Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 5 of 82
Found at i:1419519 original size:3 final size:3
Alignment explanation
Indices: 1419513--1419537 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1419503 TTCTTCTCCC
1419513 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
1419538 CATTAAAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:1421754 original size:67 final size:67
Alignment explanation
Indices: 1421646--1421779 Score: 189
Period size: 67 Copynumber: 2.0 Consensus size: 67
1421636 ACCACTTTCT
* * *
1421646 GACTCCTGCATTTTCATAATCCCATATTCTTCGAAATAAGCACAATTTAATATGAAAATAAGGCA
1 GACTCCTGCATATTCATAATCCCATATTCGTCGAAATAAGCACAATTTAATATGAAAAGAAGGCA
1421711 TA
66 TA
* ** *
1421713 GACTCCTGCATATTCGTAATCTGATATTCGGT-GAAATAAGCAGAATTTAATATGAAAAGAAGGC
1 GACTCCTGCATATTCATAATCCCATATTC-GTCGAAATAAGCACAATTTAATATGAAAAGAAGGC
1421777 ATA
65 ATA
1421780 ATAATTAAGA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
67 58 0.98
68 1 0.02
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (67 bp):
GACTCCTGCATATTCATAATCCCATATTCGTCGAAATAAGCACAATTTAATATGAAAAGAAGGCA
TA
Found at i:1440488 original size:153 final size:153
Alignment explanation
Indices: 1440303--1440583 Score: 454
Period size: 153 Copynumber: 1.8 Consensus size: 153
1440293 AGTAAGAAAT
* * *
1440303 GAGGCTACAATAAAAATAATCAAGATGAAAACCATCAGATTATCAGAATATTTCATCCTAACTCA
1 GAGGCTACAAAAAAAATAATCAAGATGAAAACCATCAAATTATCAGAATATTTCATCCTAACCCA
* *
1440368 CATAAGTAACTATTTAGCTATACTAACCCTTCCTTCAACCAAGTCCTATGTGTCAATGTTTACTA
66 AATAAGTAACTATTTAGCTATACTAACCCTTCCTTCAACCAAGTCCTATGTGCCAATGTTTACTA
1440433 AAATCTTAACCTAAGTAAAAGAA
131 AAATCTTAACCTAAGTAAAAGAA
*
1440456 GAGGCTGCAAAAAAAATAATCAAGATGAAAACCATCAAATTATCAGAATATTTCATCCTAACCCA
1 GAGGCTACAAAAAAAATAATCAAGATGAAAACCATCAAATTATCAGAATATTTCATCCTAACCCA
* * * ** *
1440521 AATAGGTAACTGTTTAGCTATACTAACCCTTCCTTCAACTAAGTTTTGTGTGCCAATGTTTAC
66 AATAAGTAACTATTTAGCTATACTAACCCTTCCTTCAACCAAGTCCTATGTGCCAATGTTTAC
1440584 CAAACACTTT
Statistics
Matches: 116, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
153 116 1.00
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (153 bp):
GAGGCTACAAAAAAAATAATCAAGATGAAAACCATCAAATTATCAGAATATTTCATCCTAACCCA
AATAAGTAACTATTTAGCTATACTAACCCTTCCTTCAACCAAGTCCTATGTGCCAATGTTTACTA
AAATCTTAACCTAAGTAAAAGAA
Found at i:1448643 original size:14 final size:14
Alignment explanation
Indices: 1448613--1448643 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1448603 CAACGCAATG
*
1448613 AAATAAAAAAATTA
1 AAATAAAAAAATAA
1448627 AAATAAAAAAATAA
1 AAATAAAAAAATAA
1448641 AAA
1 AAA
1448644 CCATGCCTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (14 bp):
AAATAAAAAAATAA
Found at i:1459593 original size:51 final size:51
Alignment explanation
Indices: 1459490--1459620 Score: 131
Period size: 51 Copynumber: 2.6 Consensus size: 51
1459480 AGAATAATAT
* * * * *
1459490 AAAATGACCTTGACTTGAATCTATCGATAGATAAGCATCTGAGAACATTTC
1 AAAATGATCTTAACTTGAATCTATCGATAGATAAGCACCCGAGAACACTTC
* * *
1459541 -AAATGGATCTTAACTTGTATCTATCGATAGAT-AGCCACCCGAGGATACTTC
1 AAAAT-GATCTTAACTTGAATCTATCGATAGATAAG-CACCCGAGAACACTTC
* * *
1459592 AAAATGATCTTGAGTTGAATTTATCGATA
1 AAAATGATCTTAACTTGAATCTATCGATA
1459621 TATATTTACA
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
50 6 0.09
51 55 0.85
52 4 0.06
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (51 bp):
AAAATGATCTTAACTTGAATCTATCGATAGATAAGCACCCGAGAACACTTC
Found at i:1464325 original size:31 final size:32
Alignment explanation
Indices: 1464288--1464369 Score: 112
Period size: 32 Copynumber: 2.6 Consensus size: 32
1464278 AGCAGCAGCC
**
1464288 AAAACATCAAGAAAAAAAA-TTCAAAGAAATA
1 AAAACATCAAGAAAAAAAAGTAAAAAGAAATA
* * *
1464319 AGAACATTAGGAAAAAAAAGTAAAAAGAAATA
1 AAAACATCAAGAAAAAAAAGTAAAAAGAAATA
1464351 AAAACATCAAGAAAAAAAA
1 AAAACATCAAGAAAAAAAA
1464370 ACATTTAAAG
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 16 0.38
32 26 0.62
ACGTcount: A:0.72, C:0.07, G:0.10, T:0.11
Consensus pattern (32 bp):
AAAACATCAAGAAAAAAAAGTAAAAAGAAATA
Found at i:1464370 original size:16 final size:16
Alignment explanation
Indices: 1464288--1464373 Score: 59
Period size: 16 Copynumber: 5.4 Consensus size: 16
1464278 AGCAGCAGCC
1464288 AAAACATCAAG-AAAA
1 AAAACATCAAGAAAAA
* *
1464303 AAAA-TTCAAAGAAATA
1 AAAACATC-AAGAAAAA
* * *
1464319 AGAACATTAGGAAAAA
1 AAAACATCAAGAAAAA
** ** *
1464335 AAAGTAAAAAGAAATA
1 AAAACATCAAGAAAAA
1464351 AAAACATCAAGAAAAA
1 AAAACATCAAGAAAAA
1464367 AAAACAT
1 AAAACAT
1464374 TTAAAGAAAA
Statistics
Matches: 49, Mismatches: 19, Indels: 5
0.67 0.26 0.07
Matches are distributed among these distances:
14 2 0.04
15 7 0.14
16 39 0.80
17 1 0.02
ACGTcount: A:0.71, C:0.08, G:0.09, T:0.12
Consensus pattern (16 bp):
AAAACATCAAGAAAAA
Found at i:1468233 original size:26 final size:26
Alignment explanation
Indices: 1468153--1468280 Score: 65
Period size: 25 Copynumber: 5.1 Consensus size: 26
1468143 ATTTTAATAG
* *
1468153 TAATATTTATTATGAAAATATTGAGAAA
1 TAATATTTATTATTAAAA-ATT-AAAAA
* * *
1468181 T-A-A-TTATTATGAATAA-TAAATAT
1 TAATATTTATTATTAAAAATTAAA-AA
1468204 TAATATTTATTATTAAAAATTAAAAA
1 TAATATTTATTATTAAAAATTAAAAA
* * * *
1468230 TAAT-TATA-TATTTAAAGTGATAAAA
1 TAATATTTATTATTAAAAATTA-AAAA
* *
1468255 -AAT-TTTATTATTAAATAGTAAAAA
1 TAATATTTATTATTAAAAATTAAAAA
1468279 TA
1 TA
1468281 GCAATATAAT
Statistics
Matches: 76, Mismatches: 16, Indels: 19
0.68 0.14 0.17
Matches are distributed among these distances:
22 2 0.03
23 3 0.04
24 21 0.28
25 27 0.36
26 17 0.22
27 5 0.07
28 1 0.01
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.41
Consensus pattern (26 bp):
TAATATTTATTATTAAAAATTAAAAA
Found at i:1468278 original size:24 final size:24
Alignment explanation
Indices: 1468204--1468280 Score: 68
Period size: 24 Copynumber: 3.1 Consensus size: 24
1468194 TAATAAATAT
*
1468204 TAATATTTATTATTAAAAATTAAAAA
1 TAAT-TTTATTATT-AAAAGTAAAAA
* *
1468230 TAATTATA-TATTTAAAGTGATAAAA
1 TAATTTTATTATTAAAAGT-A-AAAA
1468255 -AATTTTATTATTAAATAGTAAAAA
1 TAATTTTATTATTAAA-AGTAAAAA
1468279 TA
1 TA
1468281 GCAATATAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
23 4 0.10
24 15 0.37
25 15 0.37
26 7 0.17
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (24 bp):
TAATTTTATTATTAAAAGTAAAAA
Found at i:1479210 original size:31 final size:31
Alignment explanation
Indices: 1479175--1479234 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
1479165 AGTCATTATT
1479175 TTTTAA-TTACAT-TCAATCAAATTTTTATATC
1 TTTTAATTTA-ATCTCAAT-AAATTTTTATATC
*
1479206 TTTTAATTTAATCTGAATAAATTTTTATA
1 TTTTAATTTAATCTCAATAAATTTTTATA
1479235 AATAATAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 19 0.73
32 7 0.27
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (31 bp):
TTTTAATTTAATCTCAATAAATTTTTATATC
Found at i:1484752 original size:15 final size:15
Alignment explanation
Indices: 1484734--1484764 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1484724 GCTTCAATTC
*
1484734 TTTTTTCTTTTGTTT
1 TTTTTTATTTTGTTT
1484749 TTTTTTATTTTGTTT
1 TTTTTTATTTTGTTT
1484764 T
1 T
1484765 GATAGCTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.03, C:0.03, G:0.06, T:0.87
Consensus pattern (15 bp):
TTTTTTATTTTGTTT
Found at i:1487978 original size:30 final size:30
Alignment explanation
Indices: 1487944--1488012 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
1487934 GGTGATTCCA
1487944 GGTGATGGTGTGGCTCCCCCTCT-ATACCCT
1 GGTGATGGTGTGGCTCCCCCTCTAAT-CCCT
*
1487974 GGTGATGGTGTGGTTCCCCCTCTAATCCCT
1 GGTGATGGTGTGGCTCCCCCTCTAATCCCT
*
1488004 GGTGGTGGT
1 GGTGATGGT
1488013 ATTATTCCCC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 34 0.94
31 2 0.06
ACGTcount: A:0.09, C:0.28, G:0.32, T:0.32
Consensus pattern (30 bp):
GGTGATGGTGTGGCTCCCCCTCTAATCCCT
Found at i:1488021 original size:30 final size:30
Alignment explanation
Indices: 1487944--1488024 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
1487934 GGTGATTCCA
* **
1487944 GGTGATGGTGTGGCTCCCCCTCTATACCCT
1 GGTGATGGTATGATTCCCCCTCTATACCCT
* *
1487974 GGTGATGGTGTGGTTCCCCCTCTA-ATCCCT
1 GGTGATGGTATGATTCCCCCTCTATA-CCCT
* *
1488004 GGTGGTGGTATTATTCCCCCT
1 GGTGATGGTATGATTCCCCCT
1488025 TTCATTCCAG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
29 1 0.02
30 44 0.98
ACGTcount: A:0.10, C:0.30, G:0.27, T:0.33
Consensus pattern (30 bp):
GGTGATGGTATGATTCCCCCTCTATACCCT
Found at i:1489006 original size:47 final size:47
Alignment explanation
Indices: 1488948--1489037 Score: 162
Period size: 47 Copynumber: 1.9 Consensus size: 47
1488938 TTTGGCTATA
1488948 TATAACTTTAATGTTTTCACTTGTTTATGTAGAATCAAGAAATGTTG
1 TATAACTTTAATGTTTTCACTTGTTTATGTAGAATCAAGAAATGTTG
* *
1488995 TATAATTTTAATGTTTTCACTTTTTTATGTAGAATCAAGAAAT
1 TATAACTTTAATGTTTTCACTTGTTTATGTAGAATCAAGAAAT
1489038 TCTGTCATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (47 bp):
TATAACTTTAATGTTTTCACTTGTTTATGTAGAATCAAGAAATGTTG
Found at i:1492706 original size:21 final size:21
Alignment explanation
Indices: 1492682--1492741 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1492672 GTGACTAGTT
*
1492682 TTTAGGCATTGCGTGACTGAC
1 TTTAGGTATTGCGTGACTGAC
* * *
1492703 TTTAGATATTTCGTGATTGAC
1 TTTAGGTATTGCGTGACTGAC
1492724 TTT-GGATATTGCGTGACT
1 TTTAGG-TATTGCGTGACT
1492742 AATTTTTGAT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.20, C:0.13, G:0.25, T:0.42
Consensus pattern (21 bp):
TTTAGGTATTGCGTGACTGAC
Found at i:1492752 original size:21 final size:21
Alignment explanation
Indices: 1492689--1492752 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
1492679 GTTTTTAGGC
* *
1492689 ATTGCGTGACTGACTTTAGAT
1 ATTGCGTGACTAACTTTTGAT
* * * *
1492710 ATTTCGTGATTGACTTTGGAT
1 ATTGCGTGACTAACTTTTGAT
*
1492731 ATTGCGTGACTAATTTTTGAT
1 ATTGCGTGACTAACTTTTGAT
1492752 A
1 A
1492753 AGACATTGCG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.23, C:0.11, G:0.22, T:0.44
Consensus pattern (21 bp):
ATTGCGTGACTAACTTTTGAT
Found at i:1492760 original size:26 final size:26
Alignment explanation
Indices: 1492731--1493014 Score: 269
Period size: 26 Copynumber: 11.6 Consensus size: 26
1492721 GACTTTGGAT
* *
1492731 ATTGCGTGACTAATTTTTGATAAGAC
1 ATTGCGTGACTAGTTTTTGATAAGGC
* * *
1492757 ATTGCGTGATTAGTTTATGATAAGGT
1 ATTGCGTGACTAGTTTTTGATAAGGC
1492783 ATTGCGTGACTAG---TTGAT-AGGC
1 ATTGCGTGACTAGTTTTTGATAAGGC
*
1492805 ATTGCGTGACTAGTTTTTGATAAGAC
1 ATTGCGTGACTAGTTTTTGATAAGGC
* * *
1492831 ATTGCGTGACTAGTTTCTAATAGGGC
1 ATTGCGTGACTAGTTTTTGATAAGGC
*
1492857 ATTGCGTGACTAG---TTGAT-AGGT
1 ATTGCGTGACTAGTTTTTGATAAGGC
1492879 ATTGCGTGACTAGTTTTTGATAAGGC
1 ATTGCGTGACTAGTTTTTGATAAGGC
*
1492905 ATTGTGTGACTAG---TTGATAA-GC
1 ATTGCGTGACTAGTTTTTGATAAGGC
* ** *
1492927 ATTGCGTTACTA-ACTTTG----GGT
1 ATTGCGTGACTAGTTTTTGATAAGGC
* *
1492948 ATTGCATGACTAGTTTCTGATAAGGC
1 ATTGCGTGACTAGTTTTTGATAAGGC
* *
1492974 ATTGTGTGACTAGTTTCTGATAAGGC
1 ATTGCGTGACTAGTTTTTGATAAGGC
*
1493000 ATTGTGTGACTAGTT
1 ATTGCGTGACTAGTT
1493015 AATAGGCATT
Statistics
Matches: 211, Mismatches: 30, Indels: 34
0.77 0.11 0.12
Matches are distributed among these distances:
21 11 0.05
22 46 0.22
23 14 0.07
24 3 0.01
25 10 0.05
26 127 0.60
ACGTcount: A:0.25, C:0.11, G:0.26, T:0.38
Consensus pattern (26 bp):
ATTGCGTGACTAGTTTTTGATAAGGC
Found at i:1492814 original size:74 final size:74
Alignment explanation
Indices: 1492731--1493032 Score: 382
Period size: 74 Copynumber: 4.1 Consensus size: 74
1492721 GACTTTGGAT
* * * *
1492731 ATTGCGTGACTAATTTTTGATAAGACATTGCGTGATTAGTTTATGATAAGGTATTGCGTGACTAG
1 ATTGCGTGACTAGTTTTTGATAAGACATTGCGTGACTAGTTTCTGATAAGGCATTGCGTGACTAG
1492796 TTGATAGGC
66 TTGATAGGC
* *
1492805 ATTGCGTGACTAGTTTTTGATAAGACATTGCGTGACTAGTTTCTAATAGGGCATTGCGTGACTAG
1 ATTGCGTGACTAGTTTTTGATAAGACATTGCGTGACTAGTTTCTGATAAGGCATTGCGTGACTAG
*
1492870 TTGATAGGT
66 TTGATAGGC
* * *
1492879 ATTGCGTGACTAGTTTTTGATAAGGCATTGTGTGACTAG--T-TGATAA-GCATTGCGTTACTAA
1 ATTGCGTGACTAGTTTTTGATAAGACATTGCGTGACTAGTTTCTGATAAGGCATTGCGTGACT-A
* * *
1492940 CTT--TGGGT
65 GTTGATAGGC
* * * * *
1492948 ATTGCATGACTAGTTTCTGATAAGGCATTGTGTGACTAGTTTCTGATAAGGCATTGTGTGACTAG
1 ATTGCGTGACTAGTTTTTGATAAGACATTGCGTGACTAGTTTCTGATAAGGCATTGCGTGACTAG
*
1493013 TTAATAGGC
66 TTGATAGGC
1493022 ATTGCGTGACT
1 ATTGCGTGACT
1493033 TGTTAGTAAG
Statistics
Matches: 199, Mismatches: 22, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
69 41 0.21
70 12 0.06
71 8 0.04
72 10 0.05
73 11 0.06
74 117 0.59
ACGTcount: A:0.25, C:0.12, G:0.26, T:0.37
Consensus pattern (74 bp):
ATTGCGTGACTAGTTTTTGATAAGACATTGCGTGACTAGTTTCTGATAAGGCATTGCGTGACTAG
TTGATAGGC
Found at i:1492819 original size:48 final size:48
Alignment explanation
Indices: 1492731--1493055 Score: 253
Period size: 48 Copynumber: 6.7 Consensus size: 48
1492721 GACTTTGGAT
* * * *
1492731 ATTGCGTGACTAATTTTTGATAAGACATTGCGTGATTAGTTTATGATAAGGT
1 ATTGCGTGACT-A-GTTTGATAAGGCATTGCGTGACTAG-TT-TGATAAGGC
*
1492783 ATTGCGTGACTAG-TTGAT-AGGCATTGCGTGACTAGTTTTTGATAAGAC
1 ATTGCGTGACTAGTTTGATAAGGCATTGCGTGACTAG--TTTGATAAGGC
* * *
1492831 ATTGCGTGACTAGTTTCTAATAGGGCATTGCGTGACTAG-TTGAT-AGGT
1 ATTGCGTGACTAG-TT-TGATAAGGCATTGCGTGACTAGTTTGATAAGGC
*
1492879 ATTGCGTGACTAGTTTTTGATAAGGCATTGTGTGACTAG-TTGATAA-GC
1 ATTGCGTGACTAG--TTTGATAAGGCATTGCGTGACTAGTTTGATAAGGC
* * * *
1492927 ATTGCGTTACTAACTTTG----GGTATTGCATGACTAGTTTCTGATAAGGC
1 ATTGCGTGACT-AGTTTGATAAGGCATTGCGTGACTAG-TT-TGATAAGGC
* * *
1492974 ATTGTGTGACTAGTTTCTGATAAGGCATTGTGTGACTAG-TTAAT-AGGC
1 ATTGCGTGACTAG-TT-TGATAAGGCATTGCGTGACTAGTTTGATAAGGC
* * *
1493022 ATTGCGTGACTTGTTAG-TAAGGCATTGTGTGACT
1 ATTGCGTGACTAGTTTGATAAGGCATTGCGTGACT
1493056 TAGGTATTAC
Statistics
Matches: 227, Mismatches: 28, Indels: 43
0.76 0.09 0.14
Matches are distributed among these distances:
43 13 0.06
45 18 0.08
46 8 0.04
47 19 0.08
48 102 0.45
49 21 0.09
50 2 0.01
51 4 0.02
52 40 0.18
ACGTcount: A:0.25, C:0.11, G:0.26, T:0.38
Consensus pattern (48 bp):
ATTGCGTGACTAGTTTGATAAGGCATTGCGTGACTAGTTTGATAAGGC
Found at i:1493095 original size:22 final size:22
Alignment explanation
Indices: 1493067--1493171 Score: 79
Period size: 22 Copynumber: 4.9 Consensus size: 22
1493057 AGGTATTACT
* *
1493067 TAAAAATTAGTCAGGCAATATC
1 TAAAAATTAGTCACGCAATACC
*
1493089 TAAAAATTAGTCACGTAATACC
1 TAAAAATTAGTCACGCAATACC
** * *
1493111 T-AAAACCAATCACGTAATA-C
1 TAAAAATTAGTCACGCAATACC
* * * *
1493131 TTAAAATCAATCACGTAATACC
1 TAAAAATTAGTCACGCAATACC
* *
1493153 TAAAAACTAGTCACACAAT
1 TAAAAATTAGTCACGCAAT
1493172 GATTAAATCA
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
20 2 0.03
21 32 0.47
22 34 0.50
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.25
Consensus pattern (22 bp):
TAAAAATTAGTCACGCAATACC
Found at i:1493180 original size:42 final size:39
Alignment explanation
Indices: 1493099--1493196 Score: 94
Period size: 38 Copynumber: 2.5 Consensus size: 39
1493089 TAAAAATTAG
**
1493099 TCACGTAATACCT-AAAACCAATCACGTAATACTTAAAATCAA
1 TCACGTAATACCTAAAAACCAATCACACAATACTT--AA--AA
* *
1493141 TCACGTAATACCTAAAAACTAGTCACACAATGA-TT-AAA
1 TCACGTAATACCTAAAAACCAATCACACAAT-ACTTAAAA
1493179 TCACGTAATACCTAAAAA
1 TCACGTAATACCTAAAAA
1493197 TCAGTAAACT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
38 20 0.40
40 1 0.02
42 13 0.26
43 15 0.30
44 1 0.02
ACGTcount: A:0.48, C:0.22, G:0.06, T:0.23
Consensus pattern (39 bp):
TCACGTAATACCTAAAAACCAATCACACAATACTTAAAA
Found at i:1498760 original size:30 final size:30
Alignment explanation
Indices: 1498726--1498789 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
1498716 GGTGATTCCA
*
1498726 GGTGATGATGTGGTTCCCCCTCCATTCCCT
1 GGTGATGATGTGGTTCCCCCTCCAATCCCT
* *
1498756 GGTGATGGTGTGGTTCCCCCTCTAATCCCT
1 GGTGATGATGTGGTTCCCCCTCCAATCCCT
1498786 GGTG
1 GGTG
1498790 GTGGTATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.09, C:0.30, G:0.28, T:0.33
Consensus pattern (30 bp):
GGTGATGATGTGGTTCCCCCTCCAATCCCT
Found at i:1498803 original size:30 final size:30
Alignment explanation
Indices: 1498739--1498805 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
1498729 GATGATGTGG
* * *
1498739 TTCCCCCTCCATTCCCTGGTGATGGTGTGG
1 TTCCCCCTCCAATCCCTGGTGATGGTATGA
* * *
1498769 TTCCCCCTCTAATCCCTGGTGGTGGTATTA
1 TTCCCCCTCCAATCCCTGGTGATGGTATGA
1498799 TTCCCCC
1 TTCCCCC
1498806 AATCATTCCA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.09, C:0.36, G:0.21, T:0.34
Consensus pattern (30 bp):
TTCCCCCTCCAATCCCTGGTGATGGTATGA
Found at i:1517465 original size:22 final size:22
Alignment explanation
Indices: 1517427--1517477 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
1517417 AAAATATGTA
1517427 ATTATAAATAATAATTTTTAAT
1 ATTATAAATAATAATTTTTAAT
*
1517449 ATTA-AAATATATTATTTTT-AT
1 ATTATAAATA-ATAATTTTTAAT
1517470 -TTATAAAT
1 ATTATAAAT
1517478 TTTTTATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 3 0.12
21 11 0.42
22 12 0.46
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTATAAATAATAATTTTTAAT
Found at i:1519007 original size:17 final size:18
Alignment explanation
Indices: 1518985--1519022 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1518975 ATTCGGTTAG
* *
1518985 TTTAATTTTTTAAA-TAA
1 TTTAATTATTAAAATTAA
1519002 TTTAATTATTAAAATTAA
1 TTTAATTATTAAAATTAA
1519020 TTT
1 TTT
1519023 GGTTCGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTAATTATTAAAATTAA
Found at i:1524212 original size:3 final size:3
Alignment explanation
Indices: 1524204--1524278 Score: 123
Period size: 3 Copynumber: 25.0 Consensus size: 3
1524194 AAATCTCCTT
*
1524204 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
1524252 TTA TTG TTT TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1524279 CTTGAAATGG
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1526547 original size:4 final size:4
Alignment explanation
Indices: 1526538--1526562 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1526528 CTAATTAACT
1526538 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
1526563 ATTCAATTGA
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):
TTTA
Found at i:1531986 original size:69 final size:66
Alignment explanation
Indices: 1531905--1532031 Score: 191
Period size: 69 Copynumber: 1.9 Consensus size: 66
1531895 CAATTGTAGC
* * *
1531905 AGCTCAAACTGAAATCCTGGAGCAACAATATGATGAGAATATCCTTCCACTTCAAATTGAAATTC
1 AGCTCAAACTGAAATCCTGGAGCAACAATATG--G-GAAAATCCTTCCACCTCAAACTGAAATTC
1531970 CAGT
63 CAGT
*
1531974 AGCTCAAGCTGAAATCCTGGAGCAACAATATGGGAAAATCCTTCCACCTCAAACTGAA
1 AGCTCAAACTGAAATCCTGGAGCAACAATATGGGAAAATCCTTCCACCTCAAACTGAA
1532032 CAGGTTCAAG
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
66 22 0.41
67 1 0.02
69 31 0.57
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.23
Consensus pattern (66 bp):
AGCTCAAACTGAAATCCTGGAGCAACAATATGGGAAAATCCTTCCACCTCAAACTGAAATTCCAG
T
Found at i:1532381 original size:57 final size:57
Alignment explanation
Indices: 1532271--1532721 Score: 646
Period size: 57 Copynumber: 8.0 Consensus size: 57
1532261 ATTCGGTGGG
*
1532271 CCATGATCCTTTGAACATGCAT---CAGCAGCAGCAATTTTCAAGTGTCCCAAACAT
1 CCATGATCCTTTGAACATGCATCAGCAGCAGCAGCAATTTTCAAGTGCCCCAAACAT
* *
1532325 CCATGATCCTTTGAATATGCATCAGCAGCAGCAGCAATTTCCAAGTGCCCCAAACAT
1 CCATGATCCTTTGAACATGCATCAGCAGCAGCAGCAATTTTCAAGTGCCCCAAACAT
* *
1532382 CCATGATCCTTTGAACATGTCATCAGCAGCAACAGCAATTTTCAAGTGCTCCAAACAT
1 CCATGATCCTTTGAACATG-CATCAGCAGCAGCAGCAATTTTCAAGTGCCCCAAACAT
* *
1532440 CCATGATCCTTTGAACATGCATCAGCAGCAACAGCAATTTTCAGGTGCCCCAAACAT
1 CCATGATCCTTTGAACATGCATCAGCAGCAGCAGCAATTTTCAAGTGCCCCAAACAT
* * *
1532497 CCATGATCCTTTGAACATGCATCAGCAGCAACAGCAATTTTCAAGGGCTCCAAACAT
1 CCATGATCCTTTGAACATGCATCAGCAGCAGCAGCAATTTTCAAGTGCCCCAAACAT
* *
1532554 CCATGATCCTTTGAACATGCAT---CAGCAGCAGCAATTTTCAGGTGCCCCAAACTT
1 CCATGATCCTTTGAACATGCATCAGCAGCAGCAGCAATTTTCAAGTGCCCCAAACAT
* * * * *
1532608 CCCTGATCCTTCGAACATGGATCAGCAGCAGCAGCAATTTTCAGGTGGCCCAAACAT
1 CCATGATCCTTTGAACATGCATCAGCAGCAGCAGCAATTTTCAAGTGCCCCAAACAT
** * *
1532665 CCATGGCCCTTTGAACATGCATCAGCAGGAGCAGCAATTTTC-AGATGCCCCAGACAT
1 CCATGATCCTTTGAACATGCATCAGCAGCAGCAGCAATTTTCAAG-TGCCCCAAACAT
1532722 TACCGAGTTA
Statistics
Matches: 358, Mismatches: 31, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
54 67 0.19
56 1 0.00
57 236 0.66
58 54 0.15
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24
Consensus pattern (57 bp):
CCATGATCCTTTGAACATGCATCAGCAGCAGCAGCAATTTTCAAGTGCCCCAAACAT
Found at i:1532624 original size:111 final size:111
Alignment explanation
Indices: 1532271--1532721 Score: 624
Period size: 111 Copynumber: 4.0 Consensus size: 111
1532261 ATTCGGTGGG
*
1532271 CCATGATCCTTTGAACATGCATCAGCAG---CAGCAATTTTCAAGTG-TCCCAAACATCCATGAT
1 CCATGATCCTTTGAACATGCATCAGCAGCAACAGCAATTTTCAAGGGCT-CCAAACATCCATGAT
* * *
1532332 CCTTTGAATATGCATCAGCAGCAGCAGCAATTTCCAAGTGCCCCAAACAT
65 CCTTTGAACATGCAT---CAGCAGCAGCAATTTTCAGGTGCCCCAAACAT
*
1532382 CCATGATCCTTTGAACATGTCATCAGCAGCAACAGCAATTTTCAAGTGCTCCAAACATCCATGAT
1 CCATGATCCTTTGAACATG-CATCAGCAGCAACAGCAATTTTCAAGGGCTCCAAACATCCATGAT
1532447 CCTTTGAACATGCATCAGCAGCAACAGCAATTTTCAGGTGCCCCAAACAT
65 CCTTTGAACATGCATCAGCAG---CAGCAATTTTCAGGTGCCCCAAACAT
1532497 CCATGATCCTTTGAACATGCATCAGCAGCAACAGCAATTTTCAAGGGCTCCAAACATCCATGATC
1 CCATGATCCTTTGAACATGCATCAGCAGCAACAGCAATTTTCAAGGGCTCCAAACATCCATGATC
*
1532562 CTTTGAACATGCATCAGCAGCAGCAATTTTCAGGTGCCCCAAACTT
66 CTTTGAACATGCATCAGCAGCAGCAATTTTCAGGTGCCCCAAACAT
* * * * * **
1532608 CCCTGATCCTTCGAACATGGATCAGCAGCAGCAGCAATTTTCAGGTGGC-CCAAACATCCATGGC
1 CCATGATCCTTTGAACATGCATCAGCAGCAACAGCAATTTTCAAG-GGCTCCAAACATCCATGAT
* *
1532672 CCTTTGAACATGCATCAGCAGGAGCAGCAATTTTCAGATGCCCCAGACAT
65 CCTTTGAACATGCATCAGC---AGCAGCAATTTTCAGGTGCCCCAAACAT
1532722 TACCGAGTTA
Statistics
Matches: 313, Mismatches: 15, Indels: 21
0.90 0.04 0.06
Matches are distributed among these distances:
111 116 0.37
112 18 0.06
114 90 0.29
115 88 0.28
116 1 0.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24
Consensus pattern (111 bp):
CCATGATCCTTTGAACATGCATCAGCAGCAACAGCAATTTTCAAGGGCTCCAAACATCCATGATC
CTTTGAACATGCATCAGCAGCAGCAATTTTCAGGTGCCCCAAACAT
Found at i:1532678 original size:168 final size:170
Alignment explanation
Indices: 1532271--1532707 Score: 650
Period size: 168 Copynumber: 2.6 Consensus size: 170
1532261 ATTCGGTGGG
* * *
1532271 CCATGATCCTTTGAACATGCAT---CAGCAGCAGCAATTTTCAAGTGTCCCAAACATCCATGATC
1 CCATGATCCTTCGAACATGCATCAGCAGCAGCAGCAATTTTCAGGTGCCCCAAACATCCATGATC
* * *
1532333 CTTTGAATATGCATCAGCAGCAGCAGCAATTTCCAAGTGCCCCAAACATCCATGATCCTTTGAAC
66 CTTTGAACATGCATCAGCAGCAGCAGCAATTTTCAAGGGCCCCAAACATCCATGATCCTTTGAAC
*
1532398 ATGTCATCAGCAGCAACAGCAATTTTCAAGTGCTCCAAACAT
131 ATGTCATCAGCAG--ACAGCAATTTTCAAGTGCCCCAAACAT
* *
1532440 CCATGATCCTTTGAACATGCATCAGCAGCAACAGCAATTTTCAGGTGCCCCAAACATCCATGATC
1 CCATGATCCTTCGAACATGCATCAGCAGCAGCAGCAATTTTCAGGTGCCCCAAACATCCATGATC
* *
1532505 CTTTGAACATGCATCAGCAGCAACAGCAATTTTCAAGGGCTCCAAACATCCATGATCCTTTGAAC
66 CTTTGAACATGCATCAGCAGCAGCAGCAATTTTCAAGGGCCCCAAACATCCATGATCCTTTGAAC
* *
1532570 ATG-CATCAGCAG-CAGCAATTTTCAGGTGCCCCAAACTT
131 ATGTCATCAGCAGACAGCAATTTTCAAGTGCCCCAAACAT
* * * **
1532608 CCCTGATCCTTCGAACATGGATCAGCAGCAGCAGCAATTTTCAGGTGGCCCAAACATCCATGGCC
1 CCATGATCCTTCGAACATGCATCAGCAGCAGCAGCAATTTTCAGGTGCCCCAAACATCCATGATC
*
1532673 CTTTGAACATGCATCAGCAGGAGCAGCAATTTTCA
66 CTTTGAACATGCATCAGCAGCAGCAGCAATTTTCA
1532708 GATGCCCCAG
Statistics
Matches: 245, Mismatches: 20, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
168 114 0.47
169 22 0.09
171 9 0.04
172 100 0.41
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24
Consensus pattern (170 bp):
CCATGATCCTTCGAACATGCATCAGCAGCAGCAGCAATTTTCAGGTGCCCCAAACATCCATGATC
CTTTGAACATGCATCAGCAGCAGCAGCAATTTTCAAGGGCCCCAAACATCCATGATCCTTTGAAC
ATGTCATCAGCAGACAGCAATTTTCAAGTGCCCCAAACAT
Found at i:1533373 original size:60 final size:60
Alignment explanation
Indices: 1533305--1533425 Score: 242
Period size: 60 Copynumber: 2.0 Consensus size: 60
1533295 TGTCGTCAAT
1533305 CATGTGGCTGCTTCAAATGCACTTCTCCTAGTGTCTGTGCCAATGCCGTCTTCTTCCGAA
1 CATGTGGCTGCTTCAAATGCACTTCTCCTAGTGTCTGTGCCAATGCCGTCTTCTTCCGAA
1533365 CATGTGGCTGCTTCAAATGCACTTCTCCTAGTGTCTGTGCCAATGCCGTCTTCTTCCGAA
1 CATGTGGCTGCTTCAAATGCACTTCTCCTAGTGTCTGTGCCAATGCCGTCTTCTTCCGAA
1533425 C
1 C
1533426 CGCGGTGCTC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.17, C:0.31, G:0.20, T:0.33
Consensus pattern (60 bp):
CATGTGGCTGCTTCAAATGCACTTCTCCTAGTGTCTGTGCCAATGCCGTCTTCTTCCGAA
Found at i:1548172 original size:85 final size:85
Alignment explanation
Indices: 1548072--1548245 Score: 215
Period size: 85 Copynumber: 2.0 Consensus size: 85
1548062 ATATAAACAT
* * * * *
1548072 GATAAATTGATTATACTAGTTCCAATAATATTCATATATTGCAAACAATATTAATTTGGTATCAT
1 GATAAATTGATTATACCAATTCCAATAACATTCATAAATTGCAAACAATATCAATTTGGTATCAT
*
1548137 TCCT-GATATTATTCTAAATA
66 T-CTGGATATTATTCCAAATA
**** *
1548157 GATAAATTGATTATACCAATTTTTGTAACATTCATAAATTGTAAACAATATCAATTTGGTATCAT
1 GATAAATTGATTATACCAATTCCAATAACATTCATAAATTGCAAACAATATCAATTTGGTATCAT
* *
1548222 TCTGGGTATTATTCCAAATT
66 TCTGGATATTATTCCAAATA
1548242 GATA
1 GATA
1548246 TAATCATGAT
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
84 2 0.03
85 73 0.97
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (85 bp):
GATAAATTGATTATACCAATTCCAATAACATTCATAAATTGCAAACAATATCAATTTGGTATCAT
TCTGGATATTATTCCAAATA
Found at i:1550582 original size:16 final size:17
Alignment explanation
Indices: 1550552--1550589 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
1550542 AGATTATGAA
1550552 TATTT-ATTTTAAAATT
1 TATTTAATTTTAAAATT
*
1550568 T-TTTAATTTTTAAATT
1 TATTTAATTTTAAAATT
1550584 TATTTA
1 TATTTA
1550590 TTAACAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 3 0.16
16 12 0.63
17 4 0.21
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTTAATTTTAAAATT
Found at i:1551135 original size:15 final size:15
Alignment explanation
Indices: 1551101--1551151 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
1551091 CCCTTTGTTT
*
1551101 TTCTC-CTCTCTTTC
1 TTCTCTCTCTCTATC
*
1551115 TCTCTCTCTCTCTCTC
1 T-TCTCTCTCTCTATC
**
1551131 TTCTCTCAGTCTATC
1 TTCTCTCTCTCTATC
1551146 TTCTCT
1 TTCTCT
1551152 ACTTTTCTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
14 1 0.03
15 21 0.68
16 9 0.29
ACGTcount: A:0.04, C:0.41, G:0.02, T:0.53
Consensus pattern (15 bp):
TTCTCTCTCTCTATC
Found at i:1557893 original size:27 final size:27
Alignment explanation
Indices: 1557861--1557913 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
1557851 TTTTTTATTG
*
1557861 TTTAAATATGAATAATTTATAATTTAT
1 TTTAAATATGAATAATTAATAATTTAT
* *
1557888 TTTAAATATTAATAATTAATTATTTA
1 TTTAAATATGAATAATTAATAATTTA
1557914 AATATTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (27 bp):
TTTAAATATGAATAATTAATAATTTAT
Found at i:1557916 original size:22 final size:26
Alignment explanation
Indices: 1557861--1557923 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 26
1557851 TTTTTTATTG
*
1557861 TTTAAATATGAATAATTTATAATTTAT
1 TTTAAATATTAATAA-TTATAATTTAT
1557888 TTTAAATATTAATAA-T-TAA-TTA-
1 TTTAAATATTAATAATTATAATTTAT
1557910 TTTAAATATTAATA
1 TTTAAATATTAATA
1557924 TTTTATTAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
22 14 0.40
23 3 0.09
24 3 0.09
25 1 0.03
27 14 0.40
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (26 bp):
TTTAAATATTAATAATTATAATTTAT
Found at i:1557925 original size:14 final size:12
Alignment explanation
Indices: 1557882--1557951 Score: 52
Period size: 14 Copynumber: 5.3 Consensus size: 12
1557872 ATAATTTATA
*
1557882 ATTTATTTTAAAT
1 ATTTATATT-AAT
*
1557895 ATTAATAATTAATT
1 ATTTAT-ATTAA-T
1557909 ATTTAAATATTAAT
1 ATTT--ATATTAAT
1557923 ATTT-TATTAAT
1 ATTTATATTAAT
1557934 AATTTATCATTAAT
1 -ATTTAT-ATTAAT
1557948 ATTT
1 ATTT
1557952 TCAAATATCA
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
11 7 0.15
12 4 0.09
13 12 0.26
14 17 0.36
15 5 0.11
16 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTATATTAAT
Found at i:1557931 original size:22 final size:22
Alignment explanation
Indices: 1557853--1557931 Score: 77
Period size: 22 Copynumber: 3.4 Consensus size: 22
1557843 TATTTTATTT
* *
1557853 TTTTATTGTTTAAATATGAATAA
1 TTTTATTATTTAAATATTAAT-A
1557876 TTTATAATTTATTTTAAATATTAATA
1 TTT-T-A-TTA-TTTAAATATTAATA
* *
1557902 ATTAATTATTTAAATATTAATA
1 TTTTATTATTTAAATATTAATA
1557924 TTTTATTA
1 TTTTATTA
1557932 ATAATTTATC
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
22 20 0.43
23 6 0.13
24 2 0.04
25 1 0.02
26 5 0.11
27 12 0.26
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (22 bp):
TTTTATTATTTAAATATTAATA
Found at i:1564764 original size:21 final size:20
Alignment explanation
Indices: 1564725--1564762 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1564715 ATTTTAAAAG
* *
1564725 ATTCAATTTGAACTTAAATA
1 ATTCAAATTAAACTTAAATA
1564745 ATTCAAATTAAACTTAAA
1 ATTCAAATTAAACTTAAA
1564763 ATGACTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.11, G:0.03, T:0.37
Consensus pattern (20 bp):
ATTCAAATTAAACTTAAATA
Found at i:1566297 original size:28 final size:28
Alignment explanation
Indices: 1566255--1566325 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
1566245 ATCAACCACC
*
1566255 AAAAGTGAATGAATACTTTTAACTCACA
1 AAAAGTGGATGAATACTTTTAACTCACA
* * *
1566283 AGAAGTGGATGAATACTTTTAATTTACA
1 AAAAGTGGATGAATACTTTTAACTCACA
1566311 AAAAGTGGATGAATA
1 AAAAGTGGATGAATA
1566326 ATAAAAAAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.45, C:0.08, G:0.17, T:0.30
Consensus pattern (28 bp):
AAAAGTGGATGAATACTTTTAACTCACA
Found at i:1566699 original size:24 final size:22
Alignment explanation
Indices: 1566643--1566700 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 22
1566633 ATGAAGATGC
1566643 TTTAA-TATGTTCTTATTATAT
1 TTTAATTATGTTCTTATTATAT
* *
1566664 TTAAATGATATGTTCTTATTATGTGT
1 TTTAAT--TATGTTCTTATTA--TAT
1566690 TTTAATTATGT
1 TTTAATTATGT
1566701 ATTTAATGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
21 4 0.14
24 18 0.62
26 7 0.24
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.59
Consensus pattern (22 bp):
TTTAATTATGTTCTTATTATAT
Found at i:1570537 original size:16 final size:17
Alignment explanation
Indices: 1570511--1570547 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
1570501 TATGTATATC
1570511 TAGATTTGGATGTAA-AT
1 TAGATTTGGATG-AAGAT
1570528 TAGA-TTGGATGAAGAT
1 TAGATTTGGATGAAGAT
1570544 TAGA
1 TAGA
1570548 ATTTAATCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 2 0.11
16 13 0.68
17 4 0.21
ACGTcount: A:0.38, C:0.00, G:0.27, T:0.35
Consensus pattern (17 bp):
TAGATTTGGATGAAGAT
Found at i:1575068 original size:17 final size:17
Alignment explanation
Indices: 1575046--1575089 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
1575036 CCTAGGATGA
1575046 TATTTTGATTATCTTGC
1 TATTTTGATTATCTTGC
1575063 TATTTTGATTATCTTGC
1 TATTTTGATTATCTTGC
1575080 TATTTTGATT
1 TATTTTGATT
1575090 CTTGGTTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.18, C:0.09, G:0.11, T:0.61
Consensus pattern (17 bp):
TATTTTGATTATCTTGC
Found at i:1577829 original size:42 final size:42
Alignment explanation
Indices: 1577770--1577893 Score: 212
Period size: 42 Copynumber: 3.0 Consensus size: 42
1577760 TGTTGATTTG
1577770 GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
1 GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
* *
1577812 GACCCGACTATGTGCGAGTAGGAGTGCATATAAGCCGTTGCT
1 GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
* *
1577854 GACCCGGCTATGTGTGAGTGGGAGTGCACATAAGCCGTTG
1 GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTG
1577894 TTGCCCCCAT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.22, C:0.22, G:0.34, T:0.23
Consensus pattern (42 bp):
GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
Found at i:1578165 original size:26 final size:26
Alignment explanation
Indices: 1578129--1578190 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
1578119 TTGCATATGA
1578129 GATGATGATGATGGGATGATGTGCAT
1 GATGATGATGATGGGATGATGTGCAT
*
1578155 GATGATGATGATGGGATGGTGTGCAT
1 GATGATGATGATGGGATGATGTGCAT
*
1578181 GTTGATGATG
1 GATGATGATG
1578191 GGTATATGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.24, C:0.03, G:0.40, T:0.32
Consensus pattern (26 bp):
GATGATGATGATGGGATGATGTGCAT
Found at i:1578328 original size:22 final size:23
Alignment explanation
Indices: 1578282--1578342 Score: 88
Period size: 23 Copynumber: 2.6 Consensus size: 23
1578272 TTATTTTAGC
1578282 AGGATGACTTGTTTT-AAGGGAAAA
1 AGGA-GACTT-TTTTCAAGGGAAAA
*
1578306 ATGAGACTTTTTTCAAGGGAAAA
1 AGGAGACTTTTTTCAAGGGAAAA
1578329 AGGAGACTTTTTTC
1 AGGAGACTTTTTTC
1578343 CTTGATGTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 4 0.12
23 27 0.79
24 3 0.09
ACGTcount: A:0.34, C:0.08, G:0.25, T:0.33
Consensus pattern (23 bp):
AGGAGACTTTTTTCAAGGGAAAA
Found at i:1580255 original size:13 final size:13
Alignment explanation
Indices: 1580237--1580262 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1580227 GAAAAAATTC
1580237 TGTTGGAAATTTT
1 TGTTGGAAATTTT
1580250 TGTTGGAAATTTT
1 TGTTGGAAATTTT
1580263 CAATGGAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (13 bp):
TGTTGGAAATTTT
Found at i:1580582 original size:22 final size:22
Alignment explanation
Indices: 1580544--1580599 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
1580534 TTTTTATTTA
** *
1580544 AAATATATTAAGAATTTTTAA-
1 AAATATATTAATCATTTATAAG
*
1580565 AAATTTTATTAATCATTTATAAG
1 AAA-TATATTAATCATTTATAAG
1580588 AAATATATTAAT
1 AAATATATTAAT
1580600 AAAATTAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 3 0.11
22 22 0.79
23 3 0.11
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.45
Consensus pattern (22 bp):
AAATATATTAATCATTTATAAG
Found at i:1586059 original size:34 final size:34
Alignment explanation
Indices: 1586016--1586083 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
1586006 TTAACCAAGT
1586016 TAATTGACACCCTAAGCTACATCTAGAGACTCAA
1 TAATTGACACCCTAAGCTACATCTAGAGACTCAA
1586050 TAATTGACACCCTAAGCTACATCTAGAGACTCAA
1 TAATTGACACCCTAAGCTACATCTAGAGACTCAA
1586084 GATGATCACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (34 bp):
TAATTGACACCCTAAGCTACATCTAGAGACTCAA
Found at i:1590707 original size:32 final size:32
Alignment explanation
Indices: 1590657--1590737 Score: 126
Period size: 32 Copynumber: 2.5 Consensus size: 32
1590647 ATTCAACATG
* *
1590657 TTTAGAATTGAGTTTTTTGGATGGTTCATGGT
1 TTTAAAATCGAGTTTTTTGGATGGTTCATGGT
1590689 TTTAAAATCGAGTTTTTTGGATGGTTCATGGT
1 TTTAAAATCGAGTTTTTTGGATGGTTCATGGT
* *
1590721 CTTAAAATCAAGTTTTT
1 TTTAAAATCGAGTTTTT
1590738 GGACCAATTG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.23, C:0.06, G:0.22, T:0.48
Consensus pattern (32 bp):
TTTAAAATCGAGTTTTTTGGATGGTTCATGGT
Found at i:1591601 original size:7 final size:7
Alignment explanation
Indices: 1591589--1591621 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
1591579 TCTTCTCTCC
1591589 CTCCTCT
1 CTCCTCT
1591596 CTCCTCT
1 CTCCTCT
1591603 CTCCTCT
1 CTCCTCT
1591610 CTCTCTCT
1 CTC-CTCT
1591618 CTCC
1 CTCC
1591622 ACACGTGCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (7 bp):
CTCCTCT
Found at i:1594093 original size:110 final size:109
Alignment explanation
Indices: 1593973--1594192 Score: 431
Period size: 110 Copynumber: 2.0 Consensus size: 109
1593963 ATATATATAT
1593973 ATATATTATGTTACAAATGTATTGATATCACGTGACAAAATAAAACAAAATAAAAAACAAAAACA
1 ATATATTATGTTACAAATGTATTGATATCACGTGACAAAATAAAACAAAATAAAAAACAAAAACA
1594038 AGACCAAAATAAGAATTATATTTTTTAGAGGCAAGCCATGCTGA
66 AGACCAAAATAAGAATTATATTTTTTAGAGGCAAGCCATGCTGA
1594082 NATATATTATGTTACAAATGTATTGATATCACGTGACAAAATAAAACAAAATAAAAAACAAAAAC
1 -ATATATTATGTTACAAATGTATTGATATCACGTGACAAAATAAAACAAAATAAAAAACAAAAAC
1594147 AAGACCAAAATAAGAATTATATTTTTTAGAGGCAAGCCATGCTGA
65 AAGACCAAAATAAGAATTATATTTTTTAGAGGCAAGCCATGCTGA
1594192 A
1 A
1594193 ATCAGAAAGG
Statistics
Matches: 110, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
109 1 0.01
110 109 0.99
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.25
Consensus pattern (109 bp):
ATATATTATGTTACAAATGTATTGATATCACGTGACAAAATAAAACAAAATAAAAAACAAAAACA
AGACCAAAATAAGAATTATATTTTTTAGAGGCAAGCCATGCTGA
Found at i:1597664 original size:15 final size:14
Alignment explanation
Indices: 1597629--1597678 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
1597619 AGAAAATTTC
1597629 AAAAAAATCAAAAG
1 AAAAAAATCAAAAG
1597643 AAGAAAAATCAAAAG
1 AA-AAAAATCAAAAG
**
1597658 CTAAAAAAAAAAAAAG
1 --AAAAAAATCAAAAG
1597674 AAAAA
1 AAAAA
1597679 CAGAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 7 0.23
15 12 0.39
16 10 0.32
17 2 0.06
ACGTcount: A:0.80, C:0.06, G:0.08, T:0.06
Consensus pattern (14 bp):
AAAAAAATCAAAAG
Found at i:1598286 original size:19 final size:18
Alignment explanation
Indices: 1598240--1598287 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
1598230 TTTTTGTTTA
* *
1598240 TATTCTTTTTCTTAATTTT
1 TATT-TTTTTATTAATTAT
1598259 TAATTTTTTTATTAATTAT
1 T-ATTTTTTTATTAATTAT
*
1598278 TATTATTTTA
1 TATTTTTTTA
1598288 ATTCAGTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 8 0.32
19 14 0.56
20 3 0.12
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (18 bp):
TATTTTTTTATTAATTAT
Found at i:1619363 original size:33 final size:33
Alignment explanation
Indices: 1619301--1619363 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
1619291 ATATGTCACG
*
1619301 TCATCATCAATTATAATAATTTAATATATCGTA
1 TCATCATCAATTATAATAATTTAACATATCGTA
*
1619334 TCATTATCAATTATAAT-ATATTAACATATC
1 TCATCATCAATTATAATAAT-TTAACATATC
1619364 ACATTAACGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 2 0.07
33 25 0.93
ACGTcount: A:0.43, C:0.13, G:0.02, T:0.43
Consensus pattern (33 bp):
TCATCATCAATTATAATAATTTAACATATCGTA
Found at i:1619467 original size:30 final size:30
Alignment explanation
Indices: 1619431--1619489 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
1619421 TAATCACAAA
*
1619431 AGCTTATTTGATTTAAAATAAAAATATAAG
1 AGCTTATTTGAATTAAAATAAAAATATAAG
1619461 AGCTTATTTGAATTAAAATAAAAATATAA
1 AGCTTATTTGAATTAAAATAAAAATATAA
1619490 AGACTGTGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.36
Consensus pattern (30 bp):
AGCTTATTTGAATTAAAATAAAAATATAAG
Found at i:1633932 original size:17 final size:19
Alignment explanation
Indices: 1633904--1633940 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1633894 TATTTATAAA
1633904 TTTATAAATTTTT-ATTTT
1 TTTATAAATTTTTAATTTT
1633922 TTTAT-AATTTTTAATTTT
1 TTTATAAATTTTTAATTTT
1633940 T
1 T
1633941 ACATTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTATAAATTTTTAATTTT
Found at i:1633946 original size:26 final size:26
Alignment explanation
Indices: 1633893--1633953 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
1633883 AATAAAATAA
1633893 TTATTTATAAATTTATAAATTTTT-AT
1 TTATTTAT-AATTTATAAATTTTTAAT
* *
1633919 TTTTTTATAATTT-TTAATTTTTACAT
1 TTATTTATAATTTATAAATTTTTA-AT
1633945 TTATTTATA
1 TTATTTATA
1633954 TAAGATGACA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 8 0.27
25 5 0.17
26 17 0.57
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (26 bp):
TTATTTATAATTTATAAATTTTTAAT
Found at i:1644871 original size:57 final size:55
Alignment explanation
Indices: 1644775--1645218 Score: 558
Period size: 57 Copynumber: 8.0 Consensus size: 55
1644765 GAACTCGTTA
* * * * *
1644775 ATGTTTGGGGCATCTGAAAGTTGCTGCTCCTGCTTATGCATGTTCAAAGGACCATGA
1 ATGTTTGGGGCACCTGAAAATTGCTG-T-CTGCTGATGCATGTTCAAAGGATCATGG
* * *
1644832 ATGCTTGGGGCATCTGAAAATTGCTGCTCCTGCTGATGCATGTTCAAAGGACCATGG
1 ATGTTTGGGGCACCTGAAAATTGCTG-T-CTGCTGATGCATGTTCAAAGGATCATGG
* * *
1644889 ATGTTTGGGGCACCTGAAAATTGCTGCTGCTGCTGATCCATGTTCAAAGAATCAGGG
1 ATGTTTGGGGCACCTGAAAATTGCTG-T-CTGCTGATGCATGTTCAAAGGATCATGG
1644946 ATGTTTGGGGCACCTGAAAATTGCTG-CTGCTGATGCATGTTCAAAGGATCATGG
1 ATGTTTGGGGCACCTGAAAATTGCTGTCTGCTGATGCATGTTCAAAGGATCATGG
* * * *
1645000 ATGTTTGGAGCACTTGAAAATTGCTGTTGCTGCTGATGCATGTTCGAAGGATCAAGG
1 ATGTTTGGGGCACCTGAAAATTGCTG-T-CTGCTGATGCATGTTCAAAGGATCATGG
* *
1645057 ATGTATGGGGCACCTGAAAA-T--TG-CTGCTGATGCATATTCAAAGGATCATGG
1 ATGTTTGGGGCACCTGAAAATTGCTGTCTGCTGATGCATGTTCAAAGGATCATGG
* * * *
1645108 ATGTTTGGGACACTTGAAAATTGCTG-CTGCTGATGCATGTTCGAAGGATTATGG
1 ATGTTTGGGGCACCTGAAAATTGCTGTCTGCTGATGCATGTTCAAAGGATCATGG
*
1645162 ATGCTTGGGGCACCTGAAAATTGCTGTTGCTGCTGATGCATGTTCAAAGGATCATGG
1 ATGTTTGGGGCACCTGAAAATTGCTG-T-CTGCTGATGCATGTTCAAAGGATCATGG
1645219 CCCTCAGAAT
Statistics
Matches: 343, Mismatches: 35, Indels: 18
0.87 0.09 0.05
Matches are distributed among these distances:
51 42 0.12
52 1 0.00
54 101 0.29
56 1 0.00
57 198 0.58
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (55 bp):
ATGTTTGGGGCACCTGAAAATTGCTGTCTGCTGATGCATGTTCAAAGGATCATGG
Found at i:1645018 original size:111 final size:111
Alignment explanation
Indices: 1644775--1645218 Score: 580
Period size: 111 Copynumber: 4.0 Consensus size: 111
1644765 GAACTCGTTA
* * * * *
1644775 ATGTTTGGGGCA-TCTGAAAGTTGCTGCTCCTGCTTATGCATGTTCAAAGGACCATGAATGCTTG
1 ATGTTTGGGGCACT-TGAAAATTGCTGCTGCTGCTGATGCATGTTCAAAGGATCATGGATGCTTG
* *
1644839 GGGCATCTGAAAATTGCTGCTCCTGCTGATGCATGTTCAAAGGACCATGG
65 GGGCACCTGAAAATTGCTG---CTGCTGATGCATGTTCAAAGGATCATGG
* * * * *
1644889 ATGTTTGGGGCACCTGAAAATTGCTGCTGCTGCTGATCCATGTTCAAAGAATCAGGGATGTTTGG
1 ATGTTTGGGGCACTTGAAAATTGCTGCTGCTGCTGATGCATGTTCAAAGGATCATGGATGCTTGG
1644954 GGCACCTGAAAATTGCTGCTGCTGATGCATGTTCAAAGGATCATGG
66 GGCACCTGAAAATTGCTGCTGCTGATGCATGTTCAAAGGATCATGG
* * * *
1645000 ATGTTTGGAGCACTTGAAAATTGCTGTTGCTGCTGATGCATGTTCGAAGGATCAAGGATG-TATG
1 ATGTTTGGGGCACTTGAAAATTGCTGCTGCTGCTGATGCATGTTCAAAGGATCATGGATGCT-TG
*
1645064 GGGCACCTGAAAA-T--TGCTGCTGATGCATATTCAAAGGATCATGG
65 GGGCACCTGAAAATTGCTGCTGCTGATGCATGTTCAAAGGATCATGG
* * *
1645108 ATGTTTGGGACACTTGAAAA-T--TGCTGCTGCTGATGCATGTTCGAAGGATTATGGATGCTTGG
1 ATGTTTGGGGCACTTGAAAATTGCTGCTGCTGCTGATGCATGTTCAAAGGATCATGGATGCTTGG
1645170 GGCACCTGAAAATTGCTGTTGCTGCTGATGCATGTTCAAAGGATCATGG
66 GGCACCTGAAAATTGC---TGCTGCTGATGCATGTTCAAAGGATCATGG
1645219 CCCTCAGAAT
Statistics
Matches: 295, Mismatches: 26, Indels: 21
0.86 0.08 0.06
Matches are distributed among these distances:
105 48 0.16
106 2 0.01
107 1 0.00
108 47 0.16
110 2 0.01
111 124 0.42
114 71 0.24
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (111 bp):
ATGTTTGGGGCACTTGAAAATTGCTGCTGCTGCTGATGCATGTTCAAAGGATCATGGATGCTTGG
GGCACCTGAAAATTGCTGCTGCTGATGCATGTTCAAAGGATCATGG
Found at i:1645164 original size:162 final size:165
Alignment explanation
Indices: 1644775--1645215 Score: 593
Period size: 162 Copynumber: 2.7 Consensus size: 165
1644765 GAACTCGTTA
* * * * * *
1644775 ATGTTTGGGGCATCTGAAAGTTGCTGCTCCTGCTTATGCATGTTCAAAGGACCATGAATGCTTGG
1 ATGTTTGGGACACCTGAAAATTGCTG---CTGCTGATGCATGTTCAAAGGATCATGGATGCTTGG
* * * * *
1644840 GGCA-TCTGAAAATTGCTGCTCCTGCTGATGCATGTTCAAAGGACCATGGATGTTTGGGGCACCT
63 GGCACT-TGAAAATTGCTGTTGCTGCTGATGCATGTTCAAAGGATCAAGGATGTATGGGGCACCT
*
1644904 GAAAATTGCTGCTGCTGCTGATCCATGTTCAAAGAATCAGGG
127 GAAAATTGCTGCTGATGC-GAT-CA-GTTCAAAGAATCAGGG
* * *
1644946 ATGTTTGGGGCACCTGAAAATTGCTGCTGCTGATGCATGTTCAAAGGATCATGGATGTTTGGAGC
1 ATGTTTGGGACACCTGAAAATTGCTGCTGCTGATGCATGTTCAAAGGATCATGGATGCTTGGGGC
*
1645011 ACTTGAAAATTGCTGTTGCTGCTGATGCATGTTCGAAGGATCAAGGATGTATGGGGCACCTGAAA
66 ACTTGAAAATTGCTGTTGCTGCTGATGCATGTTCAAAGGATCAAGGATGTATGGGGCACCTGAAA
* *
1645076 ATTGCTGCTGATGC-AT-A-TTCAAAGGATCATGG
131 ATTGCTGCTGATGCGATCAGTTCAAAGAATCAGGG
* * *
1645108 ATGTTTGGGACACTTGAAAATTGCTGCTGCTGATGCATGTTCGAAGGATTATGGATGCTTGGGGC
1 ATGTTTGGGACACCTGAAAATTGCTGCTGCTGATGCATGTTCAAAGGATCATGGATGCTTGGGGC
*
1645173 ACCTGAAAATTGCTGTTGCTGCTGATGCATGTTCAAAGGATCA
66 ACTTGAAAATTGCTGTTGCTGCTGATGCATGTTCAAAGGATCA
1645216 TGGCCCTCAG
Statistics
Matches: 245, Mismatches: 24, Indels: 11
0.88 0.09 0.04
Matches are distributed among these distances:
162 113 0.46
164 1 0.00
166 2 0.01
168 104 0.42
169 1 0.00
171 24 0.10
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.30
Consensus pattern (165 bp):
ATGTTTGGGACACCTGAAAATTGCTGCTGCTGATGCATGTTCAAAGGATCATGGATGCTTGGGGC
ACTTGAAAATTGCTGTTGCTGCTGATGCATGTTCAAAGGATCAAGGATGTATGGGGCACCTGAAA
ATTGCTGCTGATGCGATCAGTTCAAAGAATCAGGG
Found at i:1645571 original size:66 final size:65
Alignment explanation
Indices: 1645458--1645656 Score: 272
Period size: 66 Copynumber: 3.0 Consensus size: 65
1645448 CTTGAACCTG
* * * * *
1645458 TTCAGTTTGAGGTGGAAGGATATTCCCATATTCTTGCTTCAGAATTTCTGTTCGAGCAGCTGGAA
1 TTCAGTTTGAGGTGGAAGGATATTCCCATATTGTTGCTCCAGGATTTCAGTT-GAGCTGCTGGAA
1645523 T
65 T
* *
1645524 TTCAGTTTGAGGTGGAGGGATATTCCCATATTGTTGCCCCAGGATTTCAGCTTGAGCTGCTGGAA
1 TTCAGTTTGAGGTGGAAGGATATTCCCATATTGTTGCTCCAGGATTTCAG-TTGAGCTGCTGGAA
1645589 T
65 T
* * * *
1645590 TTCAATTTGAAGTGGAAGGATATTCTCATATTGTTGCTCCAGGATTTCAGTTTGAGCTGCTGTAA
1 TTCAGTTTGAGGTGGAAGGATATTCCCATATTGTTGCTCCAGGATTTCAG-TTGAGCTGCTGGAA
1645655 T
65 T
1645656 T
1 T
1645657 GCATAATTTT
Statistics
Matches: 118, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
66 116 0.98
67 2 0.02
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.37
Consensus pattern (65 bp):
TTCAGTTTGAGGTGGAAGGATATTCCCATATTGTTGCTCCAGGATTTCAGTTGAGCTGCTGGAAT
Found at i:1659084 original size:29 final size:30
Alignment explanation
Indices: 1659050--1659110 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
1659040 TTGACGATGA
** *
1659050 TTAAATTTTCATCAAAA-TTAAAAGTTTAT
1 TTAAATTTAAATCAAAATTTAAAAATTTAT
1659079 TTAAATTTAAATCAAAATTTAAAAATTTAT
1 TTAAATTTAAATCAAAATTTAAAAATTTAT
1659109 TT
1 TT
1659111 GAACAGAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.46
Consensus pattern (30 bp):
TTAAATTTAAATCAAAATTTAAAAATTTAT
Found at i:1659842 original size:30 final size:29
Alignment explanation
Indices: 1659787--1659843 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
1659777 AACAACTAAA
* *
1659787 AATAAAAATATAGAAACGTAATTAAATAT
1 AATAAAAATATAAAAAAGTAATTAAATAT
*
1659816 AATAAAAATATAAAAAATTAAATTAAAT
1 AATAAAAATATAAAAAAGT-AATTAAAT
1659844 TTTCTTCCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.28
Consensus pattern (29 bp):
AATAAAAATATAAAAAAGTAATTAAATAT
Found at i:1666339 original size:2 final size:2
Alignment explanation
Indices: 1666332--1666365 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1666322 CAATTCAACA
1666332 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1666366 TTAATTGCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1682878 original size:3 final size:3
Alignment explanation
Indices: 1682870--1682902 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1682860 GCCAACACAT
1682870 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1682903 GAAAAATGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1686720 original size:15 final size:15
Alignment explanation
Indices: 1686683--1686723 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1686673 AGACGTTACT
1686683 GAAAAAAAAAAAAAA
1 GAAAAAAAAAAAAAA
* **
1686698 GAGAAAAATGAAAAA
1 GAAAAAAAAAAAAAA
1686713 GAAAAAAAAAA
1 GAAAAAAAAAA
1686724 GAAGTCAAAA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.02
Consensus pattern (15 bp):
GAAAAAAAAAAAAAA
Found at i:1686738 original size:27 final size:27
Alignment explanation
Indices: 1686684--1686753 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 27
1686674 GACGTTACTG
*
1686684 AAAA-AAAAAAAAAAG-AGAAAAATGA
1 AAAAGAAAAAAAAAAGAAGAAAAATCA
*
1686709 AAAAGAAAAAAAAAAGAAGTCAAAA-CA
1 AAAAGAAAAAAAAAAGAAG-AAAAATCA
* *
1686736 AAAGGAAAAATAAAAGAA
1 AAAAGAAAAAAAAAAGAA
1686754 TGATTGAGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
25 4 0.11
26 11 0.29
27 19 0.50
28 4 0.11
ACGTcount: A:0.80, C:0.03, G:0.13, T:0.04
Consensus pattern (27 bp):
AAAAGAAAAAAAAAAGAAGAAAAATCA
Found at i:1701953 original size:30 final size:30
Alignment explanation
Indices: 1701897--1701954 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
1701887 TAGTTTATTG
* *
1701897 AATTAAATTTTTATATTTTATTTTAAATTA
1 AATTAAATTTTTATAATTAATTTTAAATTA
1701927 AATT-AATTTTTATAATTAATTATTAAAT
1 AATTAAATTTTTATAATTAATT-TTAAAT
1701955 AATATTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
AATTAAATTTTTATAATTAATTTTAAATTA
Found at i:1703302 original size:34 final size:33
Alignment explanation
Indices: 1703254--1703317 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
1703244 GTCAAATTAG
1703254 TATGTTACAATATCATC-ATTTTATAATATGTCAA
1 TATGTTACAATATCATCGA--TTATAATATGTCAA
* *
1703288 TATGTTATATTATCATCGATTATAATATGT
1 TATGTTACAATATCATCGATTATAATATGT
1703318 TAGCATGTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 11 0.41
34 15 0.56
35 1 0.04
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.47
Consensus pattern (33 bp):
TATGTTACAATATCATCGATTATAATATGTCAA
Found at i:1705095 original size:28 final size:28
Alignment explanation
Indices: 1705056--1705109 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
1705046 AAAGGAAAAC
* *
1705056 AAAAGAAATTGAAAGGGAAGAAGACTTA
1 AAAAGAAATTGAAAGAGAAAAAGACTTA
1705084 AAAAGAAATTGAAAGAGAAAAAGACT
1 AAAAGAAATTGAAAGAGAAAAAGACT
1705110 ATTTTGTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.61, C:0.04, G:0.22, T:0.13
Consensus pattern (28 bp):
AAAAGAAATTGAAAGAGAAAAAGACTTA
Found at i:1706417 original size:28 final size:28
Alignment explanation
Indices: 1706386--1706439 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
1706376 AAAGGAAAAC
1706386 AAAAGAAATTGAAAGGGAACAAGACTTA
1 AAAAGAAATTGAAAGGGAACAAGACTTA
*
1706414 AAAAGAAATTGAAAGGGAAGAAGACT
1 AAAAGAAATTGAAAGGGAACAAGACT
1706440 ATTTAATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.06, G:0.24, T:0.13
Consensus pattern (28 bp):
AAAAGAAATTGAAAGGGAACAAGACTTA
Found at i:1707567 original size:19 final size:20
Alignment explanation
Indices: 1707522--1707569 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 20
1707512 AAAACTTCTT
1707522 TAAATTTTTTTAAATAATTCA
1 TAAA-TTTTTTAAATAATTCA
*
1707543 TGAATTTTTTAAA-AATAT-A
1 TAAATTTTTTAAATAAT-TCA
1707562 TAAATTTT
1 TAAATTTT
1707570 CTTTTTATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 11 0.46
20 10 0.42
21 3 0.12
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
TAAATTTTTTAAATAATTCA
Found at i:1711933 original size:167 final size:166
Alignment explanation
Indices: 1711657--1711978 Score: 635
Period size: 167 Copynumber: 1.9 Consensus size: 166
1711647 ACCCACTCAT
1711657 ATAAAGTGGTTGGACTTGGGTCGTTACACATTTAATATAAAATTGTAGTTTGCCATTTACTATGA
1 ATAAAGTGGTTGGACTTGGGTCGTTACACATTTAATATAAAATTGTAGTTTGCCATTTACTATGA
1711722 AAAGAAAGGCATGGGTTGGGCATACATCAAATTGCCATATAAAGTCAAGAGTTTAACCGTTTTTT
66 AAAGAAAGGCATGGGTTGGGCATACATCAAATTGCCATATAAAGTCAAGAGTTTAACCGTTTTTT
1711787 TTGTAATTGTTTTACTATGTTTTTCTTCTTCCATGA
131 TTGTAATTGTTTTACTATGTTTTTCTTCTTCCATGA
1711823 NATAAAGTGGTTGGACTTGGGTCGTTACACATTTAATATAAAATTGTAGTTTGCCATTTACTATG
1 -ATAAAGTGGTTGGACTTGGGTCGTTACACATTTAATATAAAATTGTAGTTTGCCATTTACTATG
1711888 AAAAGAAAGGCATGGGTTGGGCATACATCAAATTGCCATATAAAGTCAAGAGTTTAACCGTTTTT
65 AAAAGAAAGGCATGGGTTGGGCATACATCAAATTGCCATATAAAGTCAAGAGTTTAACCGTTTTT
1711953 TTTGTAATTGTTTTACTATGTTTTTC
130 TTTGTAATTGTTTTACTATGTTTTTC
1711979 CTTTTCAGAC
Statistics
Matches: 155, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
167 155 1.00
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (166 bp):
ATAAAGTGGTTGGACTTGGGTCGTTACACATTTAATATAAAATTGTAGTTTGCCATTTACTATGA
AAAGAAAGGCATGGGTTGGGCATACATCAAATTGCCATATAAAGTCAAGAGTTTAACCGTTTTTT
TTGTAATTGTTTTACTATGTTTTTCTTCTTCCATGA
Found at i:1712005 original size:2 final size:2
Alignment explanation
Indices: 1711998--1712030 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1711988 CTTAAATAAT
*
1711998 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1712031 TATGGGTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:1716254 original size:16 final size:19
Alignment explanation
Indices: 1716218--1716255 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1716208 ATCCTTAATA
1716218 TGAATAAATAAACTAATTT
1 TGAATAAATAAACTAATTT
1716237 TGAATAAA-AAA-T-ATTT
1 TGAATAAATAAACTAATTT
1716253 TGA
1 TGA
1716256 TAATTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 1 0.05
18 3 0.16
19 8 0.42
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.37
Consensus pattern (19 bp):
TGAATAAATAAACTAATTT
Found at i:1722994 original size:105 final size:105
Alignment explanation
Indices: 1722812--1723020 Score: 373
Period size: 105 Copynumber: 2.0 Consensus size: 105
1722802 TGAATCTATA
** *
1722812 AAAATAAAATAAATTAGGAGTACTATTCTTTTATATTTATTTAAAACAAATATAAGGTAAATTCA
1 AAAATAAAATAAATTAAAAGTACTACTCTTTTATATTTATTTAAAACAAATATAAGGTAAATTCA
1722877 ATCTATCTAATTTAAGAATACCCTATAAATCACCTCGTTG
66 ATCTATCTAATTTAAGAATACCCTATAAATCACCTCGTTG
1722917 AAAATAAAATAAATTAAAAGTACTACTCTTTTATATTTATTTAAAACAAATATAAGGTAAATTCA
1 AAAATAAAATAAATTAAAAGTACTACTCTTTTATATTTATTTAAAACAAATATAAGGTAAATTCA
* *
1722982 ATCTATCTAATTTAAGAATACCCTGTAAATCATCTCGTT
66 ATCTATCTAATTTAAGAATACCCTATAAATCACCTCGTT
1723021 TTTAAAAAAA
Statistics
Matches: 99, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 99 1.00
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.36
Consensus pattern (105 bp):
AAAATAAAATAAATTAAAAGTACTACTCTTTTATATTTATTTAAAACAAATATAAGGTAAATTCA
ATCTATCTAATTTAAGAATACCCTATAAATCACCTCGTTG
Found at i:1728212 original size:15 final size:15
Alignment explanation
Indices: 1728194--1728224 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1728184 TCTAATTATC
1728194 AATAATCTATCTTTG
1 AATAATCTATCTTTG
*
1728209 AATAATTTATCTTTG
1 AATAATCTATCTTTG
1728224 A
1 A
1728225 CTTTTATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.48
Consensus pattern (15 bp):
AATAATCTATCTTTG
Found at i:1730189 original size:19 final size:17
Alignment explanation
Indices: 1730174--1730208 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1730164 TTTTTTACAT
1730174 ATTATATAAATTTTTAA
1 ATTATATAAATTTTTAA
*
1730191 ATTTTATAAATATTTTAA
1 ATTATATAAAT-TTTTAA
1730209 TGGCGCCCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTATATAAATTTTTAA
Found at i:1730271 original size:20 final size:20
Alignment explanation
Indices: 1730246--1730292 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1730236 AATTAATACN
*
1730246 TTTTTACATATTATATAAAT-
1 TTTTTAAAT-TTATATAAATA
*
1730266 TTTTTAAATTTTTATAAATA
1 TTTTTAAATTTATATAAATA
1730286 TTTTTAA
1 TTTTTAA
1730293 TGGCGCCCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTTAAATTTATATAAATA
Found at i:1730311 original size:84 final size:81
Alignment explanation
Indices: 1730165--1730329 Score: 287
Period size: 84 Copynumber: 2.0 Consensus size: 81
1730155 AATTAAATTT
1730165 TTTTTACATATTATATAAATTTTTAAATTTTATAAATATTTTAATGGCGCCCTAAAATAA-TTTT
1 TTTTTACATATTATATAAATTTTTAAATTTTATAAATATTTTAATGGCGCCCTAAAATAATTTTT
1730229 ATTTAATAATTAATAC
66 ATTTAATAATTAATAC
1730245 NTTTTTACATATTATATAAATTTTTTAAATTTTTATAAATATTTTTAATGGCGCCCTAAAATAAT
1 -TTTTTACATATTATATAAA-TTTTTAAA-TTTTATAAATA-TTTTAATGGCGCCCTAAAATAAT
1730310 TTTTATTTAATAATTAATAC
62 TTTTATTTAATAATTAATAC
1730330 AAATAAAAAA
Statistics
Matches: 80, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
81 19 0.24
82 8 0.10
83 11 0.14
84 22 0.28
85 20 0.25
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.50
Consensus pattern (81 bp):
TTTTTACATATTATATAAATTTTTAAATTTTATAAATATTTTAATGGCGCCCTAAAATAATTTTT
ATTTAATAATTAATAC
Found at i:1733744 original size:2 final size:2
Alignment explanation
Indices: 1733686--1733725 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1733676 ATATACTGTA
1733686 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1733726 TGCTGNACTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1733783 original size:2 final size:2
Alignment explanation
Indices: 1733776--1733816 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1733766 TAATTACTGT
1733776 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1733817 TGCTGTTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1735531 original size:35 final size:38
Alignment explanation
Indices: 1735483--1735556 Score: 118
Period size: 35 Copynumber: 2.0 Consensus size: 38
1735473 TGGAAAGATT
*
1735483 AGGTACAGTACCAAACATCTCAGAT-A-AA-AAAAAAA
1 AGGTACAGCACCAAACATCTCAGATGAGAACAAAAAAA
1735518 AGGTACAGCACCAAACATCTCAGATGAGAACAAAAAAA
1 AGGTACAGCACCAAACATCTCAGATGAGAACAAAAAAA
1735556 A
1 A
1735557 AACTTACTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
35 24 0.69
36 1 0.03
37 2 0.06
38 8 0.23
ACGTcount: A:0.55, C:0.19, G:0.14, T:0.12
Consensus pattern (38 bp):
AGGTACAGCACCAAACATCTCAGATGAGAACAAAAAAA
Found at i:1753607 original size:22 final size:22
Alignment explanation
Indices: 1753582--1753638 Score: 53
Period size: 22 Copynumber: 2.5 Consensus size: 22
1753572 AATAAATTTA
1753582 AAATTTTTAAAATTTAAAAAAT
1 AAATTTTTAAAATTTAAAAAAT
* **
1753604 AAA-TATTAATAATTTTCAAAAT
1 AAATTTTTAA-AATTTAAAAAAT
*
1753626 ATATATTTTAAAA
1 AAAT-TTTTAAAA
1753639 AATTTTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
21 5 0.19
22 15 0.56
23 2 0.07
24 5 0.19
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
AAATTTTTAAAATTTAAAAAAT
Found at i:1754700 original size:33 final size:32
Alignment explanation
Indices: 1754662--1754723 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
1754652 TATTATAAAA
* *
1754662 ATTATATTAAGAAATAAAAATAAAATATATAAG
1 ATTATAATAA-AAATAAAAATAAAACATATAAG
*
1754695 ATTATAATAAAAATGAAAATAAAACATAT
1 ATTATAATAAAAATAAAAATAAAACATAT
1754724 GACATTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 17 0.65
33 9 0.35
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.29
Consensus pattern (32 bp):
ATTATAATAAAAATAAAAATAAAACATATAAG
Found at i:1754995 original size:15 final size:15
Alignment explanation
Indices: 1754971--1755004 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1754961 TTGCAATCAT
*
1754971 ATTACTTGTAATTAC
1 ATTACCTGTAATTAC
*
1754986 ATTACCTGTAATTAT
1 ATTACCTGTAATTAC
1755001 ATTA
1 ATTA
1755005 TATTGTAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (15 bp):
ATTACCTGTAATTAC
Found at i:1755442 original size:23 final size:23
Alignment explanation
Indices: 1755394--1755442 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
1755384 AAATAAATAT
* *
1755394 TTTTAAAATTATAAGTATTTATA
1 TTTTAAAATTATAACTATTTAAA
*
1755417 TTTTAAAATTTTTAACTA-TTAAA
1 TTTTAAAA-TTATAACTATTTAAA
1755440 TTT
1 TTT
1755443 ACTTTATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
TTTTAAAATTATAACTATTTAAA
Found at i:1760347 original size:17 final size:17
Alignment explanation
Indices: 1760325--1760357 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1760315 GGTATTATTT
1760325 TTTTTC-TTTCTATTTTG
1 TTTTTCATTT-TATTTTG
1760342 TTTTTCATTTTATTTT
1 TTTTTCATTTTATTTT
1760358 CTATCTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTTTCATTTTATTTTG
Found at i:1760368 original size:28 final size:26
Alignment explanation
Indices: 1760321--1760372 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
1760311 TTCAGGTATT
*
1760321 ATTTTTTTTCTTTCTATTTTGTTTTTC
1 ATTTTTTTTCTATCTATTTT-TTTTTC
1760348 ATTTTATTTTCTATCT-TTTTTTTTT
1 ATTTT-TTTTCTATCTATTTTTTTTT
1760373 GGGACTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 5 0.22
27 9 0.39
28 9 0.39
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.79
Consensus pattern (26 bp):
ATTTTTTTTCTATCTATTTTTTTTTC
Found at i:1760791 original size:29 final size:29
Alignment explanation
Indices: 1760759--1760814 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
1760749 TTATTAATTT
1760759 ATTAT-TATTTAATAAAAAATTATTTATAA
1 ATTATGTA-TTAATAAAAAATTATTTATAA
* * *
1760788 ATTATGTATTACTTATAAATTATTTAT
1 ATTATGTATTAATAAAAAATTATTTAT
1760815 TGAACTCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 21 0.91
30 2 0.09
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (29 bp):
ATTATGTATTAATAAAAAATTATTTATAA
Found at i:1760798 original size:18 final size:18
Alignment explanation
Indices: 1760777--1760815 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1760767 TTAATAAAAA
*
1760777 ATTATTTATAAATTATGT
1 ATTACTTATAAATTATGT
*
1760795 ATTACTTATAAATTATTT
1 ATTACTTATAAATTATGT
1760813 ATT
1 ATT
1760816 GAACTCTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (18 bp):
ATTACTTATAAATTATGT
Found at i:1765312 original size:6 final size:6
Alignment explanation
Indices: 1765302--1765372 Score: 79
Period size: 6 Copynumber: 11.8 Consensus size: 6
1765292 AATGAAAACT
* * * * * *
1765302 ACCCAT ACCCAT ACCCAT GCCCAA ACCCAA ACCCAA ACTCAA ACTCAA
1 ACCCAA ACCCAA ACCCAA ACCCAA ACCCAA ACCCAA ACCCAA ACCCAA
*
1765350 ACCCAG ACCCAA ACCCAA ACCCA
1 ACCCAA ACCCAA ACCCAA ACCCA
1765373 TGCACATAGT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.42, C:0.48, G:0.03, T:0.07
Consensus pattern (6 bp):
ACCCAA
Found at i:1774287 original size:62 final size:62
Alignment explanation
Indices: 1774190--1774312 Score: 237
Period size: 62 Copynumber: 2.0 Consensus size: 62
1774180 AGAGATATTC
*
1774190 AACTCTTATTCTTTAAGTAATAGGTATATACATCAATCATTGAGTCAAATACTCGGATGCAG
1 AACTCTTATTCTTTAAGCAATAGGTATATACATCAATCATTGAGTCAAATACTCGGATGCAG
1774252 AACTCTTATTCTTTAAGCAATAGGTATATACATCAATCATTGAGTCAAATACTCGGATGCA
1 AACTCTTATTCTTTAAGCAATAGGTATATACATCAATCATTGAGTCAAATACTCGGATGCA
1774313 CCATATTTGA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (62 bp):
AACTCTTATTCTTTAAGCAATAGGTATATACATCAATCATTGAGTCAAATACTCGGATGCAG
Found at i:1790121 original size:14 final size:13
Alignment explanation
Indices: 1790102--1790142 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
1790092 TCACCCGCCT
1790102 ACAGAACCAAGAAC
1 ACAGAACCAA-AAC
1790116 ACAGAACC-AAA-
1 ACAGAACCAAAAC
*
1790127 ACAGAACAAAAAC
1 ACAGAACCAAAAC
1790140 ACA
1 ACA
1790143 ACTTTAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
11 7 0.29
12 5 0.21
13 4 0.17
14 8 0.33
ACGTcount: A:0.63, C:0.27, G:0.10, T:0.00
Consensus pattern (13 bp):
ACAGAACCAAAAC
Found at i:1790162 original size:31 final size:32
Alignment explanation
Indices: 1790127--1790186 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
1790117 CAGAACCAAA
*
1790127 ACAGAACAAAAA-CACAACTTTAACAAAAACC
1 ACAGAACAAAAATCACAAATTTAACAAAAACC
*
1790158 ACAGAACAAAAATCGCAAATTTAACAAAA
1 ACAGAACAAAAATCACAAATTTAACAAAA
1790187 TCCCATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 12 0.46
32 14 0.54
ACGTcount: A:0.62, C:0.22, G:0.05, T:0.12
Consensus pattern (32 bp):
ACAGAACAAAAATCACAAATTTAACAAAAACC
Found at i:1811063 original size:27 final size:28
Alignment explanation
Indices: 1811002--1811078 Score: 95
Period size: 27 Copynumber: 2.8 Consensus size: 28
1810992 ATAAAAATTT
**
1811002 ATTAATTAATCAAAATATT-ATTTAATCG
1 ATTAATTAAT-AATTTATTAATTTAATCG
* *
1811030 ATAAATTAATAATTTATTAATTTATTC-
1 ATTAATTAATAATTTATTAATTTAATCG
1811057 ATTAATTAATAATTTATTAATT
1 ATTAATTAATAATTTATTAATT
1811079 ATCAAGATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 27 0.63
28 16 0.37
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.49
Consensus pattern (28 bp):
ATTAATTAATAATTTATTAATTTAATCG
Found at i:1815398 original size:25 final size:22
Alignment explanation
Indices: 1815343--1815396 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
1815333 TTTCTCATTC
1815343 TTATAATAATCCACAATTCAAG
1 TTATAATAATCCACAATTCAAG
*
1815365 TTATAATAATCCACAATTGAAG
1 TTATAATAATCCACAATTCAAG
*
1815387 TCATAATAAT
1 TTATAATAAT
1815397 AATTCTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.33
Consensus pattern (22 bp):
TTATAATAATCCACAATTCAAG
Found at i:1819850 original size:2 final size:2
Alignment explanation
Indices: 1819843--1819889 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
1819833 NNNNNNNNNN
1819843 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1819885 CA TA T
1 TA TA T
1819890 GTAAATATGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1837780 original size:61 final size:60
Alignment explanation
Indices: 1837690--1838055 Score: 319
Period size: 61 Copynumber: 6.2 Consensus size: 60
1837680 AAGAGTAAGA
* * *
1837690 AAGATTAAGCATTGTTAGAGTAAGG-GAAGATGTCATGGTCCCAAAAGAGACTCTAAGAGT
1 AAGATTGAGCATTGTTAGAGT-GGGAGAAGATGTCATGGTCCCAAAAGAGGCTCTAAGAGT
* * * *
1837750 AAGATTGAGCCATTGTTAGAGTGGGAGAAGATGTTATTGTCCCAAAAGGGGCTTTAAGAGT
1 AAGATTGAG-CATTGTTAGAGTGGGAGAAGATGTCATGGTCCCAAAAGAGGCTCTAAGAGT
* ** * * *
1837811 AAAATAAAGTATTGTTAGAGTGGG-GAAGATGTCATGGTCCCAAAA-AGGGCTTTGAGAGT
1 AAGATTGAGCATTGTTAGAGTGGGAGAAGATGTCATGGTCCCAAAAGA-GGCTCTAAGAGT
* * *
1837870 AAGATTGAGCATTGTTAAAGTGGGAGAAGATG--AGGGCTCTC-----A-GCT-TAAGA--
1 AAGATTGAGCATTGTTAGAGTGGGAGAAGATGTCATGG-TCCCAAAAGAGGCTCTAAGAGT
* * * * * *
1837920 AAGATTAAGCATTATTAGAGTGGGGGAAAGATGTCATGGTCCCAAGAGGGGCTCTTAGAGT
1 AAGATTGAGCATTGTTAGAGTGGGAG-AAGATGTCATGGTCCCAAAAGAGGCTCTAAGAGT
* * * * * * *
1837981 GAGATTGAGCATTGTTAAAGTGGGATAAAGATGTCATGGTCCCAAAAGGGGTTCTGATAGT
1 AAGATTGAGCATTGTTAGAGTGGGA-GAAGATGTCATGGTCCCAAAAGAGGCTCTAAGAGT
1838042 AAGATTGAGCATTG
1 AAGATTGAGCATTG
1838056 ATAAAGTAAG
Statistics
Matches: 246, Mismatches: 42, Indels: 35
0.76 0.13 0.11
Matches are distributed among these distances:
50 22 0.09
51 6 0.02
52 7 0.03
53 6 0.02
55 1 0.00
58 6 0.02
59 56 0.23
60 31 0.13
61 111 0.45
ACGTcount: A:0.34, C:0.10, G:0.31, T:0.26
Consensus pattern (60 bp):
AAGATTGAGCATTGTTAGAGTGGGAGAAGATGTCATGGTCCCAAAAGAGGCTCTAAGAGT
Found at i:1837847 original size:120 final size:122
Alignment explanation
Indices: 1837673--1838073 Score: 338
Period size: 111 Copynumber: 3.4 Consensus size: 122
1837663 TGGAAGATAA
*
1837673 GGGCTTTAAGAGTAAGAAAGATTAAGCATTGTTAGAGTAAGGGAAGATGTCATGGTCCC-AAAAG
1 GGGCTTTAAGAGT-A-AAAGATAAAGCATTGTTAGAGTAAGGGAAGATGTCATGGTCCCAAAAAG
*
1837737 AGACTCTAAGAGTAAGATTGAGCCATTGTTAGAGTGGGAGAAGATGTTATTGTCCCAAAAG
64 -GACTCTAAGAGTAAGATTGAG-CATTGTTAAAGTGGGAGAAGATGTTATTGTCCCAAAAG
* * *
1837798 GGGCTTTAAGAGT-AAA-ATAAAGTATTGTTAGAGT-GGGGAAGATGTCATGGTCCCAAAAAGGG
1 GGGCTTTAAGAGTAAAAGATAAAGCATTGTTAGAGTAAGGGAAGATGTCATGGTCCCAAAAAGGA
* * ** *
1837860 CTTTGAGAGTAAGATTGAGCATTGTTAAAGTGGGAGAAGATG--AGGGCTCTC---A-
66 CTCTAAGAGTAAGATTGAGCATTGTTAAAGTGGGAGAAGATGTTATTG-TCCCAAAAG
* * ** * *
1837912 --GC-TT-A-AG--AAAGATTAAGCATTATTAGAGTGGGGGAAAGATGTCATGGTCCCAAGAGGG
1 GGGCTTTAAGAGTAAAAGATAAAGCATTGTTAGAGTAAGGG-AAGATGTCATGGTCCCAAAAAGG
* * * * * *
1837970 GCTCTTAGAGTGAGATTGAGCATTGTTAAAGTGGGATAAAGATGTCATGGTCCCAAAAG
65 ACTCTAAGAGTAAGATTGAGCATTGTTAAAGTGGGA-GAAGATGTTATTGTCCCAAAAG
* * ** * *
1838029 GGG-TTCTGATAGT--AAGATTGAGCATTGATAAAGTAAGGGAAGATG
1 GGGCTT-TAAGAGTAAAAGATAAAGCATTGTTAGAGTAAGGGAAGATG
1838074 GGAGTTCTAT
Statistics
Matches: 230, Mismatches: 27, Indels: 42
0.77 0.09 0.14
Matches are distributed among these distances:
108 3 0.01
109 17 0.07
110 5 0.02
111 56 0.24
112 8 0.03
113 3 0.01
114 3 0.01
115 1 0.00
116 1 0.00
117 2 0.01
118 3 0.01
119 24 0.10
120 38 0.17
121 28 0.12
122 25 0.11
125 13 0.06
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.25
Consensus pattern (122 bp):
GGGCTTTAAGAGTAAAAGATAAAGCATTGTTAGAGTAAGGGAAGATGTCATGGTCCCAAAAAGGA
CTCTAAGAGTAAGATTGAGCATTGTTAAAGTGGGAGAAGATGTTATTGTCCCAAAAG
Found at i:1837861 original size:59 final size:60
Alignment explanation
Indices: 1837671--1837901 Score: 252
Period size: 59 Copynumber: 3.8 Consensus size: 60
1837661 GATGGAAGAT
*
1837671 AAGGGCTTTAAGAGTAAGAAAGATTAAGCATTGTTAGAGTAAGG-GAAGATGTCATGGTCCC-AA
1 AAGGGCTTTAAGAGT---AAA-ATTAAGCATTGTTAGAGT-GGGAGAAGATGTCATGGTCCCAAA
* * * * * *
1837734 AAGAGACTCTAAGAGTAAGATTGAGCCATTGTTAGAGTGGGAGAAGATGTTATTGTCCCAAA
1 AAG-GGCTTTAAGAGTAAAATTAAG-CATTGTTAGAGTGGGAGAAGATGTCATGGTCCCAAA
* * *
1837796 AGGGGCTTTAAGAGTAAAATAAAGTATTGTTAGAGTGGG-GAAGATGTCATGGTCCCAAA
1 AAGGGCTTTAAGAGTAAAATTAAGCATTGTTAGAGTGGGAGAAGATGTCATGGTCCCAAA
* * * *
1837855 AAGGGCTTTGAGAGTAAGATTGAGCATTGTTAAAGTGGGAGAAGATG
1 AAGGGCTTTAAGAGTAAAATTAAGCATTGTTAGAGTGGGAGAAGATG
1837902 AGGGCTCTCA
Statistics
Matches: 140, Mismatches: 23, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
59 50 0.36
60 28 0.20
61 45 0.32
62 4 0.03
63 3 0.02
64 10 0.07
ACGTcount: A:0.36, C:0.09, G:0.30, T:0.25
Consensus pattern (60 bp):
AAGGGCTTTAAGAGTAAAATTAAGCATTGTTAGAGTGGGAGAAGATGTCATGGTCCCAAA
Found at i:1838046 original size:172 final size:170
Alignment explanation
Indices: 1837750--1838174 Score: 529
Period size: 172 Copynumber: 2.5 Consensus size: 170
1837740 CTCTAAGAGT
* * * * *
1837750 AAGATTGAGCCATTGTTAGAGTGGGAG-AAGATGTTATTGTCCCAAAAGGGGCTTTAAGAGTAAA
1 AAGATTAAG-CATTGTTAGAGTGGGGGAAAGATGTCATGGTCCCAAAAGGGGCTTTAAGAGTAAG
** * * *
1837814 ATAAAGTATTGTTAGAGTGGGGAAGATGTCATGGTCCCAAAAAGGGCTTTGAGAGTAAGATTGAG
65 ATTGAGCATTGTTAAAGTGGGAAAGATGTCATGGTCCCAAAAAGGGCTTTGAGAGTAAGATTGAG
* * **
1837879 CATTGTTAAAGT-GGGAGAAGATGAGG-GCTCTCA-GCTTAAGA
130 CATTGATAAAGTAAGG-GAAGATG-GGAGCTCT-ATGAATAAGA
* * *
1837920 AAGATTAAGCATTATTAGAGTGGGGGAAAGATGTCATGGTCCCAAGAGGGGCTCTT-AGAGTGAG
1 AAGATTAAGCATTGTTAGAGTGGGGGAAAGATGTCATGGTCCCAAAAGGGGCT-TTAAGAGTAAG
* *
1837984 ATTGAGCATTGTTAAAGTGGGATAAAGATGTCATGGTCCC-AAAAGGGGTTCTGATAGTAAGATT
65 ATTGAGCATTGTTAAAGTGGG--AAAGATGTCATGGTCCCAAAAAGGGCTT-TGAGAGTAAGATT
*
1838048 GAGCATTGATAAAGTAAGGGAAGATGGGAGTTCTATGAATAAGA
127 GAGCATTGATAAAGTAAGGGAAGATGGGAGCTCTATGAATAAGA
* *
1838092 AAGATTAAGCATTGTTAGAGTGGGGGAAAGATGTCATGGTCCCAAAAAGGGCTTTGAGAGTAAGA
1 AAGATTAAGCATTGTTAGAGTGGGGGAAAGATGTCATGGTCCCAAAAGGGGCTTTAAGAGTAAGA
*
1838157 TTGCGCATTGTTAAAGTG
66 TTGAGCATTGTTAAAGTG
1838175 AGGGAAGCCC
Statistics
Matches: 221, Mismatches: 25, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
169 15 0.07
170 54 0.24
171 16 0.07
172 134 0.61
173 2 0.01
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (170 bp):
AAGATTAAGCATTGTTAGAGTGGGGGAAAGATGTCATGGTCCCAAAAGGGGCTTTAAGAGTAAGA
TTGAGCATTGTTAAAGTGGGAAAGATGTCATGGTCCCAAAAAGGGCTTTGAGAGTAAGATTGAGC
ATTGATAAAGTAAGGGAAGATGGGAGCTCTATGAATAAGA
Found at i:1838107 original size:111 final size:111
Alignment explanation
Indices: 1837982--1838181 Score: 303
Period size: 111 Copynumber: 1.8 Consensus size: 111
1837972 TCTTAGAGTG
* * * *
1837982 AGATTGAGCATTGTTAAAGTGGGATAAAGATGTCATGGTCCC-AAAAGGGGTTCTGATAGTAAGA
1 AGATTAAGCATTGTTAAAGTGGGAGAAAGATGTCATGGTCCCAAAAAGGGCTT-TGAGAGTAAGA
1838046 TTGAGCATTGATAAAGTAAGGGAAGATGGGAGTTCTATGAATAAGAA
65 TTGAGCATTGATAAAGTAAGGGAAGATGGGAGTTCTATGAATAAGAA
* *
1838093 AGATTAAGCATTGTTAGAGTGGGGGAAAGATGTCATGGTCCCAAAAAGGGCTTTGAGAGTAAGAT
1 AGATTAAGCATTGTTAAAGTGGGAGAAAGATGTCATGGTCCCAAAAAGGGCTTTGAGAGTAAGAT
* * *
1838158 TGCGCATTGTTAAAGTGAGGGAAG
66 TGAGCATTGATAAAGTAAGGGAAG
1838182 CCCTTTGAGA
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
111 70 0.89
112 9 0.11
ACGTcount: A:0.35, C:0.08, G:0.32, T:0.26
Consensus pattern (111 bp):
AGATTAAGCATTGTTAAAGTGGGAGAAAGATGTCATGGTCCCAAAAAGGGCTTTGAGAGTAAGAT
TGAGCATTGATAAAGTAAGGGAAGATGGGAGTTCTATGAATAAGAA
Found at i:1838291 original size:59 final size:60
Alignment explanation
Indices: 1838204--1838332 Score: 172
Period size: 59 Copynumber: 2.2 Consensus size: 60
1838194 AAGATTGAGT
* * *
1838204 ATCATTGTTAGAGTGGGGCAAGATGTCATTG-TCCC-AAAGGGGCTTTAAGAGTAAAATGA
1 ATCATTGTTAGAGTGGGGCAAGACGTCA-TGATCCCAAAAAGGGCTCTAAGAGTAAAATGA
* * *
1838263 ATCATTGTTAGAGTGGGGGAAGACGTCATGATCCCAAAAAGGGCTCTAAGAGTAAGATTA
1 ATCATTGTTAGAGTGGGGCAAGACGTCATGATCCCAAAAAGGGCTCTAAGAGTAAAATGA
*
1838323 ACCATTGTTA
1 ATCATTGTTA
1838333 AAATGGGAGA
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
58 2 0.03
59 30 0.49
60 29 0.48
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.26
Consensus pattern (60 bp):
ATCATTGTTAGAGTGGGGCAAGACGTCATGATCCCAAAAAGGGCTCTAAGAGTAAAATGA
Found at i:1838544 original size:111 final size:110
Alignment explanation
Indices: 1838265--1839110 Score: 465
Period size: 111 Copynumber: 7.6 Consensus size: 110
1838255 TAAAATGAAT
* * * * * * * *
1838265 CATTGTTAGAGTGGGGGAAGACGTCATGATCCCAAAAAGGGCTCTAAGAGTAAGATTAACCATTG
1 CATTATTAAAGTGGGGAAAGATGTCATGGTCCCAAAAGGGGCTCTAAGAGTAAGATTGAGCATTG
* * *
1838330 TTAAAATGGGAGAAGATGGGGGCTCTGAGCTTAAGAAAGATTAAG
66 TTAAAGTGGGGGAAGATGGGGGCTTTGAGCTTAAGAAAGATTAAG
* *
1838375 CATTATTAGAGTGGGGGAAAGATGTCATGGTCCCAAAAGGGACTCTAAGAGTAAGATTGAGCATT
1 CATTATTAAAGT-GGGGAAAGATGTCATGGTCCCAAAAGGGGCTCTAAGAGTAAGATTGAGCATT
*
1838440 GTTAAAGTGGGGGAAGATGGGGGCTTTGAGCTTAAGCAAGATTAAG
65 GTTAAAGTGGGGGAAGATGGGGGCTTTGAGCTTAAGAAAGATTAAG
* *
1838486 CATTATTAAAGTGGGAGAAAGATGTCATGGTCCTAAAAGGGGCTCTGAGAGTAAGATTGAGCATT
1 CATTATTAAAGTGGG-GAAAGATGTCATGGTCCCAAAAGGGGCTCTAAGAGTAAGATTGAGCATT
* * *** *** * * *
1838551 ATTAAAGTGAGGGAAATATGTCATGGTCCCAAAAGGGGTTCTGATAA-TAAGATTGAG
65 GTTAAAGTG-GGG-GA-A-G--ATGGGGGC--TTTGAG--CT--TAAGAAAGATTAAG
* * * * * *
1838608 CATTATTAAAGTGAGGGAAATATGTCATGGTCCCAAAAGGGGTTTTGATAATAAGATTGAGCATT
1 CATTATTAAAGTG-GGGAAAGATGTCATGGTCCCAAAAGGGGCTCTAAGAGTAAGATTGAGCATT
* ** * * ** *
1838673 GATAAAGTAAGGGAAGATGAGAG-TTCT-ATGAATAAGAAAGGTTAAG
65 GTTAAAGTGGGGGAAGATGGGGGCTT-TGA-GCTTAAGAAAGATTAAG
* * * *
1838719 CATTGTTATAGTGGGAGAAAGATGTCATGGTCCTAAAGGGGGCTCTAAGAGTAAGATTGCA-CAT
1 CATTATTAAAGTGGG-GAAAGATGTCATGGTCCCAAAAGGGGCTCTAAGAGTAAGATTG-AGCAT
* ** ** ** ** *
1838783 TGTTAAAGTGAGGG-A-A---GCCCTTTGAGAGTAAGATTGA-GCAT
64 TGTTAAAGTGGGGGAAGATGGGGGCTTTGAGCTTAAGAAAGATTAAG
* * * * * * * * *
1838824 CATTGTTAGAGTGGGGCAAGATGTTATTGTCCCAAATGAGGCTTTAAGAGTAAGAAAGATTAAGC
1 CATTATTAAAGTGGGGAAAGATGTCATGGTCCCAAAAGGGGCTCTAAGAGT----AAGATTGAGC
* * ** * *
1838889 ATTATTAAAGTGGGGG--GA--AGCCCTTTGAG----AGTAAGATTTAG
62 ATTGTTAAAGTGGGGGAAGATGGGGGCTTTGAGCTTAAGAAAGATTAAG
* * * * * * *
1838930 TATTGTTAAAGTAAGGG-AATATGTCATGATCCCAAAAGGGGCTTTAAGAGTAAGAAAGATTAAG
1 CATTATTAAAGT-GGGGAAAGATGTCATGGTCCCAAAAGGGGCTCTAAGAGT----AAGATTGAG
* * * * * **
1838994 AATTGTTATAGTGAGGAAAGATGAGGGCTTTGAGAGTAAGAAAGATTAAG
61 CATTGTTAAAGTGGGGGAAGATGGGGGCTTTGAGCTTAAGAAAGATTAAG
* * * * *
1839044 CATTGTTAGAGTTAGGGGAAA-ATGTCATGAT-CCTAGAGAGGGCTCTAAGAGTAAGATTGAGCA
1 CATTATTAAAG-T-GGGGAAAGATGTCATGGTCCCAAAAG-GGGCTCTAAGAGTAAGATTGAGCA
1839107 TTGT
63 TTGT
1839111 CCCAAAAGGG
Statistics
Matches: 579, Mismatches: 115, Indels: 83
0.75 0.15 0.11
Matches are distributed among these distances:
104 29 0.05
105 19 0.03
106 74 0.13
107 7 0.01
108 24 0.04
109 11 0.02
110 29 0.05
111 233 0.40
112 4 0.01
113 1 0.00
114 26 0.04
115 28 0.05
116 5 0.01
117 5 0.01
118 1 0.00
119 3 0.01
120 1 0.00
121 4 0.01
122 70 0.12
123 5 0.01
ACGTcount: A:0.35, C:0.09, G:0.30, T:0.26
Consensus pattern (110 bp):
CATTATTAAAGTGGGGAAAGATGTCATGGTCCCAAAAGGGGCTCTAAGAGTAAGATTGAGCATTG
TTAAAGTGGGGGAAGATGGGGGCTTTGAGCTTAAGAAAGATTAAG
Found at i:1838572 original size:61 final size:61
Alignment explanation
Indices: 1838477--1838687 Score: 318
Period size: 61 Copynumber: 3.5 Consensus size: 61
1838467 GAGCTTAAGC
* * * * * *
1838477 AAGATTAAGCATTATTAAAGTG-GGAGAAAGATGTCATGGTCCTAAAAGGGGCTCTGAGAGT
1 AAGATTGAGCATTATTAAAGTGAGG-GAAATATGTCATGGTCCCAAAAGGGGTTCTGATAAT
1838538 AAGATTGAGCATTATTAAAGTGAGGGAAATATGTCATGGTCCCAAAAGGGGTTCTGATAAT
1 AAGATTGAGCATTATTAAAGTGAGGGAAATATGTCATGGTCCCAAAAGGGGTTCTGATAAT
*
1838599 AAGATTGAGCATTATTAAAGTGAGGGAAATATGTCATGGTCCCAAAAGGGGTTTTGATAAT
1 AAGATTGAGCATTATTAAAGTGAGGGAAATATGTCATGGTCCCAAAAGGGGTTCTGATAAT
*
1838660 AAGATTGAGCATTGA-TAAAGTAAGGGAA
1 AAGATTGAGCATT-ATTAAAGTGAGGGAA
1838688 GATGAGAGTT
Statistics
Matches: 140, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
61 137 0.98
62 3 0.02
ACGTcount: A:0.37, C:0.09, G:0.27, T:0.27
Consensus pattern (61 bp):
AAGATTGAGCATTATTAAAGTGAGGGAAATATGTCATGGTCCCAAAAGGGGTTCTGATAAT
Found at i:1838604 original size:446 final size:439
Alignment explanation
Indices: 1837745--1838626 Score: 1061
Period size: 446 Copynumber: 2.0 Consensus size: 439
1837735 AGAGACTCTA
*
1837745 AGAGTAAGATTGAGCCATTGTTAGAGTGGGAGAAGATGTTATTGTCCCAAAAGGGGCTTTAAGAG
1 AGAGTAAGATTGAGCCATTGTTAGAGTGGGAGAAGATGTCATTGTCCCAAAAGGGGCTTTAAGAG
* * * *
1837810 TAAAATAAAGTATTGTTAGAGTGGGGAAGATGTCATGGTCCCAAAAAGGGCTTTGAGAGTAAGAT
66 TAAAATAAAGTATTGTTAGAGTGGGGAAGACGTCATGATCCCAAAAAGGGCTCTAAGAGTAAGAT
* * *
1837875 TGAGCATTGTTAAAGTGGGAGAAGATGAGGGCTCTCAGCTTAAGAAAGATTAAGCATTATTAGAG
131 TAACCATTGTTAAAATGGGAGAAGATGAGGGCTCTCAGCTTAAGAAAGATTAAGCATTATTAGAG
* * * *
1837940 TGGGGGAAAGATGTCATGGTCCCAAGAGGGGCTCTTAGAGTGAGATTGAGCATTGTTAAAGTGGG
196 TGGGGGAAAGATGTCATGGTCCCAAAAGGGACTCTAAGAGTAAGATTGAGCATTGTTAAAGTGGG
* * * *
1838005 ATAAAGATGTCATGGTCCCAAAAGGGGTTCTGATAGTAAGATTGAGCATTGATAAAGTAAGGGAA
261 AGAAAGATG---TGGTCCC-AAAGGAG-TCTGATAGCAAGATTAAGCATTGATAAAGTAAGGGAA
* * * * * *
1838070 GATGGGAGTTCTATGAATAAGAAAGATTAAGCATTGTTAGAGTGGGGGAAAGATGTCATGGTCCC
321 GATGGCAGTCCTATAAATAAGAAAGATTAAGCATTATTAAAGTGAGGGAAAGATGTCATGGTCCC
* * *
1838135 AAAAAGGGCTTTGAGAGTAAGATTGCGCATTGTTAAAGTGAGGGAAGCCCTTTG
386 AAAAAGGGCTTTGAGAATAAGATTGAGCATTATTAAAGTGAGGGAAGCCCTTTG
*
1838189 AGAGTAAGATTGAGTATCATTGTTAGAGTGGG-GCAAGATGTCATTGTCCC-AAAGGGGCTTTAA
1 AGAGTAAGATTGAG--CCATTGTTAGAGTGGGAG-AAGATGTCATTGTCCCAAAAGGGGCTTTAA
*
1838252 GAGTAAAATGAA-TCATTGTTAGAGTGGGGGAAGACGTCATGATCCCAAAAAGGGCTCTAAGAGT
63 GAGTAAAATAAAGT-ATTGTTAGAGT-GGGGAAGACGTCATGATCCCAAAAAGGGCTCTAAGAGT
* *
1838316 AAGATTAACCATTGTTAAAATGGGAGAAGATGGGGGCTCTGAGCTTAAGAAAGATTAAGCATTAT
126 AAGATTAACCATTGTTAAAATGGGAGAAGATGAGGGCTCTCAGCTTAAGAAAGATTAAGCATTAT
1838381 TAGAGTGGGGGAAAGATGTCATGGTCCCAAAAGGGACTCTAAGAGTAAGATTGAGCATTGTTAAA
191 TAGAGTGGGGGAAAGATGTCATGGTCCCAAAAGGGACTCTAAGAGTAAGATTGAGCATTGTTAAA
* ** *** * *
1838446 GTGGG-GGAAGATG-GG-GGC-TTTGAG-CTTA-AGCAAGATTAAGCATT-ATTAAAGT-GGGAG
256 GTGGGAGAAAGATGTGGTCCCAAAGGAGTCTGATAGCAAGATTAAGCATTGA-TAAAGTAAGG-G
* * *
1838503 AAAGATGTCATGGTCCTA-AAAGGGGCTCTGAGAGTAAGATTGAGCATTATTAAAGTGAGGGAAA
319 -AAGATGGCA--GTCCTATAAA-------T-A-AGAAAGATTAAGCATTATTAAAGTGAGGGAAA
* * *
1838567 TATGTCATGGTCCC-AAAAGGGGTTCTGATAATAAGATTGAGCATTATTAAAGTGAGGGAA
372 GATGTCATGGTCCCAAAAAGGGCTT-TGAGAATAAGATTGAGCATTATTAAAGTGAGGGAA
1838627 ATATGTCATG
Statistics
Matches: 375, Mismatches: 43, Indels: 38
0.82 0.09 0.08
Matches are distributed among these distances:
434 3 0.01
435 21 0.06
436 10 0.03
437 2 0.01
438 7 0.02
440 1 0.00
441 2 0.01
444 16 0.04
445 52 0.14
446 261 0.70
ACGTcount: A:0.34, C:0.10, G:0.31, T:0.25
Consensus pattern (439 bp):
AGAGTAAGATTGAGCCATTGTTAGAGTGGGAGAAGATGTCATTGTCCCAAAAGGGGCTTTAAGAG
TAAAATAAAGTATTGTTAGAGTGGGGAAGACGTCATGATCCCAAAAAGGGCTCTAAGAGTAAGAT
TAACCATTGTTAAAATGGGAGAAGATGAGGGCTCTCAGCTTAAGAAAGATTAAGCATTATTAGAG
TGGGGGAAAGATGTCATGGTCCCAAAAGGGACTCTAAGAGTAAGATTGAGCATTGTTAAAGTGGG
AGAAAGATGTGGTCCCAAAGGAGTCTGATAGCAAGATTAAGCATTGATAAAGTAAGGGAAGATGG
CAGTCCTATAAATAAGAAAGATTAAGCATTATTAAAGTGAGGGAAAGATGTCATGGTCCCAAAAA
GGGCTTTGAGAATAAGATTGAGCATTATTAAAGTGAGGGAAGCCCTTTG
Found at i:1838641 original size:233 final size:233
Alignment explanation
Indices: 1838366--1838798 Score: 602
Period size: 233 Copynumber: 1.9 Consensus size: 233
1838356 GAGCTTAAGA
* * *
1838366 AAGATTAAGCATTATTAGAGTGGGGGAAAGATGTCATGGTCCCAAAAGGGACTCTAAGAGTAAGA
1 AAGATTAAGCATTATTAAAGTGAGGGAAAGATGTCATGGTCCCAAAAGGGACTCTAAGAATAAGA
* ** * * ** *
1838431 TTGAGCATTGTTAAAGTGGGGGAAGATGGGGGCTT-TGA-GCTTAAGCAAGATTAAGCATTATTA
66 TTGAGCATTGATAAAGTAAGGGAAGATGAGAG-TTCT-ATGAATAAGAAAGATTAAGCATTATTA
*
1838494 AAGTGGGAGAAAGATGTCATGGTCCTAAAAGGGGCTCTGAGAGTAAGATTG-AGCATTATTAAAG
129 AAGTGGGAGAAAGATGTCATGGTCCTAAAAGGGGCTCTAAGAGTAAGATTGCA-CATTATTAAAG
1838558 TGAGGGAAATATGTCATGGTCCCAAAAGGGGTTCTGATAAT
193 TGAGGGAAATATGTCATGGTCCCAAAAGGGGTTCTGATAAT
* * ** * * *
1838599 AAGATTGAGCATTATTAAAGTGAGGGAAATATGTCATGGTCCCAAAAGGGGTTTTGATAATAAGA
1 AAGATTAAGCATTATTAAAGTGAGGGAAAGATGTCATGGTCCCAAAAGGGACTCTAAGAATAAGA
* * *
1838664 TTGAGCATTGATAAAGTAAGGGAAGATGAGAGTTCTATGAATAAGAAAGGTTAAGCATTGTTATA
66 TTGAGCATTGATAAAGTAAGGGAAGATGAGAGTTCTATGAATAAGAAAGATTAAGCATTATTAAA
* *
1838729 GTGGGAGAAAGATGTCATGGTCCTAAAGGGGGCTCTAAGAGTAAGATTGCACATTGTTAAAGTGA
131 GTGGGAGAAAGATGTCATGGTCCTAAAAGGGGCTCTAAGAGTAAGATTGCACATTATTAAAGTGA
1838794 GGGAA
196 GGGAA
1838799 GCCCTTTGAG
Statistics
Matches: 173, Mismatches: 24, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
232 3 0.02
233 169 0.98
234 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.30, T:0.26
Consensus pattern (233 bp):
AAGATTAAGCATTATTAAAGTGAGGGAAAGATGTCATGGTCCCAAAAGGGACTCTAAGAATAAGA
TTGAGCATTGATAAAGTAAGGGAAGATGAGAGTTCTATGAATAAGAAAGATTAAGCATTATTAAA
GTGGGAGAAAGATGTCATGGTCCTAAAAGGGGCTCTAAGAGTAAGATTGCACATTATTAAAGTGA
GGGAAATATGTCATGGTCCCAAAAGGGGTTCTGATAAT
Found at i:1838978 original size:106 final size:107
Alignment explanation
Indices: 1838780--1839009 Score: 288
Period size: 106 Copynumber: 2.1 Consensus size: 107
1838770 TAAGATTGCA
* * *
1838780 CATTGTTAAAGTGAGGGAAGCCCTTTGAGAGTAAGATTGAGCATCATTGTTAGAGTGGGGCAAGA
1 CATTATTAAAGTGAGGGAAGCCCTTTGAGAGTAAGATTGAG-ATCATTGTTAAAGTAGGGCAAGA
* *
1838845 TGTTATTGTCCCAAATGAGGCTTTAAGAGTAAGAAAGATTAAG
65 TGTCATTGTCCCAAAAGAGGCTTTAAGAGTAAGAAAGATTAAG
* * *
1838888 CATTATTAAAGTGGGGGGAAGCCCTTTGAGAGTAAGATTTAG-T-ATTGTTAAAGTAAGGG-AAT
1 CATTATTAAAGT-GAGGGAAGCCCTTTGAGAGTAAGATTGAGATCATTGTTAAAGT-AGGGCAAG
*
1838950 ATGTCA-TGATCCCAAAAGGGGCTTTAAGAGTAAGAAAGATTAAG
64 ATGTCATTG-TCCCAAAAGAGGCTTTAAGAGTAAGAAAGATTAAG
* * *
1838994 AATTGTTATAGTGAGG
1 CATTATTAAAGTGAGG
1839010 AAAGATGAGG
Statistics
Matches: 106, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
105 5 0.05
106 59 0.56
107 4 0.04
108 11 0.10
109 27 0.25
ACGTcount: A:0.35, C:0.09, G:0.28, T:0.28
Consensus pattern (107 bp):
CATTATTAAAGTGAGGGAAGCCCTTTGAGAGTAAGATTGAGATCATTGTTAAAGTAGGGCAAGAT
GTCATTGTCCCAAAAGAGGCTTTAAGAGTAAGAAAGATTAAG
Found at i:1839291 original size:114 final size:115
Alignment explanation
Indices: 1839086--1839436 Score: 524
Period size: 127 Copynumber: 3.0 Consensus size: 115
1839076 CTAGAGAGGG
*
1839086 CTCTAAGAGTAAGATTGAGCATTGTCCCAAAAGGGGCTCTGAGAGTAAGATTGAGTATTTTTAGA
1 CTCTGAGAGTAAGATTGAGCATTGTCCCAAAAGGGGCTCTGAGAGTAAGATTGAGTATTTTTAGA
* *
1839151 ATAAAGGAAAATGGGGACTCTGAGAGTAAGAAAGATTAAGCATT-AAGCC
66 ATAAGGGAAAATGGGGACTCTAAGAGTAAGAAAGATTAAGCATTGAAGCC
*
1839200 CTCTGAGAGTAAGATTGAGCATTGTCCCAAAAAGGGCTCTGAGAGTAAGATTGAGTATTTTTAGA
1 CTCTGAGAGTAAGATTGAGCATTGTCCCAAAAGGGGCTCTGAGAGTAAGATTGAGTATTTTTAGA
1839265 ATAAGGGAAAATGGGGACTCTAAGAGTAAGAAAGATTAAGCATTGTTAAAGTGGGGGAAGCC
66 ATAAGGGAAAATGGGGACTCTAAGAGTAAGAAAGATTAAGCA----T----T----GAAGCC
*
1839327 CTCTGAGAGTAAGATTGAGCATTGTCCCAAAAGGGGCTCTAAGAGTAAGATTGAGTATTTTTAGA
1 CTCTGAGAGTAAGATTGAGCATTGTCCCAAAAGGGGCTCTGAGAGTAAGATTGAGTATTTTTAGA
* *
1839392 ATAAGGAAAAATGGCGACTCTAAGAGTAAGAAAGATTAAGCATTG
66 ATAAGGGAAAATGGGGACTCTAAGAGTAAGAAAGATTAAGCATTG
1839437 TTAAAGTGGG
Statistics
Matches: 216, Mismatches: 8, Indels: 25
0.87 0.03 0.10
Matches are distributed among these distances:
114 103 0.48
115 1 0.00
118 1 0.00
119 1 0.00
122 1 0.00
123 1 0.00
127 108 0.50
ACGTcount: A:0.37, C:0.11, G:0.27, T:0.25
Consensus pattern (115 bp):
CTCTGAGAGTAAGATTGAGCATTGTCCCAAAAGGGGCTCTGAGAGTAAGATTGAGTATTTTTAGA
ATAAGGGAAAATGGGGACTCTAAGAGTAAGAAAGATTAAGCATTGAAGCC
Found at i:1839421 original size:127 final size:127
Alignment explanation
Indices: 1839195--1839471 Score: 518
Period size: 127 Copynumber: 2.2 Consensus size: 127
1839185 ATTAAGCATT
*
1839195 AAGCCCTCTGAGAGTAAGATTGAGCATTGTCCCAAAAAGGGCTCTGAGAGTAAGATTGAGTATTT
1 AAGCCCTCTGAGAGTAAGATTGAGCATTGTCCCAAAAAGGGCTCTAAGAGTAAGATTGAGTATTT
* *
1839260 TTAGAATAAGGGAAAATGGGGACTCTAAGAGTAAGAAAGATTAAGCATTGTTAAAGTGGGGG
66 TTAGAATAAGGAAAAATGGCGACTCTAAGAGTAAGAAAGATTAAGCATTGTTAAAGTGGGGG
*
1839322 AAGCCCTCTGAGAGTAAGATTGAGCATTGTCCCAAAAGGGGCTCTAAGAGTAAGATTGAGTATTT
1 AAGCCCTCTGAGAGTAAGATTGAGCATTGTCCCAAAAAGGGCTCTAAGAGTAAGATTGAGTATTT
1839387 TTAGAATAAGGAAAAATGGCGACTCTAAGAGTAAGAAAGATTAAGCATTGTTAAAGTGGGGG
66 TTAGAATAAGGAAAAATGGCGACTCTAAGAGTAAGAAAGATTAAGCATTGTTAAAGTGGGGG
1839449 AAGCCCTCTGAGAGTAAGATTGA
1 AAGCCCTCTGAGAGTAAGATTGA
1839472 AGCCCTCTGA
Statistics
Matches: 146, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
127 146 1.00
ACGTcount: A:0.36, C:0.11, G:0.28, T:0.24
Consensus pattern (127 bp):
AAGCCCTCTGAGAGTAAGATTGAGCATTGTCCCAAAAAGGGCTCTAAGAGTAAGATTGAGTATTT
TTAGAATAAGGAAAAATGGCGACTCTAAGAGTAAGAAAGATTAAGCATTGTTAAAGTGGGGG
Found at i:1839476 original size:22 final size:22
Alignment explanation
Indices: 1839448--1839493 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
1839438 TAAAGTGGGG
1839448 GAAGCCCTCTGAGAGTAAGATT
1 GAAGCCCTCTGAGAGTAAGATT
1839470 GAAGCCCTCTGAGAGTAAGATT
1 GAAGCCCTCTGAGAGTAAGATT
1839492 GA
1 GA
1839494 GCATTGTCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (22 bp):
GAAGCCCTCTGAGAGTAAGATT
Found at i:1839591 original size:149 final size:149
Alignment explanation
Indices: 1839321--1839620 Score: 582
Period size: 149 Copynumber: 2.0 Consensus size: 149
1839311 TAAAGTGGGG
1839321 GAAGCCCTCTGAGAGTAAGATTGAGCATTGTCCCAAAAGGGGCTCTAAGAGTAAGATTGAGTATT
1 GAAGCCCTCTGAGAGTAAGATTGAGCATTGTCCCAAAAGGGGCTCTAAGAGTAAGATTGAGTATT
1839386 TTTAGAATAAGGAAAAATGGCGACTCTAAGAGTAAGAAAGATTAAGCATTGTTAAAGTGGGGGAA
66 TTTAGAATAAGGAAAAATGGCGACTCTAAGAGTAAGAAAGATTAAGCATTGTTAAAGTGGGGGAA
1839451 GCCCTCTGAGAGTAAGATT
131 GCCCTCTGAGAGTAAGATT
*
1839470 GAAGCCCTCTGAGAGTAAGATTGAGCATTGTCCCAAAAGGGGCTCTGAGAGTAAGATTGAGTATT
1 GAAGCCCTCTGAGAGTAAGATTGAGCATTGTCCCAAAAGGGGCTCTAAGAGTAAGATTGAGTATT
1839535 TTTAGAATAAGGAAAAATGGCGACTCTAAGAGTAAGAAAGATTAAGCATTGTTAAAGTGGGGGAA
66 TTTAGAATAAGGAAAAATGGCGACTCTAAGAGTAAGAAAGATTAAGCATTGTTAAAGTGGGGGAA
*
1839600 GCCTTCTGAGAGTAAGATT
131 GCCCTCTGAGAGTAAGATT
1839619 GA
1 GA
1839621 GCATTGTTAG
Statistics
Matches: 149, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 149 1.00
ACGTcount: A:0.36, C:0.12, G:0.28, T:0.24
Consensus pattern (149 bp):
GAAGCCCTCTGAGAGTAAGATTGAGCATTGTCCCAAAAGGGGCTCTAAGAGTAAGATTGAGTATT
TTTAGAATAAGGAAAAATGGCGACTCTAAGAGTAAGAAAGATTAAGCATTGTTAAAGTGGGGGAA
GCCCTCTGAGAGTAAGATT
Found at i:1847813 original size:22 final size:21
Alignment explanation
Indices: 1847788--1847830 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1847778 CTCAACTTAA
*
1847788 GTCTTATTATACGTTGAGTTTG
1 GTCTAATTATACGTTGA-TTTG
*
1847810 GTCTAATTATATGTTGATTTG
1 GTCTAATTATACGTTGATTTG
1847831 TTGATTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.51
Consensus pattern (21 bp):
GTCTAATTATACGTTGATTTG
Found at i:1850336 original size:16 final size:16
Alignment explanation
Indices: 1850315--1850368 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
1850305 TATCTATGGT
1850315 AAAATTTAACATTAAA
1 AAAATTTAACATTAAA
*
1850331 AAAATTATAAGC-TT-AT
1 AAAATT-TAA-CATTAAA
*
1850347 AAAATTTAACATTACA
1 AAAATTTAACATTAAA
1850363 AAAATT
1 AAAATT
1850369 ACATACTTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 1 0.03
15 5 0.16
16 19 0.61
17 5 0.16
18 1 0.03
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.33
Consensus pattern (16 bp):
AAAATTTAACATTAAA
Found at i:1851653 original size:22 final size:23
Alignment explanation
Indices: 1851605--1851654 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
1851595 GTGCAATGTG
*
1851605 TTTAA-TTTTATATTATAAAAAA
1 TTTAATTTTTAAATTATAAAAAA
* *
1851627 ATTAATTTTTAAATTA-AAAAAT
1 TTTAATTTTTAAATTATAAAAAA
1851649 TTTAAT
1 TTTAAT
1851655 GATAAGAGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TTTAATTTTTAAATTATAAAAAA
Found at i:1852393 original size:25 final size:29
Alignment explanation
Indices: 1852347--1852401 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
1852337 ATTTAATTTA
*
1852347 TATATTTTTATTATATTTAATTAAA-AAT
1 TATATTTTTATTATATTAAATTAAATAAT
1852375 TATATTTTTA-T-T-TTAAATTAAATAAT
1 TATATTTTTATTATATTAAATTAAATAAT
1852401 T
1 T
1852402 TTTGATGATC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 9 0.36
26 5 0.20
27 1 0.04
28 10 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TATATTTTTATTATATTAAATTAAATAAT
Found at i:1853390 original size:19 final size:19
Alignment explanation
Indices: 1853354--1853398 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
1853344 TAAATTAGAC
* * *
1853354 TAAAAAATTTATGTTCAAT
1 TAAAAAATATATGATCAAA
*
1853373 TAAAAAATATGTGATCAAA
1 TAAAAAATATATGATCAAA
1853392 TAAAAAA
1 TAAAAAA
1853399 AAGTTTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.31
Consensus pattern (19 bp):
TAAAAAATATATGATCAAA
Done.