Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 4 of 168
Found at i:1002436 original size:20 final size:18
Alignment explanation
Indices: 1002389--1002437 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
1002379 CAAGATAAAC
1002389 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
1002406 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
1002426 ATTAAATTAATA
1 ATTAAATTAATA
1002438 AAATTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:1002482 original size:72 final size:71
Alignment explanation
Indices: 1002353--1002488 Score: 170
Period size: 72 Copynumber: 1.9 Consensus size: 71
1002343 TATTAAACAT
* *
1002353 TATTAAATTAATAGAATATTTATCTACAAGATAAACATTAAATTAAATTTAATATTAAGATAATC
1 TATTAAATTAATAAAATATTTATCTA-AAGATAAACATTAAATTAAATTTAATATTAAAATAATC
1002418 ACTTTAA
65 ACTTTAA
**
1002425 TATTAAATTAATAAAAT-TTTAT-T-AAGATAAGTATTAAATTAAATATTAAATCTATTAAAATA
1 TATTAAATTAATAAAATATTTATCTAAAGATAAACATTAAATTAAAT-TT-AA--TATTAAAATA
1002487 AT
62 AT
1002489 ATTATTTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
68 19 0.34
69 2 0.04
70 3 0.05
71 5 0.09
72 27 0.48
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (71 bp):
TATTAAATTAATAAAATATTTATCTAAAGATAAACATTAAATTAAATTTAATATTAAAATAATCA
CTTTAA
Found at i:1005347 original size:23 final size:23
Alignment explanation
Indices: 1005312--1005356 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1005302 TGGAGTATAA
* *
1005312 AAGTTTTATATTTTTATATGTAC
1 AAGTTTTATATTTATACATGTAC
1005335 AAGTTTTGA-ATTTATACATGTA
1 AAGTTTT-ATATTTATACATGTA
1005357 TATACAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.51
Consensus pattern (23 bp):
AAGTTTTATATTTATACATGTAC
Found at i:1005570 original size:2 final size:2
Alignment explanation
Indices: 1005563--1005590 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1005553 GCAAATATGC
1005563 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
1005591 GTTCTGTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1005771 original size:2 final size:2
Alignment explanation
Indices: 1005764--1005812 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1005754 TGTATTAAGT
1005764 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
1005806 TA TA TA T
1 TA TA TA T
1005813 GTTCGGATGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1006038 original size:41 final size:41
Alignment explanation
Indices: 1005996--1006205 Score: 282
Period size: 42 Copynumber: 5.1 Consensus size: 41
1005986 TTTATTACCA
* *
1005996 GTGAAACATTTTAGACTTTACGTCTAGCAGGCTTAATGCCA
1 GTGAAACATTTCAGACTTTACGTCTAGCAGGCTTAATGCCG
1006037 GTGAAACAATATT-AGAC-TTACGTCTAGCAGGCTTAATGCCG
1 GTGAAAC-AT-TTCAGACTTTACGTCTAGCAGGCTTAATGCCG
* * *
1006078 GTGAAATAATTCCAGACTTTACGTCTAGCAGGCTTAATACCG
1 GTGAAA-CATTTCAGACTTTACGTCTAGCAGGCTTAATGCCG
*
1006120 GTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGAAAC-ATTTCAGACTTTACGTCTAGCAGGCTTAATGCCG
* *
1006162 GTGAAACATTTCAGACTATATGTCTAGCAGGC-TAAGTGCCG
1 GTGAAACATTTCAGACTTTACGTCTAGCAGGCTTAA-TGCCG
1006203 GTG
1 GTG
1006206 TACTGAATCA
Statistics
Matches: 151, Mismatches: 11, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
40 4 0.03
41 72 0.48
42 73 0.48
43 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (41 bp):
GTGAAACATTTCAGACTTTACGTCTAGCAGGCTTAATGCCG
Found at i:1006113 original size:42 final size:41
Alignment explanation
Indices: 1005996--1006248 Score: 291
Period size: 41 Copynumber: 6.1 Consensus size: 41
1005986 TTTATTACCA
* * *
1005996 GTGAAACATTTTAGACTTTACGTCTAGCAGGCTTAATGCCA
1 GTGAAACAATTCAGACTTTACGTCTAGCAGGCTTAATGCCG
*
1006037 GTGAAACAATATTAGAC-TTACGTCTAGCAGGCTTAATGCCG
1 GTGAAACAAT-TCAGACTTTACGTCTAGCAGGCTTAATGCCG
* *
1006078 GTGAAATAATTCCAGACTTTACGTCTAGCAGGCTTAATACCG
1 GTGAAACAATT-CAGACTTTACGTCTAGCAGGCTTAATGCCG
1006120 GTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGAAACAAT-TCAGACTTTACGTCTAGCAGGCTTAATGCCG
* * *
1006162 GTGAAACATTTCAGACTATATGTCTAGCAGGC-TAAGTGCCG
1 GTGAAACAATTCAGACTTTACGTCTAGCAGGCTTAA-TGCCG
* * * *
1006203 GTG-TACTGAA-TCAGGCTTTAAGTCTAGCAGGC-TAAGTGCCA
1 GTGAAAC--AATTCAGACTTTACGTCTAGCAGGCTTAA-TGCCG
1006244 GTGAA
1 GTGAA
1006249 TCTGTTTAAA
Statistics
Matches: 187, Mismatches: 17, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
40 6 0.03
41 103 0.55
42 77 0.41
43 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (41 bp):
GTGAAACAATTCAGACTTTACGTCTAGCAGGCTTAATGCCG
Found at i:1006204 original size:83 final size:83
Alignment explanation
Indices: 1005996--1006248 Score: 318
Period size: 83 Copynumber: 3.1 Consensus size: 83
1005986 TTTATTACCA
* * *
1005996 GTGAAACATTTTAGACTTTACGTCTAGCAGGCTTAATGCCAGTGAAACAATATTAGAC-TTACGT
1 GTGAAACATTTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGT
1006060 CTAGCAGGCTTAATGCCG
66 CTAGCAGGCTTAATGCCG
* * *
1006078 GTGAAATAATTCCAGACTTTACGTCTAGCAGGCTTAATACCGGTGAAACAATATCAGACTTTACG
1 GTGAAA-CATTTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAACAATATCAGACTTTACG
1006143 TCTAGCAGGCTTAATGCCG
65 TCTAGCAGGCTTAATGCCG
* * * * * *
1006162 GTGAAACATTTCAGACTATATGTCTAGCAGGC-TAAGTGCCGGTG-TACTGA-ATCAGGCTTTAA
1 GTGAAACATTTCAGACTTTACGTCTAGCAGGCTTAA-TGCCGGTGAAAC-AATATCAGACTTTAC
*
1006224 GTCTAGCAGGC-TAAGTGCCA
64 GTCTAGCAGGCTTAA-TGCCG
1006244 GTGAA
1 GTGAA
1006249 TCTGTTTAAA
Statistics
Matches: 150, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
81 3 0.02
82 41 0.27
83 76 0.51
84 30 0.20
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (83 bp):
GTGAAACATTTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGT
CTAGCAGGCTTAATGCCG
Found at i:1013868 original size:22 final size:22
Alignment explanation
Indices: 1013809--1013870 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
1013799 GAAAGGAAGA
**
1013809 TACTAAGCTCTCATGGCTAACG
1 TACTAAGCTCTCATGTTTAACG
*
1013831 TACTAAGCTCTCATGTTTCACG
1 TACTAAGCTCTCATGTTTAACG
1013853 TACTAAGCTCTCATGTTT
1 TACTAAGCTCTCATGTTT
1013871 GAACAATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (22 bp):
TACTAAGCTCTCATGTTTAACG
Found at i:1014138 original size:29 final size:29
Alignment explanation
Indices: 1014083--1014193 Score: 107
Period size: 31 Copynumber: 3.7 Consensus size: 29
1014073 ATATCAAAAT
* *
1014083 TATACATGAACTTTGATTTAATGTGCAATTG
1 TATACATGAACTTTAATTT-A-GTGCAATTA
1014114 TATACATGAACTTTAATTTAGTGCAATTA
1 TATACATGAACTTTAATTTAGTGCAATTA
* * * *
1014143 TACACATGAAATTCTAATTGTTGTTCAATTA
1 TATACATGAACTT-TAATT-TAGTGCAATTA
1014174 TATAC-TGGAAGCTTTAATTT
1 TATACAT-GAA-CTTTAATTT
1014194 TAATTTAATC
Statistics
Matches: 68, Mismatches: 8, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
29 19 0.28
30 8 0.12
31 39 0.57
32 2 0.03
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (29 bp):
TATACATGAACTTTAATTTAGTGCAATTA
Found at i:1016397 original size:28 final size:28
Alignment explanation
Indices: 1016343--1016397 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
1016333 AAATTAGGTT
* *
1016343 AAAAGAGATGGAGAACAGAGGGAGAAAC
1 AAAAGAGATGGAAAACAAAGGGAGAAAC
*
1016371 AAAAGAGAATGGAAAATAAAGGG-GAAA
1 AAAAGAG-ATGGAAAACAAAGGGAGAAA
1016398 ATGAAAGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.58, C:0.04, G:0.33, T:0.05
Consensus pattern (28 bp):
AAAAGAGATGGAAAACAAAGGGAGAAAC
Found at i:1019673 original size:16 final size:16
Alignment explanation
Indices: 1019648--1019681 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1019638 ATGAATATAT
* *
1019648 ATGTGTAAATGTGATA
1 ATGTGCAAATATGATA
1019664 ATGTGCAAATATGATA
1 ATGTGCAAATATGATA
1019680 AT
1 AT
1019682 TGGATATTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (16 bp):
ATGTGCAAATATGATA
Found at i:1027000 original size:2 final size:2
Alignment explanation
Indices: 1026993--1027028 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1026983 ATTAAAAATG
1026993 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
1027029 CCTTAGCAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1030233 original size:20 final size:20
Alignment explanation
Indices: 1030173--1030236 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
1030163 TTTTTTCAAT
*
1030173 TTAAATTCTAATTATTTTTAA
1 TTAAATTATAATTATTTTT-A
* **
1030194 TTATGTAATTATCACAATTTTTA
1 TTA---AATTATAATTATTTTTA
1030217 TTAAATTATAATTATTTTTA
1 TTAAATTATAATTATTTTTA
1030237 AATGTATAGT
Statistics
Matches: 33, Mismatches: 7, Indels: 7
0.70 0.15 0.15
Matches are distributed among these distances:
20 14 0.42
21 3 0.09
23 4 0.12
24 12 0.36
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAAATTATAATTATTTTTA
Found at i:1032265 original size:5 final size:5
Alignment explanation
Indices: 1032255--1032301 Score: 51
Period size: 5 Copynumber: 9.2 Consensus size: 5
1032245 TGAAGTTTTC
* *
1032255 TCGAA TCGAA TCGAG T-GAGA TGGAA TTCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGA-A TCGAA -TCGAA TCGAA TCGAA TCGAA T
1032302 ATATTTGTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
4 2 0.06
5 28 0.78
6 6 0.17
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:1034581 original size:11 final size:10
Alignment explanation
Indices: 1034567--1034635 Score: 59
Period size: 10 Copynumber: 6.5 Consensus size: 10
1034557 AAAAATTAAA
1034567 AAAAGTATTTT
1 AAAA-TATTTT
1034578 AAAAATATTTTT
1 -AAAATA-TTTT
1034590 AAAATATTTT
1 AAAATATTTT
***
1034600 AAAAT-TAAA
1 AAAATATTTT
1034609 AAAAGTATTTT
1 AAAA-TATTTT
1034620 AAAAATATTTT
1 -AAAATATTTT
1034631 AAAAT
1 AAAAT
1034636 TAAAAAAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
9 5 0.11
10 15 0.32
11 15 0.32
12 12 0.26
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (10 bp):
AAAATATTTT
Found at i:1034609 original size:42 final size:40
Alignment explanation
Indices: 1034553--1034728 Score: 237
Period size: 42 Copynumber: 4.2 Consensus size: 40
1034543 CCATTTTTAT
1034553 TTTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTTAAAA
1 TTTAAAAAATTAAAAAAAGTATTTTAAAAATA-TTTTAAAA
**
1034594 TATTTTAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
1 T-TTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
*
1034635 TTAAAAAAAAATTAAAAAAAAGTATTTTAAAAATATTTTAAAA
1 TT--TAAAAAATT-AAAAAAAGTATTTTAAAAATATTTTAAAA
* *
1034678 TTTAAAAAAATT-AAAAAAGTATGTAAAAAATATTTTAAAA
1 TTT-AAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
1034718 TTTTAAAAAAT
1 -TTTAAAAAAT
1034729 AAATATATTT
Statistics
Matches: 121, Mismatches: 8, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
40 34 0.28
41 13 0.11
42 43 0.36
43 31 0.26
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (40 bp):
TTTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
Found at i:1034625 original size:31 final size:30
Alignment explanation
Indices: 1034578--1034666 Score: 115
Period size: 31 Copynumber: 2.9 Consensus size: 30
1034568 AAAGTATTTT
*
1034578 AAAAATATTTTTAAAATATTTTAAAATTAA
1 AAAAATATTTTAAAAATATTTTAAAATTAA
1034608 AAAAAGTATTTTAAAAATATTTTAAAATTAA
1 AAAAA-TATTTTAAAAATATTTTAAAATTAA
* **
1034639 AAAAAAATTAAAAAAAAGTATTTTAAAA
1 AAAAATATT-TTAAAAA-TATTTTAAAA
1034667 ATATTTTAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
30 8 0.15
31 34 0.65
32 10 0.19
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (30 bp):
AAAAATATTTTAAAAATATTTTAAAATTAA
Found at i:1034645 original size:11 final size:11
Alignment explanation
Indices: 1034631--1034655 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1034621 AAAATATTTT
1034631 AAAATTAAAAA
1 AAAATTAAAAA
1034642 AAAATTAAAAA
1 AAAATTAAAAA
1034653 AAA
1 AAA
1034656 GTATTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAATTAAAAA
Found at i:1035042 original size:14 final size:14
Alignment explanation
Indices: 1035023--1035049 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1035013 TTCAATGCAT
1035023 AATTTTTTAACACG
1 AATTTTTTAACACG
1035037 AATTTTTTAACAC
1 AATTTTTTAACAC
1035050 CATTAGTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.04, T:0.44
Consensus pattern (14 bp):
AATTTTTTAACACG
Found at i:1036200 original size:44 final size:44
Alignment explanation
Indices: 1036147--1036231 Score: 152
Period size: 44 Copynumber: 1.9 Consensus size: 44
1036137 AAATATCACA
*
1036147 TATTCGAATTTAATGAAAGTATATTAACAATAGTATTAATTGGG
1 TATTCGAATTTAATGAAAATATATTAACAATAGTATTAATTGGG
*
1036191 TATTGGAATTTAATGAAAATATATTAACAATAGTATTAATT
1 TATTCGAATTTAATGAAAATATATTAACAATAGTATTAATT
1036232 AGGTTTTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.44, C:0.04, G:0.13, T:0.40
Consensus pattern (44 bp):
TATTCGAATTTAATGAAAATATATTAACAATAGTATTAATTGGG
Found at i:1056767 original size:19 final size:17
Alignment explanation
Indices: 1056730--1056763 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1056720 CATTATTAAA
1056730 AATAAATTTTTTTATTT
1 AATAAATTTTTTTATTT
*
1056747 AATATATTTTTTTATTT
1 AATAAATTTTTTTATTT
1056764 TTAAAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
AATAAATTTTTTTATTT
Found at i:1065707 original size:16 final size:16
Alignment explanation
Indices: 1065686--1065716 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1065676 TTAACTATTA
*
1065686 TGTCTTTTGTATTTTT
1 TGTCTTTTATATTTTT
1065702 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
1065717 GCGTGCATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.06, G:0.10, T:0.74
Consensus pattern (16 bp):
TGTCTTTTATATTTTT
Found at i:1066816 original size:13 final size:13
Alignment explanation
Indices: 1066798--1066822 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1066788 GAATTGTTCA
1066798 ATTAAAGAATTTG
1 ATTAAAGAATTTG
1066811 ATTAAAGAATTT
1 ATTAAAGAATTT
1066823 TCTTGAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (13 bp):
ATTAAAGAATTTG
Found at i:1067409 original size:17 final size:16
Alignment explanation
Indices: 1067386--1067445 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
1067376 TTAATAAGAT
1067386 TTAATATTAAACTTAA
1 TTAATATTAAACTTAA
* *
1067402 TCTAATATTTATCTTAA
1 T-TAATATTAAACTTAA
* * *
1067419 TAAATCTTATA-TTAA
1 TTAATATTAAACTTAA
1067434 TTTAATATTAAA
1 -TTAATATTAAA
1067446 GTGATTAAGT
Statistics
Matches: 32, Mismatches: 10, Indels: 4
0.70 0.22 0.09
Matches are distributed among these distances:
15 4 0.12
16 14 0.44
17 14 0.44
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (16 bp):
TTAATATTAAACTTAA
Found at i:1067425 original size:21 final size:20
Alignment explanation
Indices: 1067400--1067440 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1067390 TATTAAACTT
*
1067400 AATCTAATATTTATCTTAATA
1 AATCTAATATTAAT-TTAATA
*
1067421 AATCTTATATTAATTTAATA
1 AATCTAATATTAATTTAATA
1067441 TTAAAGTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (20 bp):
AATCTAATATTAATTTAATA
Found at i:1067443 original size:11 final size:12
Alignment explanation
Indices: 1067398--1067444 Score: 50
Period size: 11 Copynumber: 4.3 Consensus size: 12
1067388 AATATTAAAC
1067398 TTAATC-TAATA
1 TTAATCTTAATA
*
1067409 TTTATCTTAATA
1 TTAATCTTAATA
1067421 --AATCTT-ATA
1 TTAATCTTAATA
1067430 TTAAT-TTAATA
1 TTAATCTTAATA
1067441 TTAA
1 TTAA
1067445 AGTGATTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
9 3 0.10
10 7 0.23
11 15 0.50
12 5 0.17
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (12 bp):
TTAATCTTAATA
Found at i:1069572 original size:40 final size:40
Alignment explanation
Indices: 1069528--1070027 Score: 509
Period size: 40 Copynumber: 12.4 Consensus size: 40
1069518 GGCACTGAAT
* * *
1069528 TACAAATAGGAGTACGTATGTGCATTTAAGGGTACCGAAG
1 TACAAACAGGAGCACGTATGTGCATTCAAGGGTACCGAAG
* * * * *
1069568 TACAAACAGGAGCATGTATGTGCATTTAGGGGTATCAAAG
1 TACAAACAGGAGCACGTATGTGCATTCAAGGGTACCGAAG
* * *
1069608 TACAAACAGGAGCACGTCTGTGCATTCAGGGGTACCAAAG
1 TACAAACAGGAGCACGTATGTGCATTCAAGGGTACCGAAG
* * * * *
1069648 TATAAATAGGAGCACGTATGTGCGTTTAAAGGTACCGAAG
1 TACAAACAGGAGCACGTATGTGCATTCAAGGGTACCGAAG
* * * * **
1069688 TACAAACAAGAGCACGTATATGTATTCAGGGGTACTAAAG
1 TACAAACAGGAGCACGTATGTGCATTCAAGGGTACCGAAG
* * *
1069728 TACAAACCGGAGCATGTTTGTGCATTC-AGAGGTACCGAAG
1 TACAAACAGGAGCACGTATGTGCATTCAAG-GGTACCGAAG
*
1069768 TACAAACAGGAGCACGTATGTGCATTCAGGGGTACCGAAG
1 TACAAACAGGAGCACGTATGTGCATTCAAGGGTACCGAAG
* * ** *** *
1069808 TACAAATAGGAGAAAATATGTATGTTGAAGGGTACCGAAG
1 TACAAACAGGAGCACGTATGTGCATTCAAGGGTACCGAAG
*
1069848 TACAAACAGGAGCACGTATGTGCATTCAAGGGTACCAAAG
1 TACAAACAGGAGCACGTATGTGCATTCAAGGGTACCGAAG
* * * *
1069888 TACAAACAGGAGCATGTTTGTGCATTCAAGGGTATCGAAA
1 TACAAACAGGAGCACGTATGTGCATTCAAGGGTACCGAAG
* * * * * *
1069928 TACAAACAGCAGGAGTACATATATGCGTTCAGGGGTACCGAAA
1 TAC-AA-A-CAGGAGCACGTATGTGCATTCAAGGGTACCGAAG
* *
1069971 TACAAACAGGAGCACGTATGTCCATTCAGGGGTACCCG-AG
1 TACAAACAGGAGCACGTATGTGCATTCAAGGGTA-CCGAAG
*
1070011 TACAATCAGGAGCACGT
1 TACAAACAGGAGCACGT
1070028 CTTCATTTCT
Statistics
Matches: 374, Mismatches: 80, Indels: 12
0.80 0.17 0.03
Matches are distributed among these distances:
39 1 0.00
40 334 0.89
41 7 0.02
42 3 0.01
43 29 0.08
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (40 bp):
TACAAACAGGAGCACGTATGTGCATTCAAGGGTACCGAAG
Found at i:1074144 original size:23 final size:23
Alignment explanation
Indices: 1074118--1074239 Score: 165
Period size: 23 Copynumber: 5.3 Consensus size: 23
1074108 ATAAGTGCCA
*
1074118 CACTGATATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
1074141 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
1074164 CACTGAAATGTAGCCGAAGCAAC
1 CACTGATATGTAGCCGAAGCTAC
* *
1074187 CACTGATATGTAGCCGTAGCTAT
1 CACTGATATGTAGCCGAAGCTAC
*
1074210 CACTGA-ATTGTAGCTGAAGCTAC
1 CACTGATA-TGTAGCCGAAGCTAC
1074233 CACTGAT
1 CACTGAT
1074240 CAATAACACT
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
22 1 0.01
23 84 0.99
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:1074189 original size:46 final size:46
Alignment explanation
Indices: 1074118--1074239 Score: 190
Period size: 46 Copynumber: 2.7 Consensus size: 46
1074108 ATAAGTGCCA
* *
1074118 CACTGATATGTAGCCAAAGCTACCACTGATATGTAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
* *
1074164 CACTGAAATGTAGCCGAAGCAACCACTGATATGTAGCCGTAGCTAT
1 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
* *
1074210 CACTGAATTGTAGCTGAAGCTACCACTGAT
1 CACTGAAATGTAGCCGAAGCTACCACTGAT
1074240 CAATAACACT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 69 1.00
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
Found at i:1075609 original size:5 final size:5
Alignment explanation
Indices: 1075575--1075642 Score: 70
Period size: 5 Copynumber: 13.4 Consensus size: 5
1075565 TTATGTTATG
*
1075575 TATAT TAT-T T-TAT TATAT AATATAA TATAT TATAT TA-AT TATAT TATAT
1 TATAT TATAT TATAT TATAT --TATAT TATAT TATAT TATAT TATAT TATAT
1075624 TATAT TATTAT ATATAT TA
1 TATAT TA-TAT -TATAT TA
1075643 AATAAAGTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
3 1 0.02
4 8 0.15
5 33 0.61
6 6 0.11
7 6 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:1082732 original size:25 final size:25
Alignment explanation
Indices: 1082685--1082735 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1082675 ACTGTTCTAC
* * **
1082685 TGTTGTTTTGCTATTGTTTTGTTGA
1 TGTTGTATTGCTATTCTAGTGTTGA
1082710 TGTTGTATTGCTATTCTAGTGTTGA
1 TGTTGTATTGCTATTCTAGTGTTGA
1082735 T
1 T
1082736 TTGCTAGAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.12, C:0.06, G:0.24, T:0.59
Consensus pattern (25 bp):
TGTTGTATTGCTATTCTAGTGTTGA
Found at i:1087583 original size:18 final size:19
Alignment explanation
Indices: 1087546--1087585 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
1087536 TGATTTATTC
1087546 TAAGATTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
1087565 TAAGATTTATCTA-CTAAA
1 TAAGATTTATCTACCTAAA
1087583 TAA
1 TAA
1087586 CTTTAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (19 bp):
TAAGATTTATCTACCTAAA
Found at i:1091462 original size:19 final size:19
Alignment explanation
Indices: 1091438--1091474 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1091428 TTATTCTAAG
*
1091438 ATTTATCTACCTATATAAA
1 ATTTATCTACCTAAATAAA
1091457 ATTTATCTACCTAAATAA
1 ATTTATCTACCTAAATAA
1091475 CTTTAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTTATCTACCTAAATAAA
Found at i:1095561 original size:22 final size:22
Alignment explanation
Indices: 1095476--1095548 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
1095466 TTGAGAAGAA
** * *
1095476 TCTCATGTTTAACGAACTAAAC
1 TCTCATGGCTAACGTACTAAGC
*
1095498 CCTCATGGCTAACGTACTAAGC
1 TCTCATGGCTAACGTACTAAGC
1095520 TCTCATGGCTAACGTACTAAGC
1 TCTCATGGCTAACGTACTAAGC
1095542 TCTCATG
1 TCTCATG
1095549 TTTCACGTAC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (22 bp):
TCTCATGGCTAACGTACTAAGC
Found at i:1102869 original size:16 final size:17
Alignment explanation
Indices: 1102848--1102890 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
1102838 GAAAGAGAAG
1102848 TAAAAAAAAGTTCG-AT-
1 TAAAAAAAAGTT-GAATA
1102864 TAAAAAAAA-TTGAATA
1 TAAAAAAAAGTTGAATA
1102880 TAAAAAAAAGT
1 TAAAAAAAAGT
1102891 GTGACGGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.04
15 4 0.17
16 18 0.75
17 1 0.04
ACGTcount: A:0.65, C:0.02, G:0.09, T:0.23
Consensus pattern (17 bp):
TAAAAAAAAGTTGAATA
Found at i:1104063 original size:22 final size:23
Alignment explanation
Indices: 1104038--1104082 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1104028 AGACATCTCC
1104038 AAATCAAATC-TCTAAGATTACA
1 AAATCAAATCTTCTAAGATTACA
*
1104060 AAATCATATCTTCTAAGATTACA
1 AAATCAAATCTTCTAAGATTACA
1104083 TATCATATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.31
Consensus pattern (23 bp):
AAATCAAATCTTCTAAGATTACA
Found at i:1104087 original size:22 final size:23
Alignment explanation
Indices: 1104038--1104092 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
1104028 AGACATCTCC
*
1104038 AAATCAAATC-TCTAAGATTACA
1 AAATCATATCTTCTAAGATTACA
1104060 AAATCATATCTTCTAAGATTAC-
1 AAATCATATCTTCTAAGATTACA
*
1104082 ATATCATATCT
1 AAATCATATCT
1104093 ACGATTGCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 19 0.63
23 11 0.37
ACGTcount: A:0.44, C:0.18, G:0.04, T:0.35
Consensus pattern (23 bp):
AAATCATATCTTCTAAGATTACA
Found at i:1107665 original size:264 final size:264
Alignment explanation
Indices: 1107195--1107726 Score: 1046
Period size: 264 Copynumber: 2.0 Consensus size: 264
1107185 TGGCAAATTG
1107195 GATTGCCGACAATTTTTTTCCTCCCATGCTTCCCTTTCTTTTCACTCGCATCATATATCAATGGT
1 GATTGCCGACAATTTTTTTCCTCCCATGCTTCCCTTTCTTTTCACTCGCATCATATATCAATGGT
*
1107260 TCGAATCAGAGATCATCATGTAATTCTTGGAAGGATGAATATCCGTATTAAGTCAGTCAAGTAAG
66 TCGAATCAGAGATCATCATGTAATTCTCGGAAGGATGAATATCCGTATTAAGTCAGTCAAGTAAG
1107325 CATAATCCAACCATAAAACCATAATCATCAAGGGGGATTACCTTAATGGTTGCCTTGCCTGTCCA
131 CATAATCCAACCATAAAACCATAATCATCAAGGGGGATTACCTTAATGGTTGCCTTGCCTGTCCA
1107390 CTCGCCAAGCCTGAGTTCCACTCCTTTAGCCACACCCGTTATGGGAATGCTTTTCGAGTTCACTG
196 CTCGCCAAGCCTGAGTTCCACTCCTTTAGCCACACCCGTTATGGGAATGCTTTTCGAGTTCACTG
1107455 TTTT
261 TTTT
*
1107459 GATTGCCGACAATTTTTTTCCTCCCATGCTTCCCTTTCTTTTCACTCGCATTATATATCAATGGT
1 GATTGCCGACAATTTTTTTCCTCCCATGCTTCCCTTTCTTTTCACTCGCATCATATATCAATGGT
1107524 TCGAATCAGAGATCATCATGTAATTCTCGGAAGGATGAATATCCGTATTAAGTCAGTCAAGTAAG
66 TCGAATCAGAGATCATCATGTAATTCTCGGAAGGATGAATATCCGTATTAAGTCAGTCAAGTAAG
1107589 CATAATCCAACCATAAAACCATAATCATCAAGGGGGATTACCTTAATGGTTGCCTTGCCTGTCCA
131 CATAATCCAACCATAAAACCATAATCATCAAGGGGGATTACCTTAATGGTTGCCTTGCCTGTCCA
1107654 CTCGCCAAGCCTGAGTTCCACTCCTTTAGCCACACCCGTTATGGGAATGCTTTTCGAGTTCACTG
196 CTCGCCAAGCCTGAGTTCCACTCCTTTAGCCACACCCGTTATGGGAATGCTTTTCGAGTTCACTG
1107719 TTTT
261 TTTT
1107723 GATT
1 GATT
1107727 CGACCCGAAT
Statistics
Matches: 266, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
264 266 1.00
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.33
Consensus pattern (264 bp):
GATTGCCGACAATTTTTTTCCTCCCATGCTTCCCTTTCTTTTCACTCGCATCATATATCAATGGT
TCGAATCAGAGATCATCATGTAATTCTCGGAAGGATGAATATCCGTATTAAGTCAGTCAAGTAAG
CATAATCCAACCATAAAACCATAATCATCAAGGGGGATTACCTTAATGGTTGCCTTGCCTGTCCA
CTCGCCAAGCCTGAGTTCCACTCCTTTAGCCACACCCGTTATGGGAATGCTTTTCGAGTTCACTG
TTTT
Found at i:1109465 original size:23 final size:22
Alignment explanation
Indices: 1109420--1109477 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
1109410 GTAAGGTATC
* * *
1109420 TACAAATCAAAT-ATCTAATAT
1 TACAAATCATATCTTCTAAGAT
1109441 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
1109464 TACATATCATATCT
1 TACAAATCATATCT
1109478 ACGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:1109475 original size:22 final size:23
Alignment explanation
Indices: 1109433--1109477 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1109423 AAATCAAATA
*
1109433 TCTAATATTACAAAATCATATCT
1 TCTAAGATTACAAAATCATATCT
*
1109456 TCTAAGATTAC-ATATCATATCT
1 TCTAAGATTACAAAATCATATCT
1109478 ACGATTGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.40, C:0.18, G:0.02, T:0.40
Consensus pattern (23 bp):
TCTAAGATTACAAAATCATATCT
Found at i:1109840 original size:16 final size:16
Alignment explanation
Indices: 1109819--1109849 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1109809 AAATACATAT
1109819 ATGTTCAGCCGCATGA
1 ATGTTCAGCCGCATGA
*
1109835 ATGTTCAGCTGCATG
1 ATGTTCAGCCGCATG
1109850 CTTTAGCTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.29
Consensus pattern (16 bp):
ATGTTCAGCCGCATGA
Found at i:1110069 original size:28 final size:28
Alignment explanation
Indices: 1110012--1110073 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
1110002 GGACAAAACA
* * *
1110012 AAGACATGATTTTAATGTGTAATATACT
1 AAGACATGATTTAAATATGTAACATACT
* *
1110040 AAGACATGATTTAAATATGTAGCATGCT
1 AAGACATGATTTAAATATGTAACATACT
1110068 AAGACA
1 AAGACA
1110074 AATTAATGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (28 bp):
AAGACATGATTTAAATATGTAACATACT
Found at i:1110694 original size:20 final size:20
Alignment explanation
Indices: 1110632--1110695 Score: 51
Period size: 21 Copynumber: 3.0 Consensus size: 20
1110622 ATATTTTAGA
1110632 TTAAATAAATAAATATTAGTTT
1 TTAAAT-AATAAATATTA-TTT
* *
1110654 ATT-AATATTTTAAT-TTGATTT
1 -TTAAATA-ATAAATATT-ATTT
1110675 TTAAATAATAAATATTATTT
1 TTAAATAATAAATATTATTT
1110695 T
1 T
1110696 ATTATTTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 11
0.69 0.08 0.23
Matches are distributed among these distances:
20 11 0.33
21 12 0.36
22 8 0.24
23 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
TTAAATAATAAATATTATTT
Found at i:1112775 original size:8 final size:8
Alignment explanation
Indices: 1112762--1112791 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
1112752 GTATCACATG
1112762 CTCTTCCC
1 CTCTTCCC
1112770 CTCTTCCC
1 CTCTTCCC
1112778 CTCTTCCC
1 CTCTTCCC
1112786 CATCTT
1 C-TCTT
1112792 TTCTTCTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 17 0.81
9 4 0.19
ACGTcount: A:0.03, C:0.57, G:0.00, T:0.40
Consensus pattern (8 bp):
CTCTTCCC
Found at i:1113868 original size:12 final size:12
Alignment explanation
Indices: 1113851--1113875 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1113841 TAAATTTATA
1113851 ATAAAAAATATT
1 ATAAAAAATATT
1113863 ATAAAAAATATT
1 ATAAAAAATATT
1113875 A
1 A
1113876 GAAATTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAAAAAATATT
Found at i:1113977 original size:66 final size:63
Alignment explanation
Indices: 1113789--1113983 Score: 205
Period size: 66 Copynumber: 3.0 Consensus size: 63
1113779 GCATAAAAAT
* * ** *
1113789 AAATAAATTTTATAAAAATTATTAGAAACTATTTAAAAAGAATAAAACTTTATAAATTTAT-AA
1 AAATAAAATTTATAAAAATTATTAGAAATTATTT-AAAATCATAAAATTTTATAAATTTATAAA
* * * * *
1113852 TAA-AAAATATTATAAAAAATATTAGAAATTTATTTAAAATCATTAAATTTTTTTTAATTTATAA
1 AAATAAAAT-TTATAAAAATTATTAGAAA-TTATTTAAAATCA-TAAAATTTTATAAATTTATAA
1113916 A
63 A
* *
1113917 AAATTAAAATTTATAAAAATTATTAGAAATTAATTTAAAATCATAAAATTTTAGAAAATTTAGAA
1 AAA-TAAAATTTATAAAAATTATTAGAAATT-ATTTAAAATCATAAAATTTTA-TAAATTTATAA
1113982 A
63 A
1113983 A
1 A
1113984 TTTTATAAAC
Statistics
Matches: 107, Mismatches: 17, Indels: 13
0.78 0.12 0.09
Matches are distributed among these distances:
62 4 0.04
63 25 0.23
64 20 0.19
65 14 0.13
66 39 0.36
67 5 0.05
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (63 bp):
AAATAAAATTTATAAAAATTATTAGAAATTATTTAAAATCATAAAATTTTATAAATTTATAAA
Found at i:1113983 original size:19 final size:20
Alignment explanation
Indices: 1113961--1114002 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1113951 TTAAAATCAT
1113961 AAAATTTTAGAAAAT-TTAG
1 AAAATTTTAGAAAATATTAG
* *
1113980 AAAATTTTATAAACTATTAG
1 AAAATTTTAGAAAATATTAG
1114000 AAA
1 AAA
1114003 CTAATTGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (20 bp):
AAAATTTTAGAAAATATTAG
Found at i:1120447 original size:348 final size:348
Alignment explanation
Indices: 1119805--1120499 Score: 819
Period size: 348 Copynumber: 2.0 Consensus size: 348
1119795 GAAGAATTTT
* *
1119805 CCTCTCTTCAAAATCTGTCAATTGATAGCTACAAGGAATTGGAAGTTCTTCCTATAACCGGAGGT
1 CCTCTCTTCAAAACCTGTCAATTGATAGCTACAAGGAATTAGAAGTTCTTCCTATAACCGGAGGT
* ** **
1119870 TGTTCATCTCTTGAAAAGCTTAGTATTTTGGGTTGTGAAAGTTTAAGCAAGATCGAAGACAAATT
66 TGTTCATCTCTTGAAAAGCTTAGCATTTTGGGTTGCAAAAAATTAAGCAAGATCGAAGACAAATT
* * * * * * * *
1119935 ATTTAGCTCCACTTGTCTGAAAGAATTATATCTATGTCATTGTTCTAATTTAAGTTCGGTTCCAG
131 ATCTACCTCCACTTGTCTGAAAGAATTAGATCTATATAATTGTCCTAATTTAAGTTCGATTCCAA
* *
1120000 ACTTGGAAGAATGTTTCTCTCTTAAAATTCTATCAATTAATAGCTGTAAGGAATTGAAAGTTCTT
196 ACTTGGAAGAATGTTTCTCTCTTAAAACTCTATCAATTAATAGCTGCAAGGAATTGAAAGTTCTT
* * * * * *
1120065 CCAGTAATAGGAAGATGTTCATCTCTTTAAAAGCTTAACATTTTCGGTTGCGAAAAAT-TAAACA
261 CCAATAATAGGAAGATGTTCATCTATTGAAAAGCTTAAAATTTCCAGTTG-GAAAAATATAAACA
* *
1120129 AGATTGGAGACGGATTATTTACCC
325 AGATCGGAGACGGATTATCTACCC
* * * * *
1120153 CCTCTCTTCAAAACCTGTCAATTGATAGTTGCAATGAGTTAGAAGTTCTTTCGT-T-ACCTGGAA
1 CCTCTCTTCAAAACCTGTCAATTGATAGCTACAAGGAATTAGAAGTTC-TTCCTATAACC-GG-A
* * * * ***
1120216 GG-TGTTTATCTCTTGAAAAGCTTAGCATTTTTGGTTGCAAAAAATTAAGCAAGATTGGAGATGG
63 GGTTGTTCATCTCTTGAAAAGCTTAGCATTTTGGGTTGCAAAAAATTAAGCAAGATCGAAGACAA
* * * *
1120280 ATTATCTACCTGCGCTTGTCTTAAAGAATTAGGTCTATATAATTGTCCTAATTTAAGTTCGATTC
128 ATTATCTACCTCCACTTGTCTGAAAGAATTAGATCTATATAATTGTCCTAATTTAAGTTCGATTC
* * * * * *
1120345 CAAATTTGGAAGGAAT-TTTCTCTCTTCAAAGCT-TGTCAATTAATAGGTGCAATGAATTGGAAG
193 CAAACTTGGAA-GAATGTTTCTCTCTT-AAAACTCTATCAATTAATAGCTGCAAGGAATTGAAAG
* *
1120408 TTCTTCCAATAACT-GGAAGATGTTTATCTATTGAAAAGCTTAAAATTTCCAGTTGTAAAAATAT
256 TTCTTCCAATAA-TAGGAAGATGTTCATCTATTGAAAAGCTTAAAATTTCCAGTTGGAAAAATAT
* *
1120472 AACCAAGATCGGAGATGGATTATCTACC
320 AAACAAGATCGGAGACGGATTATCTACC
1120500 TCCCCTTGTC
Statistics
Matches: 289, Mismatches: 51, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
347 9 0.03
348 264 0.91
349 16 0.06
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (348 bp):
CCTCTCTTCAAAACCTGTCAATTGATAGCTACAAGGAATTAGAAGTTCTTCCTATAACCGGAGGT
TGTTCATCTCTTGAAAAGCTTAGCATTTTGGGTTGCAAAAAATTAAGCAAGATCGAAGACAAATT
ATCTACCTCCACTTGTCTGAAAGAATTAGATCTATATAATTGTCCTAATTTAAGTTCGATTCCAA
ACTTGGAAGAATGTTTCTCTCTTAAAACTCTATCAATTAATAGCTGCAAGGAATTGAAAGTTCTT
CCAATAATAGGAAGATGTTCATCTATTGAAAAGCTTAAAATTTCCAGTTGGAAAAATATAAACAA
GATCGGAGACGGATTATCTACCC
Found at i:1120518 original size:210 final size:209
Alignment explanation
Indices: 1120153--1120822 Score: 862
Period size: 210 Copynumber: 3.2 Consensus size: 209
1120143 TTATTTACCC
* * * * * * ** * *
1120153 CCTCTCTTCAAAACCTGTCAATTGATAGTTGCAATGAGTTAGAAGTTCTTTCGTTACCTGGAAGG
1 CCTCTCTTCAAAACTTGTCAATTGATAGCTACAATGAATTGGAAGTTCTTCCAATAACTGGAAGA
* *** * *
1120218 TGTTTATCTCTTGAAAAGCTTAGCATTTTTGGTTGCAAAAA-ATTAAGCAAGATTGGAGATGGAT
66 TGTTTATCTCTTGAAAAGCTTAGAATTTCCAGTTGTAAAAATA-TAAGCAAGATCGGAGATGGAT
* * ** *
1120282 TATCTACCTGCGCTTGTCTTAAAGAATTAGGTCTATATAATTGTCCTAATTTAAGTTCGATTCCA
130 TATCTACCTCCACTTGTCTTAAAGAATTA-GTCTATATCTTTGTTCTAATTTAAGTTCGATTCCA
*
1120347 AATTTGGAAGGAATTTT
194 GATTTGGAAGG-ATTTT
* * * *
1120364 -CTCTCTTCAAAGCTTGTCAATTAATAGGTGCAATGAATTGGAAGTTCTTCCAATAACTGGAAGA
1 CCTCTCTTCAAAACTTGTCAATTGATAGCTACAATGAATTGGAAGTTCTTCCAATAACTGGAAGA
* * *
1120428 TGTTTATCTATTGAAAAGCTTAAAATTTCCAGTTGTAAAAATATAACCAAGATCGGAGATGGATT
66 TGTTTATCTCTTGAAAAGCTTAGAATTTCCAGTTGTAAAAATATAAGCAAGATCGGAGATGGATT
* * * *
1120493 ATCTACCTCCCCTTGTCTCAAAGAATTA-TATATATCTTTGTTCTAATTTAAGTTTGATTCCAGA
131 ATCTACCTCCACTTGTCTTAAAGAATTAGTCTATATCTTTGTTCTAATTTAAGTTCGATTCCAGA
1120557 TTTGGAAGGATTTT
196 TTTGGAAGGATTTT
* * **
1120571 CCTCTCTTCAAAA-TCTGTCAATTGATAGCTACAACGAATTGGAAGTTCTTCCCATAACAAGAAG
1 CCTCTCTTCAAAACT-TGTCAATTGATAGCTACAATGAATTGGAAGTTCTTCCAATAACTGGAAG
* * *
1120635 ATGTTCATCTCTTGAAAAGCTTAGAATTTCCAGTTGTAAAAATATAAGCAAGATCGGAGGTAGAT
65 ATGTTTATCTCTTGAAAAGCTTAGAATTTCCAGTTGTAAAAATATAAGCAAGATCGGAGATGGAT
* *
1120700 TATCTACCTCCACTTATCTTAAAGAATTAGATCTATATCTTTGTTCTAATTTAAGTTGGATTCCA
130 TATCTACCTCCACTTGTCTTAAAGAATTAG-TCTATATCTTTGTTCTAATTTAAGTTCGATTCCA
*
1120765 GATTTTGAAGGATTTT
194 GATTTGGAAGGATTTT
* *
1120781 CCTCTCTTCAAAATTTGTCAATTGATAGCTACAAGGAATTGG
1 CCTCTCTTCAAAACTTGTCAATTGATAGCTACAATGAATTGG
1120823 CGAGTTTTCA
Statistics
Matches: 403, Mismatches: 50, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
207 6 0.01
208 177 0.44
210 218 0.54
211 2 0.00
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (209 bp):
CCTCTCTTCAAAACTTGTCAATTGATAGCTACAATGAATTGGAAGTTCTTCCAATAACTGGAAGA
TGTTTATCTCTTGAAAAGCTTAGAATTTCCAGTTGTAAAAATATAAGCAAGATCGGAGATGGATT
ATCTACCTCCACTTGTCTTAAAGAATTAGTCTATATCTTTGTTCTAATTTAAGTTCGATTCCAGA
TTTGGAAGGATTTT
Found at i:1135456 original size:25 final size:25
Alignment explanation
Indices: 1135402--1135456 Score: 58
Period size: 27 Copynumber: 2.2 Consensus size: 25
1135392 AGCCCGGCCC
* * *
1135402 ATTTTTAAAATAAACATTAAAAAATT
1 ATTTTAAAAATAAAAAATAAAAAA-T
1135428 ATTTTAAAAATAAAAAAATAAAAAA-
1 ATTTTAAAAAT-AAAAAATAAAAAAT
1135453 ATTT
1 ATTT
1135457 ATTTTAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 4 0.16
26 10 0.40
27 11 0.44
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (25 bp):
ATTTTAAAAATAAAAAATAAAAAAT
Found at i:1135465 original size:28 final size:25
Alignment explanation
Indices: 1135404--1135465 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 25
1135394 CCCGGCCCAT
* *
1135404 TTTTAAAATAAACATTAAAAAATTA
1 TTTTAAAATAAAAATAAAAAAATTA
1135429 TTTTAAAAATAAAAAAATAAAAAAATTTA
1 TTTT-AAAAT--AAAAATAAAAAAA-TTA
1135458 TTTTAAAA
1 TTTTAAAA
1135466 GTATCTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 4 0.13
26 5 0.16
28 15 0.48
29 7 0.23
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (25 bp):
TTTTAAAATAAAAATAAAAAAATTA
Found at i:1136197 original size:49 final size:45
Alignment explanation
Indices: 1136102--1136199 Score: 133
Period size: 49 Copynumber: 2.1 Consensus size: 45
1136092 TTACCCTTAC
* * *
1136102 TTTTATAAAATTTTATGATAATTAATTTCTAATACTTTTTATAAA
1 TTTTATAAAATTTTATGATAATTAATTTCTAATAATTTATACAAA
1136147 TTTTATAAAATTTTATGATTTTTAATTAATTTCTAATAATTTATACAAA
1 TTTTATAAAATTTTATGA----TAATTAATTTCTAATAATTTATACAAA
1136196 TTTT
1 TTTT
1136200 TATGTTTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
45 18 0.39
49 28 0.61
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (45 bp):
TTTTATAAAATTTTATGATAATTAATTTCTAATAATTTATACAAA
Found at i:1144552 original size:11 final size:11
Alignment explanation
Indices: 1144536--1144564 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1144526 CCACCACTGG
1144536 TCTCCCCTCCC
1 TCTCCCCTCCC
1144547 TCTCCCCTCCC
1 TCTCCCCTCCC
1144558 TCTCCCC
1 TCTCCCC
1144565 CACCGTCCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.72, G:0.00, T:0.28
Consensus pattern (11 bp):
TCTCCCCTCCC
Found at i:1148329 original size:20 final size:19
Alignment explanation
Indices: 1148306--1148349 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
1148296 GGCTTGATTA
*
1148306 ATTAAGTTAATCAAGGTTT
1 ATTAAGTTAATCAAAGTTT
*
1148325 GATTAAGTTAATTAAAGTTT
1 -ATTAAGTTAATCAAAGTTT
1148345 ATTAA
1 ATTAA
1148350 TTATTAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.41, C:0.02, G:0.14, T:0.43
Consensus pattern (19 bp):
ATTAAGTTAATCAAAGTTT
Found at i:1150185 original size:13 final size:15
Alignment explanation
Indices: 1150147--1150185 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1150137 AAAGGTATGA
*
1150147 TTGATTAGGTTGAAT
1 TTGATTAAGTTGAAT
1150162 TTGATTAAGTTGAA-
1 TTGATTAAGTTGAAT
1150176 TTGA-TAAGTT
1 TTGATTAAGTT
1150186 TGATGTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 6 0.26
14 4 0.17
15 13 0.57
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (15 bp):
TTGATTAAGTTGAAT
Found at i:1153772 original size:22 final size:23
Alignment explanation
Indices: 1153719--1153774 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
1153709 CCCGTTTTTA
* * *
1153719 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
1153742 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
1153764 ATTAAAATTAA
1 ATTAAAATTAA
1153775 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:1153787 original size:16 final size:16
Alignment explanation
Indices: 1153750--1153789 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
1153740 TTAATAAAAT
* *
1153750 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
1153766 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
1153782 TAAAATTA
1 TAAAATTA
1153790 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:1153868 original size:59 final size:59
Alignment explanation
Indices: 1153800--1153968 Score: 313
Period size: 59 Copynumber: 2.9 Consensus size: 59
1153790 TCAAATTATT
*
1153800 AATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1153859 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
*
1153918 AATTATTAATTGTATTAATTGTTGTAA-CAAATCTAACATTTGATTAGTAAA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
1153969 ACAAACTTGA
Statistics
Matches: 108, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
58 23 0.21
59 85 0.79
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.45
Consensus pattern (59 bp):
AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
Found at i:1154065 original size:24 final size:24
Alignment explanation
Indices: 1154035--1154080 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
1154025 AAATAAATTT
1154035 AAAATAAAAAACTAT-TATATTTTA
1 AAAATAAAAAA-TATATATATTTTA
1154059 AAAATAAAAAATATATATATTT
1 AAAATAAAAAATATATATATTT
1154081 AATATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
AAAATAAAAAATATATATATTTTA
Found at i:1154081 original size:23 final size:23
Alignment explanation
Indices: 1154031--1154082 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
1154021 AAGTAAATAA
1154031 ATTT-AAAATAAAAAACTATTAT
1 ATTTAAAAATAAAAAACTATTAT
1154053 ATTTTAAAAATAAAAAA-TATATAT
1 A-TTTAAAAATAAAAAACTAT-TAT
1154077 ATTTAA
1 ATTTAA
1154083 TATTTTTTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 1 0.04
23 11 0.41
24 15 0.56
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
ATTTAAAAATAAAAAACTATTAT
Found at i:1163251 original size:24 final size:24
Alignment explanation
Indices: 1163214--1163286 Score: 119
Period size: 24 Copynumber: 3.0 Consensus size: 24
1163204 GGTAAGACAT
1163214 TTTCCACAGCTCCTCTCTTCACCC
1 TTTCCACAGCTCCTCTCTTCACCC
* *
1163238 TTTCCACTGTTCCTCTCTTCACCC
1 TTTCCACAGCTCCTCTCTTCACCC
*
1163262 TTTCCACAGCTCCTCTATTCACCC
1 TTTCCACAGCTCCTCTCTTCACCC
1163286 T
1 T
1163287 ATCGATTGCA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.12, C:0.47, G:0.04, T:0.37
Consensus pattern (24 bp):
TTTCCACAGCTCCTCTCTTCACCC
Found at i:1163892 original size:8 final size:8
Alignment explanation
Indices: 1163879--1163903 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1163869 AATGCCGTTC
1163879 CTGTTGTT
1 CTGTTGTT
1163887 CTGTTGTT
1 CTGTTGTT
1163895 CTGTTGTT
1 CTGTTGTT
1163903 C
1 C
1163904 CTGGTAATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.16, G:0.24, T:0.60
Consensus pattern (8 bp):
CTGTTGTT
Found at i:1164625 original size:134 final size:134
Alignment explanation
Indices: 1164461--1164730 Score: 540
Period size: 134 Copynumber: 2.0 Consensus size: 134
1164451 CCATTGGAGG
1164461 TTTTAATAAGCTTGACTGAATTTTATTTTTTTAATTCTTGTGGGGATTAGAAAGGCATATATATA
1 TTTTAATAAGCTTGACTGAATTTTATTTTTTTAATTCTTGTGGGGATTAGAAAGGCATATATATA
1164526 TTTAATACGGTTTTCAAATTACTCATAAATTCATCAAACCTTAATTAATTTAATGAAAAGATACT
66 TTTAATACGGTTTTCAAATTACTCATAAATTCATCAAACCTTAATTAATTTAATGAAAAGATACT
1164591 ATAT
131 ATAT
1164595 TTTTAATAAGCTTGACTGAATTTTATTTTTTTAATTCTTGTGGGGATTAGAAAGGCATATATATA
1 TTTTAATAAGCTTGACTGAATTTTATTTTTTTAATTCTTGTGGGGATTAGAAAGGCATATATATA
1164660 TTTAATACGGTTTTCAAATTACTCATAAATTCATCAAACCTTAATTAATTTAATGAAAAGATACT
66 TTTAATACGGTTTTCAAATTACTCATAAATTCATCAAACCTTAATTAATTTAATGAAAAGATACT
1164725 ATAT
131 ATAT
1164729 TT
1 TT
1164731 AAAAAAAAAT
Statistics
Matches: 136, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
134 136 1.00
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.43
Consensus pattern (134 bp):
TTTTAATAAGCTTGACTGAATTTTATTTTTTTAATTCTTGTGGGGATTAGAAAGGCATATATATA
TTTAATACGGTTTTCAAATTACTCATAAATTCATCAAACCTTAATTAATTTAATGAAAAGATACT
ATAT
Found at i:1168075 original size:20 final size:20
Alignment explanation
Indices: 1168050--1168091 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1168040 TACTATGTGG
1168050 TGTACTACTAATTATGTATT
1 TGTACTACTAATTATGTATT
1168070 TGTACTACTAATTATGTATT
1 TGTACTACTAATTATGTATT
1168090 TG
1 TG
1168092 GATAATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TGTACTACTAATTATGTATT
Found at i:1168353 original size:32 final size:32
Alignment explanation
Indices: 1168317--1168393 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 32
1168307 AACTTTTTCG
* ** *
1168317 GAAAATATTTTCAGGAAA-TCTGTCAAACAGCA
1 GAAAATATTTTCA-CAAATTCAATCAAACACCA
1168349 GAAAATATTTTACACAAATTCAATCAAACACCA
1 GAAAATATTTT-CACAAATTCAATCAAACACCA
1168382 GAAAATATTTTC
1 GAAAATATTTTC
1168394 CAGTAAGTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 15 0.38
33 24 0.62
ACGTcount: A:0.47, C:0.17, G:0.09, T:0.27
Consensus pattern (32 bp):
GAAAATATTTTCACAAATTCAATCAAACACCA
Found at i:1168441 original size:14 final size:14
Alignment explanation
Indices: 1168418--1168457 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1168408 ACAGAAAAGT
*
1168418 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
1168432 AAATCATTTTACGG
1 AAAACATTTTACAG
1168446 AAAACATTTTAC
1 AAAACATTTTAC
1168458 TGCCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:1168443 original size:34 final size:35
Alignment explanation
Indices: 1168383--1168449 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
1168373 CAAACACCAG
* *
1168383 AAAATATTTTCCAGTAAGTCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
1168418 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
1168450 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:1175814 original size:2 final size:2
Alignment explanation
Indices: 1175802--1175849 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1175792 ATAATTATGG
*
1175802 GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1175844 GA GA GA
1 GA GA GA
1175850 CGTGTTTGGT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1176454 original size:124 final size:124
Alignment explanation
Indices: 1176234--1176478 Score: 454
Period size: 124 Copynumber: 2.0 Consensus size: 124
1176224 ACCACCAATC
*
1176234 CGGTTTAAAAAACATTAAGATTAATATTTTATGCATTAATATTTTATATAGGATGGAAATTTGAA
1 CGGTTTAAAAAACATTAAGACTAATATTTTATGCATTAATATTTTATATAGGATGGAAATTTGAA
*
1176299 GTGTATAATTCTATGTACCATCAATCAATTTGATTATTCTCAATCATTAAGGCTTTATA
66 GTGTATAATTCAATGTACCATCAATCAATTTGATTATTCTCAATCATTAAGGCTTTATA
* *
1176358 CGGTTTAAAAAACATTGAGACTAATATTTTATGCATTAATATTTTTTATAGGATGGAAATTTGAA
1 CGGTTTAAAAAACATTAAGACTAATATTTTATGCATTAATATTTTATATAGGATGGAAATTTGAA
1176423 GTGTATAATTCAATGTACCATCAATCAATTTGATTATTCTCAATCATTAAGGCTTT
66 GTGTATAATTCAATGTACCATCAATCAATTTGATTATTCTCAATCATTAAGGCTTT
1176479 GCTTGATAGA
Statistics
Matches: 117, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
124 117 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (124 bp):
CGGTTTAAAAAACATTAAGACTAATATTTTATGCATTAATATTTTATATAGGATGGAAATTTGAA
GTGTATAATTCAATGTACCATCAATCAATTTGATTATTCTCAATCATTAAGGCTTTATA
Found at i:1181174 original size:5 final size:5
Alignment explanation
Indices: 1181144--1181186 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
1181134 TTATTGGAGG
* *
1181144 TTAAT TTGAG TTAAT TTAAAT ATTAAT TTAAT TTAAT TTAAT T
1 TTAAT TTAAT TTAAT TT-AAT -TTAAT TTAAT TTAAT TTAAT T
1181187 GTAAAATAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
5 24 0.75
6 6 0.19
7 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (5 bp):
TTAAT
Found at i:1183788 original size:21 final size:21
Alignment explanation
Indices: 1183764--1183804 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1183754 GGGGCTATCA
*
1183764 TACACGGGCATGTGGGATTTC
1 TACACGGGCATGTGCGATTTC
*
1183785 TACACGGGCGTGTGCGATTT
1 TACACGGGCATGTGCGATTT
1183805 GCCAAAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.20, G:0.34, T:0.29
Consensus pattern (21 bp):
TACACGGGCATGTGCGATTTC
Found at i:1185869 original size:46 final size:46
Alignment explanation
Indices: 1185813--1185918 Score: 114
Period size: 45 Copynumber: 2.4 Consensus size: 46
1185803 AAAATGAATA
*
1185813 GAAATAGAGAAATGGAAAAT-ATTCAAAAATGATTATGGTTTTCTCT
1 GAAAT-GAGAAATGGAAAATCATTCAAAAATGAATATGGTTTTCTCT
*** *
1185859 GAAATGGAGAAAT-G-AAATCATTTGTAAATGAATGTGGTTTTCTCT
1 GAAAT-GAGAAATGGAAAATCATTCAAAAATGAATATGGTTTTCTCT
1185904 -AAAT-AGAAATGGAAA
1 GAAATGAGAAATGGAAA
1185919 TGAGAAATGA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
42 6 0.12
43 1 0.02
44 10 0.20
45 22 0.43
46 12 0.24
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.31
Consensus pattern (46 bp):
GAAATGAGAAATGGAAAATCATTCAAAAATGAATATGGTTTTCTCT
Found at i:1190687 original size:22 final size:22
Alignment explanation
Indices: 1190645--1190685 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1190635 TAATAGGTTA
* *
1190645 ATAAGTTAATAGTAAATAAATG
1 ATAAATTAAAAGTAAATAAATG
1190667 ATAAATTAAAAGT-AATAAA
1 ATAAATTAAAAGTAAATAAA
1190686 ATAACACTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (22 bp):
ATAAATTAAAAGTAAATAAATG
Found at i:1191545 original size:25 final size:25
Alignment explanation
Indices: 1191500--1191622 Score: 103
Period size: 25 Copynumber: 5.0 Consensus size: 25
1191490 GTCATTAGGG
* *
1191500 TTACCGAT-TTCAGCTCTTATGAGC
1 TTACCGATATTCAACTCATATGAGC
1191524 TTACCGATATTCAACTCATATGAGC
1 TTACCGATATTCAACTCATATGAGC
* * *
1191549 TTACCGTTATTCAGCTCGA-AGGAGC
1 TTACCGATATTCAACTC-ATATGAGC
** *
1191574 TTACC-ATTATTCAACTCGGAGGAGC
1 TTACCGA-TATTCAACTCATATGAGC
*
1191599 TTACCG-T-TTACAACTCGTATGAGC
1 TTACCGATATT-CAACTCATATGAGC
1191623 ATACATGTAC
Statistics
Matches: 83, Mismatches: 10, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
23 2 0.02
24 21 0.25
25 59 0.71
26 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (25 bp):
TTACCGATATTCAACTCATATGAGC
Found at i:1196072 original size:27 final size:27
Alignment explanation
Indices: 1195942--1196088 Score: 134
Period size: 27 Copynumber: 5.4 Consensus size: 27
1195932 CACATCAAGA
** * *
1195942 AAGAATAGCCTTTGTGGTGAACCCTAA
1 AAGAATAGCCTTTGTGGAAAACTCTAG
* * *
1195969 AAGAATAGCCTTTATGGCAAACTCTAA
1 AAGAATAGCCTTTGTGGAAAACTCTAG
* * *
1195996 AAGAATAGTCTTTGTAGAAAACTCTGG
1 AAGAATAGCCTTTGTGGAAAACTCTAG
* * **
1196023 AAGAATATCCTTTGTAGCGAACTCTAG
1 AAGAATAGCCTTTGTGGAAAACTCTAG
* *
1196050 AAGAATAGCCTTTTTGGAAAACTC-CG
1 AAGAATAGCCTTTGTGGAAAACTCTAG
1196076 AGAGAATAGCCTT
1 A-AGAATAGCCTT
1196089 AATGACAAAT
Statistics
Matches: 98, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
26 2 0.02
27 96 0.98
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (27 bp):
AAGAATAGCCTTTGTGGAAAACTCTAG
Found at i:1199453 original size:205 final size:205
Alignment explanation
Indices: 1199094--1199509 Score: 751
Period size: 205 Copynumber: 2.0 Consensus size: 205
1199084 TAAAAAGCTG
* * * *
1199094 AAAAATATCCATTAAATCTTTAAAAAACTCCAAAATTTCAGATCTTGAAATTTAGGTTTTTATTT
1 AAAAATATCCATTAAATCTTTAAAAAACCCCAAAATTTCAAATCTAGAAATTTAGGTTTTTATTG
* *
1199159 ATCAAGATTTAGCAAGAAAACAAGAGAGAGAAAGATCTTACACAAGCTAGATTCTATGGGCGACA
66 ATCAAGATTTAGCAAGAAAACAAGAGAGAGAAAGATCTTACACAAGCTAGATGCTATGAGCGACA
*
1199224 ATGGCACTTCTTGGAAATAATAGGGATCAATCTTGGAGACTTAATATTTCATATTTGGGGCTGAT
131 ATGGCACTTCTTGGAAACAATAGGGATCAATCTTGGAGACTTAATATTTCATATTTGGGGCTGAT
1199289 TTAATTAGAT
196 TTAATTAGAT
*
1199299 AAAAATATCCATTAAATCTTTAAAAATCCCCAAAATTTCAAATCTAGAAATTTAGGTTTTTATTG
1 AAAAATATCCATTAAATCTTTAAAAAACCCCAAAATTTCAAATCTAGAAATTTAGGTTTTTATTG
1199364 ATCAAGATTTAGCAAGAAAACAAGAGAGAGAAAGATCTTACACAAGCTAGATGCTATGAGCGACA
66 ATCAAGATTTAGCAAGAAAACAAGAGAGAGAAAGATCTTACACAAGCTAGATGCTATGAGCGACA
*
1199429 ATGGCACTTCTTGGAAACAATAGGGATCAATCTTGGAGACTTAATATTTCATATTTTGGGCTGAT
131 ATGGCACTTCTTGGAAACAATAGGGATCAATCTTGGAGACTTAATATTTCATATTTGGGGCTGAT
1199494 TTAATTAGAT
196 TTAATTAGAT
1199504 AAAAAT
1 AAAAAT
1199510 GGAAGCAATA
Statistics
Matches: 202, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
205 202 1.00
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (205 bp):
AAAAATATCCATTAAATCTTTAAAAAACCCCAAAATTTCAAATCTAGAAATTTAGGTTTTTATTG
ATCAAGATTTAGCAAGAAAACAAGAGAGAGAAAGATCTTACACAAGCTAGATGCTATGAGCGACA
ATGGCACTTCTTGGAAACAATAGGGATCAATCTTGGAGACTTAATATTTCATATTTGGGGCTGAT
TTAATTAGAT
Found at i:1201421 original size:21 final size:23
Alignment explanation
Indices: 1201397--1201444 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
1201387 AATAATCTTT
*
1201397 TCCT-GCTCACC-GCCTTATTTC
1 TCCTAGCTCACCTCCCTTATTTC
*
1201418 TCCTACTCTCACCTCCCTTATTTC
1 TCCTA-GCTCACCTCCCTTATTTC
1201442 TCC
1 TCC
1201445 ATATAGGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 4 0.18
23 6 0.27
24 12 0.55
ACGTcount: A:0.10, C:0.46, G:0.04, T:0.40
Consensus pattern (23 bp):
TCCTAGCTCACCTCCCTTATTTC
Found at i:1212492 original size:21 final size:21
Alignment explanation
Indices: 1212468--1212527 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
1212458 TCATTTTTAG
1212468 CAACTTCTTCTTCTTCAACAA
1 CAACTTCTTCTTCTTCAACAA
* *
1212489 CAACTTCCTCTTCTAT-AGCAA
1 CAACTTCTTCTTCT-TCAACAA
1212510 CAA-TT-TTCTTC-TCAACAA
1 CAACTTCTTCTTCTTCAACAA
1212528 TAGTATCCTC
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
17 1 0.03
18 4 0.12
19 5 0.15
20 2 0.06
21 20 0.61
22 1 0.03
ACGTcount: A:0.30, C:0.32, G:0.02, T:0.37
Consensus pattern (21 bp):
CAACTTCTTCTTCTTCAACAA
Found at i:1216626 original size:44 final size:44
Alignment explanation
Indices: 1216562--1216650 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 44
1216552 GGGACAAGTG
* *
1216562 AAAGTTTTTTTCTCCCGATCCTCTGGTGCAATAGCAATTTTATT
1 AAAGTTTTTTTCTCCCGATCCTCTAGTGCAATAGCAATTTGATT
*
1216606 AAAGTTTTTTTCTCCTGATCCTCTAGTGCAATAGCAATTTGATT
1 AAAGTTTTTTTCTCCCGATCCTCTAGTGCAATAGCAATTTGATT
1216650 A
1 A
1216651 TACCCAGAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (44 bp):
AAAGTTTTTTTCTCCCGATCCTCTAGTGCAATAGCAATTTGATT
Found at i:1218699 original size:21 final size:21
Alignment explanation
Indices: 1218658--1218699 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1218648 TATCTGAGTG
***
1218658 TGTTGATTGTAATTTTGTTGT
1 TGTTGATTGTAATTCCCTTGT
1218679 TGTTGATTGTAATTCCCTTGT
1 TGTTGATTGTAATTCCCTTGT
1218700 CTGGGATTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.14, C:0.07, G:0.21, T:0.57
Consensus pattern (21 bp):
TGTTGATTGTAATTCCCTTGT
Found at i:1222314 original size:13 final size:13
Alignment explanation
Indices: 1222288--1222328 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1222278 AAATGTCTCC
*
1222288 TTTCATATATCCA
1 TTTCATATAACCA
1222301 TTTCCATA-AACCA
1 TTT-CATATAACCA
1222314 TTTCATATAACCA
1 TTTCATATAACCA
1222327 TT
1 TT
1222329 CTAATTTACT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 4 0.16
13 17 0.68
14 4 0.16
ACGTcount: A:0.34, C:0.24, G:0.00, T:0.41
Consensus pattern (13 bp):
TTTCATATAACCA
Found at i:1224853 original size:19 final size:19
Alignment explanation
Indices: 1224829--1224867 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1224819 GAGAAAGAAA
*
1224829 TTATTCTCAGGTTTTTATT
1 TTATTCTCAGATTTTTATT
*
1224848 TTATTCTTAGATTTTTATT
1 TTATTCTCAGATTTTTATT
1224867 T
1 T
1224868 CGTTCTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.18, C:0.08, G:0.08, T:0.67
Consensus pattern (19 bp):
TTATTCTCAGATTTTTATT
Found at i:1226747 original size:6 final size:6
Alignment explanation
Indices: 1226736--1226762 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1226726 AATACATATG
1226736 TGGGCA TGGGCA TGGGCA TGGGCA TGG
1 TGGGCA TGGGCA TGGGCA TGGGCA TGG
1226763 AGAGAGGATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.52, T:0.19
Consensus pattern (6 bp):
TGGGCA
Found at i:1229355 original size:272 final size:272
Alignment explanation
Indices: 1228847--1229534 Score: 1119
Period size: 272 Copynumber: 2.5 Consensus size: 272
1228837 TTCTGTAGGA
*
1228847 CTTCA-TTCATTTAAATT-TTTTACACGGATTCTTTACTATTTAGTAGCAGGTATAAATCCCCCT
1 CTTCACTT-ATTT-AATTGTTTTACATGGATTCTTTACTATTTAGTAGCAGGTATAAATCCCCCT
*
1228910 CCCATGAGAGAAAAAAAATGTTGTATTGATTGATGTTTCTTTTGGTTCAATAAGAAATTTCCTAA
64 CCCATGAGAGAAAAAAAATGTTGTATTGATTGATGTTTCTTTTGGTTCATTAAGAAATTTCCTAA
* *
1228975 AAAGCTATCAATGACTTTCAATGGTTTCTCTTAGGCTTAAAGGAAATGCATTGTCTCTGTGGTCT
129 AAAGCTATCAATGACTTTCAATGGTTTCTCTTAGGCTTAAAGGAAATGCATTATCTATGTGGTCT
*
1229040 CTATTATGATGACTGGAAAACAAACTCCTCTATCATTATATGCTTTTGCATACATGTTCACATTT
194 CTATTATGATGACTGGAAAACAAACTCCTCTATCATCATATGCTTTTGCATACATGTTCACATTT
1229105 TATTTTCCAAGTGG
259 TATTTTCCAAGTGG
*
1229119 CTTCACTTTTTTAATTGTTTTACATGGATTCTTTACTATTTAGTAGCAGGTATAAATCCCCCTCC
1 CTTCACTTATTTAATTGTTTTACATGGATTCTTTACTATTTAGTAGCAGGTATAAATCCCCCTCC
1229184 CATGAGAGAAAAAAAATGTTGTATTGATTGATGTTTCTTTTGGTTCATTAAGAAATTTCCTAAAA
66 CATGAGAGAAAAAAAATGTTGTATTGATTGATGTTTCTTTTGGTTCATTAAGAAATTTCCTAAAA
*
1229249 AGCTATCAATGACTTTCAATGGTTTCTCTTAGGCTTGAAGGAAATGCATTATCTATGTGGTCTCT
131 AGCTATCAATGACTTTCAATGGTTTCTCTTAGGCTTAAAGGAAATGCATTATCTATGTGGTCTCT
*
1229314 ATTATGATGACTGGAAAACGAACTCCTCTATCATCATATGCTTTTGCATACATGTTCACATTTTA
196 ATTATGATGACTGGAAAACAAACTCCTCTATCATCATATGCTTTTGCATACATGTTCACATTTTA
1229379 TTTTCCAAGTGG
261 TTTTCCAAGTGG
1229391 CTTCACTTATTTAATTGTTTTACATGGATTCTTTACTATTTAGTAGCAGGTATAAATCCCCCTCA
1 CTTCACTTATTTAATTGTTTTACATGGATTCTTTACTATTTAGTAGCAGGTATAAATCCCCCTC-
* * * *** *
1229456 CTCCTAAAAGAAGTAATTTATGTTGTATTGATTGATGTTACAGTTCTTCTGGTTCATTAAGAAAT
65 C-CATGAGAGAA--AAAAAATGTTGTATTGATTGATG-T----TTCTTTTGGTTCATTAAGAAAT
*
1229521 TTCCTAGAAAGCTA
122 TTCCTAAAAAGCTA
1229535 CAGACTCGAT
Statistics
Matches: 388, Mismatches: 17, Indels: 13
0.93 0.04 0.03
Matches are distributed among these distances:
271 4 0.01
272 319 0.82
273 3 0.01
274 7 0.02
276 20 0.05
277 1 0.00
281 34 0.09
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.40
Consensus pattern (272 bp):
CTTCACTTATTTAATTGTTTTACATGGATTCTTTACTATTTAGTAGCAGGTATAAATCCCCCTCC
CATGAGAGAAAAAAAATGTTGTATTGATTGATGTTTCTTTTGGTTCATTAAGAAATTTCCTAAAA
AGCTATCAATGACTTTCAATGGTTTCTCTTAGGCTTAAAGGAAATGCATTATCTATGTGGTCTCT
ATTATGATGACTGGAAAACAAACTCCTCTATCATCATATGCTTTTGCATACATGTTCACATTTTA
TTTTCCAAGTGG
Found at i:1234867 original size:12 final size:12
Alignment explanation
Indices: 1234852--1234877 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1234842 TAAACTAACC
1234852 TCAAATTCCTGG
1 TCAAATTCCTGG
1234864 TCAAATTCCTGG
1 TCAAATTCCTGG
1234876 TC
1 TC
1234878 CAGATGCTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (12 bp):
TCAAATTCCTGG
Found at i:1239788 original size:13 final size:13
Alignment explanation
Indices: 1239762--1239836 Score: 86
Period size: 13 Copynumber: 6.1 Consensus size: 13
1239752 AATTTGGCAA
* *
1239762 TGCTTTTCAGAAG
1 TGCTTTTGAAAAG
1239775 TGCTTTTGAAAA-
1 TGCTTTTGAAAAG
1239787 -G--TTTGAAAAG
1 TGCTTTTGAAAAG
1239797 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
1239810 TGCTTTTCAAAAG
1 TGCTTTTGAAAAG
*
1239823 TGTTTTTGAAAAG
1 TGCTTTTGAAAAG
1239836 T
1 T
1239837 TTGATTTAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
9 8 0.15
11 2 0.04
13 43 0.81
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:1240170 original size:27 final size:26
Alignment explanation
Indices: 1240119--1240170 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
1240109 AATATAACCA
*
1240119 TTAAATATTTGTAATTAGTATTTTTT
1 TTAAATATTTGTAATTAATATTTTTT
*
1240145 TTAAATTATTTTTAATTAATGATTTT
1 TTAAA-TATTTGTAATTAAT-ATTTT
1240171 AACACATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.23
27 12 0.55
28 5 0.23
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.62
Consensus pattern (26 bp):
TTAAATATTTGTAATTAATATTTTTT
Found at i:1253839 original size:29 final size:29
Alignment explanation
Indices: 1253770--1253840 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
1253760 TTACAATTCA
* * *
1253770 GACTTATTTGATTCATTTTAATAATATAGG
1 GACTGATTTGA-TCATTTTAATAATAGAAG
* *
1253800 GACTGAATTGATCATTTTAATAATAGAAT
1 GACTGATTTGATCATTTTAATAATAGAAG
1253829 GACT-AGTTTGAT
1 GACTGA-TTTGAT
1253841 ACGGTCCCTA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
28 1 0.03
29 24 0.71
30 9 0.26
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.42
Consensus pattern (29 bp):
GACTGATTTGATCATTTTAATAATAGAAG
Found at i:1254172 original size:20 final size:21
Alignment explanation
Indices: 1254119--1254178 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
1254109 ACAAATAATT
*
1254119 TTAAAAAGATTAAAACAAAAATA
1 TTAAAAAG-TTCAAA-AAAAATA
*
1254142 TTTAAAA-TTCAAAAAAAATA
1 TTAAAAAGTTCAAAAAAAATA
*
1254162 -TAAAAAGTTCATAAAAA
1 TTAAAAAGTTCAAAAAAA
1254179 TTCAAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
19 5 0.16
20 16 0.50
21 5 0.16
23 6 0.19
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.25
Consensus pattern (21 bp):
TTAAAAAGTTCAAAAAAAATA
Found at i:1257618 original size:46 final size:46
Alignment explanation
Indices: 1257567--1257662 Score: 147
Period size: 46 Copynumber: 2.1 Consensus size: 46
1257557 AAAGCTAGGT
*
1257567 TAAAATGTTGATTAAGCTCAAAGAATTTATGCAAACCCCTACACAA
1 TAAAATGTTGATTAAGCTCAAAGAACTTATGCAAACCCCTACACAA
* * * *
1257613 TAAAATGTTGATTCAGCTCAAAGAACTTATGCAATCCCCTGCTCAA
1 TAAAATGTTGATTAAGCTCAAAGAACTTATGCAAACCCCTACACAA
1257659 TAAA
1 TAAA
1257663 GCCAAGACCC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.41, C:0.21, G:0.11, T:0.27
Consensus pattern (46 bp):
TAAAATGTTGATTAAGCTCAAAGAACTTATGCAAACCCCTACACAA
Found at i:1264266 original size:5 final size:5
Alignment explanation
Indices: 1264256--1264286 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
1264246 TAACATTAGG
1264256 CATAT CATAT CATAT CATAT CATAT CATAT C
1 CATAT CATAT CATAT CATAT CATAT CATAT C
1264287 TTAGACTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (5 bp):
CATAT
Found at i:1268171 original size:13 final size:13
Alignment explanation
Indices: 1268155--1268179 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1268145 TTCAAGAGTG
1268155 GTAGAAAAGTGTT
1 GTAGAAAAGTGTT
1268168 GTAGAAAAGTGT
1 GTAGAAAAGTGT
1268180 AGTTTATTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.32, T:0.28
Consensus pattern (13 bp):
GTAGAAAAGTGTT
Found at i:1268442 original size:10 final size:10
Alignment explanation
Indices: 1268421--1268450 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1268411 AATAAATAAG
1268421 ATTTAA-ATA
1 ATTTAATATA
1268430 ATTTAATATA
1 ATTTAATATA
1268440 ATTTAATATA
1 ATTTAATATA
1268450 A
1 A
1268451 AATATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.30
10 14 0.70
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
ATTTAATATA
Found at i:1279117 original size:17 final size:18
Alignment explanation
Indices: 1279084--1279123 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
1279074 AAATTTTATT
1279084 TTATAATAAGATAATATC
1 TTATAATAAGATAATATC
*
1279102 TTATAATAA-TTAATATC
1 TTATAATAAGATAATATC
1279119 TTATA
1 TTATA
1279124 TAAACTTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (18 bp):
TTATAATAAGATAATATC
Found at i:1287535 original size:37 final size:37
Alignment explanation
Indices: 1287484--1287578 Score: 113
Period size: 37 Copynumber: 2.5 Consensus size: 37
1287474 ATTCCAAAAA
*
1287484 TAATATTATTTTAATAGT-TTTCTATTAAATTAA-ATT
1 TAATATTATCTTAATAGTATTT-TATTAAATTAATATT
*
1287520 TAATACTTATCTTAATAGTATTTTATTAATTTAATATT
1 TAATA-TTATCTTAATAGTATTTTATTAAATTAATATT
*
1287558 AAAGTGATTATCTTAATAGTA
1 TAA-T-ATTATCTTAATAGTA
1287579 AATTTAATAT
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
36 5 0.10
37 22 0.43
38 8 0.16
39 15 0.29
40 1 0.02
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.52
Consensus pattern (37 bp):
TAATATTATCTTAATAGTATTTTATTAAATTAATATT
Found at i:1287629 original size:69 final size:68
Alignment explanation
Indices: 1287509--1287636 Score: 193
Period size: 69 Copynumber: 1.9 Consensus size: 68
1287499 AGTTTTCTAT
* * *
1287509 TAAATTAAATTTAATACTTATCTTAATAGTATTTTATTAATTTAATATTAAAGTGATTATCTTAA
1 TAAATTAAATATAATACTTATCTTAATAATATTATATTAATTTAATATTAAAGTGATTATCTTAA
1287574 TAG
66 TAG
* * *
1287577 TAAATTTAATATAATATTTATCTTTATAAATATTATATTAATTTAATATTAAAGTGATTA
1 TAAATTAAATATAATACTTATCTTAAT-AATATTATATTAATTTAATATTAAAGTGATTA
1287637 AGTTTAATCA
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
68 23 0.43
69 30 0.57
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (68 bp):
TAAATTAAATATAATACTTATCTTAATAATATTATATTAATTTAATATTAAAGTGATTATCTTAA
TAG
Found at i:1292380 original size:30 final size:30
Alignment explanation
Indices: 1292344--1292406 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
1292334 TTGTTTCTAG
1292344 TAAAGCCATGCCATACACAAGTCATGTACC
1 TAAAGCCATGCCATACACAAGTCATGTACC
1292374 TAAAGCCATGCCATACACAAGTCATGTACC
1 TAAAGCCATGCCATACACAAGTCATGTACC
1292404 TAA
1 TAA
1292407 CATATCGACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.38, C:0.29, G:0.13, T:0.21
Consensus pattern (30 bp):
TAAAGCCATGCCATACACAAGTCATGTACC
Found at i:1295414 original size:33 final size:33
Alignment explanation
Indices: 1295372--1295440 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
1295362 AGTATTGTTC
1295372 AAGATTTTAGATGTTGACATTGTTGAATAGTTT
1 AAGATTTTAGATGTTGACATTGTTGAATAGTTT
1295405 AAGATTTTAGATGTTGACATTGTTGAATAGTTT
1 AAGATTTTAGATGTTGACATTGTTGAATAGTTT
1295438 AAG
1 AAG
1295441 TATTAGGGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.32, C:0.03, G:0.22, T:0.43
Consensus pattern (33 bp):
AAGATTTTAGATGTTGACATTGTTGAATAGTTT
Found at i:1296386 original size:16 final size:18
Alignment explanation
Indices: 1296365--1296402 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1296355 GATTGATATT
1296365 GAAATG-ACA-AAGATGA
1 GAAATGAACATAAGATGA
*
1296381 GAAATGAATATAAGATGA
1 GAAATGAACATAAGATGA
1296399 GAAA
1 GAAA
1296403 ATATTGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 2 0.11
18 11 0.58
ACGTcount: A:0.58, C:0.03, G:0.24, T:0.16
Consensus pattern (18 bp):
GAAATGAACATAAGATGA
Found at i:1296408 original size:43 final size:43
Alignment explanation
Indices: 1296360--1296445 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
1296350 TATGTGATTG
*
1296360 ATATTGAAATGACAAAGATGAG-AAATGAATATAAGATGAGAAA
1 ATATTGAAATGACAAAGATG-GTAAATGAATATAAAATGAGAAA
* *
1296403 ATATTGAAATGGCAAAGATGGTAATTGAATATAAAATGAGAAA
1 ATATTGAAATGACAAAGATGGTAAATGAATATAAAATGAGAAA
1296446 TGAAATATGA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
42 1 0.03
43 38 0.97
ACGTcount: A:0.53, C:0.02, G:0.21, T:0.23
Consensus pattern (43 bp):
ATATTGAAATGACAAAGATGGTAAATGAATATAAAATGAGAAA
Found at i:1302484 original size:22 final size:20
Alignment explanation
Indices: 1302442--1302484 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
1302432 ATCTTGCTGG
**
1302442 AAATTGTTGGTTGAGTTATT
1 AAATTGTTGGTTGAGAAATT
1302462 AAATTGTATGGTATGAGAAATT
1 AAATTGT-TGGT-TGAGAAATT
1302484 A
1 A
1302485 TTACTTTAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 4 0.21
22 8 0.42
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (20 bp):
AAATTGTTGGTTGAGAAATT
Found at i:1305739 original size:75 final size:75
Alignment explanation
Indices: 1305652--1305793 Score: 175
Period size: 75 Copynumber: 1.9 Consensus size: 75
1305642 AGGCGCAATA
* * *
1305652 TTTGTTGTTTTAT-TCAACTAGTGCTAGG-CACACCATTATACTTGTT-GATTTATCCGACTAGT
1 TTTGTTGTTTTATCT-AACTAGTACT-GGACACACCATTATA-TTGTTCGATTTACCCGACTAGC
1305714 GCTGGGCATAACC
63 GCTGGGCATAACC
* *
1305727 TTTGTTAG-TTTATCTAACTAGTACTGGACACACCATTATATTTTTCGGTTTACCCGACTAGCGC
1 TTTGTT-GTTTTATCTAACTAGTACTGGACACACCATTATATTGTTCGATTTACCCGACTAGCGC
1305791 TGG
65 TGG
1305794 ACGCAACTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
74 6 0.10
75 50 0.86
76 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (75 bp):
TTTGTTGTTTTATCTAACTAGTACTGGACACACCATTATATTGTTCGATTTACCCGACTAGCGCT
GGGCATAACC
Found at i:1306491 original size:2 final size:2
Alignment explanation
Indices: 1306486--1306512 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1306476 TACTCATGTC
1306486 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 T
1306513 GTTTGGTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1308602 original size:23 final size:23
Alignment explanation
Indices: 1308572--1308624 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
1308562 AGTGTTATTG
1308572 ATCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
*
1308595 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
1308618 ATCAGTG
1 ATCAGTG
1308625 TGGCACTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (23 bp):
ATCAGTGGTAGCTACGGCTACAT
Found at i:1313010 original size:22 final size:22
Alignment explanation
Indices: 1312982--1313030 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
1312972 TATTTAATGG
1312982 TATACAATGTTATGAAAAGAGT
1 TATACAATGTTATGAAAAGAGT
1313004 TATACAATGTTATGAAAAGAGT
1 TATACAATGTTATGAAAAGAGT
1313026 T-TACA
1 TATACA
1313031 TATTGTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (22 bp):
TATACAATGTTATGAAAAGAGT
Found at i:1313578 original size:2 final size:2
Alignment explanation
Indices: 1313571--1313607 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1313561 AGCTTCGTGT
1313571 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1313608 TTTATATATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1313913 original size:2 final size:2
Alignment explanation
Indices: 1313906--1313956 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1313896 GTAACCATCA
1313906 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1313948 TC TC TC TC T
1 TC TC TC TC T
1313957 ACAGCTGGTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1324014 original size:9 final size:9
Alignment explanation
Indices: 1323973--1324015 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
1323963 ATATTTATTA
1323973 TTTTATAAC
1 TTTTATAAC
1323982 TTTTA-ATAC
1 TTTTATA-AC
*
1323991 TTTAATAAC
1 TTTTATAAC
*
1324000 TTTTATAAA
1 TTTTATAAC
1324009 TTTTATA
1 TTTTATA
1324016 TACAACTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
8 1 0.03
9 27 0.93
10 1 0.03
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (9 bp):
TTTTATAAC
Found at i:1324127 original size:10 final size:10
Alignment explanation
Indices: 1324084--1324174 Score: 82
Period size: 10 Copynumber: 9.3 Consensus size: 10
1324074 TCTAAATTTA
*
1324084 TTTATAGTAT
1 TTTATAATAT
1324094 TTATATAATAT
1 TT-TATAATAT
*
1324105 TTTCAT-ATTT
1 TTT-ATAATAT
*
1324115 TTTATAACAT
1 TTTATAATAT
1324125 TTTATAATA-
1 TTTATAATAT
*
1324134 TTTAAAATAT
1 TTTATAATAT
*
1324144 CTTATAATAT
1 TTTATAATAT
*
1324154 TGTATAAT-T
1 TTTATAATAT
1324163 TTTATAA-AT
1 TTTATAATAT
1324172 TTT
1 TTT
1324175 CTTTGTAATG
Statistics
Matches: 65, Mismatches: 11, Indels: 11
0.75 0.13 0.13
Matches are distributed among these distances:
9 21 0.32
10 33 0.51
11 11 0.17
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.57
Consensus pattern (10 bp):
TTTATAATAT
Found at i:1324167 original size:19 final size:19
Alignment explanation
Indices: 1324084--1324173 Score: 67
Period size: 19 Copynumber: 4.6 Consensus size: 19
1324074 TCTAAATTTA
*
1324084 TTTATAGTATTTATATAATAT
1 TTTATAATATTTA-A-AATAT
* * * *
1324105 TTTCATATTTTTTATAACAT
1 TTT-ATAATATTTAAAATAT
1324125 TTTATAATATTTAAAATAT
1 TTTATAATATTTAAAATAT
* *
1324144 CTTATAATATTGTATAAT-T
1 TTTATAATATT-TAAAATAT
1324163 TTTATAA-ATTT
1 TTTATAATATTT
1324174 TCTTTGTAAT
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
17 1 0.02
18 3 0.05
19 29 0.52
20 12 0.21
21 3 0.05
22 8 0.14
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTATAATATTTAAAATAT
Found at i:1324602 original size:38 final size:38
Alignment explanation
Indices: 1324559--1324631 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
1324549 CTTTAAAATC
* *
1324559 AAACCTTGAAAAGGTAAATAGATATTTAT-TTAAAGCAT
1 AAACCTTAAAAAAGTAAATAGATATTT-TCTTAAAGCAT
**
1324597 AAACCTTAAAAAAGTAGGTAGATATTTTCTTAAAG
1 AAACCTTAAAAAAGTAAATAGATATTTTCTTAAAG
1324632 TATGAGAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 1 0.03
38 29 0.97
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.32
Consensus pattern (38 bp):
AAACCTTAAAAAAGTAAATAGATATTTTCTTAAAGCAT
Found at i:1327776 original size:21 final size:22
Alignment explanation
Indices: 1327743--1327783 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1327733 GATATAATGC
*
1327743 ATTTTAAACATATA-ATTTACT
1 ATTTGAAACATATATATTTACT
*
1327764 ATTTGAAATATATATATTTA
1 ATTTGAAACATATATATTTA
1327784 ATTTAGTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (22 bp):
ATTTGAAACATATATATTTACT
Found at i:1332799 original size:19 final size:20
Alignment explanation
Indices: 1332777--1332842 Score: 75
Period size: 19 Copynumber: 3.4 Consensus size: 20
1332767 AAAATTTTGT
*
1332777 AAAAATTTCAAAAATTATAA
1 AAAAATTTCAAAAATTATTA
* *
1332797 AAAAATATT--TAAATTATTT
1 AAAAAT-TTCAAAAATTATTA
1332816 AAAAA-TTCAAAAATTATTA
1 AAAAATTTCAAAAATTATTA
1332835 AAAAATTT
1 AAAAATTT
1332843 AGAAAAGAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
17 2 0.05
19 25 0.68
20 8 0.22
21 2 0.05
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAATTTCAAAAATTATTA
Found at i:1332856 original size:38 final size:39
Alignment explanation
Indices: 1332776--1332857 Score: 96
Period size: 38 Copynumber: 2.1 Consensus size: 39
1332766 TAAAATTTTG
* ** *
1332776 TAAAAATTTCAAAAATTATAAAAAAATATTTAAATTATT
1 TAAAAATTTCAAAAATTATAAAAAAATATTGAAAAGAAT
*
1332815 TAAAAA-TTCAAAAATTATTAAAAAAT-TTAGAAAAGAAT
1 TAAAAATTTCAAAAATTATAAAAAAATATT-GAAAAGAAT
1332853 TAAAA
1 TAAAA
1332858 TTTATATATT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
37 2 0.05
38 29 0.78
39 6 0.16
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (39 bp):
TAAAAATTTCAAAAATTATAAAAAAATATTGAAAAGAAT
Found at i:1334678 original size:6 final size:6
Alignment explanation
Indices: 1334655--1334693 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
1334645 AAAATAAATA
* *
1334655 AATAAC AATGAT AATAAC AATAAC AATAAC AATAAC AAT
1 AATAAC AATAAC AATAAC AATAAC AATAAC AATAAC AAT
1334694 GATAACAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.64, C:0.13, G:0.03, T:0.21
Consensus pattern (6 bp):
AATAAC
Found at i:1335958 original size:33 final size:33
Alignment explanation
Indices: 1335916--1335981 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1335906 TATATGATTT
1335916 GTTGCTTCAATCTACTCTACTGCAACTTCAGGG
1 GTTGCTTCAATCTACTCTACTGCAACTTCAGGG
**
1335949 GTTGCTTCAATCTACTCTACTTTAACTTCAGGG
1 GTTGCTTCAATCTACTCTACTGCAACTTCAGGG
1335982 AGATTAGACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (33 bp):
GTTGCTTCAATCTACTCTACTGCAACTTCAGGG
Found at i:1336020 original size:44 final size:44
Alignment explanation
Indices: 1335952--1336496 Score: 270
Period size: 44 Copynumber: 11.9 Consensus size: 44
1335942 TTCAGGGGTT
* * ** * *
1335952 GCTTCAATCTACTCTACTTTAACTTCAGGGAGATTAGACTCGTA
1 GCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGACTTGTA
* * * *
1335996 GCTTTAATCTACTCCACTGCAACTTTAGGAAGATGAGACTCGTA
1 GCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGACTTGTA
* * * *
1336040 TCTTTAATCTACTTCATTGCAACTTCAAGGAGATAAGATTTGTAGCTTGTA
1 GCTTTAATCTACTCCACTGCAACTTCAGGGAGAT-A-A---G-A-CTTGTA
* * * *
1336091 GTTTTAATCTATTCCACTGCAACTTTAGGGAGATAATACTTACTATGGTA
1 GCTTTAATCTACTCCACTGCAACTTCAGGGAGAT-A-A--GACT-T-GTA
* * * * * *
1336141 GATTTAATCCGAC-CTACTGTAACTTCAGAGG-TATAGGAC-T-TA
1 GCTTTAAT-CTACTCCACTGCAACTTCAG-GGAGATAAGACTTGTA
* * * ** * * *
1336183 TCATTTCAATCTGCTCTACTAAAATTTCAGAGAGATAAGATTTGTAA
1 GC-TTT-AATCTACTCCACTGCAACTTCAGGGAGATAAGACTTGT-A
** * * *
1336230 TTTGTAACTTTAATCTGTTCCATTGCAACTTTCAGGGAAATAAGATTTGTA
1 ---G---CTTTAATCTACTCCACTGCAAC-TTCAGGGAGATAAGACTTGTA
* * * * * *
1336281 GTTTTAATCTACTCCATTGCAATTTCAAGGAGATAAGATTTGTG
1 GCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGACTTGTA
* * * * * *
1336325 GCTTTAATATGCTCCACTGCAACTTCAAGGAGACAATATTTGTA
1 GCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGACTTGTA
* ** * * * *
1336369 TCTCCAATATACTCTACTGCAACTTCAGGGAAATAAGATTTGTA
1 GCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGACTTGTA
* * * * *
1336413 ACTTCAATCTACTCCACTGCAACTTTAGGGAGATAAGATTTGTG
1 GCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGACTTGTA
* *
1336457 GCTTTAATCTACTCTATTGCAACTTCAGGGAGATAAGACT
1 GCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGACT
1336497 CATCACGATG
Statistics
Matches: 385, Mismatches: 91, Indels: 50
0.73 0.17 0.10
Matches are distributed among these distances:
42 2 0.01
43 6 0.02
44 246 0.64
45 19 0.05
46 4 0.01
47 1 0.00
48 3 0.01
49 4 0.01
50 26 0.07
51 52 0.14
52 21 0.05
53 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (44 bp):
GCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGACTTGTA
Found at i:1346505 original size:42 final size:43
Alignment explanation
Indices: 1346409--1346523 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 43
1346399 AGCTCGTACA
* * *
1346409 ATGCCAATGTCTCAGAC-GAGCTCTTACATGTAATCAAATATCG
1 ATGCCAATGTCCCAGACAG-GGTCTTACACGTAATCAAATATCG
* * * *
1346452 ATGCCACTGTCCGAGACAGGGTTTTACACGTAATCATATA-CG
1 ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCAAATATCG
*
1346494 ATGCCAATGTCCCAGACATGGTCTTACACG
1 ATGCCAATGTCCCAGACAGGGTCTTACACG
1346524 AGGTCTTACA
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
42 28 0.47
43 31 0.52
44 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCAAATATCG
Found at i:1350009 original size:18 final size:17
Alignment explanation
Indices: 1349987--1350041 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 17
1349977 GAAAATAAAT
1349987 AAATAAAAATGATAATA
1 AAATAAAAATGATAATA
*
1350004 ATAATAACAATGATAATA
1 A-AATAAAAATGATAATA
*
1350022 AAATATAAATG-TATATA
1 AAATAAAAATGATA-ATA
1350039 AAA
1 AAA
1350042 GGAATATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 2 0.06
17 15 0.45
18 16 0.48
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.27
Consensus pattern (17 bp):
AAATAAAAATGATAATA
Done.