Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009633.1 Hibiscus syriacus cultivar Beakdansim tig00117032_pilon, whole genome shotgun sequence
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: 2608659
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 13
Found at i:1231357 original size:26 final size:26
Alignment explanation
Indices: 1231327--1231380 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
1231317 CATTTCAAGC
*
1231327 CTATTTTTTATTCAATATTCATTTTG
1 CTATTTTTCATTCAATATTCATTTTG
1231353 CTATTTTTCATTCAATATTCATTTTG
1 CTATTTTTCATTCAATATTCATTTTG
1231379 CT
1 CT
1231381 TTCAAGAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.22, C:0.15, G:0.04, T:0.59
Consensus pattern (26 bp):
CTATTTTTCATTCAATATTCATTTTG
Found at i:1243864 original size:17 final size:17
Alignment explanation
Indices: 1243842--1243876 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1243832 TGATTAAGCG
*
1243842 TTGAATGATTCAATGGC
1 TTGAATGATTCAAAGGC
1243859 TTGAATGATTCAAAGGC
1 TTGAATGATTCAAAGGC
1243876 T
1 T
1243877 CTGTATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.34
Consensus pattern (17 bp):
TTGAATGATTCAAAGGC
Found at i:1258897 original size:35 final size:33
Alignment explanation
Indices: 1258858--1258942 Score: 82
Period size: 35 Copynumber: 2.5 Consensus size: 33
1258848 GTATTTCAGT
*
1258858 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTT-A-A-CACTTATTG
*
1258893 TAATTTGGTTATCATTTACCATTTAACACTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAACACTTATTG
* *
1258928 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
1258943 TAAAATTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 26 0.62
36 2 0.05
37 2 0.05
38 9 0.21
ACGTcount: A:0.27, C:0.09, G:0.11, T:0.53
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAACACTTATTG
Found at i:1262554 original size:42 final size:42
Alignment explanation
Indices: 1262501--1262600 Score: 173
Period size: 42 Copynumber: 2.4 Consensus size: 42
1262491 CGCGGCGGTA
*
1262501 CCTGCCCCGCGCTATATATAATTATAAAGGTCAGGCACGACC
1 CCTGACCCGCGCTATATATAATTATAAAGGTCAGGCACGACC
* *
1262543 CTTGACCCGCGCTATATATAATTATAAAGGTCAGGCACGGCC
1 CCTGACCCGCGCTATATATAATTATAAAGGTCAGGCACGACC
1262585 CCTGACCCGCGCTATA
1 CCTGACCCGCGCTATA
1262601 CCCTACGTGG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.22
Consensus pattern (42 bp):
CCTGACCCGCGCTATATATAATTATAAAGGTCAGGCACGACC
Found at i:1264565 original size:2 final size:2
Alignment explanation
Indices: 1264558--1264585 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1264548 GAATTCAAAG
1264558 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1264586 CCGATAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1267199 original size:21 final size:21
Alignment explanation
Indices: 1267175--1267216 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1267165 TTATCTGATT
*
1267175 ACTGTCACTTGCCACCAGAAA
1 ACTGTCACTTCCCACCAGAAA
1267196 ACTGTCACTTCCCACCAGAAA
1 ACTGTCACTTCCCACCAGAAA
1267217 GCTAAAAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.36, G:0.12, T:0.19
Consensus pattern (21 bp):
ACTGTCACTTCCCACCAGAAA
Found at i:1271424 original size:34 final size:36
Alignment explanation
Indices: 1271380--1271454 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 36
1271370 AAAATACTTC
*
1271380 AATTTAGGG-TTTAGAATATAATTAAAGTATTTTGG
1 AATTTAGGGTTTTAGAATATAATTAAAGTATTTTGA
* * *
1271415 AATTT-GGGTTTTAGAATGTAATTGAAGTGTTTTGA
1 AATTTAGGGTTTTAGAATATAATTAAAGTATTTTGA
1271450 AATTT
1 AATTT
1271455 TGAACATGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 3 0.09
35 32 0.91
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.45
Consensus pattern (36 bp):
AATTTAGGGTTTTAGAATATAATTAAAGTATTTTGA
Found at i:1274584 original size:19 final size:19
Alignment explanation
Indices: 1274528--1274584 Score: 51
Period size: 22 Copynumber: 2.8 Consensus size: 19
1274518 CTGTTATTTG
** *
1274528 ATTAGTTAGGCTGTTGTTA
1 ATTAGTTAGATTGTTATTA
*
1274547 ATTACTTAGATTGCAGTTATTA
1 ATTAGTTAGATT---GTTATTA
1274569 ATTAGTTAGATTGTTA
1 ATTAGTTAGATTGTTA
1274585 GTTAGGCTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
19 13 0.43
22 17 0.57
ACGTcount: A:0.28, C:0.05, G:0.19, T:0.47
Consensus pattern (19 bp):
ATTAGTTAGATTGTTATTA
Found at i:1274782 original size:13 final size:13
Alignment explanation
Indices: 1274764--1274788 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1274754 ATTTTAGGGA
1274764 TTTCTCTTCTCCT
1 TTTCTCTTCTCCT
1274777 TTTCTCTTCTCC
1 TTTCTCTTCTCC
1274789 ACAGCAGCCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTCTCTTCTCCT
Found at i:1283233 original size:30 final size:31
Alignment explanation
Indices: 1283167--1283238 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
1283157 ATTAAACCCG
1283167 TCCCCGTTTAACATAAACGATTTTTCTCCAA
1 TCCCCGTTTAACATAAACGATTTTTCTCCAA
** * *
1283198 TCCCCGTTTAGTATAAACTATTTTT-TCCCA
1 TCCCCGTTTAACATAAACGATTTTTCTCCAA
1283228 TCCCCGTTTAA
1 TCCCCGTTTAA
1283239 TTCAATTTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 14 0.39
31 22 0.61
ACGTcount: A:0.25, C:0.29, G:0.07, T:0.39
Consensus pattern (31 bp):
TCCCCGTTTAACATAAACGATTTTTCTCCAA
Found at i:1284123 original size:26 final size:25
Alignment explanation
Indices: 1284053--1284123 Score: 65
Period size: 26 Copynumber: 2.8 Consensus size: 25
1284043 TGAATAGATC
*
1284053 AAAGAAAAAATGTAGA-AAATAAAAA
1 AAAGAAAAAA-ATAGATAAATAAAAA
*
1284078 AAAGAAAAATAATCA-TTAAATCAAAAA
1 AAAGAAAAA-AAT-AGATAAAT-AAAAA
*
1284105 AAGGAAAAAAATAGATAAA
1 AAAGAAAAAAATAGATAAA
1284124 ATAGAGAGGA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
25 11 0.30
26 13 0.35
27 13 0.35
ACGTcount: A:0.73, C:0.03, G:0.10, T:0.14
Consensus pattern (25 bp):
AAAGAAAAAAATAGATAAATAAAAA
Found at i:1284125 original size:27 final size:26
Alignment explanation
Indices: 1284068--1284126 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
1284058 AAAAATGTAG
1284068 AAAATAAAAAAAAGAAAAATAATCAT
1 AAAATAAAAAAAAGAAAAATAATCAT
* * *
1284094 TAAATCAAAAAAAGGAAAAA-AATAGAT
1 AAAAT-AAAAAAAAGAAAAATAAT-CAT
1284121 AAAATA
1 AAAATA
1284127 GAGAGGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
26 8 0.30
27 19 0.70
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (26 bp):
AAAATAAAAAAAAGAAAAATAATCAT
Found at i:1284635 original size:12 final size:12
Alignment explanation
Indices: 1284618--1284648 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1284608 GGTGGCCTCT
1284618 CCACCGCGCCGG
1 CCACCGCGCCGG
*
1284630 CCACCGTGCCGG
1 CCACCGCGCCGG
1284642 CCACCGC
1 CCACCGC
1284649 CGGCGGTGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.58, G:0.29, T:0.03
Consensus pattern (12 bp):
CCACCGCGCCGG
Found at i:1285274 original size:16 final size:15
Alignment explanation
Indices: 1285248--1285278 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1285238 ATGTATGACC
1285248 GGTCATCCCGGGATG
1 GGTCATCCCGGGATG
1285263 GGTCAGTCCCGGGATG
1 GGTCA-TCCCGGGATG
1285279 CCGGCCGGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.13, C:0.26, G:0.42, T:0.19
Consensus pattern (15 bp):
GGTCATCCCGGGATG
Found at i:1285457 original size:4 final size:4
Alignment explanation
Indices: 1285426--1285485 Score: 59
Period size: 4 Copynumber: 15.0 Consensus size: 4
1285416 GACCTGAAAC
* * **
1285426 AAAT -AAT AAAT AAGT AAAT GAAAA AAAT AAAT AAAT AAAT AAAT GGAT
1 AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT
*
1285474 AAAT TAAT AAAT
1 AAAT AAAT AAAT
1285486 TAATTAAAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
3 3 0.07
4 38 0.86
5 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:1285468 original size:25 final size:24
Alignment explanation
Indices: 1285420--1285485 Score: 78
Period size: 25 Copynumber: 2.7 Consensus size: 24
1285410 ATCCTGGACC
* *
1285420 TGAAACAAATAATAAATAAGTAAA
1 TGAAAAAAATAATAAATAAATAAA
1285444 TGAAAAAAATAAATAAATAAATAAA
1 TGAAAAAAAT-AATAAATAAATAAA
* * *
1285469 TGGATAAATTAATAAAT
1 TGAAAAAAATAATAAAT
1285486 TAATTAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
24 16 0.44
25 20 0.56
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.24
Consensus pattern (24 bp):
TGAAAAAAATAATAAATAAATAAA
Found at i:1285574 original size:35 final size:35
Alignment explanation
Indices: 1285489--1285695 Score: 274
Period size: 35 Copynumber: 5.8 Consensus size: 35
1285479 AATAAATTAA
* *
1285489 TTAAAAAC--ATTTTTAAAACTATACAATATATACTT
1 TTAAAAACTAATTTTCAAAACTATATAATATAT--TT
*
1285524 TTAAAAAAAATAATTTTCAAAACTATATAATATATTT
1 TT--AAAAACTAATTTTCAAAACTATATAATATATTT
1285561 TTAAAAACTAATTTTCAAAACTATATAATATATTT
1 TTAAAAACTAATTTTCAAAACTATATAATATATTT
1285596 TTAAAAACTAATTTTCAAAACTATATAATATATATATT
1 TTAAAAACTAATTTTCAAAACTATAT-A-ATATAT-TT
* *
1285634 TTAAAAACTAATTTTCAAAATTATATAATATATAT
1 TTAAAAACTAATTTTCAAAACTATATAATATATTT
* *
1285669 TTAGAAACTAATTTTCAAAATTATATA
1 TTAAAAACTAATTTTCAAAACTATATA
1285696 TACGTTTTTT
Statistics
Matches: 158, Mismatches: 7, Indels: 14
0.88 0.04 0.08
Matches are distributed among these distances:
35 87 0.55
36 7 0.04
37 16 0.10
38 27 0.17
39 21 0.13
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (35 bp):
TTAAAAACTAATTTTCAAAACTATATAATATATTT
Found at i:1285580 original size:13 final size:13
Alignment explanation
Indices: 1285559--1285653 Score: 51
Period size: 13 Copynumber: 7.6 Consensus size: 13
1285549 TATAATATAT
1285559 TTTTAAAAACTAA
1 TTTTAAAAACTAA
*
1285572 TTTTCAAAACT-A
1 TTTTAAAAACTAA
* * *
1285584 -TAT-AATA-TAT
1 TTTTAAAAACTAA
1285594 TTTTAAAAACTAA
1 TTTTAAAAACTAA
*
1285607 TTTTCAAAACT-A
1 TTTTAAAAACTAA
* *
1285619 -TATAATATA-TATA
1 TTTTAA-AAACTA-A
1285632 TTTTAAAAACTAA
1 TTTTAAAAACTAA
1285645 TTTTCAAAA
1 TTTT-AAAA
1285654 TTATATAATA
Statistics
Matches: 59, Mismatches: 13, Indels: 19
0.65 0.14 0.21
Matches are distributed among these distances:
9 1 0.02
10 3 0.05
11 8 0.14
12 7 0.12
13 30 0.51
14 10 0.17
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.42
Consensus pattern (13 bp):
TTTTAAAAACTAA
Found at i:1285662 original size:73 final size:71
Alignment explanation
Indices: 1285528--1285811 Score: 278
Period size: 73 Copynumber: 4.0 Consensus size: 71
1285518 ATACTTTTAA
*
1285528 AAAAAATAATTTTCAAAACTATAT-AATATATTTTTAAAAACTAATTTTCAAAACTATATAATAT
1 AAAAACTAATTTTCAAAACTATATAAATATATTTTTAAAAACTAATTTTCAAAACTATATAATAT
*
1285592 ATTTTT
66 ATATTT
*
1285598 AAAAACTAATTTTCAAAACTATATAATATATATATTTTAAAAACTAATTTTCAAAATTATATAAT
1 AAAAACTAATTTTCAAAACTATATAA-ATATAT-TTTTAAAAACTAATTTTCAAAACTATATAAT
1285663 ATATATTT
64 ATATATTT
* * * ** * * *
1285671 AGAAACTAATTTTCAAAATTATATATACGT-TTTTTCAAAA-T-GTTTTTAAAAGCTATATATTA
1 AAAAACTAATTTTCAAAACTATATAAATATATTTTTAAAAACTAATTTTCAAAA-CTATATA--A
*
1285733 TATATACTT
63 TATATATTT
* * * * * *
1285742 AAAAA--AAGTTTTCAAAACAATATAATATGTATTTTCAAAAA-T-GTTTTCAAAAATTATATAT
1 AAAAACTAA-TTTTCAAAACTATATAA-ATATATTTTTAAAAACTAATTTTC-AAAACTATATAA
1285803 TATATATTT
63 TATATATTT
1285812 TCGAAATATT
Statistics
Matches: 180, Mismatches: 24, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
68 8 0.04
69 9 0.05
70 53 0.29
71 18 0.10
72 28 0.16
73 64 0.36
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (71 bp):
AAAAACTAATTTTCAAAACTATATAAATATATTTTTAAAAACTAATTTTCAAAACTATATAATAT
ATATTT
Found at i:1285782 original size:35 final size:35
Alignment explanation
Indices: 1285489--1285812 Score: 246
Period size: 35 Copynumber: 9.0 Consensus size: 35
1285479 AATAAATTAA
* * *
1285489 TTAAAAACATTTTTAAAACTATACAATATATACTTT
1 TTAAAAAAATTTTCAAAACTATATAATATATA-TTT
*
1285525 TAAAAAAAATAATTTTCAAAACTATAT-A-ATATATTT
1 T--TAAAAA-AATTTTCAAAACTATATAATATATATTT
1285561 TTAAAAACTAATTTTCAAAACTATAT-A-ATATATTT
1 TTAAAAA--AATTTTCAAAACTATATAATATATATTT
1285596 TTAAAAACTAATTTTCAAAACTATATAATATATATATT
1 TTAAAAA--AATTTTCAAAACTATATAATATATAT-TT
*
1285634 TTAAAAACTAATTTTCAAAATTATATAATATATATTT
1 TTAAAAA--AATTTTCAAAACTATATAATATATATTT
** ** * **
1285671 AGAAACTAATTTTCAAAATTATAT-ATACGT-TTT
1 TTAAAAAAATTTTCAAAACTATATAATATATATTT
* ** * * **
1285704 TTCAAAATGTTTTTAAAAGCTATATATTATATATAC
1 TTAAAAAAATTTTCAAAA-CTATATAATATATATTT
* *
1285740 TTAAAAAAAGTTTTCAAAACAATATAATATGTATTT
1 TTAAAAAAA-TTTTCAAAACTATATAATATATATTT
* ** * *
1285776 TCAAAAATGTTTTCAAAAATTATATATTATATATTT
1 TTAAAAAAATTTTC-AAAACTATATAATATATATTT
1285812 T
1 T
1285813 CGAAATATTT
Statistics
Matches: 234, Mismatches: 42, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
33 13 0.06
34 14 0.06
35 78 0.33
36 49 0.21
37 24 0.10
38 42 0.18
39 14 0.06
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (35 bp):
TTAAAAAAATTTTCAAAACTATATAATATATATTT
Found at i:1285811 original size:36 final size:35
Alignment explanation
Indices: 1285491--1285854 Score: 219
Period size: 35 Copynumber: 10.1 Consensus size: 35
1285481 TAAATTAATT
* * * * *
1285491 AAAAACATTTTTAAAACTATACAATATATACTTTTAAA
1 AAAAATATTTTCAAAACTATATATTATATA-TTTT--C
*
1285529 AAAAATAATTTTCAAAACTATATA--ATATATTTTT
1 AAAAAT-ATTTTCAAAACTATATATTATATATTTTC
*
1285563 AAAAACTAATTTTCAAAACTATATA--ATATATTTTT
1 AAAAA-T-ATTTTCAAAACTATATATTATATATTTTC
1285598 AAAAACTAATTTTCAAAACTATATAATATATATATTTT-
1 AAAAA-T-ATTTTCAAAACTATAT-AT-TATATATTTTC
* *
1285636 AAAAACTAATTTTCAAAATTATATAATATATA-TTT-
1 AAAAA-T-ATTTTCAAAACTATATATTATATATTTTC
* * ** *
1285671 AGAAACTAATTTTCAAAATTATATA-TACGTTTTTTC
1 A-AAAAT-ATTTTCAAAACTATATATTATATATTTTC
* * *
1285707 -AAAATGTTTTTAAAAGCTATATATTATATATACTT-
1 AAAAATATTTTCAAAA-CTATATATTATATAT-TTTC
* * * *
1285742 AAAAAAAGTTTTCAAAACAATATAATATGTATTTTC
1 AAAAATA-TTTTCAAAACTATATATTATATATTTTC
* *
1285778 AAAAATGTTTTCAAAAATTATATATTATATATTTTC
1 AAAAATATTTTC-AAAACTATATATTATATATTTTC
* ** *
1285814 -GAAATATTTAAAAAAAACCATATATTATATAATTTTC
1 AAAAATATTT--TCAAAACTATATATTATAT-ATTTTC
1285851 AAAA
1 AAAA
1285855 TGATTTCAAA
Statistics
Matches: 268, Mismatches: 38, Indels: 40
0.77 0.11 0.12
Matches are distributed among these distances:
33 8 0.03
34 18 0.07
35 97 0.36
36 71 0.26
37 20 0.07
38 30 0.11
39 24 0.09
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (35 bp):
AAAAATATTTTCAAAACTATATATTATATATTTTC
Found at i:1286751 original size:84 final size:84
Alignment explanation
Indices: 1286499--1287307 Score: 710
Period size: 84 Copynumber: 9.8 Consensus size: 84
1286489 AAGTTGAATA
* * * *
1286499 TAATCGAACTCGAAGGTC-TT--TAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGAT
1 TAATCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGAT
*
1286561 GTGCCCTCGAAGCTGAGTG
66 GTGCCCTTGAAGCTGAGTG
* ** * * * * *
1286580 TAATCGAACTTGGGGGTC-TT--TGGCAGATAGCTCTTCTCGACTTAAGCTATACTGCAAATGAT
1 TAATCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGAT
*
1286642 GTG-CCTTGGAGCTGAGTG
66 GTGCCCTTGAAGCTGAGTG
* * * * * * * *
1286660 TAGTCGAACTCGAAGGTC-TTGGTGGGCAGATAGCCCTTCTGGCCTTGAGCTATGCTGTAAATAA
1 TAATCGAACTCGAAGGTCTTTGGT-GGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGA
*
1286724 TATGCCCTTGAAGCTGAGTG
65 TGTGCCCTTGAAGCTGAGTG
* * * *
1286744 TAATCGAACT-TAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATG
1 TAATCGAACTCGAA-GGTCTTT-GGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATG
**
1286808 ATGTG-CCTTCGAAGCTGAACG
64 ATGTGCCCTT-GAAGCTGAGTG
* * * * * * * *
1286829 CAGTCGAACTCAAAGGTCTTGGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGAT
1 TAATCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGAT
*
1286894 ATGCCCTTGAAGCTGAGTG
66 GTGCCCTTGAAGCTGAGTG
* * * *
1286913 TAATCGAACT-TAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATG
1 TAATCGAACTCGAA-GGTCTTT-GGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATG
**
1286977 ATGTG-CCTTCGAAGCTGAACG
64 ATGTGCCCTT-GAAGCTGAGTG
* * * * * *
1286998 TAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGAT
1 TAATCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGAT
*
1287063 ATGCCCTTGAAGCTGAGTG
66 GTGCCCTTGAAGCTGAGTG
** * * *
1287082 TAATCGAACTTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATG
1 TAATCGAACTCGAA-GGTCTTT-GGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATG
**
1287147 ATGTG-CCTTCGAAGCTGAACG
64 ATGTGCCCTT-GAAGCTGAGTG
* * * * * * *
1287168 TAGTCGAACTCGAGGGTC-TT--TGGCATATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGAT
1 TAATCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGAT
* *
1287230 ATGCCTTTG-AGC---GTAG
66 GTGCCCTTGAAGCTGAGT-G
* * * * *
1287246 T--T-GAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGAT
1 TAATCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGAT
1287308 TTGTTTAAAA
Statistics
Matches: 593, Mismatches: 112, Indels: 49
0.79 0.15 0.06
Matches are distributed among these distances:
75 11 0.02
76 3 0.01
78 35 0.06
80 32 0.05
81 99 0.17
82 4 0.01
83 40 0.07
84 158 0.27
85 147 0.25
86 64 0.11
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (84 bp):
TAATCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGAT
GTGCCCTTGAAGCTGAGTG
Found at i:1286836 original size:85 final size:82
Alignment explanation
Indices: 1286521--1287236 Score: 677
Period size: 85 Copynumber: 8.6 Consensus size: 82
1286511 AAGGTCTTTA
* * * *
1286521 GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 GCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGTG-CCTTGAAGCTGAGTGTAATCG
**
1286586 AACTTGGGGGTC-T-TTG
65 AACTTAAGGGTCTTGTTG
* * * * *
1286602 GCAGATAGCTCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCCTTGAAGCTGAGTGTAATCGA
* *
1286667 ACTCGAA-GGTCTTGGTGG
66 ACT-TAAGGGTCTT-GTTG
* * * * * * * * *
1286685 GCAGATAGCCCTTCTGGCCTTGAGCTATGCTGTAAATAATATGCCCTTGAAGCTGAGTGTAATCG
1 GCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGTG-CCTTGAAGCTGAGTGTAATCG
1286750 AACTTAAGGGTCTTTAGTTG
65 AACTTAAGGGTC-TT-GTTG
* ** * *
1286770 GCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGCAGTCG
1 GCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCCTT-GAAGCTGAGTGTAATCG
* * *
1286835 AACTCAAAGGTCTTGGGTG
65 AACTTAAGGGTCTT-GTTG
* * * * * * *
1286854 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCG
1 GCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGTG-CCTTGAAGCTGAGTGTAATCG
1286919 AACTTAAGGGTCTTTAGTTG
65 AACTTAAGGGTC-TT-GTTG
* ** *
1286939 GCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCG
1 GCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCCTT-GAAGCTGAGTGTAATCG
* * *
1287004 AACTCAAAGGTCTTTGGTG
65 AACTTAAGGGTC-TTGTTG
* * * * * * *
1287023 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCG
1 GCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGTG-CCTTGAAGCTGAGTGTAATCG
1287088 AACTTTAAGGGTCTTTAGTTG
65 AAC-TTAAGGGTC-TT-GTTG
* ** *
1287109 GCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCG
1 GCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCCTT-GAAGCTGAGTGTAATCG
**
1287174 AACTCGAGGGTC-T-TTG
65 AACTTAAGGGTCTTGTTG
* * * * *
1287190 GCATATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATATGCCTT
1 GCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCCTT
1287237 TGAGCGTAGT
Statistics
Matches: 522, Mismatches: 98, Indels: 30
0.80 0.15 0.05
Matches are distributed among these distances:
80 26 0.05
81 86 0.16
83 40 0.08
84 155 0.30
85 159 0.30
86 56 0.11
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (82 bp):
GCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCCTTGAAGCTGAGTGTAATCGA
ACTTAAGGGTCTTGTTG
Found at i:1286885 original size:169 final size:168
Alignment explanation
Indices: 1286502--1287239 Score: 1037
Period size: 169 Copynumber: 4.4 Consensus size: 168
1286492 TTGAATATAA
* * * * * * *
1286502 TCGAACTCGAAGGTCTT--T-AGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TCGAACTCAAAGGTCTTGGTGA-CAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATATG
* ** * * *
1286564 CCCTCGAAGCTGAGTGTAATCGAACTTGGGGGTC--T--TTGGCAGATAGCTCTTCTCGACTTAA
65 CCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAA
* * **
1286625 GCTATACTGCAAATGATGTGCCTT-GGAGCTGAGTGTAG
130 GTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAG
* * * * *
1286663 TCGAACTCGAAGGTCTTGGTGGGCAGATAGCCCTTCTGGCCTTGAGCTATGCTGTAAATAATATG
1 TCGAACTCAAAGGTCTTGGT-GACAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATATG
1286728 CCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAA
65 CCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAA
*
1286793 GTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGCAG
130 GTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAG
*
1286832 TCGAACTCAAAGGTCTTGGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATG
1 TCGAACTCAAAGGTCTT-GGTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATATG
1286897 CCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAA
65 CCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAA
1286962 GTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAG
130 GTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAG
*
1287001 TCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATG
1 TCGAACTCAAAGGTC-TTGGTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATATG
1287066 CCCTTGAAGCTGAGTGTAATCGAACTTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTA
65 CCCTTGAAGCTGAGTGTAATCGAAC-TTAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTA
1287131 AGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAG
129 AGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAG
* * * * * * * * * *
1287171 TCGAACTCGAGGGTCTT--TGGCATATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATATGC
1 TCGAACTCAAAGGTCTTGGTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATATGC
*
1287234 CTTTGA
66 CCTTGA
1287240 GCGTAGTTGA
Statistics
Matches: 528, Mismatches: 37, Indels: 18
0.91 0.06 0.03
Matches are distributed among these distances:
161 17 0.03
163 1 0.00
164 67 0.13
166 1 0.00
167 42 0.08
168 46 0.09
169 257 0.49
170 97 0.18
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (168 bp):
TCGAACTCAAAGGTCTTGGTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATATGC
CCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAAG
TTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAG
Found at i:1290690 original size:18 final size:19
Alignment explanation
Indices: 1290649--1290693 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1290639 AGTTAATGTG
1290649 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
1290668 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
1290686 AATGCAAA
1 AATGCAAA
1290694 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:1291341 original size:17 final size:17
Alignment explanation
Indices: 1291311--1291343 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1291301 TGCAAACAAT
1291311 GAACACAAAATAAAAGA
1 GAACACAAAATAAAAGA
1291328 GAACA-AAAAGTAAAAG
1 GAACACAAAA-TAAAAG
1291344 GGTTAGTGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.70, C:0.09, G:0.15, T:0.06
Consensus pattern (17 bp):
GAACACAAAATAAAAGA
Found at i:1292473 original size:26 final size:25
Alignment explanation
Indices: 1292403--1292473 Score: 65
Period size: 26 Copynumber: 2.8 Consensus size: 25
1292393 TGAATAGATC
*
1292403 AAAGAAAAAATGTAGA-AAATAAAAA
1 AAAGAAAAAA-ATAGATAAATAAAAA
*
1292428 AAAGAAAAATAATCA-TTAAATCAAAAA
1 AAAGAAAAA-AAT-AGATAAAT-AAAAA
*
1292455 AAGGAAAAAAATAGATAAA
1 AAAGAAAAAAATAGATAAA
1292474 ATAGAGAGGA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
25 11 0.30
26 13 0.35
27 13 0.35
ACGTcount: A:0.73, C:0.03, G:0.10, T:0.14
Consensus pattern (25 bp):
AAAGAAAAAAATAGATAAATAAAAA
Found at i:1292475 original size:27 final size:26
Alignment explanation
Indices: 1292418--1292476 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
1292408 AAAAATGTAG
1292418 AAAATAAAAAAAAGAAAAATAATCAT
1 AAAATAAAAAAAAGAAAAATAATCAT
* * *
1292444 TAAATCAAAAAAAGGAAAAA-AATAGAT
1 AAAAT-AAAAAAAAGAAAAATAAT-CAT
1292471 AAAATA
1 AAAATA
1292477 GAGAGGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
26 8 0.30
27 19 0.70
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (26 bp):
AAAATAAAAAAAAGAAAAATAATCAT
Found at i:1292985 original size:12 final size:12
Alignment explanation
Indices: 1292968--1292998 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1292958 GGTGGCCTCT
1292968 CCACCGCGCCGG
1 CCACCGCGCCGG
*
1292980 CCACCGTGCCGG
1 CCACCGCGCCGG
1292992 CCACCGC
1 CCACCGC
1292999 CGGCGGTGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.58, G:0.29, T:0.03
Consensus pattern (12 bp):
CCACCGCGCCGG
Found at i:1293624 original size:16 final size:15
Alignment explanation
Indices: 1293598--1293628 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1293588 ATGTATGACC
1293598 GGTCATCCCGGGATG
1 GGTCATCCCGGGATG
1293613 GGTCAGTCCCGGGATG
1 GGTCA-TCCCGGGATG
1293629 CCGGCCGGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.13, C:0.26, G:0.42, T:0.19
Consensus pattern (15 bp):
GGTCATCCCGGGATG
Found at i:1293807 original size:4 final size:4
Alignment explanation
Indices: 1293776--1293835 Score: 59
Period size: 4 Copynumber: 15.0 Consensus size: 4
1293766 GACCTGAAAC
* * **
1293776 AAAT -AAT AAAT AAGT AAAT GAAAA AAAT AAAT AAAT AAAT AAAT GGAT
1 AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT
*
1293824 AAAT TAAT AAAT
1 AAAT AAAT AAAT
1293836 TAATTAAAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
3 3 0.07
4 38 0.86
5 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:1293818 original size:25 final size:24
Alignment explanation
Indices: 1293770--1293835 Score: 78
Period size: 25 Copynumber: 2.7 Consensus size: 24
1293760 ATCCTGGACC
* *
1293770 TGAAACAAATAATAAATAAGTAAA
1 TGAAAAAAATAATAAATAAATAAA
1293794 TGAAAAAAATAAATAAATAAATAAA
1 TGAAAAAAAT-AATAAATAAATAAA
* * *
1293819 TGGATAAATTAATAAAT
1 TGAAAAAAATAATAAAT
1293836 TAATTAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
24 16 0.44
25 20 0.56
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.24
Consensus pattern (24 bp):
TGAAAAAAATAATAAATAAATAAA
Found at i:1293924 original size:35 final size:35
Alignment explanation
Indices: 1293839--1294041 Score: 279
Period size: 35 Copynumber: 5.8 Consensus size: 35
1293829 AATAAATTAA
* *
1293839 TTAAAAAC--ATTTTTAAAACTATACAATATATACTT
1 TTAAAAACTAATTTTCAAAACTATATAATATAT--TT
*
1293874 TTAAAAAAAATAATTTTCAAAACTATATAATATATTT
1 TT--AAAAACTAATTTTCAAAACTATATAATATATTT
1293911 TTAAAAACTAATTTTCAAAACTATATAATATATTT
1 TTAAAAACTAATTTTCAAAACTATATAATATATTT
1293946 TTAAAAACTAATTTTCAAAACTATATAATATATATT
1 TTAAAAACTAATTTTCAAAACTATATAATATAT-TT
*
1293982 TTAAAAACTAATTTTCAAAATTATATAATATA--T
1 TTAAAAACTAATTTTCAAAACTATATAATATATTT
* *
1294015 TTAGAAACTAATTTTCAAAATTATATA
1 TTAAAAACTAATTTTCAAAACTATATA
1294042 TACGTTTTTT
Statistics
Matches: 157, Mismatches: 6, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
33 27 0.17
35 67 0.43
36 33 0.21
37 9 0.06
39 21 0.13
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.41
Consensus pattern (35 bp):
TTAAAAACTAATTTTCAAAACTATATAATATATTT
Found at i:1293991 original size:36 final size:36
Alignment explanation
Indices: 1293878--1294158 Score: 280
Period size: 35 Copynumber: 8.0 Consensus size: 36
1293868 ATACTTTTAA
*
1293878 AAAAAATAATTTTCAAAACTATATAATATAT-TTTT
1 AAAAACTAATTTTCAAAACTATATAATATATATTTT
1293913 AAAAACTAATTTTCAAAACTATATAATATAT-TTTT
1 AAAAACTAATTTTCAAAACTATATAATATATATTTT
1293948 AAAAACTAATTTTCAAAACTATATAATATATATTTT
1 AAAAACTAATTTTCAAAACTATATAATATATATTTT
*
1293984 AAAAACTAATTTTCAAAATTATAT-A-ATATA-TTT
1 AAAAACTAATTTTCAAAACTATATAATATATATTTT
* * ** *
1294017 AGAAACTAATTTTCAAAATTATAT-ATACGTTTTTT
1 AAAAACTAATTTTCAAAACTATATAATATATATTTT
* * * * *
1294052 CAAAA-T-GTTTTTAAAAGCTATATATTATATATACTT
1 AAAAACTAATTTTCAAAA-CTATATAATATATAT-TTT
* *
1294088 AAAAA--AAGTTTTCAAAACAATATAATATGTATTTT
1 AAAAACTAA-TTTTCAAAACTATATAATATATATTTT
* * *
1294123 CAAAAA-T-GTTTTCAAAAATTATATATTATATATTTT
1 -AAAAACTAATTTTC-AAAACTATATAATATATATTTT
1294159 CGAAATATTT
Statistics
Matches: 207, Mismatches: 28, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
33 35 0.17
34 13 0.06
35 83 0.40
36 68 0.33
37 8 0.04
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.43
Consensus pattern (36 bp):
AAAAACTAATTTTCAAAACTATATAATATATATTTT
Found at i:1294159 original size:36 final size:35
Alignment explanation
Indices: 1293841--1294200 Score: 215
Period size: 35 Copynumber: 10.1 Consensus size: 35
1293831 TAAATTAATT
* * * * *
1293841 AAAAACATTTTTAAAACTATACAATATATACTTTTAAA
1 AAAAATATTTTCAAAACTATATATTATATA-TTTT--C
*
1293879 AAAAATAATTTTCAAAACTATATA--ATATATTTTT
1 AAAAAT-ATTTTCAAAACTATATATTATATATTTTC
*
1293913 AAAAACTAATTTTCAAAACTATATA--ATATATTTTT
1 AAAAA-T-ATTTTCAAAACTATATATTATATATTTTC
*
1293948 AAAAACTAATTTTCAAAACTATATAATATATATTTT-
1 AAAAA-T-ATTTTCAAAACTATATATTATATATTTTC
*
1293984 AAAAACTAATTTTCAAAA-T-TATATAATATA-TTT-
1 AAAAA-T-ATTTTCAAAACTATATATTATATATTTTC
* * ** *
1294017 AGAAACTAATTTTCAAAATTATATA-TACGTTTTTTC
1 A-AAAAT-ATTTTCAAAACTATATATTATATATTTTC
* * *
1294053 -AAAATGTTTTTAAAAGCTATATATTATATATACTT-
1 AAAAATATTTTCAAAA-CTATATATTATATAT-TTTC
* * * *
1294088 AAAAAAAGTTTTCAAAACAATATAATATGTATTTTC
1 AAAAATA-TTTTCAAAACTATATATTATATATTTTC
* *
1294124 AAAAATGTTTTCAAAAATTATATATTATATATTTTC
1 AAAAATATTTTC-AAAACTATATATTATATATTTTC
* ** *
1294160 -GAAATATTTAAAAAAAACCATATATTATATAATTTTC
1 AAAAATATTT--TCAAAACTATATATTATAT-ATTTTC
1294197 AAAA
1 AAAA
1294201 TGATTTCAAA
Statistics
Matches: 263, Mismatches: 39, Indels: 40
0.77 0.11 0.12
Matches are distributed among these distances:
33 24 0.09
34 30 0.11
35 80 0.30
36 79 0.30
37 28 0.11
38 7 0.03
39 15 0.06
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (35 bp):
AAAAATATTTTCAAAACTATATATTATATATTTTC
Found at i:1296465 original size:17 final size:17
Alignment explanation
Indices: 1296445--1296497 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
1296435 AAAAAAATAT
*
1296445 TTTTCAATTAATATTTA
1 TTTTAAATTAATATTTA
*
1296462 TTTTAAATTAAT-TTAA
1 TTTTAAATTAATATTTA
* *
1296478 TTTTAAAATAATATATA
1 TTTTAAATTAATATTTA
1296495 TTT
1 TTT
1296498 ACTAACTATA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 14 0.47
17 16 0.53
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTAAATTAATATTTA
Found at i:1296482 original size:16 final size:17
Alignment explanation
Indices: 1296445--1296491 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
1296435 AAAAAAATAT
* *
1296445 TTTTCAATTAATATTTA
1 TTTTAAATTAATATTAA
1296462 TTTTAAATTAAT-TTAA
1 TTTTAAATTAATATTAA
*
1296478 TTTTAAAATAATAT
1 TTTTAAATTAATAT
1296492 ATATTTACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 14 0.54
17 12 0.46
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTAAATTAATATTAA
Found at i:1300467 original size:42 final size:42
Alignment explanation
Indices: 1300403--1300488 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
1300393 TACGCTATTA
* *
1300403 TATTTCTAAAGGATACATGATGCATTAATTATGACTTAATCT
1 TATTTCTAAAGGATACAGGATGCATTAACTATGACTTAATCT
*
1300445 TATTTCTAAAGGATACAGGATGCATTAACTATGCCTTAATCT
1 TATTTCTAAAGGATACAGGATGCATTAACTATGACTTAATCT
1300487 TA
1 TA
1300489 GCGCAATTAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (42 bp):
TATTTCTAAAGGATACAGGATGCATTAACTATGACTTAATCT
Found at i:1302909 original size:29 final size:29
Alignment explanation
Indices: 1302871--1302961 Score: 103
Period size: 29 Copynumber: 3.1 Consensus size: 29
1302861 ATTTGACTCT
*
1302871 CATTCTAAATTGATCCTTAAACTTTTGAA
1 CATTCTAAATTGATCCTCAAACTTTTGAA
* * * *
1302900 CATTCCAAATTCATCCTCAAA-TTATGACT
1 CATTCTAAATTGATCCTCAAACTTTTGA-A
* *
1302929 CATTCTAAGTTGATCCCCAAACTTTTGAA
1 CATTCTAAATTGATCCTCAAACTTTTGAA
1302958 CATT
1 CATT
1302962 GCAATAATGT
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
28 5 0.10
29 39 0.80
30 5 0.10
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (29 bp):
CATTCTAAATTGATCCTCAAACTTTTGAA
Found at i:1304428 original size:17 final size:17
Alignment explanation
Indices: 1304406--1304443 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1304396 TCATGTGACT
1304406 TTGTTTTGCAGCTATAA
1 TTGTTTTGCAGCTATAA
1304423 TTGTTTTGCAGCTATAA
1 TTGTTTTGCAGCTATAA
1304440 TTGT
1 TTGT
1304444 CACAGTAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.50
Consensus pattern (17 bp):
TTGTTTTGCAGCTATAA
Found at i:1307659 original size:20 final size:20
Alignment explanation
Indices: 1307615--1307662 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1307605 GAATATGTAA
* *
1307615 ATCGCAATGCGATTATGATT
1 ATCGCAACGCGATTATGACT
*
1307635 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTATGACT
*
1307655 GTCGCAAC
1 ATCGCAAC
1307663 ACTGAATTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (20 bp):
ATCGCAACGCGATTATGACT
Found at i:1310753 original size:18 final size:18
Alignment explanation
Indices: 1310720--1310754 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1310710 AGAAAAAGGC
**
1310720 AATCAAAATCGTAATCAA
1 AATCAAAATCCCAATCAA
1310738 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
1310755 CAACCGGCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.23, G:0.03, T:0.20
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:1310939 original size:20 final size:20
Alignment explanation
Indices: 1310914--1311112 Score: 128
Period size: 20 Copynumber: 10.8 Consensus size: 20
1310904 TTACACATTC
*
1310914 ATTTGAATATCGCAACACGA
1 ATTTGAATATCGCAACGCGA
* *
1310934 ATTTGATTATCGCAACTC-A
1 ATTTGAATATCGCAACGCGA
*
1310953 A----AA-ATCACAACGCGA
1 ATTTGAATATCGCAACGCGA
* *
1310968 ATTTGACTATCGCAACACGA
1 ATTTGAATATCGCAACGCGA
* *
1310988 ATATGACTATCGCAACGC-A
1 ATTTGAATATCGCAACGCGA
1311007 A----AA-ATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
**
1311022 ATTTGTCTATCGCAA--CG-
1 ATTTGAATATCGCAACGCGA
*
1311039 A---GAAAATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
*
1311056 ATTTGAGTATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
* * *
1311076 ATTTGATTATCGCAACGGGT
1 ATTTGAATATCGCAACGCGA
*
1311096 ATTTGACTATCGCAACG
1 ATTTGAATATCGCAACG
1311113 AGAAAATCGT
Statistics
Matches: 139, Mismatches: 22, Indels: 36
0.71 0.11 0.18
Matches are distributed among these distances:
14 26 0.19
15 6 0.04
16 2 0.01
17 2 0.01
18 2 0.01
19 5 0.04
20 96 0.69
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.24
Consensus pattern (20 bp):
ATTTGAATATCGCAACGCGA
Found at i:1310999 original size:54 final size:54
Alignment explanation
Indices: 1310914--1311037 Score: 194
Period size: 54 Copynumber: 2.3 Consensus size: 54
1310904 TTACACATTC
* * * *
1310914 ATTTGAATATCGCAACACGAATTTGATTATCGCAACTCAAAAATCACAACGCGA
1 ATTTGACTATCGCAACACGAATATGACTATCGCAACGCAAAAATCACAACGCGA
*
1310968 ATTTGACTATCGCAACACGAATATGACTATCGCAACGCAAAAATCGCAACGCGA
1 ATTTGACTATCGCAACACGAATATGACTATCGCAACGCAAAAATCACAACGCGA
*
1311022 ATTTGTCTATCGCAAC
1 ATTTGACTATCGCAAC
1311038 GAGAAAATCG
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 64 1.00
ACGTcount: A:0.38, C:0.24, G:0.15, T:0.23
Consensus pattern (54 bp):
ATTTGACTATCGCAACACGAATATGACTATCGCAACGCAAAAATCACAACGCGA
Found at i:1311014 original size:34 final size:35
Alignment explanation
Indices: 1310976--1311146 Score: 170
Period size: 34 Copynumber: 4.8 Consensus size: 35
1310966 GAATTTGACT
* *
1310976 ATCGCAACACGAATATGACTATCGCAACGCA-AAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCAGAAA
*
1311010 ATCGCAACGCGAATTTGTCTATCGCAACG-AGAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCAGAAA
*
1311044 ATCGCAACGCGAATTTGAGTATCGCAACGC-GAATTTGA
1 ATCGCAACGCGAATTTGACTATCGCAACGCAGAA----A
* *
1311082 TTATCGCAACGGGTATTTGACTATCGCAACG-AGAAA
1 --ATCGCAACGCGAATTTGACTATCGCAACGCAGAAA
* * * *
1311118 ATCGTAAAGCGTATTAGACTATCGCAACG
1 ATCGCAACGCGAATTTGACTATCGCAACG
1311147 TGAATTGACT
Statistics
Matches: 116, Mismatches: 12, Indels: 18
0.79 0.08 0.12
Matches are distributed among these distances:
33 1 0.01
34 84 0.72
36 1 0.01
38 1 0.01
40 29 0.25
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (35 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCAGAAA
Found at i:1311106 original size:74 final size:74
Alignment explanation
Indices: 1311010--1311152 Score: 205
Period size: 74 Copynumber: 1.9 Consensus size: 74
1311000 CAACGCAAAA
* * * *
1311010 ATCGCAACGCGAATTTGTCTATCGCAACGAGAAAATCGCAACGCGAATTTGAGTATCGCAACGCG
1 ATCGCAACGCGAATTTGACTATCGCAACGAGAAAATCGCAAAGCGAATTAGACTATCGCAACGCG
1311075 AATTTGATT
66 AATTTGATT
* * * * *
1311084 ATCGCAACGGGTATTTGACTATCGCAACGAGAAAATCGTAAAGCGTATTAGACTATCGCAACGTG
1 ATCGCAACGCGAATTTGACTATCGCAACGAGAAAATCGCAAAGCGAATTAGACTATCGCAACGCG
1311149 AATT
66 AATT
1311153 GACTTTCGCG
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
74 60 1.00
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (74 bp):
ATCGCAACGCGAATTTGACTATCGCAACGAGAAAATCGCAAAGCGAATTAGACTATCGCAACGCG
AATTTGATT
Found at i:1311180 original size:20 final size:20
Alignment explanation
Indices: 1311151--1311208 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
1311141 GCAACGTGAA
1311151 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCGTTGCGATT
* * *
1311171 TTGTCTTTCGCATTGTGATT
1 TTGACTTTCGCGTTGCGATT
* *
1311191 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCGTTGCGA
1311209 AAGTGTACCT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.12, C:0.16, G:0.26, T:0.47
Consensus pattern (20 bp):
TTGACTTTCGCGTTGCGATT
Found at i:1312851 original size:42 final size:42
Alignment explanation
Indices: 1312755--1312864 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 42
1312745 TAGAATGTTA
* * * *
1312755 GGAG-GGACCTCTTTAACGATGACAGTGGCCTCTTGAACGGTG
1 GGAGAGGA-CTCTTGAAAGATGACAGGGGCCTCTTGAACGATG
* **
1312797 GGAGGGGACTCTTGAGGGATGACAGGGGCCTCTTGAACGATAG
1 GGAGAGGACTCTTGAAAGATGACAGGGGCCTCTTGAACGAT-G
*
1312840 GG-GAGGCCTCTTGAAAGATGACAGG
1 GGAGAGGACTCTTGAAAGATGACAGG
1312865 TGAGTCAGAC
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
42 51 0.89
43 6 0.11
ACGTcount: A:0.24, C:0.18, G:0.38, T:0.20
Consensus pattern (42 bp):
GGAGAGGACTCTTGAAAGATGACAGGGGCCTCTTGAACGATG
Found at i:1313385 original size:20 final size:20
Alignment explanation
Indices: 1313360--1313436 Score: 118
Period size: 20 Copynumber: 3.9 Consensus size: 20
1313350 ATCGCAACAC
*
1313360 AAATGACTATTGCAACGCGA
1 AAATGACTATCGCAACGCGA
1313380 AAATGACTATCGCAACGCGA
1 AAATGACTATCGCAACGCGA
1313400 AAATGACTATCGCAACGCGA
1 AAATGACTATCGCAACGCGA
** *
1313420 ATTTGACTATCGTAACG
1 AAATGACTATCGCAACG
1313437 AGAGAATCGC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGA
Found at i:1313504 original size:20 final size:20
Alignment explanation
Indices: 1313479--1313524 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1313469 GCGATTCTTT
1313479 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
1313499 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
1313519 CGTTGC
1 CGTTGC
1313525 AAAAGTAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1314057 original size:21 final size:20
Alignment explanation
Indices: 1314033--1314107 Score: 57
Period size: 21 Copynumber: 3.8 Consensus size: 20
1314023 GTGACATAAT
1314033 AGGTGATGGCTCTCGTTGTGG
1 AGGTGATGGCTCTCGTTGT-G
* ** *
1314054 AGGTGTATAG-TCGGGTTGATC
1 AGGTG-ATGGCTCTCGTTG-TG
*
1314075 AGGTGATGGCTCT-G-GGTG
1 AGGTGATGGCTCTCGTTGTG
1314093 AGGTGATGGCTCTCG
1 AGGTGATGGCTCTCG
1314108 AAGTGGAGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
18 14 0.33
19 2 0.05
20 4 0.10
21 18 0.43
22 4 0.10
ACGTcount: A:0.13, C:0.13, G:0.43, T:0.31
Consensus pattern (20 bp):
AGGTGATGGCTCTCGTTGTG
Found at i:1315499 original size:19 final size:19
Alignment explanation
Indices: 1315440--1315526 Score: 86
Period size: 20 Copynumber: 4.5 Consensus size: 19
1315430 TCTGAAACTT
* *
1315440 AAAATCGCAACACAAAAATG
1 AAAATCGCAACGC-GAAATG
*
1315460 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCG-AAATG
**
1315480 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
1315499 AAAATTGCAACGCGAAACT-
1 AAAATCGCAACGCGAAA-TG
1315518 AAAATCGCA
1 AAAATCGCA
1315527 TTGCGATTCT
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
19 27 0.47
20 30 0.53
ACGTcount: A:0.51, C:0.22, G:0.15, T:0.13
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:1316155 original size:20 final size:20
Alignment explanation
Indices: 1316130--1316333 Score: 203
Period size: 20 Copynumber: 10.1 Consensus size: 20
1316120 TCGCATTACA
*
1316130 ATAGTCAGCATCGCGTTGCG
1 ATAGTCAGAATCGCGTTGCG
* * *
1316150 ACAGTCAGAATCGCATTACG
1 ATAGTCAGAATCGCGTTGCG
*
1316170 ATAGTCAGCATCGCGTTGCG
1 ATAGTCAGAATCGCGTTGCG
*
1316190 ACAGTCAGAATCGCGTTGCG
1 ATAGTCAGAATCGCGTTGCG
*
1316210 ATAGTCAGAATCTCGTTGCG
1 ATAGTCAGAATCGCGTTGCG
1316230 ATAGTCAGAATCGCGTTGCG
1 ATAGTCAGAATCGCGTTGCG
* * *
1316250 ATAGTCATACTCGCATTGCG
1 ATAGTCAGAATCGCGTTGCG
* ***
1316270 ATAGTCGGAAAATCGCAACGCG
1 ATAGTC--AGAATCGCGTTGCG
* * **
1316292 A-ATTTAGAAAATCGCAATGCG
1 ATAGTCAG--AATCGCGTTGCG
1316313 ATAGTCAGAATCGCGTTGCG
1 ATAGTCAGAATCGCGTTGCG
1316333 A
1 A
1316334 ATCTGACTAC
Statistics
Matches: 151, Mismatches: 28, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
19 1 0.01
20 121 0.80
21 14 0.09
22 15 0.10
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (20 bp):
ATAGTCAGAATCGCGTTGCG
Found at i:1316623 original size:18 final size:18
Alignment explanation
Indices: 1316576--1316623 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
1316566 ACAATTATAG
*
1316576 TTATTATTATATTTTTTA
1 TTATTATTATATTTATTA
* *
1316594 TTCTT-TACATATTTATTA
1 TTATTAT-TATATTTATTA
1316612 TTATTATTATAT
1 TTATTATTATAT
1316624 ATATATATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 4
0.72 0.16 0.12
Matches are distributed among these distances:
17 1 0.04
18 21 0.91
19 1 0.04
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATTATTATATTTATTA
Found at i:1318647 original size:12 final size:12
Alignment explanation
Indices: 1318626--1318655 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1318616 CAAAACACGT
1318626 AAAA-AATAATA
1 AAAATAATAATA
1318637 AAAATAATAATA
1 AAAATAATAATA
1318649 AAAATAA
1 AAAATAA
1318656 ACAAAATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (12 bp):
AAAATAATAATA
Found at i:1318721 original size:17 final size:17
Alignment explanation
Indices: 1318694--1318747 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
1318684 AGACACATAT
* *
1318694 AAAGGAAAAAAATTAAT
1 AAAGTAAAAAAATTAAA
* *
1318711 AGAGTAAAAAAATAAAA
1 AAAGTAAAAAAATTAAA
1318728 AAAGTAAAAGAAATTAAA
1 AAAGTAAAA-AAATTAAA
1318746 AA
1 AA
1318748 GGAATAAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 21 0.70
18 9 0.30
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (17 bp):
AAAGTAAAAAAATTAAA
Found at i:1318748 original size:17 final size:16
Alignment explanation
Indices: 1318694--1318758 Score: 58
Period size: 17 Copynumber: 3.8 Consensus size: 16
1318684 AGACACATAT
*
1318694 AAAGGAAAAAAATTAA
1 AAAGTAAAAAAATTAA
* *
1318710 TAGAGTAAAAAAATAAAA
1 -AAAGTAAAAAAAT-TAA
1318728 AAAGTAAAAGAAATTAA
1 AAAGTAAAA-AAATTAA
*
1318745 AAAGGAATAAAAAT
1 AAAGTAA-AAAAAT
1318759 AATGTGTACA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 31 0.79
18 8 0.21
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.15
Consensus pattern (16 bp):
AAAGTAAAAAAATTAA
Found at i:1318966 original size:35 final size:32
Alignment explanation
Indices: 1318885--1318980 Score: 104
Period size: 35 Copynumber: 2.9 Consensus size: 32
1318875 AAAAATGAAG
* *
1318885 TAAAAATATAATATATATA-TAAATAAATAAAAA
1 TAAAAATATAATAT-TA-AGAAAATATATAAAAA
*
1318918 TAAAAATAGAATATTAAGAAAATATATAAAAA
1 TAAAAATATAATATTAAGAAAATATATAAAAA
*
1318950 CGTATAAAATATAATATTAAGAAAAAATATA
1 --TA-AAAATATAATATTAAGAAAATATATA
1318981 TATATAGTAA
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
31 1 0.02
32 14 0.26
33 13 0.24
34 2 0.04
35 24 0.44
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (32 bp):
TAAAAATATAATATTAAGAAAATATATAAAAA
Found at i:1319075 original size:25 final size:27
Alignment explanation
Indices: 1319027--1319077 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
1319017 ATACATACAT
* *
1319027 ATATATATATATATATAATGATATAAG
1 ATATATATATATATAAAATAATATAAG
1319054 ATATATATA-ATA-AAAATAATATAA
1 ATATATATATATATAAAATAATATAA
1319078 TATAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 3 0.14
27 9 0.41
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (27 bp):
ATATATATATATATAAAATAATATAAG
Found at i:1320750 original size:110 final size:108
Alignment explanation
Indices: 1320541--1320799 Score: 326
Period size: 110 Copynumber: 2.4 Consensus size: 108
1320531 AGTATTGTTC
* * ** *
1320541 CGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG--GAACTGGGAAATTGTTTGTTGA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAGAACTGAAAAATTATTTGTTGA
* *
1320604 CAGCCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCT
66 CAACCAGCCGCCCCTTCGCTATGAAGTTGAGCTTGTGTTGTCT
* *
1320647 CGAGTTCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACT-AAAAAGTTATTTGT
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA-G-AACTGAAAAA-TTATTTGT
* * * *
1320711 TGACAATCAGCCGCCCCTTCGTTATGAATTTGAGTTTGTGTTGTCT
63 TGACAACCAGCCGCCCCTTCGCTATGAAGTTGAGCTTGTGTTGTCT
* * *
1320757 TGAGTCCAATATCCCTCGCTGTGAAGTTGAAATTGGCTCTGAA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA
1320800 ACTGGGAAGC
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
106 37 0.28
109 4 0.03
110 89 0.68
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.34
Consensus pattern (108 bp):
CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAGAACTGAAAAATTATTTGTTGA
CAACCAGCCGCCCCTTCGCTATGAAGTTGAGCTTGTGTTGTCT
Found at i:1321611 original size:68 final size:65
Alignment explanation
Indices: 1321516--1321673 Score: 194
Period size: 68 Copynumber: 2.4 Consensus size: 65
1321506 AAGATATATG
* * * * *
1321516 TTGTTTCATGAAAAACGGTCTTAAGGGAAACAAAATTTTGTTTTAAGG-GAAATAAATGT-GAAG
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAA-TTTGTTTT-AGGAGAAATAAAT-TCAAAG
1321579 ATTT
63 A-TT
*
1321583 TGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGAGAAATAAATTCAAAGAT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAGGAGAAATAAATTCAAAGAT
1321648 T
65 T
*
1321649 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGAGAAACTGTCTCAAG
1321674 AGAGACGGAA
Statistics
Matches: 81, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
65 23 0.28
66 7 0.09
67 22 0.27
68 29 0.36
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.32
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAGGAGAAATAAATTCAAAGATT
Found at i:1321647 original size:67 final size:68
Alignment explanation
Indices: 1321503--1321699 Score: 206
Period size: 65 Copynumber: 2.9 Consensus size: 68
1321493 GGAAACGATC
* * * * * *
1321503 TCAAAGATATATGTTGTTTCATGAAAAACGGTCTTAAGGGAAACAAAATTTTGTTTTAAGG-GAA
1 TCAAAGAT-TTTG-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTT-AGGAGAA
1321567 ATAAATG
62 ATAAATG
*
1321574 T-GAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGAGAAATAA
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGAGAAATAA
1321638 AT-
66 ATG
* * ** * *
1321640 TCAAAGA-TTT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACGGAATTTGTTTCAAGAGAAA
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGAGAAA
1321700 CTGTCTCAAG
Statistics
Matches: 110, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
65 44 0.40
66 7 0.06
67 21 0.19
68 29 0.26
69 3 0.03
70 5 0.05
71 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.31
Consensus pattern (68 bp):
TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGAGAAATAA
ATG
Found at i:1321690 original size:101 final size:101
Alignment explanation
Indices: 1321585--1321970 Score: 395
Period size: 102 Copynumber: 3.8 Consensus size: 101
1321575 GAAGATTTTG
* * *
1321585 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTT-TAGGAGAAATAAATTCAAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTATTTCAAGG-GAAATATATTCAAAG-TT
* **
1321649 T-TGTTTCAAGGGAAACTGTCTCAAGAGAGACGGAATT
64 TATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * * *
1321686 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTATTTCAAGGGAAATATATTCAAAGTTTA
1321751 TGTTTCAAGAGAAACTGTCTCAA-AGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGA-GAGACAAAA-TT
* * ** * * * * *
1321788 TGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTATTTCAAGGGAAATATATTCAAAGTTTA
*
1321853 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
66 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * * * * * *
1321889 TAGTTCCAAAAGAAAATGTCTCAAGGGAGACGAAA-TTAGTTTCAATGAAAACAGATTCAAA-TA
1 T-GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTA-TTTCAAGGGAAATATATTCAAAGT-
* *
1321952 TTTTGTTTCAAGGGAAACT
63 TTATGTTTCAAGAGAAACT
1321971 TGGAAACTGT
Statistics
Matches: 239, Mismatches: 38, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
100 4 0.02
101 84 0.35
102 151 0.63
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (101 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTATTTCAAGGGAAATATATTCAAAGTTTA
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:1321700 original size:36 final size:36
Alignment explanation
Indices: 1321648--1321735 Score: 149
Period size: 36 Copynumber: 2.4 Consensus size: 36
1321638 ATTCAAAGAT
*
1321648 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGGAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
*
1321684 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
*
1321720 TTTATTTCAAGGGAAA
1 TTTGTTTCAAGGGAAA
1321736 TGTTTTCAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.27
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
Found at i:1321802 original size:37 final size:36
Alignment explanation
Indices: 1321751--1321837 Score: 102
Period size: 37 Copynumber: 2.4 Consensus size: 36
1321741 TCAATGTTTA
* * *
1321751 TGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTT
1 TGTTTCAAGGGAAACTATCTCAAACGAGACAAAA-TT
* *
1321788 TGTTTCAAGGGAAACTATCTCAATCGAGATAAAATT
1 TGTTTCAAGGGAAACTATCTCAAACGAGACAAAATT
**
1321824 CATTTCAAGGGAAA
1 TGTTTCAAGGGAAA
1321838 TGTTTTCAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 14 0.33
37 29 0.67
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTATCTCAAACGAGACAAAATT
Found at i:1322312 original size:106 final size:106
Alignment explanation
Indices: 1322120--1322440 Score: 462
Period size: 106 Copynumber: 3.0 Consensus size: 106
1322110 TATTGTTCCA
* * * * * * **
1322120 AGTCCAATATCCTCCGCCGTGAAGTTAAAATTGGCTTTGGAACTAAGAAATTATTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAAC
* * * *
1322185 CAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTGG
66 CAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCG
*
1322226 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAAC
* * *
1322291 CAGCCGTCTCTTCGTTATGAAGTTGAACTTGTGTTGTCTCG
66 CAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCG
* *
1322332 AGTCCAATATCCTTCGCTGGGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAAC
* *
1322397 CAGTCGTCCCTTCGCTGTGGAGTTGAACTTGTGTTGTCTCG
66 CAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCG
1322438 AGT
1 AGT
1322441 GGTACGATAT
Statistics
Matches: 191, Mismatches: 24, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
106 191 1.00
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (106 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAAC
CAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCG
Found at i:1322997 original size:138 final size:138
Alignment explanation
Indices: 1322749--1323025 Score: 518
Period size: 138 Copynumber: 2.0 Consensus size: 138
1322739 GTTATTTTGT
*
1322749 TGTCAGACAGTCGCCCCTTCGCTGTGAGGTAGAGCAACCACCATGTGCTTTTGAATTGAGCATCC
1 TGTCAGACAGTCGCCCCTTCGCTGTGAGGTAGAGCAACCACCATGTGCTTTTGAATCGAGCATCC
*
1322814 TTCATCTTGAAGTTGAAACTTGACTCTAAAAGCTGCAAAAACTTATGTATACAAAAAATGATAAA
66 TTCATCTTGAAGTTGAAACTTGACTCTAAAAGCTGCAAAAACTTATGTATACAAAAAATGAAAAA
*
1322879 TGTGATGC
131 TGCGATGC
*
1322887 TGTCAGATAGTCGCCCCTTCGCTGTGAGGTAGAGCAACCACCATGTGCTTTTGAATCGAGCATCC
1 TGTCAGACAGTCGCCCCTTCGCTGTGAGGTAGAGCAACCACCATGTGCTTTTGAATCGAGCATCC
1322952 TTCATCTTGAAGTTGAAACTTGACTCTAAAAGCTGCAAAAACTTATGTATACAAAAAATGAAAAA
66 TTCATCTTGAAGTTGAAACTTGACTCTAAAAGCTGCAAAAACTTATGTATACAAAAAATGAAAAA
1323017 TGCGATGC
131 TGCGATGC
1323025 T
1 T
1323026 CTTAAGTATG
Statistics
Matches: 135, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
138 135 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (138 bp):
TGTCAGACAGTCGCCCCTTCGCTGTGAGGTAGAGCAACCACCATGTGCTTTTGAATCGAGCATCC
TTCATCTTGAAGTTGAAACTTGACTCTAAAAGCTGCAAAAACTTATGTATACAAAAAATGAAAAA
TGCGATGC
Found at i:1323276 original size:32 final size:33
Alignment explanation
Indices: 1323174--1323264 Score: 139
Period size: 32 Copynumber: 2.8 Consensus size: 33
1323164 ATTCCCAAAG
* * *
1323174 ATGCTCCAATATTCGATGTTGAATCTAAAAAAA
1 ATGCCCCAACATTTGATGTTGAATCTAAAAAAA
*
1323207 ATGCCCCAACATTTGATGTTAAATCT-AAAAAA
1 ATGCCCCAACATTTGATGTTGAATCTAAAAAAA
1323239 ATGCCCCAACATTTGATGTTGAATCT
1 ATGCCCCAACATTTGATGTTGAATCT
1323265 TCAAAGATGC
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
32 31 0.58
33 22 0.42
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (33 bp):
ATGCCCCAACATTTGATGTTGAATCTAAAAAAA
Found at i:1324297 original size:69 final size:69
Alignment explanation
Indices: 1324182--1324319 Score: 188
Period size: 69 Copynumber: 2.0 Consensus size: 69
1324172 TGTCTCTCTC
*
1324182 TTGATGCTCCATGATCTTCGAGTAGAGTGATGAAGTAATTCAGAAATGATTGTGTTTGATCAATC
1 TTGATGCTCCATGATCTTCGAGTAGAGTGATGAAGTAATTCAGAAATGATTGTGCTTGATCAATC
1324247 TCAT
66 TCAT
* * * ** * *
1324251 TTGATGCTCTATGATCTTTGAGT-GAAGTGGTTCAGTGATTCGGAAATGATTGTGCTTGATCAAT
1 TTGATGCTCCATGATCTTCGAGTAG-AGTGATGAAGTAATTCAGAAATGATTGTGCTTGATCAAT
1324315 CTCAT
65 CTCAT
1324320 AATTTAAATC
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
68 1 0.02
69 59 0.98
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (69 bp):
TTGATGCTCCATGATCTTCGAGTAGAGTGATGAAGTAATTCAGAAATGATTGTGCTTGATCAATC
TCAT
Found at i:1324416 original size:14 final size:13
Alignment explanation
Indices: 1324398--1324439 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 13
1324388 TTAATTTTCC
1324398 TTTTTTTCT-TTT
1 TTTTTTTCTCTTT
*
1324410 TTATTTTCTCTTT
1 TTTTTTTCTCTTT
1324423 GTTTTTTTCTCTTT
1 -TTTTTTTCTCTTT
1324437 TTT
1 TTT
1324440 GTCTTTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 8 0.31
13 6 0.23
14 12 0.46
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.83
Consensus pattern (13 bp):
TTTTTTTCTCTTT
Found at i:1324430 original size:21 final size:21
Alignment explanation
Indices: 1324380--1324430 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 21
1324370 TCTTGTCTTC
1324380 TTTTTTCTTTAATTTTCCTTT-
1 TTTTTT-TTTAATTTTCCTTTG
*
1324401 TTTTCTTTTTTATTTTCTCTTTG
1 TTTT-TTTTTAATTTTC-CTTTG
1324424 TTTTTTT
1 TTTTTTT
1324431 CTCTTTTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 13 0.50
22 9 0.35
23 4 0.15
ACGTcount: A:0.06, C:0.12, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTTTTTTTAATTTTCCTTTG
Found at i:1324448 original size:25 final size:26
Alignment explanation
Indices: 1324398--1324450 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
1324388 TTAATTTTCC
* *
1324398 TTTTTTTCTTTTTTATTTTCTCTTTG
1 TTTTTTTCTCTTTTATTGTCTCTTTG
*
1324424 TTTTTTTCTCTTTT-TTGTCTTTTTG
1 TTTTTTTCTCTTTTATTGTCTCTTTG
1324449 TT
1 TT
1324451 CTGATTGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.02, C:0.11, G:0.06, T:0.81
Consensus pattern (26 bp):
TTTTTTTCTCTTTTATTGTCTCTTTG
Found at i:1327560 original size:22 final size:22
Alignment explanation
Indices: 1327529--1327605 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 22
1327519 CAAACGTGAG
1327529 AATAATAAATAAAACAAG-AAAA
1 AATAA-AAATAAAACAAGTAAAA
1327551 AATGAAAAATAACAAAACAAGTAAAA
1 AAT-AAAAAT---AAAACAAGTAAAA
* *
1327577 AATAATAAT-AAA-AATTAAAAA
1 AATAAAAATAAAACAAGT-AAAA
1327598 AATAAAAA
1 AATAAAAA
1327606 AATGAATAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
20 3 0.07
21 14 0.30
22 7 0.15
23 2 0.04
25 13 0.28
26 7 0.15
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.16
Consensus pattern (22 bp):
AATAAAAATAAAACAAGTAAAA
Found at i:1327569 original size:25 final size:25
Alignment explanation
Indices: 1327539--1327587 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1327529 AATAATAAAT
1327539 AAAACAAG-AAAAAATGAAAAATAAC
1 AAAACAAGTAAAAAAT-AAAAATAAC
*
1327564 AAAACAAGTAAAAAATAATAATAA
1 AAAACAAGTAAAAAATAAAAATAA
1327588 AAATTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.12
Consensus pattern (25 bp):
AAAACAAGTAAAAAATAAAAATAAC
Found at i:1327604 original size:27 final size:27
Alignment explanation
Indices: 1327574--1327630 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
1327564 AAAACAAGTA
1327574 AAAAATAAT-AATAAAAAT-TAAAAAAAT
1 AAAAA-AATGAAT-AAAATGTAAAAAAAT
*
1327601 AAAAAAATGAATAAAATGTTAAAAAAT
1 AAAAAAATGAATAAAATGTAAAAAAAT
1327628 AAA
1 AAA
1327631 GACACAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 8 0.30
27 19 0.70
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (27 bp):
AAAAAAATGAATAAAATGTAAAAAAAT
Found at i:1327616 original size:18 final size:18
Alignment explanation
Indices: 1327574--1327617 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
1327564 AAAACAAGTA
*
1327574 AAAAATAATAATAAAAATT
1 AAAAA-AATAATAAAAATG
1327593 AAAAAAATAA-AAAAATG
1 AAAAAAATAATAAAAATG
*
1327610 AATAAAAT
1 AAAAAAAT
1327618 GTTAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 13 0.57
18 5 0.22
19 5 0.22
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.20
Consensus pattern (18 bp):
AAAAAAATAATAAAAATG
Found at i:1327895 original size:32 final size:34
Alignment explanation
Indices: 1327859--1327928 Score: 90
Period size: 35 Copynumber: 2.1 Consensus size: 34
1327849 ATATATATAT
1327859 AAATAAATAAAAA-CA-AAAATAGAATATTAAGA
1 AAATAAATAAAAAGCATAAAATAGAATATTAAGA
* * *
1327891 AAATATATAAAAATGTATAAAATATAATATTAAGA
1 AAATAAATAAAAA-GCATAAAATAGAATATTAAGA
1327926 AAA
1 AAA
1327929 AATATATACA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 12 0.38
34 1 0.03
35 19 0.59
ACGTcount: A:0.69, C:0.01, G:0.06, T:0.24
Consensus pattern (34 bp):
AAATAAATAAAAAGCATAAAATAGAATATTAAGA
Found at i:1327980 original size:2 final size:2
Alignment explanation
Indices: 1327959--1328063 Score: 126
Period size: 2 Copynumber: 53.5 Consensus size: 2
1327949 AGAAAAATTA
* * * * *
1327959 AT AT AT CT AT AC AT AC AT AT AT AT AT AT AG AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1328001 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1328042 GAT AT A- AG AT AT AT AT A- AT AT A
1 -AT AT AT AT AT AT AT AT AT AT AT A
1328064 AATAAAAAAA
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
1 3 0.03
2 83 0.94
3 2 0.02
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1328075 original size:25 final size:27
Alignment explanation
Indices: 1327997--1328075 Score: 74
Period size: 26 Copynumber: 3.0 Consensus size: 27
1327987 AGATATATAC
* * * *
1327997 ATATATATATATATAT-ATATATATAT
1 ATATATATATATATATAATAAAAAAAG
* * *
1328023 ATATATATATATATATAATGATATAAG
1 ATATATATATATATATAATAAAAAAAG
1328050 ATATATATA-ATATA-AATAAAAAAAG
1 ATATATATATATATATAATAAAAAAAG
1328075 A
1 A
1328076 GGAATATAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
25 9 0.21
26 21 0.50
27 12 0.29
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (27 bp):
ATATATATATATATATAATAAAAAAAG
Found at i:1335034 original size:4 final size:4
Alignment explanation
Indices: 1335025--1335049 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1335015 ACGATAAGAT
1335025 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
1335050 GAGTTACTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:1335242 original size:13 final size:14
Alignment explanation
Indices: 1335209--1335246 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
1335199 TAATTTTTAA
*
1335209 CAAATAGATTAAATT
1 CAAATA-ATTAAATC
1335224 CAAATAATTAAA-C
1 CAAATAATTAAATC
1335237 CAAATAATTA
1 CAAATAATTA
1335247 CTAGTGATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
14 6 0.27
15 6 0.27
ACGTcount: A:0.58, C:0.11, G:0.03, T:0.29
Consensus pattern (14 bp):
CAAATAATTAAATC
Found at i:1336160 original size:34 final size:34
Alignment explanation
Indices: 1336101--1336167 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
1336091 TTCTTGAGAG
*
1336101 TTGTTTTCTCCTTTTTATCAAGAGAGAA-TTGTTA
1 TTGTTTTCTCCTTTTGATC-AGAGAGAAGTTGTTA
1336135 TTGTTTTCTCCTTGTTAGATC-GAGAGAAGTTGT
1 TTGTTTTCTCCTT-TT-GATCAGAGAGAAGTTGT
1336168 AATTCCTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 20 0.69
35 6 0.21
36 3 0.10
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (34 bp):
TTGTTTTCTCCTTTTGATCAGAGAGAAGTTGTTA
Found at i:1339031 original size:3 final size:3
Alignment explanation
Indices: 1339025--1339089 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
1339015 TCATTTAAAT
** * *
1339025 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA GTA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1339073 TTA TATA TTA TTTA TTA
1 TTA T-TA TTA -TTA TTA
1339090 AATATTACAA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
3 46 0.88
4 6 0.12
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:1340652 original size:19 final size:19
Alignment explanation
Indices: 1340628--1340664 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1340618 GATATGTTTA
*
1340628 ATTTATATTTTAGATATTT
1 ATTTATATTTTAAATATTT
*
1340647 ATTTATTTTTTAAATATT
1 ATTTATATTTTAAATATT
1340665 GAAGGAAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
ATTTATATTTTAAATATTT
Found at i:1341337 original size:20 final size:21
Alignment explanation
Indices: 1341314--1341365 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
1341304 AGAAATTAAA
1341314 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
1341334 AATTCTTTTCTTTAAAATTTTT
1 AATTCATTTATTT-AAATTTTT
1341356 -ATT-ATTTATT
1 AATTCATTTATT
1341366 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:1348572 original size:114 final size:114
Alignment explanation
Indices: 1348364--1348588 Score: 351
Period size: 114 Copynumber: 2.0 Consensus size: 114
1348354 AAGTGCCATA
*
1348364 TGCTCATAGTAGAAATAAGGAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * * * * *
1348429 TGGTTTGGTATGAACTCCAAAATCAATCATTGGATTTGAAAGATGAATT
66 TGATTCGGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAATT
*
1348478 TGCTCATGGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* *
1348543 TGATTCGGTAGGAACCCCAGAACCGATCATTGGAATTAAAAGATGA
66 TGATTCGGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGA
1348589 GCTGCATGAT
Statistics
Matches: 100, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 100 1.00
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (114 bp):
TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGATTCGGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAATT
Found at i:1350741 original size:54 final size:54
Alignment explanation
Indices: 1350659--1350770 Score: 170
Period size: 54 Copynumber: 2.1 Consensus size: 54
1350649 CAATGATTGA
***
1350659 GAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGCACTGTCAAATGTTTTAC
** *
1350713 GAACATCTGAGCAGAAGCCACAGGAAAGGATGAATGCACTGTTAAATGTTTTAC
1 GAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGCACTGTCAAATGTTTTAC
1350767 GAAC
1 GAAC
1350771 CTGCTATTCG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.22
Consensus pattern (54 bp):
GAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGCACTGTCAAATGTTTTAC
Found at i:1351203 original size:22 final size:22
Alignment explanation
Indices: 1351135--1351214 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 22
1351125 TACATCTGCA
* *
1351135 CTTTTTAAAGATAATAGATTCT
1 CTTTTCAAAGATGATAGATTCT
** * * * *
1351157 CACTTCAGAGATGACAAATTTT
1 CTTTTCAAAGATGATAGATTCT
*
1351179 CTTTTTAAAGATGATAGATTCT
1 CTTTTCAAAGATGATAGATTCT
*
1351201 CTTTTCAAAAATGA
1 CTTTTCAAAGATGA
1351215 AAGCTTTATG
Statistics
Matches: 41, Mismatches: 17, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.40
Consensus pattern (22 bp):
CTTTTCAAAGATGATAGATTCT
Found at i:1352017 original size:76 final size:76
Alignment explanation
Indices: 1351891--1353364 Score: 2762
Period size: 76 Copynumber: 19.5 Consensus size: 76
1351881 CTATTTCCCA
*
1351891 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1351956 AGCCTTCGGGT
66 AGCCTTCGGGT
1351967 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1352031 AGCCTTCGGGT
66 AGCCTTCGGGT
1352042 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1352107 AGCCTTCGGGT
66 AGCCTTCGGGT
1352118 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1352183 AGCCTTCGGGT
66 AGCCTTCGGGT
1352194 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1352258 AGCCTTCGGGT
66 AGCCTTCGGGT
*
1352269 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAACGCCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1352333 AGCCTTTGGGT
66 AGCCTTCGGGT
* *
1352344 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCTTTCTGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1352409 AGCCTTCGGGT
66 AGCCTTCGGGT
* * *
1352420 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCTTTCTGGAGGTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1352485 AGCCTTCGGGT
66 AGCCTTCGGGT
1352496 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1352561 AGCCTTCGGGT
66 AGCCTTCGGGT
1352572 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1352637 AGCCTTCGGGT
66 AGCCTTCGGGT
*
1352648 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1352713 AGCCTTCGGGT
66 AGCCTTCGGGT
*
1352724 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1352788 AGCCTTCGGGT
66 AGCCTTCGGGT
1352799 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1352864 AGCCTTCGGGT
66 AGCCTTCGGGT
1352875 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1352940 AGCCTTCGGGT
66 AGCCTTCGGGT
1352951 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1353015 AGCCTGCGGGT
66 AGCCTTCGGGT
1353026 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1353091 AGCCTTCGGGT
66 AGCCTTCGGGT
1353102 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1353167 AGCCTTCGGGT
66 AGCCTTCGGGT
*
1353178 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1353243 AGCCTTCGGGT
66 AGCCTTCGGGT
*
1353254 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1353319 AACC-TCAGGGT
66 AGCCTTC-GGGT
*
1353330 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
1353365 CATTTCCATC
Statistics
Matches: 1372, Mismatches: 21, Indels: 10
0.98 0.01 0.01
Matches are distributed among these distances:
75 370 0.27
76 1002 0.73
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:1352286 original size:227 final size:227
Alignment explanation
Indices: 1351891--1353364 Score: 2756
Period size: 227 Copynumber: 6.5 Consensus size: 227
1351881 CTATTTCCCA
*
1351891 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1351956 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
1352021 GATG-TTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
1352085 GGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
196 GGGAGCTTTTTGATG-TTTCAAAGCCTTCGGGT
1352118 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1352183 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
1352248 GATG-TTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAACGCCTTC
131 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
*
1352312 GGGAGCTTTTTGATGTTTCAAAGCCTTTGGGT
196 GGGAGCTTTTTGATGTTTCAAAGCCTTCGGGT
* *
1352344 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCTTTCTGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* * *
1352409 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCTTTCTGGAGGTTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
1352474 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
1352539 GGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
196 GGGAGCTTTTTGATG-TTTCAAAGCCTTCGGGT
1352572 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1352637 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
1352702 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
1352767 GGGAGCTTTTTGATGTTTCAAAGCCTTCGGGT
196 GGGAGCTTTTTGATGTTTCAAAGCCTTCGGGT
1352799 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1352864 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
1352929 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
*
1352994 GGGAGCTTTTTGATGTTTCAAAGCCTGCGGGT
196 GGGAGCTTTTTGATGTTTCAAAGCCTTCGGGT
1353026 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1353091 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
1353156 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
1353221 GGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
196 GGGAGCTTTTTGATG-TTTCAAAGCCTTCGGGT
*
1353254 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
1353319 AACC-TCAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAA
66 AGCCTTC-GGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
1353365 CATTTCCATC
Statistics
Matches: 1218, Mismatches: 25, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
226 145 0.12
227 733 0.60
228 340 0.28
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.35
Consensus pattern (227 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
GGGAGCTTTTTGATGTTTCAAAGCCTTCGGGT
Found at i:1353498 original size:3 final size:3
Alignment explanation
Indices: 1353492--1353556 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
1353482 TCATTTAAAT
** * *
1353492 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA GTA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1353540 TTA TATA TTA TTTA TTA
1 TTA T-TA TTA -TTA TTA
1353557 AATATTACAA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
3 46 0.88
4 6 0.12
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:1355037 original size:4 final size:4
Alignment explanation
Indices: 1355030--1355054 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1355020 TAATAAATAA
1355030 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
1355055 TCTATGAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:1355120 original size:19 final size:19
Alignment explanation
Indices: 1355096--1355132 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1355086 GATATGTTTA
*
1355096 ATTTATATTTTAGATATTT
1 ATTTATATTTTAAATATTT
*
1355115 ATTTATTTTTTAAATATT
1 ATTTATATTTTAAATATT
1355133 GAAGGAAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
ATTTATATTTTAAATATTT
Found at i:1359759 original size:229 final size:227
Alignment explanation
Indices: 1359354--1359802 Score: 799
Period size: 229 Copynumber: 2.0 Consensus size: 227
1359344 GTAAATTATC
* * *
1359354 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
*
1359419 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
1359484 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
1359549 AAACATAAATTACATAACTTTTAAAAAAGTATA
196 AAACATAAATTACATAAC-TTTAAAAAAGTATA
*
1359582 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
* *
1359647 TTAATATTTTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATT
* *
1359712 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
1359777 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
1359803 GCAGTTTTAA
Statistics
Matches: 211, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
228 43 0.20
229 168 0.80
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:1359891 original size:20 final size:19
Alignment explanation
Indices: 1359868--1359913 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
1359858 CGATATACCA
1359868 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
1359888 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
1359908 GGTAAA
1 GGTAAA
1359914 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1360058 original size:20 final size:19
Alignment explanation
Indices: 1360035--1360081 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1360025 CGATATAACA
1360035 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
1360055 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
1360075 GGTAAAA
1 GGTAAAA
1360082 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1360083 original size:17 final size:19
Alignment explanation
Indices: 1360044--1360086 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1360034 AGGTAAAAAT
1360044 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
1360064 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
1360081 ATGATA
1 ATGATA
1360087 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:1362356 original size:21 final size:21
Alignment explanation
Indices: 1362309--1362373 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
1362299 AAGATAATCA
* *
1362309 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
1362331 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
1362351 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
1362372 AG
1 AG
1362374 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:1362449 original size:33 final size:33
Alignment explanation
Indices: 1362407--1362472 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1362397 AAATAGATGG
1362407 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
1362440 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1362473 TATTAAGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1365052 original size:23 final size:23
Alignment explanation
Indices: 1365021--1365169 Score: 208
Period size: 23 Copynumber: 6.5 Consensus size: 23
1365011 ATAGGTAAAC
*
1365021 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1365044 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
1365067 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1365090 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
1365113 TTATAATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1365136 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
1365159 ATATATTGTAA
1 ATATAATGTAA
1365170 AGTATCTATC
Statistics
Matches: 110, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 110 1.00
ACGTcount: A:0.34, C:0.05, G:0.19, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1365080 original size:46 final size:46
Alignment explanation
Indices: 1365021--1365169 Score: 262
Period size: 46 Copynumber: 3.2 Consensus size: 46
1365011 ATAGGTAAAC
*
1365021 ATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
*
1365067 ATATAATGTAATAGGTAGTGCTTATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
*
1365113 TTATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
*
1365159 ATATATTGTAA
1 ATATAATGTAA
1365170 AGTATCTATC
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 97 1.00
ACGTcount: A:0.34, C:0.05, G:0.19, T:0.41
Consensus pattern (46 bp):
ATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
Found at i:1365613 original size:18 final size:18
Alignment explanation
Indices: 1365592--1365628 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1365582 GTAATTGGAG
1365592 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1365610 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
1365628 T
1 T
1365629 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1365636 original size:24 final size:24
Alignment explanation
Indices: 1365584--1365630 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1365574 TTTCATATGT
* *
1365584 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
1365608 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
1365631 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:1366386 original size:23 final size:23
Alignment explanation
Indices: 1366355--1366427 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
1366345 ATAGGTAAAA
*
1366355 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
1366378 ATATAATGTAATAAGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1366401 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
1366424 ATAT
1 ATAT
1366428 TGTAAAGTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1376452 original size:11 final size:11
Alignment explanation
Indices: 1376438--1376464 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1376428 CCAAAATGAC
1376438 CAACAAATTCG
1 CAACAAATTCG
1376449 CAACAAATTCG
1 CAACAAATTCG
1376460 CAACA
1 CAACA
1376465 CGAACTCCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.30, G:0.07, T:0.15
Consensus pattern (11 bp):
CAACAAATTCG
Found at i:1376520 original size:20 final size:21
Alignment explanation
Indices: 1376496--1376704 Score: 181
Period size: 20 Copynumber: 10.4 Consensus size: 21
1376486 AGTTTCTAAT
1376496 TTCGCAACGCGAATATGT-AAA
1 TTCGCAACGCG-ATATGTCAAA
* *
1376517 -TCGCAACAC-ATAAGTCAAA
1 TTCGCAACGCGATATGTCAAA
1376536 TTCGCAACGCGATA-GTCAAA
1 TTCGCAACGCGATATGTCAAA
* * *
1376556 TTCGCAACAC-AAAAGTCAAA
1 TTCGCAACGCGATATGTCAAA
1376576 TTCGCAACGCGAT-TGTCAAA
1 TTCGCAACGCGATATGTCAAA
* *
1376596 TTCGCAATGCGAATCTGT-AAA
1 TTCGCAACGCG-ATATGTCAAA
* *
1376617 -TCGTAACGCGAATTTGT-AAA
1 TTCGCAACGCG-ATATGTCAAA
* * *
1376637 -TCGCAACAC-ATAAGTTAAA
1 TTCGCAACGCGATATGTCAAA
1376656 TTCGCAACGCGATA-GTCAAA
1 TTCGCAACGCGATATGTCAAA
* *
1376676 TTCGCAACGCGAAATTTCAAA
1 TTCGCAACGCGATATGTCAAA
1376697 TTCGCAAC
1 TTCGCAAC
1376705 TAGATTTTTG
Statistics
Matches: 157, Mismatches: 20, Indels: 22
0.79 0.10 0.11
Matches are distributed among these distances:
18 9 0.06
19 8 0.05
20 112 0.71
21 25 0.16
22 3 0.02
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.22
Consensus pattern (21 bp):
TTCGCAACGCGATATGTCAAA
Found at i:1376540 original size:40 final size:41
Alignment explanation
Indices: 1376496--1376683 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 41
1376486 AGTTTCTAAT
1376496 TTCGCAACGCGAATATGT-AAA-TCGCAACACATAAGTCAAA
1 TTCGCAACGCG-ATATGTCAAATTCGCAACACATAAGTCAAA
*
1376536 TTCGCAACGCGATA-GTCAAATTCGCAACACAAAAGTCAAA
1 TTCGCAACGCGATATGTCAAATTCGCAACACATAAGTCAAA
**
1376576 TTCGCAACGCGAT-TGTCAAATTCGCAATGCGA-ATCTGT-AAA
1 TTCGCAACGCGATATGTCAAATTCGCAA--C-ACATAAGTCAAA
* * *
1376617 -TCGTAACGCGAATTTGT-AAA-TCGCAACACATAAGTTAAA
1 TTCGCAACGCG-ATATGTCAAATTCGCAACACATAAGTCAAA
1376656 TTCGCAACGCGATA-GTCAAATTCGCAAC
1 TTCGCAACGCGATATGTCAAATTCGCAAC
1376684 GCGAAATTTC
Statistics
Matches: 126, Mismatches: 9, Indels: 26
0.78 0.06 0.16
Matches are distributed among these distances:
37 1 0.01
38 9 0.07
39 14 0.11
40 86 0.68
41 8 0.06
42 7 0.06
43 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.22
Consensus pattern (41 bp):
TTCGCAACGCGATATGTCAAATTCGCAACACATAAGTCAAA
Found at i:1376719 original size:41 final size:38
Alignment explanation
Indices: 1376674--1376763 Score: 110
Period size: 41 Copynumber: 2.3 Consensus size: 38
1376664 GCGATAGTCA
*
1376674 AATTCGCAACGCGAAATTTCAAATTCGCAACTAGATTTTTG
1 AATTCGCAACACG-AATTT-AAATTCGCAAC-AGATTTTTG
* *
1376715 AATTCGCAACACGAATTTAATTTCGCAACAGATTTTAG
1 AATTCGCAACACGAATTTAAATTCGCAACAGATTTTTG
*
1376753 -TTTCGCAACAC
1 AATTCGCAACAC
1376764 AAATGTTTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
37 10 0.22
38 8 0.18
39 10 0.22
40 5 0.11
41 12 0.27
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.31
Consensus pattern (38 bp):
AATTCGCAACACGAATTTAAATTCGCAACAGATTTTTG
Found at i:1376740 original size:80 final size:80
Alignment explanation
Indices: 1376557--1376743 Score: 202
Period size: 80 Copynumber: 2.3 Consensus size: 80
1376547 ATAGTCAAAT
* * * * *
1376557 TCGCAACACAAAAGTCAAATTCGCAACGCGATTGTCAAATTCGCAATGCGAATCTGTAAATCGTA
1 TCGCAACACAGAAGTTAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAATCTGTAAATCGCA
*
1376622 ACGCGAATTTGTAAA
66 ACGAGAATTTGTAAA
*
1376637 TCGCAACACATAAGTTAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAAAT-T-TCAAATTC
1 TCGCAACACAGAAGTTAAATTCGCAACGCGATAGTCAAATTCGCAACGCG-AATCTGT-AAA-TC
* * *
1376700 GCAACTAG-ATTTTTGAAT
63 GCAACGAGAATTTGT-AAA
* *
1376718 TCGCAACAC-GAATTTAATTTCGCAAC
1 TCGCAACACAGAAGTTAAATTCGCAAC
1376744 AGATTTTAGT
Statistics
Matches: 91, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
79 1 0.01
80 69 0.76
81 21 0.23
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.26
Consensus pattern (80 bp):
TCGCAACACAGAAGTTAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAATCTGTAAATCGCA
ACGAGAATTTGTAAA
Found at i:1376751 original size:18 final size:18
Alignment explanation
Indices: 1376697--1376762 Score: 71
Period size: 18 Copynumber: 3.5 Consensus size: 18
1376687 AAATTTCAAA
1376697 TTCGCAACTAGATTTTTGAA-
1 TTCGCAAC-AGA-TTTT-AAT
*
1376717 TTCGCAACACGAATTTAAT
1 TTCGCAACA-GATTTTAAT
*
1376736 TTCGCAACAGATTTTAGT
1 TTCGCAACAGATTTTAAT
1376754 TTCGCAACA
1 TTCGCAACA
1376763 CAAATGTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
18 18 0.44
19 13 0.32
20 10 0.24
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.35
Consensus pattern (18 bp):
TTCGCAACAGATTTTAAT
Found at i:1377552 original size:12 final size:12
Alignment explanation
Indices: 1377531--1377564 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1377521 ACCACATTTC
*
1377531 CAATACCAAACA
1 CAATATCAAACA
1377543 CAATATCAAACA
1 CAATATCAAACA
*
1377555 CAATCTCAAA
1 CAATATCAAA
1377565 ACCCACAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1382042 original size:21 final size:21
Alignment explanation
Indices: 1382018--1382116 Score: 112
Period size: 21 Copynumber: 4.7 Consensus size: 21
1382008 GCGGGCGAGA
*
1382018 CCTCTTGAACGATGACAGGGG
1 CCTCTTGAACGATGAGAGGGG
* *
1382039 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGAGAGGGG
*
1382060 CCTCTTCG-ATGATGAGAGGGG
1 CCTCTT-GAACGATGAGAGGGG
*
1382081 CCTCTTGAACGAT-AGGAGGCG
1 CCTCTTGAACGATGA-GAGGGG
*
1382102 CCTCTTGAATGATGA
1 CCTCTTGAACGATGA
1382117 TAGGTGCATC
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
20 2 0.03
21 61 0.94
22 2 0.03
ACGTcount: A:0.21, C:0.21, G:0.35, T:0.22
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:1382064 original size:42 final size:42
Alignment explanation
Indices: 1381998--1382116 Score: 141
Period size: 42 Copynumber: 2.8 Consensus size: 42
1381988 GTGAATCGGG
* * * * *
1381998 CTCTTGAACGGCGGGCGAGACCTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGCCTCTTGAATGATGACAGGGGC
*
1382040 CTCTTGAACGGTGGGAGGGGCCTCTTCG-ATGATGAGAGGGGC
1 CTCTTGAACGGTGGGAGGGGCCTCTT-GAATGATGACAGGGGC
* * *
1382082 CTCTTGAACGATAGGAGGCGCCTCTTGAATGATGA
1 CTCTTGAACGGTGGGAGGGGCCTCTTGAATGATGA
1382117 TAGGTGCATC
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
41 1 0.02
42 64 0.97
43 1 0.02
ACGTcount: A:0.21, C:0.22, G:0.36, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGCCTCTTGAATGATGACAGGGGC
Found at i:1384766 original size:22 final size:21
Alignment explanation
Indices: 1384720--1384770 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
1384710 TCTGAGAGAT
*
1384720 GGAGAT-GGACGGATTTCGCC
1 GGAGATGGGACGAATTTCGCC
* *
1384740 AGAGATGGGAACGAATTTCGTC
1 GGAGATGGG-ACGAATTTCGCC
1384762 GGAGATGGG
1 GGAGATGGG
1384771 GACGGATGTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 5 0.20
21 2 0.08
22 18 0.72
ACGTcount: A:0.25, C:0.14, G:0.41, T:0.20
Consensus pattern (21 bp):
GGAGATGGGACGAATTTCGCC
Found at i:1384782 original size:22 final size:22
Alignment explanation
Indices: 1384726--1384782 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
1384716 AGATGGAGAT
*
1384726 GGACGGATTTCGCCAGAGATGG
1 GGACGGATTTCGTCAGAGATGG
* * *
1384748 GAACGAATTTCGTCGGAGATGG
1 GGACGGATTTCGTCAGAGATGG
*
1384770 GGACGGATGTCGT
1 GGACGGATTTCGT
1384783 TGTAGAGAGT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.23, C:0.16, G:0.40, T:0.21
Consensus pattern (22 bp):
GGACGGATTTCGTCAGAGATGG
Found at i:1384917 original size:20 final size:20
Alignment explanation
Indices: 1384892--1385081 Score: 147
Period size: 20 Copynumber: 9.4 Consensus size: 20
1384882 ATTGTGTTTC
*
1384892 GCGTTGCAAATTTGACTATT
1 GCGTTGCGAATTTGACTATT
*
1384912 GCGTTGCGAATTTGACTTTT
1 GCGTTGCGAATTTGACTATT
* *
1384932 GTGTTGCGAATTTGA-AATT
1 GCGTTGCGAATTTGACTATT
* *
1384951 CAGTGTTGCGAATTTGACTATC
1 --GCGTTGCGAATTTGACTATT
* * *
1384973 GCGCTGCGAATTTGATTTTT
1 GCGTTGCGAATTTGACTATT
* **
1384993 GTGTTGCGGCTTTGACTATT
1 GCGTTGCGAATTTGACTATT
* *
1385013 GCGTTGCGATTTTGACTTTT
1 GCGTTGCGAATTTGACTATT
* *
1385033 GTGTTGCG-ATTT-ACAAATT
1 GCGTTGCGAATTTGAC-TATT
1385052 CGCGTTGCG-ATTT-ACATATT
1 -GCGTTGCGAATTTGAC-TATT
1385072 CGCGTTGCGA
1 -GCGTTGCGA
1385082 TATTGGAAAC
Statistics
Matches: 136, Mismatches: 28, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
18 2 0.01
19 7 0.05
20 110 0.81
21 15 0.11
22 2 0.01
ACGTcount: A:0.18, C:0.15, G:0.25, T:0.42
Consensus pattern (20 bp):
GCGTTGCGAATTTGACTATT
Found at i:1384958 original size:21 final size:21
Alignment explanation
Indices: 1384914--1384967 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
1384904 TGACTATTGC
* **
1384914 GTTGCGAATTTG-ACTTTTGT
1 GTTGCGAATTTGAAATTCAGT
1384934 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTGAAATTCAGT
1384955 GTTGCGAATTTGA
1 GTTGCGAATTTGA
1384968 CTATCGCGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.40
21 18 0.60
ACGTcount: A:0.22, C:0.09, G:0.26, T:0.43
Consensus pattern (21 bp):
GTTGCGAATTTGAAATTCAGT
Found at i:1385098 original size:20 final size:20
Alignment explanation
Indices: 1385075--1385121 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
1385065 ACATATTCGC
1385075 GTTGCGATATTGGAAACTGG
1 GTTGCGATATTGGAAACTGG
1385095 GTTGCGATATTGGAAACTGG
1 GTTGCGATATTGGAAACTGG
1385115 GTTGCGA
1 GTTGCGA
1385122 ATTTGTTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.23, C:0.11, G:0.36, T:0.30
Consensus pattern (20 bp):
GTTGCGATATTGGAAACTGG
Found at i:1389251 original size:34 final size:33
Alignment explanation
Indices: 1389208--1389290 Score: 139
Period size: 34 Copynumber: 2.5 Consensus size: 33
1389198 CGAGGATTTG
*
1389208 GTGTTTCAAGAGAAACATTTTCAAAGGTTTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGG-TTTTTT
1389242 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTT
*
1389275 GTATTTCAAGAGAAAC
1 GTGTTTCAAGAGAAAC
1389291 TGTATTCAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
33 21 0.45
34 26 0.55
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.39
Consensus pattern (33 bp):
GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTT
Found at i:1389299 original size:34 final size:33
Alignment explanation
Indices: 1389211--1389300 Score: 119
Period size: 34 Copynumber: 2.6 Consensus size: 33
1389201 GGATTTGGTG
*
1389211 TTTCAAGAGAAACATTTTCAAAGGTTTTTTTGTG
1 TTTCAAGAGAAAC-TTTTCAAAGGTTTTTTTGTA
*
1389245 TTTCAAGAGAAACAATTTCAAAGG-TTTTTTGTA
1 TTTCAAGAGAAAC-TTTTCAAAGGTTTTTTTGTA
1389278 TTTCAAGAGAAACTGTATTCAAA
1 TTTCAAGAGAAACT-T-TTCAAA
1389301 TATTGAAGTT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
33 22 0.43
34 29 0.57
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.39
Consensus pattern (33 bp):
TTTCAAGAGAAACTTTTCAAAGGTTTTTTTGTA
Done.