCAACCC
*
1690347 ACTGCAACTTCAATGGTATAGGATTTGTA
66 ACTGCAACTTCAAGGGTATAGGATTTGTA
* * * * *
1690376 GCTTCATCTTGTTTCC-CTACAACTTTAAGAAGATAAGATTTGCTATTGTAGTTTCATTCCAATC
1 GCTTCATCTTG-CTCCACTACAACTTTAAGGAGATAAGATTTGCTATGGTAGCTTCATTCCAACC
* * * *
1690440 CACTGCAACTTTATGAGTATAGGATTTATA
65 CACTGCAACTTCAAGGGTATAGGATTTGTA
* * * **
1690470 GTTTCATCTTGCTCCACTACAACTTTAAGGAGATAAGATTCGCTATGATAGCTTCATTCTGACCC
1 GCTTCATCTTGCTCCACTACAACTTTAAGGAGATAAGATTTGCTATGGTAGCTTCATTCCAACCC
* * * *
1690535 ACTTCATCTTTAAGGGCATAGGATTTGTA
66 ACTGCAACTTCAAGGGTATAGGATTTGTA
* * * * * *
1690564 ACTTCATCTTGCTTCACTAGAACTTCAGGGAGATAAGATTTGCTATGGTAGCTTCATTCCGACCC
1 GCTTCATCTTGCTCCACTACAACTTTAAGGAGATAAGATTTGCTATGGTAGCTTCATTCCAACCC
* * * **
1690629 ACT-CAATTTGAAGGGCATAATATTTGTA
66 ACTGCAACTTCAAGGGTATAGGATTTGTA
* * * * * * * *
1690657 GTTTCATCTTACTCCACTGCAACTTTAGGGAGATAAAATTAGTTATGGTAGCTTCAAT-CAGACC
1 GCTTCATCTTGCTCCACTACAACTTTAAGGAGATAAGATTTGCTATGGTAGCTTCATTCCA-ACC
* * * *
1690721 TACTACAACTTCAGGGGTATATGATTTGTA
65 CACTGCAACTTCAAGGGTATAGGATTTGTA
* * *
1690751 GCTTCATCTTGCTCTACTATAACTTTAGGGAGATAAGATTTGCTATGGTAGCTTCATTCCAACCC
1 GCTTCATCTTGCTCCACTACAACTTTAAGGAGATAAGATTTGCTATGGTAGCTTCATTCCAACCC
* * *
1690816 ACTGGAACTTCAGGGGTATAGAATTTGTA
66 ACTGCAACTTCAAGGGTATAGGATTTGTA
* * * *
1690845 GCTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAGATTCGTTATGGTAGCTTCA
1 GCTTCATCTTGCTCCACTACAACTTTAAGGAGATAAGATTTGCTATGGTAGCTTCA
1690901 ATCTGACCTA
Statistics
Matches: 432, Mismatches: 87, Indels: 11
0.82 0.16 0.02
Matches are distributed among these distances:
92 1 0.00
93 91 0.21
94 338 0.78
95 2 0.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (94 bp):
GCTTCATCTTGCTCCACTACAACTTTAAGGAGATAAGATTTGCTATGGTAGCTTCATTCCAACCC
ACTGCAACTTCAAGGGTATAGGATTTGTA
Found at i:1690862 original size:44 final size:44
Alignment explanation
Indices: 1690726--1690871 Score: 109
Period size: 44 Copynumber: 3.2 Consensus size: 44
1690716 AGACCTACTA
* *
1690726 CAACTTCAGGGGTATATG-ATTTGTAGCTTCATCTTGCTCTACTA
1 CAACTTCAGGGGTATA-GAATTTGTAGCTTCATCTTGCTCCACTG
* * * ***
1690770 TAACTTTAGGGAG-ATAAGATTTGCTATGGTAGCTTCATTCCAAC-CCACTG
1 CAACTTCAGGG-GTAT-AGA-AT--T-T-GTAGCTTCA-TCTTGCTCCACTG
*
1690820 GAACTTCAGGGGTATAGAATTTGTAGCTTCATCTTGCTCCACTG
1 CAACTTCAGGGGTATAGAATTTGTAGCTTCATCTTGCTCCACTG
1690864 CAACTTCA
1 CAACTTCA
1690872 AGGAGATAAG
Statistics
Matches: 76, Mismatches: 15, Indels: 22
0.67 0.13 0.19
Matches are distributed among these distances:
43 3 0.04
44 34 0.45
45 3 0.04
46 2 0.03
48 2 0.03
49 5 0.07
50 24 0.32
51 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.34
Consensus pattern (44 bp):
CAACTTCAGGGGTATAGAATTTGTAGCTTCATCTTGCTCCACTG
Found at i:1694890 original size:77 final size:76
Alignment explanation
Indices: 1694803--1694956 Score: 299
Period size: 77 Copynumber: 2.0 Consensus size: 76
1694793 GTTTTCATAA
1694803 GAAACCCTTATAGGGACTATTTTGCAAAAGATGTAAATGTGTGGTAGAAATGAGGAAAATAATGA
1 GAAACCCTTATAGGGACTATTTTGCAAAAGATGTAAATGTGTGGTAGAAATGAGGAAAATAATGA
1694868 AAAATGTGGGTT
66 AAAA-GTGGGTT
1694880 GAAACCCTTATAGGGACTATTTTGCAAAAGATGTAAATGTGTGGTAGAAATGAGGAAAATAATGA
1 GAAACCCTTATAGGGACTATTTTGCAAAAGATGTAAATGTGTGGTAGAAATGAGGAAAATAATGA
1694945 AAAAGTGGGTT
66 AAAAGTGGGTT
1694956 G
1 G
1694957 CCATAAGAGA
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
76 8 0.10
77 69 0.90
ACGTcount: A:0.40, C:0.06, G:0.27, T:0.27
Consensus pattern (76 bp):
GAAACCCTTATAGGGACTATTTTGCAAAAGATGTAAATGTGTGGTAGAAATGAGGAAAATAATGA
AAAAGTGGGTT
Found at i:1707713 original size:22 final size:22
Alignment explanation
Indices: 1707672--1707713 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1707662 TTACAACATA
*
1707672 TTTTTCTTTTCATTTTTTTTGT
1 TTTTTCTTTTCATTTGTTTTGT
1707694 TTTTTCTTTATC-TTTGTTTT
1 TTTTTCTTT-TCATTTGTTTT
1707714 TTTATCCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.05, C:0.10, G:0.05, T:0.81
Consensus pattern (22 bp):
TTTTTCTTTTCATTTGTTTTGT
Found at i:1707969 original size:17 final size:18
Alignment explanation
Indices: 1707947--1707995 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
1707937 TTATTTTTGA
1707947 TTTATTTATTTGGTTT-T
1 TTTATTTATTTGGTTTAT
*
1707964 TTTATTTATTTGATTTAT
1 TTTATTTATTTGGTTTAT
*
1707982 TATTATTTTTTTGG
1 T-TTATTTATTTGG
1707996 GCTGAACGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 15 0.56
18 2 0.07
19 10 0.37
ACGTcount: A:0.16, C:0.00, G:0.10, T:0.73
Consensus pattern (18 bp):
TTTATTTATTTGGTTTAT
Found at i:1708620 original size:18 final size:18
Alignment explanation
Indices: 1708597--1708639 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
1708587 AAGGTACAAT
1708597 ATGATAATTCTAATTTTC
1 ATGATAATTCTAATTTTC
1708615 ATGATAATTCTAATTTTC
1 ATGATAATTCTAATTTTC
1708633 ATGATAA
1 ATGATAA
1708640 CGTGACCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (18 bp):
ATGATAATTCTAATTTTC
Found at i:1709209 original size:18 final size:18
Alignment explanation
Indices: 1709186--1709228 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
1709176 AAGGTACAAT
1709186 ATGATAATTCTAATTTTC
1 ATGATAATTCTAATTTTC
1709204 ATGATAATTCTAATTTTC
1 ATGATAATTCTAATTTTC
1709222 ATGATAA
1 ATGATAA
1709229 CGTGACCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (18 bp):
ATGATAATTCTAATTTTC
Found at i:1709501 original size:589 final size:588
Alignment explanation
Indices: 1708385--1709554 Score: 2331
Period size: 589 Copynumber: 2.0 Consensus size: 588
1708375 ACCTGAGCGG
1708385 TTCAAGCCCATTCGACTTAAACTTTCCCTTTGGTCACGGGCTGCCACTTCTTTGCGATTAAGAAG
1 TTCAAGCCCATTCGACTTAAACTTTCCCTTTGGTCACGGGCTGCCACTTCTTTGCGATTAAGAAG
1708450 CGTCACTGCAACAGTTTCTTACTCTTCAGGAGAAAATGAAATTGATGAGGGAATAAATGGCTGCA
66 CGTCACTGCAACAGTTTCTTACTCTTCAGGAGAAAATGAAATTGATGAGGGAATAAATGGCTGCA
1708515 CAAAGTGCACAATTTGAGCGACAGCAGACTTTCCAACAGGTGATATTGAAGTAGAATGAGAAACT
131 CAAAGTGCACAATTTGAGCGACAGCAGACTTTCCAACAGGTGATATTGAAGTAGAATGAGAAACT
1708580 TAATAGAAAGGTACAATATGATAATTCTAATTTTCATGATAATTCTAATTTTCATGATAACGTGA
196 TAATAGAAAGGTACAATATGATAATTCTAATTTTCATGATAATTCTAATTTTCATGATAACGTGA
1708645 CCATGCAAAATGAAGGTCTAGGCTTGAATGCAAAGAAATGACAGAACGAGTTGGATGCATTACAG
261 CCATGCAAAATGAAGGTCTAGGCTTGAATGCAAAGAAATGACAGAACGAGTTGGATGCATTACAG
1708710 CGAGATGTGAGGGCATTGCATCCTAAGTCTAGGGACATGGACTGGATTTTCTATTCTAACAATCC
326 CGAGATGTGAGGGCATTGCATCCTAAGTCTAGGGACATGGACTGGATTTTCTATTCTAACAATCC
1708775 GTTGGCCCCGGAGATAACAACAATAAGTCTATCACGTGATTTTAAGGTCCCAAAAGACATGTTCG
391 GTTGGCCCCGGAGATAACAACAATAAGTCTATCACGTGATTTTAAGGTCCCAAAAGACATGTTCG
1708840 AGTGTAGGAGAGACCCACAAGCCCACCTGATGTAATATAACAATTATATTAACGTATTGGGAGCT
456 AGTGTAGGAGAGACCCACAAGCCCACCTGATGTAATATAACAATTATATTAACGTATTGGGAGCT
1708905 TCGAACTTTACAAATTGTAAAGTTCTTTCCACAACACTTAAGGAAAGTATGAAGGATTGGTNTGG
521 TCGAACTTTACAAATTGTAAAGTTCTTTCCACAACACTTAAGGAAAGTATGAAGGATTGGT-TGG
1708970 GCGT
585 GCGT
1708974 TTCAAGCCCATTCGACTTAAACTTTCCCTTTGGTCACGGGCTGCCACTTCTTTGCGATTAAGAAG
1 TTCAAGCCCATTCGACTTAAACTTTCCCTTTGGTCACGGGCTGCCACTTCTTTGCGATTAAGAAG
1709039 CGTCACTGCAACAGTTTCTTACTCTTCAGGAGAAAATGAAATTGATGAGGGAATAAATGGCTGCA
66 CGTCACTGCAACAGTTTCTTACTCTTCAGGAGAAAATGAAATTGATGAGGGAATAAATGGCTGCA
1709104 CAAAGTGCACAATTTGAGCGACAGCAGACTTTCCAACAGGTGATATTGAAGTAGAATGAGAAACT
131 CAAAGTGCACAATTTGAGCGACAGCAGACTTTCCAACAGGTGATATTGAAGTAGAATGAGAAACT
1709169 TAATAGAAAGGTACAATATGATAATTCTAATTTTCATGATAATTCTAATTTTCATGATAACGTGA
196 TAATAGAAAGGTACAATATGATAATTCTAATTTTCATGATAATTCTAATTTTCATGATAACGTGA
1709234 CCATGCAAAATGAAGGTCTAGGCTTGAATGCAAAGAAATGACAGAACGAGTTGGATGCATTACAG
261 CCATGCAAAATGAAGGTCTAGGCTTGAATGCAAAGAAATGACAGAACGAGTTGGATGCATTACAG
1709299 CGAGATGTGAGGGCATTGCATCCTAAGTCTAGGGACATGGACTGGATTTTCTATTCTAACAATCC
326 CGAGATGTGAGGGCATTGCATCCTAAGTCTAGGGACATGGACTGGATTTTCTATTCTAACAATCC
1709364 GTTGGCCCCGGAGATAACAACAATAAGTCTATCACGTGATTTTAAGGTCCCAAAAGACATGTTCG
391 GTTGGCCCCGGAGATAACAACAATAAGTCTATCACGTGATTTTAAGGTCCCAAAAGACATGTTCG
1709429 AGTGTAGGAGAGACCCACAAGCCCACCTGATGTAATATAACAATTATATTAACGTATTGGGAGCT
456 AGTGTAGGAGAGACCCACAAGCCCACCTGATGTAATATAACAATTATATTAACGTATTGGGAGCT
1709494 TCGAACTTTACAAATTGTAAAGTTCTTTCCACAACACTTAAGGAAAGTATGAAGGATTGGT
521 TCGAACTTTACAAATTGTAAAGTTCTTTCCACAACACTTAAGGAAAGTATGAAGGATTGGT
1709555 ACTTGTCCCT
Statistics
Matches: 581, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
589 581 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (588 bp):
TTCAAGCCCATTCGACTTAAACTTTCCCTTTGGTCACGGGCTGCCACTTCTTTGCGATTAAGAAG
CGTCACTGCAACAGTTTCTTACTCTTCAGGAGAAAATGAAATTGATGAGGGAATAAATGGCTGCA
CAAAGTGCACAATTTGAGCGACAGCAGACTTTCCAACAGGTGATATTGAAGTAGAATGAGAAACT
TAATAGAAAGGTACAATATGATAATTCTAATTTTCATGATAATTCTAATTTTCATGATAACGTGA
CCATGCAAAATGAAGGTCTAGGCTTGAATGCAAAGAAATGACAGAACGAGTTGGATGCATTACAG
CGAGATGTGAGGGCATTGCATCCTAAGTCTAGGGACATGGACTGGATTTTCTATTCTAACAATCC
GTTGGCCCCGGAGATAACAACAATAAGTCTATCACGTGATTTTAAGGTCCCAAAAGACATGTTCG
AGTGTAGGAGAGACCCACAAGCCCACCTGATGTAATATAACAATTATATTAACGTATTGGGAGCT
TCGAACTTTACAAATTGTAAAGTTCTTTCCACAACACTTAAGGAAAGTATGAAGGATTGGTTGGG
CGT
Found at i:1716144 original size:20 final size:20
Alignment explanation
Indices: 1716092--1716135 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1716082 ACCATTTCAA
* * *
1716092 ATTTTCTTATTTTCCTTTGC
1 ATTTTATTACTTTCCATTGC
1716112 ATTTTATTACTTTCCATTGC
1 ATTTTATTACTTTCCATTGC
1716132 ATTT
1 ATTT
1716136 ACTTTCTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.18, G:0.05, T:0.61
Consensus pattern (20 bp):
ATTTTATTACTTTCCATTGC
Found at i:1720198 original size:56 final size:56
Alignment explanation
Indices: 1720107--1720286 Score: 290
Period size: 56 Copynumber: 3.2 Consensus size: 56
1720097 ACCATGGCAT
** * * *
1720107 CGATATATGTGTACGAGTAAGATCACGTTTCATACGTTGGCATCGATATGTAACTC
1 CGATATATGTGTGTGAGTAAGACCACGTTTTATACGTTGGCATCGATATGTGACTC
*
1720163 TGATATATGTGTGTGAGTAAGACCACGTTTTATACGTTGGCATCGATATGTGACTC
1 CGATATATGTGTGTGAGTAAGACCACGTTTTATACGTTGGCATCGATATGTGACTC
*
1720219 CGATATATGTGTGTGAGTAAGACCACG-TTTATACATTGGCATCGATATGTGACTC
1 CGATATATGTGTGTGAGTAAGACCACGTTTTATACGTTGGCATCGATATGTGACTC
1720274 CGATATATGTGTG
1 CGATATATGTGTG
1720287 CAAGTAAAAA
Statistics
Matches: 116, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
55 40 0.34
56 76 0.66
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.34
Consensus pattern (56 bp):
CGATATATGTGTGTGAGTAAGACCACGTTTTATACGTTGGCATCGATATGTGACTC
Found at i:1720315 original size:111 final size:111
Alignment explanation
Indices: 1720107--1720326 Score: 273
Period size: 111 Copynumber: 2.0 Consensus size: 111
1720097 ACCATGGCAT
* * *
1720107 CGATATATGTGTACGAGTAAGATCACGTTTCATACGTTGGCATCGATATGTAACTCTGATATATG
1 CGATATATGTGTACGAGTAAGACCACGTTTCATACATTGGCATCGATATGTAACTCCGATATATG
** * * * * *
1720172 TGTGTGAGTAAGACCACGTTTTATACGTTGGCATCGATATGTGACTC
66 TGTGCAAGTAAAACCAC-TCTGAGACGGTGGCATCGATATGTGACTC
** *
1720219 CGATATATGTGTGTGAGTAAGACCACGTTT-ATACATTGGCATCGATATGTGACTCCGATATATG
1 CGATATATGTGTACGAGTAAGACCACGTTTCATACATTGGCATCGATATGTAACTCCGATATATG
*
1720283 TGTGCAAGTAAAAACCTA-TCTGGGACGGTGGCATCGATATGTGA
66 TGTGCAAGT-AAAACC-ACTCTGAGACGGTGGCATCGATATGTGA
1720327 TTACATGTAA
Statistics
Matches: 92, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
111 59 0.64
112 32 0.35
113 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.32
Consensus pattern (111 bp):
CGATATATGTGTACGAGTAAGACCACGTTTCATACATTGGCATCGATATGTAACTCCGATATATG
TGTGCAAGTAAAACCACTCTGAGACGGTGGCATCGATATGTGACTC
Found at i:1721939 original size:21 final size:21
Alignment explanation
Indices: 1721898--1721939 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1721888 GAACTATAGA
* *
1721898 ATTGAAATATGTTAGTTTGAT
1 ATTGAAATATATTAGTATGAT
1721919 ATTGAAATTATATTAG-ATGAT
1 ATTGAAA-TATATTAGTATGAT
1721940 TAACTATGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (21 bp):
ATTGAAATATATTAGTATGAT
Found at i:1727853 original size:28 final size:28
Alignment explanation
Indices: 1727755--1727853 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
1727745 CATGAGATTG
* * **
1727755 GCACTAAGTGTGCGGGTTTAAATTGCATA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
*
1727784 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
1727812 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
1727840 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
1727854 GACTTACTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
28 46 0.73
29 17 0.27
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:1730148 original size:131 final size:131
Alignment explanation
Indices: 1729914--1730435 Score: 1008
Period size: 131 Copynumber: 4.0 Consensus size: 131
1729904 NNNNNNNNNN
1729914 CTCTCACCATTAGACCATTTGGAATGCTATCGAGTATTCATTAAGCCTCAAACATAAGGTGTAAT
1 CTCTCACCATTAGACCATTTGGAATGCTATCGAGTATTCATTAAGCCTCAAACATAAGGTGTAAT
1729979 GCCACATCCCAGACATGGTCTTACATTGGCTCATCCATCAAGTCGATGCCATGTCCCATACATGG
66 GCCACATCCCAGACATGGTCTTACATTGGCTCATCCATCAAGTCGATGCCATGTCCCATACATGG
1730044 T
131 T
1730045 CTCTCACCATTAGACCATTTGGAATGCTATCGAGTATTCATTAAGCCTCAAACATAAGGTGTAAT
1 CTCTCACCATTAGACCATTTGGAATGCTATCGAGTATTCATTAAGCCTCAAACATAAGGTGTAAT
1730110 GCCACATCCCAGACATGGTCTTACATTGGCTCATCCATCAAGTCGATGCCATGTCCCATACATGG
66 GCCACATCCCAGACATGGTCTTACATTGGCTCATCCATCAAGTCGATGCCATGTCCCATACATGG
1730175 T
131 T
*
1730176 CTCTCACCATTAGACCATTTGGAGTGCTATCGAGTATTCATTAAGCCTCAAACATAAGGTGTAAT
1 CTCTCACCATTAGACCATTTGGAATGCTATCGAGTATTCATTAAGCCTCAAACATAAGGTGTAAT
1730241 GCCACATCCCAGACATGGTCTTACATTGGCTCATCCATCAAGTCGATGCCATGTCCCATACATGG
66 GCCACATCCCAGACATGGTCTTACATTGGCTCATCCATCAAGTCGATGCCATGTCCCATACATGG
1730306 T
131 T
* *
1730307 CTCTCACCATTAGACCATTTGGAATGCTATCAAGTATTCATTAAGCCTCAAACATAAGGTGCAAT
1 CTCTCACCATTAGACCATTTGGAATGCTATCGAGTATTCATTAAGCCTCAAACATAAGGTGTAAT
*
1730372 GCCACATCCCAGACATGGTCTTACATTGGCTCATCCATCAAGTCGATGCCATGTTCCATACATG
66 GCCACATCCCAGACATGGTCTTACATTGGCTCATCCATCAAGTCGATGCCATGTCCCATACATG
1730436 ATCTTACACT
Statistics
Matches: 386, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
131 386 1.00
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (131 bp):
CTCTCACCATTAGACCATTTGGAATGCTATCGAGTATTCATTAAGCCTCAAACATAAGGTGTAAT
GCCACATCCCAGACATGGTCTTACATTGGCTCATCCATCAAGTCGATGCCATGTCCCATACATGG
T
Found at i:1730656 original size:46 final size:47
Alignment explanation
Indices: 1730470--1730720 Score: 187
Period size: 46 Copynumber: 5.3 Consensus size: 47
1730460 AGGCCGACAC
* * * *
1730470 CATGTCCCAAACATGGTCTTACATTGGCTCTTACATCTC-TGTGCCGATG
1 CATGTCCCAGACAT-GTCTTACACTAGCTC-TACATCTCAAG-GCCGATG
* * *
1730519 CCATGTCCCAGACATGGTCTTACACT-G-AC-ACATCTCGTA-GCTGATG
1 -CATGTCCCAGACAT-GTCTTACACTAGCTCTACATCTC-AAGGCCGATG
* *
1730565 CATGTCCCAGACATGTCTTACACTAGCT-TACATCTCGAGGTCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTACATCTCAAGGCCGATG
* * *
1730611 CATGTCCCAGACATGTCTTACGCTAGCTCT-CGTCTCAATGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTACATCTCAAGGCCGATG
* * * * * * *
1730657 CCATGACCTAGACATGGTCTTACACTGGCTCTTAGA-AT-ATGGTCGATG
1 -CATGTCCCAGACAT-GTCTTACACTAGCTC-TACATCTCAAGGCCGATG
1730705 CATGTCCCAGACATGT
1 CATGTCCCAGACATGT
1730721 AACACCCCTT
Statistics
Matches: 164, Mismatches: 26, Indels: 26
0.76 0.12 0.12
Matches are distributed among these distances:
44 10 0.06
45 16 0.10
46 66 0.40
47 25 0.15
48 21 0.13
49 3 0.02
50 23 0.14
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (47 bp):
CATGTCCCAGACATGTCTTACACTAGCTCTACATCTCAAGGCCGATG
Found at i:1737012 original size:28 final size:28
Alignment explanation
Indices: 1736944--1737067 Score: 151
Period size: 29 Copynumber: 4.4 Consensus size: 28
1736934 CATGAGATTG
* *
1736944 GCACTAAGTGTGCAGGTTTAAATT-TCATA
1 GCACTAAGTGTGCAAGTTT-GATTAT-ATA
1736973 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCAAGTTTGATTATATA
* * *
1737001 GCACTAACTGTGCGAGTTTGATTATGTAA
1 GCACTAAGTGTGCAAGTTTGATTATAT-A
*
1737030 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCAAGTTTGATTATATA
*
1737058 ACACTAAGTG
1 GCACTAAGTG
1737068 CGCGGACTTA
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
28 40 0.47
29 45 0.53
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.34
Consensus pattern (28 bp):
GCACTAAGTGTGCAAGTTTGATTATATA
Found at i:1739676 original size:9 final size:9
Alignment explanation
Indices: 1739647--1739676 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1739637 TGAATTTTAC
1739647 AATTCGAAT
1 AATTCGAAT
*
1739656 AACTCGAAT
1 AATTCGAAT
1739665 AATTCGAAT
1 AATTCGAAT
1739674 AAT
1 AAT
1739677 ATATTAGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:1739776 original size:20 final size:19
Alignment explanation
Indices: 1739745--1739817 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
1739735 CTCTCGAAAC
1739745 AAAAATTACAAAATAATTTT
1 AAAAATT-CAAAATAATTTT
*
1739765 CAAAAATTCAAAACAATTTT
1 -AAAAATTCAAAATAATTTT
* *
1739785 TAAAATT-AAAAAAATTTAT
1 AAAAATTCAAAATAATTT-T
1739804 AAAAATTTCAAAAT
1 AAAAA-TTCAAAAT
1739818 TTATATTTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
18 9 0.20
19 11 0.25
20 13 0.30
21 11 0.25
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:1739791 original size:19 final size:19
Alignment explanation
Indices: 1739746--1739807 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 19
1739736 TCTCGAAACA
* *
1739746 AAAATTACAAAATAATTTTCA
1 AAAATT-CAAAAAAATTTT-T
*
1739767 AAAATTCAAAACAATTTTT
1 AAAATTCAAAAAAATTTTT
*
1739786 AAAATT-AAAAAAATTTAT
1 AAAATTCAAAAAAATTTTT
1739804 AAAA
1 AAAA
1739808 ATTTCAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
18 14 0.38
19 6 0.16
20 11 0.30
21 6 0.16
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAATTCAAAAAAATTTTT
Found at i:1739808 original size:19 final size:19
Alignment explanation
Indices: 1739745--1739875 Score: 80
Period size: 19 Copynumber: 6.9 Consensus size: 19
1739735 CTCTCGAAAC
1739745 AAAAATTACAAAATAATTT-T
1 AAAAATTA-AAAA-AATTTAT
*
1739765 CAAAAATTCAAAACAATTT-T
1 -AAAAATT-AAAAAAATTTAT
*
1739785 TAAAATTAAAAAAATTTAT
1 AAAAATTAAAAAAATTTAT
**
1739804 AAAAATT-TCAAAATTTAT
1 AAAAATTAAAAAAATTTAT
*
1739822 ---ATTTAAAAAAA-TTAT
1 AAAAATTAAAAAAATTTAT
* *
1739837 AAAATTTTAAAAAAATCTA-
1 AAAA-ATTAAAAAAATTTAT
1739856 AAAATATATAAAAAAATTTA
1 AAAA-AT-TAAAAAAATTTA
1739876 AAATTTTATA
Statistics
Matches: 89, Mismatches: 12, Indels: 19
0.74 0.10 0.16
Matches are distributed among these distances:
15 7 0.08
16 4 0.04
18 19 0.21
19 29 0.33
20 19 0.21
21 10 0.11
22 1 0.01
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAATTAAAAAAATTTAT
Found at i:1739831 original size:24 final size:24
Alignment explanation
Indices: 1739798--1739843 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1739788 AATTAAAAAA
*
1739798 ATTTATAAAAATT-TCAAAATTTAT
1 ATTTAAAAAAATTAT-AAAATTTAT
1739822 ATTTAAAAAAATTATAAAATTT
1 ATTTAAAAAAATTATAAAATTT
1739844 TAAAAAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
ATTTAAAAAAATTATAAAATTTAT
Found at i:1739851 original size:20 final size:21
Alignment explanation
Indices: 1739786--1739888 Score: 78
Period size: 19 Copynumber: 5.0 Consensus size: 21
1739776 AACAATTTTT
* *
1739786 AAAATTAAAAAAATTTAT--A
1 AAAATTATAAAATTTTATAAA
1739805 AAAATT-TCAAAATTTATATTTAAA
1 AAAATTAT-AAAATTT-TA--TAAA
1739829 AAAATTATAAAA-TTT-TAAA
1 AAAATTATAAAATTTTATAAA
*
1739848 AAAATCTA-AAAA-TATATAAA
1 AAAAT-TATAAAATTTTATAAA
1739868 AAAATT-TAAAATTTTATAAA
1 AAAATTATAAAATTTTATAAA
1739888 A
1 A
1739889 TAATAATTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 21
0.73 0.04 0.22
Matches are distributed among these distances:
19 32 0.46
20 21 0.30
22 2 0.03
23 2 0.03
24 11 0.16
25 1 0.01
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAATTATAAAATTTTATAAA
Found at i:1739878 original size:19 final size:19
Alignment explanation
Indices: 1739820--1739888 Score: 79
Period size: 19 Copynumber: 3.6 Consensus size: 19
1739810 TTCAAAATTT
1739820 ATATTTAAAAAAATTATAAA
1 ATATTTAAAAAAATT-TAAA
*
1739840 AT-TTTAAAAAAATCTAAAA
1 ATATTTAAAAAAAT-TTAAA
*
1739859 ATATATAAAAAAATTTAAA
1 ATATTTAAAAAAATTTAAA
1739878 AT-TTTATAAAA
1 ATATTTA-AAAA
1739889 TAATAATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
18 3 0.07
19 26 0.62
20 13 0.31
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (19 bp):
ATATTTAAAAAAATTTAAA
Found at i:1742416 original size:3 final size:3
Alignment explanation
Indices: 1742410--1742450 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1742400 AATGGATTCT
1742410 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1742451 TTGGTTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1742745 original size:44 final size:44
Alignment explanation
Indices: 1742688--1742942 Score: 162
Period size: 44 Copynumber: 5.5 Consensus size: 44
1742678 TGCCCCATTG
* * * *
1742688 CAACTTTAAGGAGATAGGATTTGTGGCTTCATCTTGCTCCACTG
1 CAACTTTAGGGAGATAAGATTTGTAGCTTCATCTTGCTCCACTA
*
1742732 CATCTTTAGGGAGATAAGATTCGCCATGGTAGCTTCAATC-TGAC-CCACTA
1 CAACTTTAGGGAGATAAGATT-----T-GTAGCTTC-ATCTTG-CTCCACTA
* * *
1742782 CAACTTCAGGG-GTATAGGATTTGTAGCTTCATCTTGCTCTACTA
1 CAACTTTAGGGAG-ATAAGATTTGTAGCTTCATCTTGCTCCACTA
* *
1742826 CAACTTTAGGGAGATAAGATTAGCCATGGTAGCTTCAATC-TGACT-AACTG
1 CAACTTTAGGGAGATAAGATT-----T-GTAGCTTC-ATCTTG-CTCCACTA
* * * * *
1742876 CAACTTCAGGG-GTATAGGATTTGTAGCTTTATCTTGCACCATTA
1 CAACTTTAGGGAG-ATAAGATTTGTAGCTTCATCTTGCTCCACTA
*
1742920 CAACTTCAGGGAGATAAGATTTG
1 CAACTTTAGGGAGATAAGATTTG
1742943 CTATTGTAGC
Statistics
Matches: 166, Mismatches: 21, Indels: 48
0.71 0.09 0.20
Matches are distributed among these distances:
43 8 0.05
44 81 0.49
45 4 0.02
49 4 0.02
50 60 0.36
51 9 0.05
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (44 bp):
CAACTTTAGGGAGATAAGATTTGTAGCTTCATCTTGCTCCACTA
Found at i:1742811 original size:94 final size:94
Alignment explanation
Indices: 1742701--1742992 Score: 422
Period size: 94 Copynumber: 3.1 Consensus size: 94
1742691 CTTTAAGGAG
* * * *
1742701 ATAGGATTTGTGGCTTCATCTTGCTCCACTGCATCTTTAGGGAGATAAGATTCGCCATGGTAGCT
1 ATAGGATTTGTAGCTTCATCTTGCTCCACTACAACTTTAGGGAGATAAGATTAGCCATGGTAGCT
1742766 TCAATCTGACCCACTACAACTTCAGGGGT
66 TCAATCTGACCCACTACAACTTCAGGGGT
*
1742795 ATAGGATTTGTAGCTTCATCTTGCTCTACTACAACTTTAGGGAGATAAGATTAGCCATGGTAGCT
1 ATAGGATTTGTAGCTTCATCTTGCTCCACTACAACTTTAGGGAGATAAGATTAGCCATGGTAGCT
** *
1742860 TCAATCTGACTAACTGCAACTTCAGGGGT
66 TCAATCTGACCCACTACAACTTCAGGGGT
* * * * * * *
1742889 ATAGGATTTGTAGCTTTATCTTGCACCATTACAACTTCAGGGAGATAAGATTTGCTATTGTAGCT
1 ATAGGATTTGTAGCTTCATCTTGCTCCACTACAACTTTAGGGAGATAAGATTAGCCATGGTAGCT
** *
1742954 TCAATCCAACCCACTACAACTTCAGAGGT
66 TCAATCTGACCCACTACAACTTCAGGGGT
1742983 ATAGGATTTG
1 ATAGGATTTG
1742993 AGGACACTGA
Statistics
Matches: 176, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
94 176 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (94 bp):
ATAGGATTTGTAGCTTCATCTTGCTCCACTACAACTTTAGGGAGATAAGATTAGCCATGGTAGCT
TCAATCTGACCCACTACAACTTCAGGGGT
Found at i:1742881 original size:50 final size:49
Alignment explanation
Indices: 1742739--1742978 Score: 143
Period size: 50 Copynumber: 5.0 Consensus size: 49
1742729 CTGCATCTTT
**
1742739 AGGGAGATAAGATTCGCCATGGTAGCTTCAATCTGACCCACTACAACTTC
1 AGGGAGATAAGATT-GCCATGGTAGCTTCAATCTGACTAACTACAACTTC
* * *
1742789 AGGG-GTATAGGATT----T-GTAGCTTC-ATCTTG-CTCTACTACAACTTT
1 AGGGAG-ATAAGATTGCCATGGTAGCTTCAATC-TGACT-AACTACAACTTC
*
1742833 AGGGAGATAAGATTAGCCATGGTAGCTTCAATCTGACTAACTGCAACTTC
1 AGGGAGATAAGATT-GCCATGGTAGCTTCAATCTGACTAACTACAACTTC
* * * *
1742883 AGGG-GTATAGGATT----T-GTAGCTT-TATCTTGCAC-CATTACAACTTC
1 AGGGAG-ATAAGATTGCCATGGTAGCTTCAATC-TG-ACTAACTACAACTTC
* * ** **
1742927 AGGGAGATAAGATTTGCTATTGTAGCTTCAATCCAACCCACTACAACTTC
1 AGGGAGATAAGA-TTGCCATGGTAGCTTCAATCTGACTAACTACAACTTC
1742977 AG
1 AG
1742979 AGGTATAGGA
Statistics
Matches: 148, Mismatches: 18, Indels: 48
0.69 0.08 0.22
Matches are distributed among these distances:
43 7 0.05
44 58 0.39
45 8 0.05
49 6 0.04
50 61 0.41
51 8 0.05
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (49 bp):
AGGGAGATAAGATTGCCATGGTAGCTTCAATCTGACTAACTACAACTTC
Found at i:1759907 original size:40 final size:40
Alignment explanation
Indices: 1759809--1760111 Score: 405
Period size: 40 Copynumber: 7.6 Consensus size: 40
1759799 TCCTCGTTCA
* * * * *
1759809 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
1759848 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1759888 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1759928 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1759968 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
1760008 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
1760048 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
1760088 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
1760112 CAGCATTCAA
Statistics
Matches: 240, Mismatches: 20, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
39 37 0.15
40 195 0.81
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:1769600 original size:40 final size:39
Alignment explanation
Indices: 1769502--1769764 Score: 278
Period size: 40 Copynumber: 6.6 Consensus size: 39
1769492 TCCTCGTTCA
* * * *
1769502 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
1769541 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
1769580 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
1769620 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
1769660 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
1769700 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
1769741 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
1769765 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
39 40 0.20
40 145 0.74
41 12 0.06
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:1769724 original size:120 final size:119
Alignment explanation
Indices: 1769502--1769764 Score: 307
Period size: 120 Copynumber: 2.2 Consensus size: 119
1769492 TCCTCGTTCA
* * *
1769502 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
* * *
1769567 TAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAAC-TCGCAC
66 TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
* * * * *
1769620 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACATAACCCGG-
* * ** * *
1769685 ATTT-GTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
63 ATTTAATAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAATAACTTAGCAC
*
1769741 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
1769765 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 37 0.31
120 75 0.62
121 9 0.07
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
Found at i:1769773 original size:41 final size:41
Alignment explanation
Indices: 1769696--1769773 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
1769686 TTTGTATCTC
* * *
1769696 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
1769737 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
1769774 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:1773439 original size:50 final size:49
Alignment explanation
Indices: 1773326--1773497 Score: 186
Period size: 50 Copynumber: 3.4 Consensus size: 49
1773316 TATGCATAGC
* **
1773326 AGCCTGCACTTAGTACTACACATGTGACCAACAGTCTGGTACACGTAGT
1 AGCCTGCACTTAGTACTACACACGTGACCAACAGTCTAATACACGTAGT
* *
1773375 AGCCTGCACTTAGTACTACGCACGTGACCTCACCA-TCTAATACACGTAGT
1 AGCCTGCACTTAGTACTACACACGTGA-C-CAACAGTCTAATACACGTAGT
* *** * *
1773425 AGCCTGCACTTAGTACTACACACGTGATC-ACAGTTTTCGGGTACGCATAGT
1 AGCCTGCACTTAGTACTACACACGTGACCAACAG---TCTAATACACGTAGT
1773476 AGCCTGCACTTAGTACTACACA
1 AGCCTGCACTTAGTACTACACA
1773498 TGCGACCTCA
Statistics
Matches: 104, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
49 25 0.24
50 40 0.38
51 36 0.35
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (49 bp):
AGCCTGCACTTAGTACTACACACGTGACCAACAGTCTAATACACGTAGT
Found at i:1773505 original size:101 final size:99
Alignment explanation
Indices: 1773326--1773508 Score: 260
Period size: 101 Copynumber: 1.8 Consensus size: 99
1773316 TATGCATAGC
* * *
1773326 AGCCTGCACTTAGTACTACACATGTGACCAACAGTCTGGTACACGTAGTAGCCTGCACTTAGTAC
1 AGCCTGCACTTAGTACTACACACGTGACCAACAGTCGGGTACACATAGTAGCCTGCACTTAGTAC
* *
1773391 TACGCACGTGACCTCACCATCTAATACACGTAGT
66 TACACACGCGACCTCACCATCTAATACACGTAGT
* *
1773425 AGCCTGCACTTAGTACTACACACGTGATC-ACAGTTTTCGGGTACGCATAGTAGCCTGCACTTAG
1 AGCCTGCACTTAGTACTACACACGTGACCAACAG---TCGGGTACACATAGTAGCCTGCACTTAG
*
1773489 TACTACACATGCGACCTCAC
63 TACTACACACGCGACCTCAC
1773509 AATAGATCAT
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
98 4 0.05
99 27 0.37
101 42 0.58
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.25
Consensus pattern (99 bp):
AGCCTGCACTTAGTACTACACACGTGACCAACAGTCGGGTACACATAGTAGCCTGCACTTAGTAC
TACACACGCGACCTCACCATCTAATACACGTAGT
Found at i:1773838 original size:14 final size:16
Alignment explanation
Indices: 1773806--1773844 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
1773796 ATTTACATAA
*
1773806 CATATATCACATATTT
1 CATATATCACATATGT
1773822 CATATATCAC-T-TGT
1 CATATATCACATATGT
1773836 CATATATCA
1 CATATATCA
1773845 TCATTTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.50
15 1 0.05
16 10 0.45
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.41
Consensus pattern (16 bp):
CATATATCACATATGT
Found at i:1775743 original size:43 final size:43
Alignment explanation
Indices: 1775693--1775778 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
1775683 TATGTGATTC
* *
1775693 CGATATGTGTTTACAAGTCAGACC-CTGTCTGGGACAG-TGGCAT
1 CGATATGTGGTTACAAGTAAGACCAC-GTCTGGGAC-GTTGGCAT
*
1775736 CGATATGTGGTTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGATATGTGGTTACAAGTAAGACCACGTCTGGGACGTTGGCAT
1775779 TGTACCATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 1 0.03
43 36 0.95
44 1 0.03
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (43 bp):
CGATATGTGGTTACAAGTAAGACCACGTCTGGGACGTTGGCAT
Found at i:1783809 original size:43 final size:43
Alignment explanation
Indices: 1783746--1783831 Score: 115
Period size: 43 Copynumber: 2.0 Consensus size: 43
1783736 TATGTGATTC
*
1783746 CGATATGTGTTTACGAGTAAGACC-CTGTCTGGGACAG-TGGCAT
1 CGATATGTGGTTACGAGTAAGACCAC-GTCTGGGAC-GTTGGCAT
1783789 CGATATGTGGTTAC-ATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGATATGTGGTTACGA-GTAAGACCACGTCTGGGACGTTGGCAT
1783832 TGTACCATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
42 2 0.05
43 36 0.92
44 1 0.03
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (43 bp):
CGATATGTGGTTACGAGTAAGACCACGTCTGGGACGTTGGCAT
Found at i:1797463 original size:61 final size:61
Alignment explanation
Indices: 1797393--1797511 Score: 229
Period size: 61 Copynumber: 2.0 Consensus size: 61
1797383 TTACTTTAGG
1797393 CATTTATTTTTCTTGCAATTTAATTTAATTTTATTATTATTTATTAACTTAGTTTTTCTGC
1 CATTTATTTTTCTTGCAATTTAATTTAATTTTATTATTATTTATTAACTTAGTTTTTCTGC
*
1797454 CATTTATTTTTCTTGCAATTTAATTTAATTTTTTTATTATTTATTAACTTAGTTTTTC
1 CATTTATTTTTCTTGCAATTTAATTTAATTTTATTATTATTTATTAACTTAGTTTTTC
1797512 CTTCTCTTGG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.24, C:0.09, G:0.04, T:0.62
Consensus pattern (61 bp):
CATTTATTTTTCTTGCAATTTAATTTAATTTTATTATTATTTATTAACTTAGTTTTTCTGC
Found at i:1802657 original size:96 final size:96
Alignment explanation
Indices: 1802544--1802741 Score: 360
Period size: 96 Copynumber: 2.1 Consensus size: 96
1802534 TATTTTTAAT
*
1802544 TATCAATTTTGATTTTCCTTTATGAGTAATTATTATTCCTAATATCCCCTAAAAAGTTCCTAATT
1 TATCAATTTCGATTTTCCTTTATGAGTAATTATTATTCCTAATATCCCCTAAAAAGTTCCTAATT
1802609 TTATCACAGTTATATAGAGCTCTTAAGCTCA
66 TTATCACAGTTATATAGAGCTCTTAAGCTCA
*
1802640 TATCAATTTCGGTTTTCCTTTATGAGTAATTATTATTCCTAATATCCCCTAAAAAGTTCCTAATT
1 TATCAATTTCGATTTTCCTTTATGAGTAATTATTATTCCTAATATCCCCTAAAAAGTTCCTAATT
*
1802705 TTATCACAGTTATATAGATCTCTTAAGCTCA
66 TTATCACAGTTATATAGAGCTCTTAAGCTCA
1802736 TCATCA
1 T-ATCA
1802742 CATAGGAACT
Statistics
Matches: 98, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
96 94 0.96
97 4 0.04
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (96 bp):
TATCAATTTCGATTTTCCTTTATGAGTAATTATTATTCCTAATATCCCCTAAAAAGTTCCTAATT
TTATCACAGTTATATAGAGCTCTTAAGCTCA
Found at i:1805789 original size:40 final size:40
Alignment explanation
Indices: 1805662--1805792 Score: 156
Period size: 40 Copynumber: 3.3 Consensus size: 40
1805652 ACACTCTTTG
* *
1805662 TCTGGCGTGTTTCAGTTGGATTAGCTCTTATG-TGCTTCTG
1 TCTGGCGTGTTTCAATTGGATTAGCTCTTATGAT-CTTCTA
* * * *
1805702 TCTGGCGTGTTTCAAGTGGATTAGCTCTTATGAGCGTCTT
1 TCTGGCGTGTTTCAATTGGATTAGCTCTTATGATCTTCTA
* * *
1805742 TCCGGTGTGTTTCAATTGGATTAGCTCTTACGATCTTCTA
1 TCTGGCGTGTTTCAATTGGATTAGCTCTTATGATCTTCTA
*
1805782 TCTGGTGTGTT
1 TCTGGCGTGTT
1805793 CGATTTATCT
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
40 77 1.00
ACGTcount: A:0.13, C:0.18, G:0.26, T:0.44
Consensus pattern (40 bp):
TCTGGCGTGTTTCAATTGGATTAGCTCTTATGATCTTCTA
Found at i:1807938 original size:21 final size:19
Alignment explanation
Indices: 1807895--1807938 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
1807885 TTTCCTTTTG
**
1807895 CTTTCCCCCAAAGCATTAA
1 CTTTCCCCCAAAGCAAAAA
1807914 CTTTCCCCCAAATCGCAAAAA
1 CTTTCCCCCAAA--GCAAAAA
1807935 CTTT
1 CTTT
1807939 TTTTTTTCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.57
21 9 0.43
ACGTcount: A:0.32, C:0.36, G:0.05, T:0.27
Consensus pattern (19 bp):
CTTTCCCCCAAAGCAAAAA
Found at i:1808676 original size:12 final size:12
Alignment explanation
Indices: 1808661--1808722 Score: 54
Period size: 13 Copynumber: 4.9 Consensus size: 12
1808651 AGTTTAGTAT
1808661 TATTTTTAAAAG
1 TATTTTTAAAAG
*
1808673 TATTTTTAAAAAA
1 TATTTTT-AAAAG
*
1808686 TATTTTAAAAATG
1 TATTTTTAAAA-G
*
1808699 TGA-TTTTGAAAG
1 T-ATTTTTAAAAG
1808711 ATATTTTTAAAA
1 -TATTTTTAAAA
1808723 AGTTTGATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
12 13 0.33
13 25 0.64
14 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (12 bp):
TATTTTTAAAAG
Found at i:1808684 original size:13 final size:13
Alignment explanation
Indices: 1808661--1808725 Score: 64
Period size: 12 Copynumber: 5.1 Consensus size: 13
1808651 AGTTTAGTAT
1808661 TATTTTT-AAAAG
1 TATTTTTAAAAAG
*
1808673 TATTTTTAAAAAA
1 TATTTTTAAAAAG
1808686 TA-TTTTAAAAATG
1 TATTTTTAAAAA-G
* *
1808699 TGATTTTGAAAGA-
1 T-ATTTTTAAAAAG
1808712 TATTTTTAAAAAG
1 TATTTTTAAAAAG
1808725 T
1 T
1808726 TTGATTTAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
12 25 0.60
13 9 0.21
14 1 0.02
15 7 0.17
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.46
Consensus pattern (13 bp):
TATTTTTAAAAAG
Found at i:1808714 original size:26 final size:28
Alignment explanation
Indices: 1808661--1808736 Score: 74
Period size: 27 Copynumber: 2.9 Consensus size: 28
1808651 AGTTTAGTAT
*
1808661 TATTTTT-AAAAGTAT--TTTTAAAAAA
1 TATTTTTAAAAAGTGTGATTTTAAAAAA
* *
1808686 TA-TTTTAAAAA-TGTGATTTTGAAAGA
1 TATTTTTAAAAAGTGTGATTTTAAAAAA
*
1808712 TATTTTTAAAAAGTTTGA-TTTAAAA
1 TATTTTTAAAAAGTGTGATTTTAAAA
1808737 TTTAAATATT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
24 6 0.15
25 6 0.15
26 10 0.24
27 15 0.37
28 4 0.10
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.46
Consensus pattern (28 bp):
TATTTTTAAAAAGTGTGATTTTAAAAAA
Found at i:1820453 original size:19 final size:19
Alignment explanation
Indices: 1820429--1820469 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
1820419 AATTTAATTA
1820429 AATTCAATATTTAATTTTT
1 AATTCAATATTTAATTTTT
1820448 AATTCAATATTTAATTTTT
1 AATTCAATATTTAATTTTT
1820467 AAT
1 AAT
1820470 GATATACTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (19 bp):
AATTCAATATTTAATTTTT
Found at i:1820582 original size:15 final size:14
Alignment explanation
Indices: 1820548--1820586 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1820538 TTGACAACAA
* *
1820548 TTATTTTTCAGTAT
1 TTATTTTTTAATAT
1820562 TTATTTTTTAATAT
1 TTATTTTTTAATAT
1820576 TTAATTTTTTA
1 TT-ATTTTTTA
1820587 GTTTATCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (14 bp):
TTATTTTTTAATAT
Found at i:1831447 original size:3 final size:3
Alignment explanation
Indices: 1831433--1831514 Score: 85
Period size: 3 Copynumber: 27.3 Consensus size: 3
1831423 TAAGCAAATA
** *
1831433 AAT AAGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT CCT AGT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
1831479 AGT AAT AAA AAT -AT AAT AGT AAT GAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1831515 TAAAAAATAT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
2 2 0.03
3 61 0.92
4 3 0.05
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1831601 original size:17 final size:16
Alignment explanation
Indices: 1831569--1831630 Score: 58
Period size: 17 Copynumber: 3.8 Consensus size: 16
1831559 ATACATGGAG
*
1831569 ATATAATATAT-A-AA
1 ATATAATAGATAAGAA
1831583 ATATAATA-ATAACTGAA
1 ATATAATAGATAA--GAA
1831600 ATATAAATAGATAAGAA
1 ATAT-AATAGATAAGAA
1831617 ATATAAATAGATAA
1 ATAT-AATAGATAA
1831631 ATAAATAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
13 2 0.05
14 9 0.21
17 23 0.55
18 4 0.10
19 4 0.10
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (16 bp):
ATATAATAGATAAGAA
Found at i:1831630 original size:25 final size:23
Alignment explanation
Indices: 1831602--1831667 Score: 70
Period size: 19 Copynumber: 3.0 Consensus size: 23
1831592 TAACTGAAAT
1831602 ATAAATAGATAAGAAATATAAATAG
1 ATAAATA-ATAAGAAA-ATAAATAG
1831627 ATAAATAA-ATA-AAAAT---TAG
1 ATAAATAATA-AGAAAATAAATAG
1831646 ATAAATAATAAGAAAATAAATA
1 ATAAATAATAAGAAAATAAATA
1831668 TCGATGAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
19 12 0.34
20 6 0.17
22 2 0.06
23 6 0.17
24 2 0.06
25 7 0.20
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (23 bp):
ATAAATAATAAGAAAATAAATAG
Done.