Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 83 of 120
Found at i:24119970 original size:30 final size:31
Alignment explanation
Indices: 24119911--24119977 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
24119901 ATTAATAAAA
* *
24119911 ATAAAATTATACTTTAATTTTTTTTAAAATG
1 ATAAAATTATAATTTAATTTTTTTAAAAATG
* *
24119942 ATAAAATTTTAATTTAA-TTTTTTAAAAATT
1 ATAAAATTATAATTTAATTTTTTTAAAAATG
24119972 ATAAAA
1 ATAAAA
24119978 AATATAAACT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 17 0.53
31 15 0.47
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (31 bp):
ATAAAATTATAATTTAATTTTTTTAAAAATG
Found at i:24120029 original size:22 final size:22
Alignment explanation
Indices: 24119969--24120029 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
24119959 TTTTTTAAAA
*
24119969 ATTATAAAAAATATAA---ACT
1 ATTATAAAAATTATAATTTACT
* *
24119988 ATGAT-AAAATTATATTTTTACT
1 ATTATAAAAATTATA-ATTTACT
24120010 ATTATAAAAATTATAATTTA
1 ATTATAAAAATTATAATTTA
24120030 ATTTTTACTT
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
18 8 0.25
19 4 0.12
22 11 0.34
23 9 0.28
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (22 bp):
ATTATAAAAATTATAATTTACT
Found at i:24122642 original size:43 final size:43
Alignment explanation
Indices: 24122581--24122677 Score: 142
Period size: 43 Copynumber: 2.3 Consensus size: 43
24122571 TCAGACACAC
** *
24122581 CTTTTTCATATTTCCTGCCTATTTATCTAAAC-AGAGCATCAAT
1 CTTTTTCATATTTCCTGCCTAGCTAT-TAAACAAAAGCATCAAT
*
24122624 CTTTTTCATATTTCCTGCCTAGCTATTACACAAAAGCATCAAT
1 CTTTTTCATATTTCCTGCCTAGCTATTAAACAAAAGCATCAAT
24122667 CTTTTTCATAT
1 CTTTTTCATAT
24122678 ACATCATTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 4 0.08
43 45 0.92
ACGTcount: A:0.28, C:0.24, G:0.06, T:0.42
Consensus pattern (43 bp):
CTTTTTCATATTTCCTGCCTAGCTATTAAACAAAAGCATCAAT
Found at i:24125551 original size:31 final size:29
Alignment explanation
Indices: 24125513--24125670 Score: 108
Period size: 31 Copynumber: 5.2 Consensus size: 29
24125503 AAATTTAGGC
*
24125513 ACCAAATTAAGAAAAAATGCCAAGTTCAGGT
1 ACCAAATTAGGAAAAAA-G-CAAGTTCAGGT
* *
24125544 ACCAAATTAGGTCCAAAAA--AAGTTTAGGT
1 ACCAAATTAGG--AAAAAAGCAAGTTCAGGT
* *
24125573 ACTAAATTAGGAAAAAGGGTCAAGTTCAGGT
1 ACCAAATTAGGAAAAA-AG-CAAGTTCAGGT
* *
24125604 ACCAAATTGGGTCAAAAAA--AAGTTAAGGT
1 ACCAAATTAGG--AAAAAAGCAAGTTCAGGT
* * *
24125633 ACAAAATTAGGAAAAAGTGTCAAGTTCAGAT
1 ACCAAATTAGGAAAAA-AG-CAAGTTCAGGT
24125664 ACCAAAT
1 ACCAAAT
24125671 GTTATATTAA
Statistics
Matches: 98, Mismatches: 17, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
27 9 0.09
29 37 0.38
31 42 0.43
33 10 0.10
ACGTcount: A:0.47, C:0.13, G:0.19, T:0.22
Consensus pattern (29 bp):
ACCAAATTAGGAAAAAAGCAAGTTCAGGT
Found at i:24125572 original size:29 final size:28
Alignment explanation
Indices: 24125534--24125643 Score: 98
Period size: 29 Copynumber: 3.8 Consensus size: 28
24125524 AAAAAATGCC
24125534 AAGTTCAGGTACCAAATTAGGTCCAAAAA
1 AAGTTCAGGTACCAAATTAGGT-CAAAAA
* *
24125563 AAGTTTAGGTACTAAATTAGG--AAAAA
1 AAGTTCAGGTACCAAATTAGGTCAAAAA
*
24125589 GGGTCAAGTTCAGGTACCAAATTGGGTCAAAAAA
1 -----AAGTTCAGGTACCAAATTAGGTC-AAAAA
* *
24125623 AAGTTAAGGTACAAAATTAGG
1 AAGTTCAGGTACCAAATTAGG
24125644 AAAAAGTGTC
Statistics
Matches: 65, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
26 5 0.08
29 37 0.57
31 18 0.28
34 5 0.08
ACGTcount: A:0.45, C:0.11, G:0.22, T:0.23
Consensus pattern (28 bp):
AAGTTCAGGTACCAAATTAGGTCAAAAA
Found at i:24125599 original size:60 final size:60
Alignment explanation
Indices: 24125506--24125670 Score: 231
Period size: 60 Copynumber: 2.8 Consensus size: 60
24125496 ATTTAATAAA
* * * * * *
24125506 TTTAGGCACCAAATTAAGAAAAAATGCCAAGTTCAGGTACCAAATTAGGTCCAAAAAAAG
1 TTTAGGTACAAAATTAGGAAAAAGTGTCAAGTTCAGGTACCAAATTAGGTCAAAAAAAAG
* * *
24125566 TTTAGGTACTAAATTAGGAAAAAGGGTCAAGTTCAGGTACCAAATTGGGTCAAAAAAAAG
1 TTTAGGTACAAAATTAGGAAAAAGTGTCAAGTTCAGGTACCAAATTAGGTCAAAAAAAAG
* *
24125626 TTAAGGTACAAAATTAGGAAAAAGTGTCAAGTTCAGATACCAAAT
1 TTTAGGTACAAAATTAGGAAAAAGTGTCAAGTTCAGGTACCAAAT
24125671 GTTATATTAA
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 93 1.00
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.22
Consensus pattern (60 bp):
TTTAGGTACAAAATTAGGAAAAAGTGTCAAGTTCAGGTACCAAATTAGGTCAAAAAAAAG
Found at i:24126905 original size:178 final size:177
Alignment explanation
Indices: 24126606--24126952 Score: 495
Period size: 178 Copynumber: 2.0 Consensus size: 177
24126596 TAATATATAG
* * * * *
24126606 AGCTAAATAAACTAAAGTAAACTGAAGATTAAGCTTTACATTTCTGGTTCTCTGAACACCTTTAA
1 AGCTAAATAAACTAAACTAAACTGAAGATCAAGCTTTACAATTCTAGTTCTCTGAACACCTGTAA
*
24126671 CCACCACAAAAGCAAACAAAACATTTGATCACAGTCACAGAATATGCAATGGATTTGTTTCTAAA
66 CCACCACAAAAGCAAACAAAACATTTGATCACAGCCACAGAATATGCAATGGATTTG-TTCTAAA
*
24126736 GCACACAACAAAAAAATAAGTCGCAA-GATTAATTCCCAAAACAGATAA
130 GCACACAACAAAAAAATAAGTC-CAATGATTAACTCCCAAAACAGATAA
*
24126784 AGCTAAATATACTAAACTAAACTGAAGATCAAGC-TTACCAATTCTAGTTCTCTGAACACCTCGT
1 AGCTAAATAAACTAAACTAAACTGAAGATCAAGCTTTA-CAATTCTAGTTCTCTGAACACCT-GT
* **
24126848 -ACCGA-CACAAAAGCAAACAAAACATTTTATCGGAGCCACAGAATATGCAATGGATTTGTTCTA
64 AACC-ACCACAAAAGCAAACAAAACATTTGATCACAGCCACAGAATATGCAATGGATTTGTTCTA
* * *
24126911 AGGCACACAACAAAATAATAAGTCTAATGATTAACTCCCAAA
128 AAGCACACAACAAAAAAATAAGTCCAATGATTAACTCCCAAA
24126953 TTAGATAACA
Statistics
Matches: 151, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
176 2 0.01
177 43 0.28
178 104 0.69
179 2 0.01
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.24
Consensus pattern (177 bp):
AGCTAAATAAACTAAACTAAACTGAAGATCAAGCTTTACAATTCTAGTTCTCTGAACACCTGTAA
CCACCACAAAAGCAAACAAAACATTTGATCACAGCCACAGAATATGCAATGGATTTGTTCTAAAG
CACACAACAAAAAAATAAGTCCAATGATTAACTCCCAAAACAGATAA
Found at i:24129463 original size:2 final size:2
Alignment explanation
Indices: 24129456--24129506 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
24129446 GCAGTAACGT
24129456 GA GA GA 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
24129498 GA GA GA GA G
1 GA GA GA GA G
24129507 GATGGGGAGA
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:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:24129624 original size:25 final size:25
Alignment explanation
Indices: 24129588--24129637 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
24129578 GAGGGTCTTT
* *
24129588 TTATTTTTATTTAGCATTAATATAA
1 TTATTTTAATTTAACATTAATATAA
*
24129613 TTATTTTAATTTAATATTAATATAA
1 TTATTTTAATTTAACATTAATATAA
24129638 AATTTAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (25 bp):
TTATTTTAATTTAACATTAATATAA
Found at i:24129658 original size:23 final size:24
Alignment explanation
Indices: 24129603--24129660 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
24129593 TTTATTTAGC
* *
24129603 ATTAATATAATTATTTTAATTTAAT
1 ATTAATATAA-AATTTAAATTTAAT
*
24129628 ATTAATATAAAATTTAAATTTATT
1 ATTAATATAAAATTTAAATTTAAT
24129652 ATTATATAT
1 ATTA-ATAT
24129661 TTTTTGAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 15 0.52
25 14 0.48
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
ATTAATATAAAATTTAAATTTAAT
Found at i:24132352 original size:13 final size:12
Alignment explanation
Indices: 24132323--24132357 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
24132313 TGTTAAAATG
*
24132323 AATAAAAAATAT
1 AATAAAAATTAT
24132335 AATAAAAATTAT
1 AATAAAAATTAT
24132347 ATATAAAAATT
1 A-ATAAAAATT
24132358 GAGAATTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AATAAAAATTAT
Found at i:24144508 original size:18 final size:17
Alignment explanation
Indices: 24144485--24144518 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
24144475 ATAAATTGTG
24144485 ATAATTACACATTTAAAA
1 ATAATTACA-ATTTAAAA
*
24144503 ATAATTATAATTTAAA
1 ATAATTACAATTTAAA
24144519 TTACAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAATTACAATTTAAAA
Found at i:24147399 original size:37 final size:37
Alignment explanation
Indices: 24147327--24147399 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
24147317 TTGCTGATGC
*
24147327 ATAATGACTTGTGTTGTATAACTTGATTTGCCTATGT
1 ATAATGACTTGTGTTGTATAACTTGATTCGCCTATGT
*
24147364 ATAATGACTTGTGTTGTATAACTTGATTCGTCTATG
1 ATAATGACTTGTGTTGTATAACTTGATTCGCCTATG
24147400 CTTTTGGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.45
Consensus pattern (37 bp):
ATAATGACTTGTGTTGTATAACTTGATTCGCCTATGT
Found at i:24147944 original size:21 final size:21
Alignment explanation
Indices: 24147918--24147963 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
24147908 CGGGTGAGCT
24147918 CACGAGCATGT-GGAGTAGCCA
1 CACGAGCATGTGGGA-TAGCCA
**
24147939 CACGAGTGTGTGGGATAGCCA
1 CACGAGCATGTGGGATAGCCA
24147960 CACG
1 CACG
24147964 CGGTCTGGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.26, C:0.24, G:0.35, T:0.15
Consensus pattern (21 bp):
CACGAGCATGTGGGATAGCCA
Found at i:24150577 original size:16 final size:16
Alignment explanation
Indices: 24150552--24150582 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
24150542 AGATAAAACG
*
24150552 TAAAACTAAAATAAAA
1 TAAAAATAAAATAAAA
24150568 TAAAAATAAAATAAA
1 TAAAAATAAAATAAA
24150583 TAAGTTAAAC
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:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (16 bp):
TAAAAATAAAATAAAA
Found at i:24156834 original size:15 final size:16
Alignment explanation
Indices: 24156797--24156834 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
24156787 GGCATGAAAG
24156797 TAAAT-AACAAATAAA
1 TAAATAAACAAATAAA
24156812 TAAATAAACAAA-AAA
1 TAAATAAACAAATAAA
24156827 TAAATAAA
1 TAAATAAA
24156835 TTAAATGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.18
Consensus pattern (16 bp):
TAAATAAACAAATAAA
Found at i:24157639 original size:45 final size:45
Alignment explanation
Indices: 24157560--24157755 Score: 223
Period size: 45 Copynumber: 4.3 Consensus size: 45
24157550 GATTTAAGGA
* * * *
24157560 TAAATGATTGGATTTGGTGACTTCAATCTGCCCCTTTGGATTAGGGG
1 TAAAAGATTGGA--TGGTGGCTTCAATCTGCCCCTCTAGATTAGGGG
* * * *
24157607 TAAAAGATTAGATGGTGGCTTTAATCTACCCCTCTGGATTAGGGG
1 TAAAAGATTGGATGGTGGCTTCAATCTGCCCCTCTAGATTAGGGG
* *
24157652 TAAAAGATTGGATGGTGGGTTCAATCTGTCCCTCTAGATCT-GGGG
1 TAAAAGATTGGATGGTGGCTTCAATCTGCCCCTCTAGAT-TAGGGG
* * * *
24157697 TAAAAGACTGGATGGTGGCTTCAATCTGCCCTTTTAAATTAGGGG
1 TAAAAGATTGGATGGTGGCTTCAATCTGCCCCTCTAGATTAGGGG
*
24157742 TAAAAGACTGGATG
1 TAAAAGATTGGATG
24157756 TGGTGACTTT
Statistics
Matches: 129, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
44 1 0.01
45 117 0.91
46 1 0.01
47 10 0.08
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.32
Consensus pattern (45 bp):
TAAAAGATTGGATGGTGGCTTCAATCTGCCCCTCTAGATTAGGGG
Found at i:24157862 original size:48 final size:48
Alignment explanation
Indices: 24157809--24157973 Score: 172
Period size: 49 Copynumber: 3.4 Consensus size: 48
24157799 TCGTTTCGGA
* * *
24157809 TTCAATCTTTCCCTCTTCAGTTTTAAGGTGTTAGATCTGCCGTTAGGC
1 TTCAATCTATCCCTCTTCAGTTTTAAGGTGTTAGATCTACCGTTAGGT
* * * *
24157857 TTCAATCTATCCCTCTTCAGTTTTAATGTGTAAGATCCACCGTTGTGGT
1 TTCAATCTATCCCTCTTCAGTTTTAAGGTGTTAGATCTACCGTT-AGGT
* * * *
24157906 TTCAATCTTTCTCTCTTC-GATTTT-AGGATGTTAGGTCTATCGTTATGGT
1 TTCAATCTATCCCTCTTCAG-TTTTAAGG-TGTTAGATCTACCGTTA-GGT
*
24157955 TTCAACCTATCCCTCTTCA
1 TTCAATCTATCCCTCTTCA
24157974 ACTCTAGGAT
Statistics
Matches: 94, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
48 42 0.45
49 52 0.55
ACGTcount: A:0.18, C:0.23, G:0.16, T:0.43
Consensus pattern (48 bp):
TTCAATCTATCCCTCTTCAGTTTTAAGGTGTTAGATCTACCGTTAGGT
Found at i:24157930 original size:49 final size:48
Alignment explanation
Indices: 24157809--24157923 Score: 149
Period size: 48 Copynumber: 2.4 Consensus size: 48
24157799 TCGTTTCGGA
* **
24157809 TTCAATCTTTCCCTCTTCAGTTTTAAGGTGTTAGATCTGCCGTTAGGC
1 TTCAATCTTTCCCTCTTCAGTTTTAAGGTGTAAGATCCACCGTTAGGC
* * * *
24157857 TTCAATCTATCCCTCTTCAGTTTTAATGTGTAAGATCCACCGTTGTGGT
1 TTCAATCTTTCCCTCTTCAGTTTTAAGGTGTAAGATCCACCGTT-AGGC
*
24157906 TTCAATCTTTCTCTCTTC
1 TTCAATCTTTCCCTCTTC
24157924 GATTTTAGGA
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
48 39 0.68
49 18 0.32
ACGTcount: A:0.17, C:0.24, G:0.15, T:0.43
Consensus pattern (48 bp):
TTCAATCTTTCCCTCTTCAGTTTTAAGGTGTAAGATCCACCGTTAGGC
Found at i:24159056 original size:18 final size:18
Alignment explanation
Indices: 24159021--24159076 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
24159011 TCATCTCGGC
* * *
24159021 CCTTCTTTTTCTTTTTTT
1 CCTTTTTTTTCCTCTTTT
24159039 CCTTTTTTTTCCTCTTTT
1 CCTTTTTTTTCCTCTTTT
**
24159057 TTTTTTTTTTCTCTCTTTT
1 CCTTTTTTTTC-CTCTTTT
24159076 C
1 C
24159077 TGTTTCTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
18 24 0.77
19 7 0.23
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (18 bp):
CCTTTTTTTTCCTCTTTT
Found at i:24159075 original size:27 final size:27
Alignment explanation
Indices: 24159024--24159076 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
24159014 TCTCGGCCCT
* *
24159024 TCTTTTTCTTTTTTTCCTTTTTTTTCC
1 TCTTTTTCTTTTTTTCCTCTCTTTTCC
* *
24159051 TCTTTTTTTTTTTTTTCTCTCTTTTC
1 TCTTTTTCTTTTTTTCCTCTCTTTTC
24159077 TGTTTCTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (27 bp):
TCTTTTTCTTTTTTTCCTCTCTTTTCC
Found at i:24160251 original size:70 final size:67
Alignment explanation
Indices: 24160132--24160264 Score: 194
Period size: 70 Copynumber: 1.9 Consensus size: 67
24160122 ATAAACAATA
* * *
24160132 TAATGGTTTTGCCTTTTAACTTAATGGGTAAACATTTATCAAAATGACATAATTTTACCTTTTAA
1 TAATGGTTTTGACTTTTAACTTAAAGGGTAAACATTTATCAAAACGACATAATTTTACCTTTTAA
24160197 CT
66 CT
* *
24160199 TAATGGTTTTGACTTTTAACTTTAGAAAGGGTAAACATTTATCAAAACGACATAGTTTTGCCTTT
1 TAATGGTTTTGACTTTTAAC-TT--AAAGGGTAAACATTTATCAAAACGACATAATTTTACCTTT
24160264 T
63 T
24160265 CTTATTGGGA
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
67 19 0.33
68 2 0.03
70 37 0.64
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (67 bp):
TAATGGTTTTGACTTTTAACTTAAAGGGTAAACATTTATCAAAACGACATAATTTTACCTTTTAA
CT
Found at i:24163612 original size:3 final size:3
Alignment explanation
Indices: 24163604--24163649 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
24163594 GTGAGGATCT
* * *
24163604 TTA TTA TTA TTA TTA TTA TTA TTA TCA TTT TTA TGA TT- TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
24163650 AATTTAATGT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
2 4 0.11
3 32 0.89
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:24166347 original size:26 final size:26
Alignment explanation
Indices: 24166318--24166368 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
24166308 ATCACAAATA
24166318 CAACATACATAAAATAAAATGCAAAG
1 CAACATACATAAAATAAAATGCAAAG
*
24166344 CAACATATATAAAATAAAATGCAAA
1 CAACATACATAAAATAAAATGCAAA
24166369 AGATCACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.63, C:0.14, G:0.06, T:0.18
Consensus pattern (26 bp):
CAACATACATAAAATAAAATGCAAAG
Found at i:24167389 original size:16 final size:16
Alignment explanation
Indices: 24167365--24167405 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
24167355 AAAATATGGC
24167365 ATATAAATAAATAAAA
1 ATATAAATAAATAAAA
* *
24167381 ATATCAATAAATAAAT
1 ATATAAATAAATAAAA
24167397 ATATGAAAT
1 ATAT-AAAT
24167406 GCAATCATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 18 0.86
17 3 0.14
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (16 bp):
ATATAAATAAATAAAA
Found at i:24167615 original size:13 final size:13
Alignment explanation
Indices: 24167579--24167628 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 13
24167569 AAATGGCTTG
24167579 AAAATAAATAACA-
1 AAAATAAATAA-AT
24167592 ACAAGATAAATAAAT
1 A-AA-ATAAATAAAT
24167607 AAAATAAATAAAT
1 AAAATAAATAAAT
24167620 AAAAATAAA
1 -AAAATAAA
24167629 GATTAAATAC
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
13 11 0.33
14 13 0.39
15 9 0.27
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:24167643 original size:33 final size:33
Alignment explanation
Indices: 24167580--24167661 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 33
24167570 AATGGCTTGA
* *
24167580 AAATAAATAACAA-CAAGATAAATAAATAAAAT
1 AAATAAATAAAAATAAAGATAAATAAATAAAAT
*
24167612 AAATAAATAAAAATAAAGATTAAAT-ACTAAAAT
1 AAATAAATAAAAATAAAGA-TAAATAAATAAAAT
* * *
24167645 AAACAAACAAATATAAA
1 AAATAAATAAAAATAAA
24167662 CAATAAAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
32 12 0.29
33 25 0.60
34 5 0.12
ACGTcount: A:0.72, C:0.06, G:0.02, T:0.20
Consensus pattern (33 bp):
AAATAAATAAAAATAAAGATAAATAAATAAAAT
Found at i:24167710 original size:15 final size:16
Alignment explanation
Indices: 24167690--24167728 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
24167680 TTAGGCATGA
* *
24167690 AAATAAATGACAAAT-
1 AAATAAATAAAAAATG
24167705 AAATAAATAAAAAATG
1 AAATAAATAAAAAATG
24167721 AAATAAAT
1 AAATAAAT
24167729 TAAATGTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.21
Consensus pattern (16 bp):
AAATAAATAAAAAATG
Found at i:24171570 original size:28 final size:29
Alignment explanation
Indices: 24171510--24171570 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
24171500 GCAATGTCAA
24171510 CTTGTGTGAGCAAATTCATAAAATGTTAG
1 CTTGTGTGAGCAAATTCATAAAATGTTAG
24171539 CTTGTGTGAGCAAATTCAT-AAATGTTAG
1 CTTGTGTGAGCAAATTCATAAAATGTTAG
24171567 CTTG
1 CTTG
24171571 GTTACCAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 13 0.41
29 19 0.59
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.36
Consensus pattern (29 bp):
CTTGTGTGAGCAAATTCATAAAATGTTAG
Found at i:24171899 original size:16 final size:18
Alignment explanation
Indices: 24171862--24171901 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
24171852 GTAACCATAG
24171862 ACAATTATTCAATAACAT
1 ACAATTATTCAATAACAT
24171880 --AATTATTC-A-AACAT
1 ACAATTATTCAATAACAT
24171894 ACAATTAT
1 ACAATTAT
24171902 AAGTTAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
14 5 0.25
15 1 0.05
16 14 0.70
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (18 bp):
ACAATTATTCAATAACAT
Found at i:24175577 original size:18 final size:20
Alignment explanation
Indices: 24175541--24175581 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
24175531 TCTTTCAAAA
24175541 AAATGTTATTTTTAATATTT
1 AAATGTTATTTTTAATATTT
*
24175561 AAAT-TTATTTTT-CTATTT
1 AAATGTTATTTTTAATATTT
24175579 AAA
1 AAA
24175582 AATATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 8 0.40
20 4 0.20
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (20 bp):
AAATGTTATTTTTAATATTT
Found at i:24176038 original size:2 final size:2
Alignment explanation
Indices: 24176033--24176069 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
24176023 AAAAAAAAGA
24176033 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
24176070 CATAAAACAG
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:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:24183145 original size:24 final size:24
Alignment explanation
Indices: 24183113--24183174 Score: 97
Period size: 24 Copynumber: 2.5 Consensus size: 24
24183103 AACTAATAAT
*
24183113 AGTTTAATTGAAACAAATAAATAG
1 AGTTTAATTGAAACAAATAAACAG
*
24183137 AGTTTAATTGAAACAAATAAACAT
1 AGTTTAATTGAAACAAATAAACAG
24183161 AGTTTAACTTGAAA
1 AGTTTAA-TTGAAA
24183175 ATTATTTCTC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
24 29 0.83
25 6 0.17
ACGTcount: A:0.52, C:0.06, G:0.11, T:0.31
Consensus pattern (24 bp):
AGTTTAATTGAAACAAATAAACAG
Found at i:24189369 original size:5 final size:5
Alignment explanation
Indices: 24189359--24189383 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
24189349 TCAATTTTTT
24189359 AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA
24189384 TTATTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:24192441 original size:24 final size:24
Alignment explanation
Indices: 24192414--24192466 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
24192404 AGTTTGACTC
* **
24192414 AAATAAATAAACAGGGTTTAATTG
1 AAATAAACAAACAGAATTTAATTG
24192438 AAATAAACAAACAGAATTTAATTG
1 AAATAAACAAACAGAATTTAATTG
24192462 AAATA
1 AAATA
24192467 TTATTTCTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.57, C:0.06, G:0.11, T:0.26
Consensus pattern (24 bp):
AAATAAACAAACAGAATTTAATTG
Found at i:24194238 original size:24 final size:24
Alignment explanation
Indices: 24194209--24194281 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
24194199 TTTGACTCAG
*
24194209 ACAAATAAATAGAGTTTAATTGAA
1 ACAAATAAACAGAGTTTAATTGAA
*
24194233 AGAAATAAACAGAGTTTAATTGAA
1 ACAAATAAACAGAGTTTAATTGAA
* *
24194257 ACAATTAAACAGAGTTTAACTGAA
1 ACAAATAAACAGAGTTTAATTGAA
24194281 A
1 A
24194282 TATTATTTCT
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:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (24 bp):
ACAAATAAACAGAGTTTAATTGAA
Found at i:24198185 original size:15 final size:15
Alignment explanation
Indices: 24198165--24198194 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
24198155 TTTTGAACAG
*
24198165 GATTCAGTTTCTGAA
1 GATTCAGATTCTGAA
24198180 GATTCAGATTCTGAA
1 GATTCAGATTCTGAA
24198195 TATTGATCTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (15 bp):
GATTCAGATTCTGAA
Found at i:24201353 original size:18 final size:18
Alignment explanation
Indices: 24201330--24201367 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
24201320 CTTCATCAAA
24201330 GTCTTCATCCTTATCCAT
1 GTCTTCATCCTTATCCAT
24201348 GTCTTCATCCTTATCCAT
1 GTCTTCATCCTTATCCAT
24201366 GT
1 GT
24201368 AATCCTCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.32, G:0.08, T:0.45
Consensus pattern (18 bp):
GTCTTCATCCTTATCCAT
Found at i:24201376 original size:18 final size:18
Alignment explanation
Indices: 24201334--24201380 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
24201324 ATCAAAGTCT
**
24201334 TCATCCTTATCCATGTCT
1 TCATCCTTATCCATGTAA
24201352 TCATCCTTATCCATGTAA
1 TCATCCTTATCCATGTAA
*
24201370 TCCTCCTTATC
1 TCATCCTTATC
24201381 TAGATACTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.19, C:0.34, G:0.04, T:0.43
Consensus pattern (18 bp):
TCATCCTTATCCATGTAA
Found at i:24212486 original size:44 final size:44
Alignment explanation
Indices: 24212423--24212507 Score: 152
Period size: 44 Copynumber: 1.9 Consensus size: 44
24212413 TAATTTAGAG
*
24212423 CTTAGAAGGTCAAGTGTCCATGTGGCTTCATTCCAAGATGGGAA
1 CTTAGAAGGTCAAGTGTCCATATGGCTTCATTCCAAGATGGGAA
*
24212467 CTTAGAAGGTCAAGTGTCCATATGGCTTCCTTCCAAGATGG
1 CTTAGAAGGTCAAGTGTCCATATGGCTTCATTCCAAGATGG
24212508 TCAATTTATC
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:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (44 bp):
CTTAGAAGGTCAAGTGTCCATATGGCTTCATTCCAAGATGGGAA
Found at i:24215504 original size:28 final size:28
Alignment explanation
Indices: 24215464--24215517 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
24215454 TATTTTAAAA
*
24215464 CTTCAGCTCTTACTACTATCTTCAAGAG
1 CTTCAACTCTTACTACTATCTTCAAGAG
24215492 CTTCAACTCTTACTACTATCTTCAAG
1 CTTCAACTCTTACTACTATCTTCAAG
24215518 CTAAACTTTA
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:0.26, C:0.30, G:0.07, T:0.37
Consensus pattern (28 bp):
CTTCAACTCTTACTACTATCTTCAAGAG
Found at i:24217841 original size:39 final size:39
Alignment explanation
Indices: 24217758--24217877 Score: 152
Period size: 39 Copynumber: 3.1 Consensus size: 39
24217748 TCGATCTGGT
* * * *
24217758 ATTACGG-AGTTTACAGTGTCACCGTCAGTTTAATATTAC
1 ATTACGGTA-TTTACAGTGTTACCGTCAGTTCAGTATCAC
*
24217797 GTTACGGTATTTACAGTGTTACCGTCAGTTCAGTATCAC
1 ATTACGGTATTTACAGTGTTACCGTCAGTTCAGTATCAC
* * *
24217836 ATTACGATATTTTCAGTGTTACCGTCAGTTCAGTATCTC
1 ATTACGGTATTTACAGTGTTACCGTCAGTTCAGTATCAC
24217875 ATT
1 ATT
24217878 GTAGTGGTTA
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
39 70 0.99
40 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.38
Consensus pattern (39 bp):
ATTACGGTATTTACAGTGTTACCGTCAGTTCAGTATCAC
Found at i:24220165 original size:16 final size:18
Alignment explanation
Indices: 24220137--24220178 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
24220127 GATATTATTT
24220137 ATTAAATTAATTTT-TCA
1 ATTAAATTAATTTTCTCA
24220154 ATTAAA-TAATTTTCTCA
1 ATTAAATTAATTTTCTCA
*
24220171 ATTCAATT
1 ATTAAATT
24220179 CTAATTTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 7 0.32
17 14 0.64
18 1 0.05
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTAAATTAATTTTCTCA
Found at i:24221296 original size:25 final size:26
Alignment explanation
Indices: 24221267--24221323 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
24221257 TTTCATCCCA
24221267 ATTTTACT-CTAGTAAAATTTTGATG
1 ATTTTACTCCTAGTAAAATTTTGATG
*
24221292 CTTTTACTCCTAGTAAAATTTTGATG
1 ATTTTACTCCTAGTAAAATTTTGATG
24221318 ATTTTA
1 ATTTTA
24221324 GCCCCCTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 7 0.24
26 22 0.76
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.49
Consensus pattern (26 bp):
ATTTTACTCCTAGTAAAATTTTGATG
Found at i:24221334 original size:26 final size:25
Alignment explanation
Indices: 24221279--24221338 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 25
24221269 TTTACTCTAG
* *
24221279 TAAAATTTTGATGCTTTTACTCCTA
1 TAAAATTTTGATGATTTTACCCCTA
24221304 GTAAAATTTTGATGATTTTAGCCCCCT-
1 -TAAAATTTTGATGATTTTA--CCCCTA
24221331 TAAAATTT
1 TAAAATTT
24221339 CGAGAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 26 0.87
28 4 0.13
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (25 bp):
TAAAATTTTGATGATTTTACCCCTA
Found at i:24224935 original size:158 final size:158
Alignment explanation
Indices: 24224647--24224973 Score: 501
Period size: 158 Copynumber: 2.1 Consensus size: 158
24224637 TAACATCTCC
* *
24224647 ATAACATGTAATGCTCACAGGAGCTGTGAAATGAGCATGCTCACACGAGCTGCGGGTCGAGATGT
1 ATAACATGTAATGCTCACACGAGCTGTGAAATGAGCATACTCACACGAGCTGCGGGTCGAGATGT
*
24224712 TAGGCTACACGATGCTACTCACACGAGCTGTGGAGAATCCGCAATAAATGCAAGATCTCAACCAT
66 TAGGATACACGATGCTACTCACACGAGCTGTGGAGAATCCGCAATAAATGCAAGATCTCAACCAT
* *
24224777 CGGTAGGACATCTAAGACCAGCACCCAT
131 CGGTAAGACATCTAAGACCAACACCCAT
* * * * * *
24224805 ATAACTTGTAGTGCTCACACGAGCTGTGAAGTGGGCCTACTCACACGAGCTGTGGGTCGAGATGT
1 ATAACATGTAATGCTCACACGAGCTGTGAAATGAGCATACTCACACGAGCTGCGGGTCGAGATGT
* * * *
24224870 TGGGATACACGATGCTACTCACACGAGCTGTGGAGAATCCGCAATAAATGTAGGATCTTAACCAT
66 TAGGATACACGATGCTACTCACACGAGCTGTGGAGAATCCGCAATAAATGCAAGATCTCAACCAT
*
24224935 CGGTAAGACATCTAAGACCAACACTCAT
131 CGGTAAGACATCTAAGACCAACACCCAT
*
24224963 ATAACCTGTAA
1 ATAACATGTAA
24224974 ATCCCGAAAT
Statistics
Matches: 151, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
158 151 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (158 bp):
ATAACATGTAATGCTCACACGAGCTGTGAAATGAGCATACTCACACGAGCTGCGGGTCGAGATGT
TAGGATACACGATGCTACTCACACGAGCTGTGGAGAATCCGCAATAAATGCAAGATCTCAACCAT
CGGTAAGACATCTAAGACCAACACCCAT
Found at i:24228369 original size:34 final size:35
Alignment explanation
Indices: 24228331--24228396 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
24228321 CACTTAATAA
*
24228331 AATAAAA-TATATTTCCCTTTTTAATCCCCCACTT
1 AATAAAAGTATATTCCCCTTTTTAATCCCCCACTT
24228365 AATAAAAGTATATTCCCCTTTTTAATCCCCCA
1 AATAAAAGTATATTCCCCTTTTTAATCCCCCA
24228397 AAATGACTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 7 0.23
35 23 0.77
ACGTcount: A:0.33, C:0.27, G:0.02, T:0.38
Consensus pattern (35 bp):
AATAAAAGTATATTCCCCTTTTTAATCCCCCACTT
Found at i:24234008 original size:28 final size:27
Alignment explanation
Indices: 24233976--24234338 Score: 120
Period size: 29 Copynumber: 12.6 Consensus size: 27
24233966 AAAACTCTGA
* *
24233976 AAAGGTAAGCCTATGTGGTGAACTTGTT
1 AAAGG-AAGCCTTTGTGGTGATCTTGTT
* * *
24234004 AAAGGACAAGCCTTTATGGCGATTTCTGTT
1 AAAGG--AAGCCTTTGTGGTGATCT-TGTT
*
24234034 AAAGGAAGCCTTTGTGGTGATCTTTATT
1 AAAGGAAGCCTTTGTGGTGATC-TTGTT
* * *
24234062 AAAGAGAAGCCTTTGTGGTAAAACTCT-AT
1 AAAG-GAAGCCTTTGTGGT-GATCT-TGTT
* * * * *
24234091 AAACGTAAGCCTTTATGGTGAACCTCTT
1 AAA-GGAAGCCTTTGTGGTGATCTTGTT
* * * *
24234119 CAAGGATAATCCTTTATGGCGATCTATGTT
1 AAAGG--AAGCCTTTGTGGTGATCT-TGTT
* * **
24234149 AAAGGAACACCTTTGTAGCAATCTCTG-T
1 AAAGGAA-GCCTTTGTGGTGATCT-TGTT
* * *
24234177 AAATGAAGCCTTTGTGGCGACCTCTGTT
1 AAAGGAAGCCTTTGTGGTGATCT-TGTT
* ** * **
24234205 AAAGGAAGCCTTCGTGGCAAAACTCT-AA
1 AAAGGAAGCCTTTGTGG-TGATCT-TGTT
* * * *
24234233 AAAGGTAAGCCTTTGTGGCGAACCTCTT
1 AAAGG-AAGCCTTTGTGGTGATCTTGTT
* * * *
24234261 AATGGGCAAGCCTTTGCGGTAATTTCTGTT
1 AA-AGG-AAGCCTTTGTGGTGATCT-TGTT
*
24234291 AAAGGTAAGCCATTGGTGGTGATCTATGTT
1 AAAGG-AAGCC-TTTGTGGTGATCT-TGTT
24234321 AAAGGAACGCCTTTGTGG
1 AAAGGAA-GCCTTTGTGG
24234339 CGTGGTCTAA
Statistics
Matches: 249, Mismatches: 66, Indels: 39
0.70 0.19 0.11
Matches are distributed among these distances:
27 18 0.07
28 67 0.27
29 118 0.47
30 46 0.18
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (27 bp):
AAAGGAAGCCTTTGTGGTGATCTTGTT
Found at i:24234015 original size:58 final size:58
Alignment explanation
Indices: 24233953--24234138 Score: 164
Period size: 58 Copynumber: 3.2 Consensus size: 58
24233943 CAATAAAGAG
* *
24233953 AAGCCTTTATGGCAAAACTCTGAAAAGGTAAGCCTATGTGGTGAACTTGTTAAAGGAC
1 AAGCCTTTATGGCAAAACTCTGAAAAGGTAAGCCTTTGTGGTGAACTTATTAAAGGAC
* ** * * *
24234011 AAGCCTTTATGGC-GATTTCTGTTAAAGG-AAGCCTTTGTGGTGATCTTTATTAAA-GAG
1 AAGCCTTTATGGCAAAACTCTG-AAAAGGTAAGCCTTTGTGGTGAAC-TTATTAAAGGAC
* * * * * * * *
24234068 AAGCCTTTGTGGTAAAACTCT-ATAAACGTAAGCCTTTATGGTGAACCTCTTCAAGGAT
1 AAGCCTTTATGGCAAAACTCTGA-AAAGGTAAGCCTTTGTGGTGAACTTATTAAAGGAC
*
24234126 AATCCTTTATGGC
1 AAGCCTTTATGGC
24234139 GATCTATGTT
Statistics
Matches: 98, Mismatches: 24, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
57 42 0.43
58 56 0.57
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (58 bp):
AAGCCTTTATGGCAAAACTCTGAAAAGGTAAGCCTTTGTGGTGAACTTATTAAAGGAC
Found at i:24234149 original size:115 final size:116
Alignment explanation
Indices: 24233946--24234164 Score: 298
Period size: 115 Copynumber: 1.9 Consensus size: 116
24233936 TAAACACCAA
* * * *
24233946 TAAAGAGAAGCCTTTATGGCAAAACTCTGAAAAGGTAAGCCTATGTGGTGAACTTGTTAAAGGAC
1 TAAAGAGAAGCCTTTATGGCAAAACTCTGAAAACGTAAGCCTATATGGTGAACCTCTTAAAGGAC
* * *
24234011 AAGCCTTTATGGCGATTTCTGTTAAAGGAA-GCCTTTGTGGTGATCTTTAT
66 AAGCCTTTATGGCGATCTATGTTAAAGGAACACCTTTGTGGTGATCTTTAT
* * * *
24234061 TAAAGAGAAGCCTTTGTGGTAAAACTCT-ATAAACGTAAGCCTTTATGGTGAACCTCTTCAAGGA
1 TAAAGAGAAGCCTTTATGGCAAAACTCTGA-AAACGTAAGCCTATATGGTGAACCTCTTAAAGGA
* *
24234125 TAATCCTTTATGGCGATCTATGTTAAAGGAACACCTTTGT
65 CAAGCCTTTATGGCGATCTATGTTAAAGGAACACCTTTGT
24234165 AGCAATCTCT
Statistics
Matches: 89, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
114 1 0.01
115 81 0.91
116 7 0.08
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.32
Consensus pattern (116 bp):
TAAAGAGAAGCCTTTATGGCAAAACTCTGAAAACGTAAGCCTATATGGTGAACCTCTTAAAGGAC
AAGCCTTTATGGCGATCTATGTTAAAGGAACACCTTTGTGGTGATCTTTAT
Found at i:24234191 original size:27 final size:28
Alignment explanation
Indices: 24234145--24234216 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
24234135 TGGCGATCTA
* *
24234145 TGTTAAAGGAACACCTTTGTAGCAATCTC
1 TGTTAAAGGAA-GCCTTTGTAGCAACCTC
* * *
24234174 TG-TAAATGAAGCCTTTGTGGCGACCTC
1 TGTTAAAGGAAGCCTTTGTAGCAACCTC
24234201 TGTTAAAGGAAGCCTT
1 TGTTAAAGGAAGCCTT
24234217 CGTGGCAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
27 15 0.42
28 19 0.53
29 2 0.06
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (28 bp):
TGTTAAAGGAAGCCTTTGTAGCAACCTC
Found at i:24234295 original size:142 final size:144
Alignment explanation
Indices: 24234028--24234340 Score: 328
Period size: 142 Copynumber: 2.2 Consensus size: 144
24234018 TATGGCGATT
* * * * * *
24234028 TCTGTTAAAGGAAGCCTTTGTGGTGATCTTTATTAAAGAGAAGCCTTTGTGGTAAAACTCTATAA
1 TCTGTTAAAGGAAGCCTTTGTGGCGACCTCTATTAAAGAGAAGCCTTCGTGGCAAAACTCTAAAA
* * * * *
24234093 ACGTAAGCCTTTATGGTGAACCTCTTCAAGGATAATCCTTTATGGCGATCTATGTTAAAGGAACA
66 ACGTAAGCCTTTATGGCGAACCTCTTCAAGGACAAGCCTTTACGGCAATCTATGTTAAAGGAACA
24234158 CCTTTGTAGCAATC
131 CCTTTGTAGCAATC
* *
24234172 TCTG-TAAATGAAGCCTTTGTGGCGACCTCTGTTAAAG-GAAGCCTTCGTGGCAAAACTCTAAAA
1 TCTGTTAAAGGAAGCCTTTGTGGCGACCTCTATTAAAGAGAAGCCTTCGTGGCAAAACTCTAAAA
* * * * * * *
24234235 AGGTAAGCCTTTGTGGCGAACCTCTT-AATGGGCAAGCCTTTGCGGTAATTTCTGTTAAAGGTAA
66 ACGTAAGCCTTTATGGCGAACCTCTTCAA-GGACAAGCCTTTACGGCAATCTATGTTAAAGG-AA
* * * **
24234299 GC-CATTGGTGGTGATC
129 -CACCTTTGTAGCAATC
*
24234315 TATGTTAAAGGAACGCCTTTGTGGCG
1 TCTGTTAAAGGAA-GCCTTTGTGGCG
24234341 TGGTCTAAGG
Statistics
Matches: 137, Mismatches: 27, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
141 2 0.01
142 69 0.50
143 42 0.31
144 12 0.09
145 12 0.09
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (144 bp):
TCTGTTAAAGGAAGCCTTTGTGGCGACCTCTATTAAAGAGAAGCCTTCGTGGCAAAACTCTAAAA
ACGTAAGCCTTTATGGCGAACCTCTTCAAGGACAAGCCTTTACGGCAATCTATGTTAAAGGAACA
CCTTTGTAGCAATC
Found at i:24244896 original size:20 final size:20
Alignment explanation
Indices: 24244868--24244919 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
24244858 AGTCTTCAAG
24244868 GTATCGGTAGAACTGAAGTT
1 GTATCGGTAGAACTGAAGTT
* *
24244888 GTATTGGTAGAAGTGAAGTT
1 GTATCGGTAGAACTGAAGTT
* *
24244908 CTACCGGTAGAA
1 GTATCGGTAGAA
24244920 GTCTCATGCC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.29
Consensus pattern (20 bp):
GTATCGGTAGAACTGAAGTT
Found at i:24247043 original size:12 final size:12
Alignment explanation
Indices: 24247028--24247052 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24247018 GTTCAATTGT
24247028 AAATTTAGGATA
1 AAATTTAGGATA
24247040 AAATTTAGGATA
1 AAATTTAGGATA
24247052 A
1 A
24247053 CAACATGTAT
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:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (12 bp):
AAATTTAGGATA
Found at i:24255249 original size:30 final size:29
Alignment explanation
Indices: 24255158--24255297 Score: 99
Period size: 29 Copynumber: 4.8 Consensus size: 29
24255148 TATGGATACC
* *
24255158 CGGGGGCAAAGTGGTAATTTTGGTG-A-AAT
1 CGGGGGTAAAATGGTAATTTT--TGAAGAAT
* ** *
24255187 CGGGGTTAAAAATGG-AATTTTAAAAGATT
1 CGGGGGT-AAAATGGTAATTTTTGAAGAAT
*
24255216 CGGGGGTAAAATGGTAATTTTTGATGAAAT
1 CGGGGGTAAAATGGTAATTTTTGAAG-AAT
* * **
24255246 CGGGGTTAAAAATGG-AATTTTAGAAGCTT
1 CGGGGGT-AAAATGGTAATTTTTGAAGAAT
*
24255275 CGAGGGTAAAATGGTAATTTTTG
1 CGGGGGTAAAATGGTAATTTTTG
24255298 GAAGTTTTGG
Statistics
Matches: 85, Mismatches: 19, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
28 15 0.18
29 40 0.47
30 23 0.27
31 7 0.08
ACGTcount: A:0.34, C:0.05, G:0.30, T:0.31
Consensus pattern (29 bp):
CGGGGGTAAAATGGTAATTTTTGAAGAAT
Found at i:24255255 original size:59 final size:59
Alignment explanation
Indices: 24255158--24255297 Score: 219
Period size: 59 Copynumber: 2.4 Consensus size: 59
24255148 TATGGATACC
* * *
24255158 CGGGGGCAAAGTGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* *
24255216 CGGGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
*
24255275 CGAGGGTAAAATGGTAATTTTTG
1 CGGGGGTAAAATGGTAATTTTTG
24255298 GAAGTTTTGG
Statistics
Matches: 75, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
58 15 0.20
59 60 0.80
ACGTcount: A:0.34, C:0.05, G:0.30, T:0.31
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
Found at i:24255285 original size:29 final size:28
Alignment explanation
Indices: 24255186--24255324 Score: 104
Period size: 30 Copynumber: 4.8 Consensus size: 28
24255176 TTTGGTGAAA
*
24255186 TCGGGGTTAAAAATGG-AATTTTAAAAGAT
1 TCGGGG-T-AAAATGGTAATTTTAGAAGAT
* * *
24255215 TCGGGGGTAAAATGGTAATTTTTGATGAAA
1 TC-GGGGTAAAATGGTAATTTTAGAAG-AT
*
24255245 TCGGGGTTAAAAATGG-AATTTTAGAAGCT
1 TCGGGG-T-AAAATGGTAATTTTAGAAGAT
* *
24255274 TCGAGGGTAAAATGGTAATTTTTGGAAGTT
1 TCG-GGGTAAAATGGTAA-TTTTAGAAGAT
*
24255304 TTGGGGTCAAAAT-GTAATTTT
1 TCGGGGT-AAAATGGTAATTTT
24255325 GGAAAAGTTT
Statistics
Matches: 90, Mismatches: 11, Indels: 19
0.75 0.09 0.16
Matches are distributed among these distances:
28 18 0.20
29 29 0.32
30 36 0.40
31 7 0.08
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.35
Consensus pattern (28 bp):
TCGGGGTAAAATGGTAATTTTAGAAGAT
Found at i:24255333 original size:30 final size:30
Alignment explanation
Indices: 24255299--24255700 Score: 572
Period size: 30 Copynumber: 13.4 Consensus size: 30
24255289 TAATTTTTGG
*
24255299 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATATAATTTTGGAA
24255329 AAGTTTTGGGGTCAAAATATAATTTTGGAA
1 AAGTTTTGGGGTCAAAATATAATTTTGGAA
* *
24255359 AAGTTTCGGGGTCAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATATAATTTTGGAA
* *
24255389 AAGTTTTGAGGTTAAAATATAATTTTGGAA
1 AAGTTTTGGGGTCAAAATATAATTTTGGAA
** *
24255419 AAGTTTCAGGGTCAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATATAATTTTGGAA
* * *
24255449 AAGTTTTAGGGTTAAAATATAATTTTAGAA
1 AAGTTTTGGGGTCAAAATATAATTTTGGAA
* *
24255479 AAGTTTCGGGGTCAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATATAATTTTGGAA
* * *
24255509 AAGTTTTAGGGT-TAAATATAATTTTAGAA
1 AAGTTTTGGGGTCAAAATATAATTTTGGAA
* * *
24255538 AAGTATCGGGGTCAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATATAATTTTGGAA
24255568 AAGTTTTGGGGTCAAAATATAATTTTGGAA
1 AAGTTTTGGGGTCAAAATATAATTTTGGAA
*
24255598 AAGTTTTGGGGTCAACATATAATTTTGGAA
1 AAGTTTTGGGGTCAAAATATAATTTTGGAA
* *
24255628 AAGTTTTGGGGTTAAAATATAATTTTGAAA
1 AAGTTTTGGGGTCAAAATATAATTTTGGAA
* *
24255658 AAGTTTTGGGGTAAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATATAATTTTGGAA
*
24255688 AAGTTTTAGGGTC
1 AAGTTTTGGGGTC
24255701 GAAAGATGAT
Statistics
Matches: 327, Mismatches: 44, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
29 23 0.07
30 304 0.93
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (30 bp):
AAGTTTTGGGGTCAAAATATAATTTTGGAA
Found at i:24256945 original size:16 final size:16
Alignment explanation
Indices: 24256924--24256972 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
24256914 ATTACCCATA
24256924 TTTATTAATGTTATTT
1 TTTATTAATGTTATTT
*
24256940 TTTATTAAAAGTTA-TT
1 TTTATT-AATGTTATTT
* *
24256956 ATTATTAATATTATTT
1 TTTATTAATGTTATTT
24256972 T
1 T
24256973 ACATTAGCTC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
15 5 0.19
16 15 0.58
17 6 0.23
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (16 bp):
TTTATTAATGTTATTT
Found at i:24257503 original size:18 final size:15
Alignment explanation
Indices: 24257470--24257500 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
24257460 GTGGTGGTTG
24257470 GAGCTGGTGGTGGCA
1 GAGCTGGTGGTGGCA
24257485 GAGCTGGTGGTGGCA
1 GAGCTGGTGGTGGCA
24257500 G
1 G
24257501 CAGCATAGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.55, T:0.19
Consensus pattern (15 bp):
GAGCTGGTGGTGGCA
Found at i:24260870 original size:23 final size:23
Alignment explanation
Indices: 24260844--24260963 Score: 163
Period size: 23 Copynumber: 5.2 Consensus size: 23
24260834 ACACTAGCGC
24260844 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
24260867 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
24260890 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
24260915 GCTCTCCGATTAGCACT-TGTGT
1 GCTCTCTGATTAGCACTGTGTGT
*
24260937 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
24260960 GCTC
1 GCTC
24260964 AGTACTTTGT
Statistics
Matches: 86, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
22 24 0.28
23 43 0.50
25 16 0.19
26 3 0.03
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:24260913 original size:48 final size:45
Alignment explanation
Indices: 24260844--24260963 Score: 168
Period size: 48 Copynumber: 2.6 Consensus size: 45
24260834 ACACTAGCGC
* *
24260844 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCT-GT
* *
24260890 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCTGT
*
24260937 GCTCTCTGATTAGCACTTTGTGTGCTC
1 GCTCTCTGATTAGCACTGTGTGTGCTC
24260964 AGTACTTTGT
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
45 18 0.27
46 8 0.12
47 10 0.15
48 31 0.46
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (45 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCTGT
Found at i:24260997 original size:23 final size:23
Alignment explanation
Indices: 24260962--24261055 Score: 77
Period size: 23 Copynumber: 4.0 Consensus size: 23
24260952 CTTTGTGTGC
*
24260962 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* * *
24260985 TTAGCACTTTGTGTGCTCTCTAT
1 TCAGCACTTTGTGTACTCTCTGT
24261008 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
* *
24261033 TCAGTACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
24261055 T
1 T
24261056 TGTTCCGTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.28
23 20 0.35
25 8 0.14
26 7 0.12
27 4 0.07
ACGTcount: A:0.13, C:0.26, G:0.18, T:0.44
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:24263097 original size:30 final size:31
Alignment explanation
Indices: 24263051--24263215 Score: 165
Period size: 30 Copynumber: 5.6 Consensus size: 31
24263041 GGATACCCGA
*
24263051 GGGT-AAAATGGTAATTTTTGGTGAAATAGG
1 GGGTAAAAATGGTAATTTTTGGTGAAATCGG
* *
24263081 GGTTAAAAATGG-AA-TTTT-G-GAAGTTCGG
1 GGGTAAAAATGGTAATTTTTGGTGAA-ATCGG
24263109 GGGT-AAAATGGTAATTTTTGGTGAAATCGG
1 GGGTAAAAATGGTAATTTTTGGTGAAATCGG
*
24263139 GGCTAAAAATGG-AA-TTTT-G-GAAAGTTCGG
1 GGGTAAAAATGGTAATTTTTGGTGAAA--TCGG
*
24263168 GGGT-AAAATGGTAATTTTTGGTGAAATCGA
1 GGGTAAAAATGGTAATTTTTGGTGAAATCGG
*
24263198 GGTTAAAAATGG-AATTTT
1 GGGTAAAAATGGTAATTTT
24263216 GGAAGTTCGG
Statistics
Matches: 112, Mismatches: 9, Indels: 28
0.75 0.06 0.19
Matches are distributed among these distances:
27 14 0.12
28 17 0.15
29 21 0.19
30 31 0.28
31 25 0.22
32 4 0.04
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.33
Consensus pattern (31 bp):
GGGTAAAAATGGTAATTTTTGGTGAAATCGG
Found at i:24263193 original size:59 final size:58
Alignment explanation
Indices: 24263051--24263233 Score: 330
Period size: 58 Copynumber: 3.1 Consensus size: 58
24263041 GGATACCCGA
*
24263051 GGGTAAAATGGTAATTTTTGGTGAAATAGGGGTTAAAAATGGAATTTTGGAAGTTCGG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCGG
*
24263109 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGCTAAAAATGGAATTTTGGAAAGTTCGG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGG-AAGTTCGG
*
24263168 GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAGTTCGG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCGG
24263226 GGGTAAAA
1 GGGTAAAA
24263234 AGGAAATGGA
Statistics
Matches: 120, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
58 64 0.53
59 56 0.47
ACGTcount: A:0.33, C:0.03, G:0.32, T:0.31
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCGG
Found at i:24263234 original size:29 final size:28
Alignment explanation
Indices: 24263079--24263238 Score: 150
Period size: 28 Copynumber: 5.6 Consensus size: 28
24263069 TGGTGAAATA
*
24263079 GGGGTTAAAAATGGAATTTTGGAAGTTC
1 GGGGGTAAAAATGGAATTTTGGAAGTTC
*
24263107 GGGGGT-AAAATGGTAATTTTTGGTGAA-ATC
1 GGGGGTAAAAATGG-AA-TTTT-G-GAAGTTC
*
24263137 GGGGCTAAAAATGGAATTTTGGAAAGTTC
1 GGGGGTAAAAATGGAATTTTGG-AAGTTC
*
24263166 GGGGGT-AAAATGGTAATTTTTGGTGAA-ATC
1 GGGGGTAAAAATGG-AA-TTTT-G-GAAGTTC
* *
24263196 GAGGTTAAAAATGGAATTTTGGAAGTTC
1 GGGGGTAAAAATGGAATTTTGGAAGTTC
24263224 GGGGGTAAAAA-GGAA
1 GGGGGTAAAAATGGAA
24263239 ATGGAATTTT
Statistics
Matches: 108, Mismatches: 11, Indels: 27
0.74 0.08 0.18
Matches are distributed among these distances:
27 15 0.14
28 29 0.27
29 21 0.19
30 22 0.20
31 20 0.19
32 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.33, T:0.29
Consensus pattern (28 bp):
GGGGGTAAAAATGGAATTTTGGAAGTTC
Found at i:24263331 original size:28 final size:28
Alignment explanation
Indices: 24263295--24263464 Score: 107
Period size: 28 Copynumber: 5.9 Consensus size: 28
24263285 TTTTGGTGTT
*
24263295 GGGTTAAATGG-AATTTTGGAAAGTTTGG
1 GGGTAAAATGGTAATTTTGG-AAGTTTGG
24263323 GGGTAAAATGGTAATTTTTGGAAGTTTTGG
1 GGGTAAAATGGTAA-TTTTGGAAG-TTTGG
* * **
24263353 GGTTAAAAT-GAAATTTTAAAAGGTTTAGG
1 GGGTAAAATGGTAATTTTGGAA-GTTT-GG
* * *
24263382 GTAGTAAAATGGTAATTTTAGAAGTTTCGA
1 G-GGTAAAATGGTAATTTTGGAAGTTT-GG
* * ** *
24263412 GGTTAAAA--ATAGATTTTAAAAGGTTT-A
1 GGGTAAAATGGTA-ATTTTGGAA-GTTTGG
24263439 GGGTAAAATGGTAATTTTGGAAGTTT
1 GGGTAAAATGGTAATTTTGGAAGTTT
24263465 TGGGACCTAT
Statistics
Matches: 112, Mismatches: 19, Indels: 23
0.73 0.12 0.15
Matches are distributed among these distances:
27 14 0.12
28 34 0.30
29 23 0.21
30 31 0.28
31 10 0.09
ACGTcount: A:0.35, C:0.01, G:0.28, T:0.37
Consensus pattern (28 bp):
GGGTAAAATGGTAATTTTGGAAGTTTGG
Found at i:24263347 original size:29 final size:29
Alignment explanation
Indices: 24263295--24263468 Score: 103
Period size: 30 Copynumber: 6.0 Consensus size: 29
24263285 TTTTGGTGTT
*
24263295 GGGTTAAATGGAATTTTGGAAAG-TTTGG
1 GGGTAAAATGGAATTTTGGAAAGTTTTGG
24263323 GGGTAAAATGGTAATTTTTGG-AAGTTTTGG
1 GGGTAAAATGG-AA-TTTTGGAAAGTTTTGG
* * * *
24263353 GGTTAAAATGAAATTTT-AAAAGGTTTAGG
1 GGGTAAAATGGAATTTTGGAAA-GTTTTGG
* * * *
24263382 GTAGTAAAATGGTAATTTTAG-AAGTTTCGA
1 G-GGTAAAATGG-AATTTTGGAAAGTTTTGG
* * * * *
24263412 GGTTAAAAATAG-ATTTT-AAAAGGTTT-A
1 GGGT-AAAATGGAATTTTGGAAAGTTTTGG
24263439 GGGTAAAATGGTAATTTTGG-AAGTTTTGG
1 GGGTAAAATGG-AATTTTGGAAAGTTTTGG
24263468 G
1 G
24263469 ACCTATAAAT
Statistics
Matches: 110, Mismatches: 22, Indels: 27
0.69 0.14 0.17
Matches are distributed among these distances:
26 6 0.05
27 4 0.04
28 37 0.34
29 16 0.15
30 39 0.35
31 8 0.07
ACGTcount: A:0.34, C:0.01, G:0.29, T:0.37
Consensus pattern (29 bp):
GGGTAAAATGGAATTTTGGAAAGTTTTGG
Found at i:24263429 original size:59 final size:56
Alignment explanation
Indices: 24263323--24263464 Score: 196
Period size: 59 Copynumber: 2.5 Consensus size: 56
24263313 GAAAGTTTGG
* *
24263323 GGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTTAAAATGAAATTTTAAAAGGTTTA
1 GGGTAAAATGGTAA-TTTTGGAAGTTTCGAGGTTAAAATGAAATTTTAAAAGGTTTA
* *
24263380 GGGTAGTAAAATGGTAATTTTAGAAGTTTCGAGGTTAAAAAT-AGATTTTAAAAGGTTTA
1 -GG--GTAAAATGGTAATTTTGGAAGTTTCGAGGTT-AAAATGAAATTTTAAAAGGTTTA
24263439 GGGTAAAATGGTAATTTTGGAAGTTT
1 GGGTAAAATGGTAATTTTGGAAGTTT
24263465 TGGGACCTAT
Statistics
Matches: 76, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
56 23 0.30
58 4 0.05
59 32 0.42
60 17 0.22
ACGTcount: A:0.36, C:0.01, G:0.26, T:0.37
Consensus pattern (56 bp):
GGGTAAAATGGTAATTTTGGAAGTTTCGAGGTTAAAATGAAATTTTAAAAGGTTTA
Found at i:24263730 original size:161 final size:161
Alignment explanation
Indices: 24263525--24263866 Score: 483
Period size: 161 Copynumber: 2.1 Consensus size: 161
24263515 ACAGGCATCC
* * *
24263525 AACAGTCAAGGGATTAAATTGTAAACCTAAAAAATTTCTGGGCCAATTTTATAATTAAATAAGA-
1 AACAGTCAAAGGACTAAATTATAAACCTAAAAAATTTCTGGGCCAATTTTATAATTAAATAA-AT
* * *
24263589 GTTGATTTGGGGATTAAATTAAAATAAATTCAAAATATCAGGGACTAAATGAATAAATAAGCC-A
65 GTTGATTTAGGGATTAAATTAAAACAAATTAAAAATATCAGGGACTAAATGAATAAATAAGCCAA
* *
24263653 AAAGTGACACGTGGTAACCCCTGGTGTAGTCA
130 AAAGTGACACGTGGCAACCCCTGGTGCAGTCA
* *
24263685 AACAGTCAAAGGACTAATTTATAAACCTTAAAAAATTGT-TGGGCCAATTTTGTAATTAAATAAA
1 AACAGTCAAAGGACTAAATTATAAACC-TAAAAAATT-TCTGGGCCAATTTTATAATTAAATAAA
* * *
24263749 TGTTTATTTAGGGATTAAATTAAAACAAATTAAAAATGTTAGGGACTAAATGAATAAATAAGCCA
64 TGTTGATTTAGGGATTAAATTAAAACAAATTAAAAATATCAGGGACTAAATGAATAAATAAGCCA
* * *
24263814 AAAAGTGACATGTGGCAGCCTCTGGTGCAGTCA
129 AAAAGTGACACGTGGCAACCCCTGGTGCAGTCA
*
24263847 AACAGTCAAAGGATTAAATT
1 AACAGTCAAAGGACTAAATT
24263867 GAAAAACTAA
Statistics
Matches: 160, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
160 24 0.15
161 89 0.56
162 47 0.29
ACGTcount: A:0.43, C:0.11, G:0.18, T:0.28
Consensus pattern (161 bp):
AACAGTCAAAGGACTAAATTATAAACCTAAAAAATTTCTGGGCCAATTTTATAATTAAATAAATG
TTGATTTAGGGATTAAATTAAAACAAATTAAAAATATCAGGGACTAAATGAATAAATAAGCCAAA
AAGTGACACGTGGCAACCCCTGGTGCAGTCA
Found at i:24264398 original size:16 final size:16
Alignment explanation
Indices: 24264374--24264407 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
24264364 AAAGAAACCG
24264374 AACCCAGATCTGGAAA
1 AACCCAGATCTGGAAA
*
24264390 AACCTAGATCTGGAAA
1 AACCCAGATCTGGAAA
24264406 AA
1 AA
24264408 GATTCAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.21, G:0.18, T:0.15
Consensus pattern (16 bp):
AACCCAGATCTGGAAA
Found at i:24264685 original size:16 final size:16
Alignment explanation
Indices: 24264620--24264689 Score: 58
Period size: 16 Copynumber: 4.6 Consensus size: 16
24264610 ATGGTTTGAT
24264620 ATTATTAATTATTA--
1 ATTATTAATTATTATC
*
24264634 A-TATTAATTATAATC
1 ATTATTAATTATTATC
* * *
24264649 ATAAATATTTATT-TC
1 ATTATTAATTATTATC
*
24264664 AGTTATTAATTATTATG
1 A-TTATTAATTATTATC
24264681 ATTATTAAT
1 ATTATTAAT
24264690 AATATTTTTA
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
15 4 0.10
16 24 0.57
17 2 0.05
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (16 bp):
ATTATTAATTATTATC
Found at i:24264702 original size:15 final size:15
Alignment explanation
Indices: 24264682--24264711 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
24264672 ATTATTATGA
24264682 TTATTAATAATATTT
1 TTATTAATAATATTT
*
24264697 TTATTAATGATATTT
1 TTATTAATAATATTT
24264712 ATGAAATTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (15 bp):
TTATTAATAATATTT
Found at i:24265439 original size:5 final size:5
Alignment explanation
Indices: 24265431--24265490 Score: 57
Period size: 5 Copynumber: 11.0 Consensus size: 5
24265421 TTAAACTTAC
*
24265431 AAATT AAATTT AAATT AAATT CAAACTT AAATT AAATT AAAATTT AAAAT
1 AAATT AAA-TT AAATT AAATT -AAA-TT AAATT AAATT -AAA-TT AAATT
*
24265481 AAATT TAATT
1 AAATT AAATT
24265491 TCAAAGTAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
5 26 0.55
6 17 0.36
7 4 0.09
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:24265447 original size:11 final size:11
Alignment explanation
Indices: 24265431--24265488 Score: 73
Period size: 11 Copynumber: 5.2 Consensus size: 11
24265421 TTAAACTTAC
24265431 AAATTAAATTT
1 AAATTAAATTT
*
24265442 AAATTAAATTC
1 AAATTAAATTT
24265453 AAACTTAAA-TT
1 AAA-TTAAATTT
24265464 AAATTAAAATTT
1 AAATT-AAATTT
*
24265476 AAAATAAATTT
1 AAATTAAATTT
24265487 AA
1 AA
24265489 TTTCAAAGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
10 2 0.05
11 28 0.68
12 11 0.27
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (11 bp):
AAATTAAATTT
Found at i:24265462 original size:17 final size:16
Alignment explanation
Indices: 24265431--24265502 Score: 81
Period size: 17 Copynumber: 4.3 Consensus size: 16
24265421 TTAAACTTAC
24265431 AAATTAAATTTAAATT
1 AAATTAAATTTAAATT
*
24265447 AAATTCAAACTTAAATT
1 AAATT-AAATTTAAATT
*
24265464 AAATTAAAATTTAAAAT
1 AAATT-AAATTTAAATT
* *
24265481 AAATTTAATTTCAAAGT
1 AAATTAAATTT-AAATT
24265498 AAATT
1 AAATT
24265503 CTAAAATGGT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
16 10 0.21
17 38 0.79
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (16 bp):
AAATTAAATTTAAATT
Found at i:24265755 original size:18 final size:18
Alignment explanation
Indices: 24265713--24265782 Score: 74
Period size: 18 Copynumber: 3.9 Consensus size: 18
24265703 TAAAAAATAC
24265713 AAATATTTTGAATTTTTA
1 AAATATTTTGAATTTTTA
*
24265731 TAATATTTTGAA-TTTTA
1 AAATATTTTGAATTTTTA
*
24265748 AAAT-TATTTCAATTTTTGA
1 AAATAT-TTTGAATTTTT-A
*
24265767 AAGTATTTTG-ATTTTT
1 AAATATTTTGAATTTTT
24265783 TTTTGTAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
16 1 0.02
17 13 0.30
18 21 0.49
19 7 0.16
20 1 0.02
ACGTcount: A:0.34, C:0.01, G:0.07, T:0.57
Consensus pattern (18 bp):
AAATATTTTGAATTTTTA
Found at i:24272123 original size:9 final size:9
Alignment explanation
Indices: 24272109--24272144 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
24272099 AATTTAATTA
24272109 TTTTTAAAG
1 TTTTTAAAG
24272118 TTTTTAAAG
1 TTTTTAAAG
24272127 TTTTTAAAG
1 TTTTTAAAG
*
24272136 ATTTTAAAG
1 TTTTTAAAG
24272145 GACGGTACCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (9 bp):
TTTTTAAAG
Found at i:24273510 original size:31 final size:31
Alignment explanation
Indices: 24273474--24273538 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
24273464 ACCGCCGGAG
*
24273474 ACACCACCGCCTTTGTCGTTTGAACACCTGC
1 ACACCACCGCCTTTGCCGTTTGAACACCTGC
24273505 ACACCACCGCCTTTGCCGTTTGAACACCTGC
1 ACACCACCGCCTTTGCCGTTTGAACACCTGC
24273536 ACA
1 ACA
24273539 AATAATACCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.22, C:0.40, G:0.15, T:0.23
Consensus pattern (31 bp):
ACACCACCGCCTTTGCCGTTTGAACACCTGC
Found at i:24274180 original size:30 final size:29
Alignment explanation
Indices: 24274119--24274180 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
24274109 TTTTTTGCAT
*
24274119 ATTTTAATTATTTACAATTTTGCCCTGTA
1 ATTTTAATTATTTACAATTTAGCCCTGTA
* *
24274148 ATTTTAATTAATTCT-CAATTTAGTCCTTTA
1 ATTTTAATT-ATT-TACAATTTAGCCCTGTA
24274178 ATT
1 ATT
24274181 GTTTGACGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 9 0.32
30 18 0.64
31 1 0.04
ACGTcount: A:0.29, C:0.13, G:0.05, T:0.53
Consensus pattern (29 bp):
ATTTTAATTATTTACAATTTAGCCCTGTA
Found at i:24274450 original size:30 final size:30
Alignment explanation
Indices: 24274414--24274657 Score: 253
Period size: 30 Copynumber: 8.1 Consensus size: 30
24274404 TAAGTTGTCC
24274414 AAAAATTACATTTTGACCCTAAAACTTTCT
1 AAAAATTACATTTTGACCCTAAAACTTTCT
* * * *
24274444 AAAAATTGCATTTTAACCCTAAAATTTTCC
1 AAAAATTACATTTTGACCCTAAAACTTTCT
* * * *
24274474 CAAAATTATATTTTAACCCCAAAACTTTCT
1 AAAAATTACATTTTGACCCTAAAACTTTCT
*
24274504 AAAAATTATATTTTGACCCTAAAACTTTTCT
1 AAAAATTACATTTTGACCCTAAAAC-TTTCT
24274535 -AAAATTACATTTTGACCCTAAAACTTT-T
1 AAAAATTACATTTTGACCCTAAAACTTTCT
* *
24274563 CCAAAATTACATTTTGACTCTAAAACTTT-T
1 -AAAAATTACATTTTGACCCTAAAACTTTCT
* * * *
24274593 CCAAAATTATACTTTGACCCCAAAACTTTC-
1 -AAAAATTACATTTTGACCCTAAAACTTTCT
* **
24274623 AAAAATTACCATTTTTACCCCCAAACTTTCCT
1 AAAAATTA-CATTTTGACCCTAAAACTTT-CT
24274655 AAA
1 AAA
24274658 TCCCATTTTT
Statistics
Matches: 183, Mismatches: 24, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
28 1 0.01
29 10 0.05
30 163 0.89
31 6 0.03
32 3 0.02
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.36
Consensus pattern (30 bp):
AAAAATTACATTTTGACCCTAAAACTTTCT
Found at i:24274487 original size:60 final size:60
Alignment explanation
Indices: 24274415--24274651 Score: 291
Period size: 60 Copynumber: 4.0 Consensus size: 60
24274405 AAGTTGTCCA
* * *
24274415 AAAATTACATTTTGACCCTAAAACTTTCTAAAAATTGCATTTTAACCCTAAAA-TTTTCCC
1 AAAATTACATTTTGACCCCAAAACTTTCTAAAAATTACATTTTGACCCTAAAACTTTT-CC
* * * *
24274475 AAAATTATATTTTAACCCCAAAACTTTCTAAAAATTATATTTTGACCCTAAAACTTTTCT
1 AAAATTACATTTTGACCCCAAAACTTTCTAAAAATTACATTTTGACCCTAAAACTTTTCC
* * *
24274535 AAAATTACATTTTGACCCTAAAACTTT-TCCAAAATTACATTTTGACTCTAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTCT-AAAAATTACATTTTGACCCTAAAACTTTTCC
* * * **
24274595 AAAATTATACTTTGACCCCAAAACTTTC-AAAAATTACCATTTTTACCCCCAAACTTT
1 AAAATTACATTTTGACCCCAAAACTTTCTAAAAATTA-CATTTTGACCCTAAAACTTT
24274652 CCTAAATCCC
Statistics
Matches: 151, Mismatches: 22, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
59 8 0.05
60 139 0.92
61 4 0.03
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.37
Consensus pattern (60 bp):
AAAATTACATTTTGACCCCAAAACTTTCTAAAAATTACATTTTGACCCTAAAACTTTTCC
Found at i:24274567 original size:90 final size:90
Alignment explanation
Indices: 24274413--24274651 Score: 295
Period size: 90 Copynumber: 2.6 Consensus size: 90
24274403 CTAAGTTGTC
* *
24274413 CAAAAATTACATTTTGACCCTAAAACTTTCTAAAAATTGCATTTTAACCCTAAAA-TTTTCCCAA
1 CAAAAATTATATTTTGACCCTAAAACTTTCT-AAAATTACATTTTAACCCTAAAACTTTTCCCAA
*
24274477 AATTATATTTTAACCCCAAAAC-TTT
65 AATTACATTTTAACCCCAAAACTTTT
*
24274502 CTAAAAATTATATTTTGACCCTAAAACTTTTCTAAAATTACATTTTGACCCTAAAACTTTT-CCA
1 C-AAAAATTATATTTTGACCCTAAAAC-TTTCTAAAATTACATTTTAACCCTAAAACTTTTCCCA
* * *
24274566 AAATTACATTTTGACTCTAAAACTTTT
64 AAATTACATTTTAACCCCAAAACTTTT
* * * * * **
24274593 CCAAAATTATACTTTGACCCCAAAACTTTCAAAAATTACCATTTTTACCCCCAAACTTT
1 CAAAAATTATATTTTGACCCTAAAACTTTCTAAAATTA-CATTTTAACCCTAAAACTTT
24274652 CCTAAATCCC
Statistics
Matches: 131, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
89 12 0.09
90 106 0.81
91 13 0.10
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.37
Consensus pattern (90 bp):
CAAAAATTATATTTTGACCCTAAAACTTTCTAAAATTACATTTTAACCCTAAAACTTTTCCCAAA
ATTACATTTTAACCCCAAAACTTTT
Found at i:24286820 original size:76 final size:76
Alignment explanation
Indices: 24286689--24287114 Score: 631
Period size: 76 Copynumber: 5.6 Consensus size: 76
24286679 GAGCAACGTC
* * *
24286689 ATCCCCTTGAAATTGAAGTAGAG-TGAGACAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
1 ATCCTCTTGAAATTGAAGTAGAGTTG-GATAGCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
24286753 AGATCTTTTCCT
65 AGATCTTTTCCT
* *
24286765 ATCCGCTTGAAATTGAAGTAGAGTTGGATAGCAAGTATTTATCTCTGAAATTGAAGTAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAGAGTTGGATAGCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
24286830 GATCTTTTCCT
66 GATCTTTTCCT
* * *
24286841 ATCCTCTTGAAATTGAAGTAGAGTTGGA-CGACAAGTTTTTATCTCTGAAATTGAAGTAAGAACA
1 ATCCTCTTGAAATTGAAGTAGAGTTGGATAG-CAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
24286905 AGATCTTTTCCT
65 AGATCTTTTCCT
* *
24286917 ATCCGCTTGAAATTGAAGTAGAGTTGGATAGCACGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAGAGTTGGATAGCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
24286982 GATCTTTTCCT
66 GATCTTTTCCT
* * * ** * *
24286993 ATCCTTTTGAAATTGAAGTAAAGCTGGATATTACGTCTTTATCTCTGAAACTGAAGTAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAGAGTTGGATAGCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
* *
24287058 GATCTCTTCCC
66 GATCTTTTCCT
* *
24287069 ATCCTATTGAAATTGAAGTAAAGTTGGATAGCAAGTCTTTATCTCT
1 ATCCTCTTGAAATTGAAGTAGAGTTGGATAGCAAGTCTTTATCTCT
24287115 CTAAAGAAGC
Statistics
Matches: 320, Mismatches: 27, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
75 1 0.00
76 316 0.99
77 3 0.01
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.33
Consensus pattern (76 bp):
ATCCTCTTGAAATTGAAGTAGAGTTGGATAGCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
GATCTTTTCCT
Found at i:24286908 original size:152 final size:151
Alignment explanation
Indices: 24286544--24287114 Score: 780
Period size: 152 Copynumber: 3.8 Consensus size: 151
24286534 ATTATTTCTA
* * *
24286544 ATCCGCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGT-AGAAGCAA
1 ATCCTCTTGAAATTGAAGTAGAGTGGACAACAAGTCTTTATCTCTGAAATTGAAGTAAGAA-C-A
* * * * *
24286608 AGATCATTTCCAATCCACTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTG
64 AGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAGCAAGTCTTTATCTCTGAAATTG
* *
24286673 AAGAAAGAGC-A-A-C--GT-C-
129 AAGTAAGAGCAAGATCTTTTCCT
* *
24286689 ATCCCCTTGAAATTGAAGTAGAGTGAGACAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAGAGTG-GACAACAAGTCTTTATCTCTGAAATTGAAGTAAGAACAA
*
24286754 GATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAGCAAGTATTTATCTCTGAAATTGA
65 GATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAGCAAGTCTTTATCTCTGAAATTGA
24286819 AGTAAGAGCAAGATCTTTTCCT
130 AGTAAGAGCAAGATCTTTTCCT
* *
24286841 ATCCTCTTGAAATTGAAGTAGAGTTGGACGACAAGTTTTTATCTCTGAAATTGAAGTAAGAACAA
1 ATCCTCTTGAAATTGAAGTAGAG-TGGACAACAAGTCTTTATCTCTGAAATTGAAGTAAGAACAA
*
24286906 GATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAGCACGTCTTTATCTCTGAAATTGA
65 GATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAGCAAGTCTTTATCTCTGAAATTGA
24286971 AGTAAGAGCAAGATCTTTTCCT
130 AGTAAGAGCAAGATCTTTTCCT
* * * ** * * *
24286993 ATCCTTTTGAAATTGAAGTAAAGCTGGATATTACGTCTTTATCTCTGAAACTGAAGTAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAGAG-TGGACAACAAGTCTTTATCTCTGAAATTGAAGTAAGAACAA
* * ** *
24287058 GATCTCTTCCCATCCTATTGAAATTGAAGTAAAGTTGGATAGCAAGTCTTTATCTCT
65 GATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAGCAAGTCTTTATCTCT
24287115 CTAAAGAAGC
Statistics
Matches: 381, Mismatches: 35, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
145 93 0.24
146 31 0.08
147 4 0.01
148 1 0.00
150 1 0.00
151 1 0.00
152 248 0.65
153 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.32
Consensus pattern (151 bp):
ATCCTCTTGAAATTGAAGTAGAGTGGACAACAAGTCTTTATCTCTGAAATTGAAGTAAGAACAAG
ATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAGCAAGTCTTTATCTCTGAAATTGAA
GTAAGAGCAAGATCTTTTCCT
Found at i:24286994 original size:228 final size:219
Alignment explanation
Indices: 24286544--24287114 Score: 741
Period size: 228 Copynumber: 2.5 Consensus size: 219
24286534 ATTATTTCTA
*
24286544 ATCCGCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGT-AGAAGCAA
1 ATCCGCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAG-AGC-A
* * *
24286608 AGATCATTTCCAATCCACTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTG
64 AGATCTTTTCCAATCCTCTTGAAATTGAAGTAGAGTTGGA-AACAAGTCTTTATCTCTGAAATTG
*
24286673 AAGAAAGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGAGACAACAAGTCTTTATCTCTGAA
128 AAGAAAGAACAACGTCATCCCCTTGAAATTGAAGTAGAGTGAGACAACAAGTCTTTATCTCTGAA
24286738 ATTGAAGTAAGAGCAAGATCTTTTCCT
193 ATTGAAGTAAGAGCAAGATCTTTTCCT
* *
24286765 ATCCGCTTGAAATTGAAGTAGAGTTGGATAGCAAGTATTTATCTCTGAAATTGAAGTAAGAGCAA
1 ATCCGCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
* * *
24286830 GATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGACGACAAGTTTTTATCTCTGAAATTGA
65 GATCTTTTCCAATCCTCTTGAAATTGAAGTAGAGTTGGA-AACAAGTCTTTATCTCTGAAATTGA
* * * * * *
24286895 AGTAAGAACAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTG-GATAGCACGTCTTTAT
129 AGAAAGAAC-A-A-C--GT-C-ATCCCCTTGAAATTGAAGTAGAG-TGAGACAACAAGTCTTTAT
24286959 CTCTGAAATTGAAGTAAGAGCAAGATCTTTTCCT
186 CTCTGAAATTGAAGTAAGAGCAAGATCTTTTCCT
** * ** * *
24286993 ATCCTTTTGAAATTGAAGTAAAGCTGGATATTACGTCTTTATCTCTGAAACTGAAGTAAGAGCAA
1 ATCCGCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
* * * * *
24287058 GATCTCTTCCCATCCTATTGAAATTGAAGTAAAGTTGGATAGCAAGTCTTTATCTCT
65 GATCTTTTCCAATCCTCTTGAAATTGAAGTAGAGTTGGA-AACAAGTCTTTATCTCT
24287115 CTAAAGAAGC
Statistics
Matches: 306, Mismatches: 34, Indels: 13
0.87 0.10 0.04
Matches are distributed among these distances:
221 90 0.29
222 34 0.11
223 3 0.01
224 1 0.00
226 1 0.00
227 1 0.00
228 174 0.57
229 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.32
Consensus pattern (219 bp):
ATCCGCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAG
ATCTTTTCCAATCCTCTTGAAATTGAAGTAGAGTTGGAAACAAGTCTTTATCTCTGAAATTGAAG
AAAGAACAACGTCATCCCCTTGAAATTGAAGTAGAGTGAGACAACAAGTCTTTATCTCTGAAATT
GAAGTAAGAGCAAGATCTTTTCCT
Found at i:24287459 original size:12 final size:12
Alignment explanation
Indices: 24287415--24287463 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
24287405 AATTGATTTT
*
24287415 ATTTCAATTTAA
1 ATTTTAATTTAA
24287427 A-TTT-ATCTTAA
1 ATTTTAAT-TTAA
*
24287438 A-TTTACTTTAA
1 ATTTTAATTTAA
24287449 ATTTTAATTTAA
1 ATTTTAATTTAA
24287461 ATT
1 ATT
24287464 AAAATTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
10 2 0.06
11 15 0.48
12 14 0.45
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTTTAATTTAA
Found at i:24287465 original size:28 final size:27
Alignment explanation
Indices: 24287412--24287466 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
24287402 TTCAATTGAT
* **
24287412 TTTATTTCAATTTAAATTTATCTTAAA
1 TTTATTTAAATTTAAATTTAAATTAAA
*
24287439 TTTACTTTAAATTTTAATTTAAATTAAA
1 TTTA-TTTAAATTTAAATTTAAATTAAA
24287467 ATTAAAATAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (27 bp):
TTTATTTAAATTTAAATTTAAATTAAA
Found at i:24288341 original size:31 final size:31
Alignment explanation
Indices: 24288305--24288369 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
24288295 ACCGCCGGAG
*
24288305 ACACCACCGCTTTTGCCGTTTGAACACCTGC
1 ACACCACCGCCTTTGCCGTTTGAACACCTGC
24288336 ACACCACCGCCTTTGCCGTTTGAACACCTGC
1 ACACCACCGCCTTTGCCGTTTGAACACCTGC
24288367 ACA
1 ACA
24288370 AATAATACCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.22, C:0.40, G:0.15, T:0.23
Consensus pattern (31 bp):
ACACCACCGCCTTTGCCGTTTGAACACCTGC
Found at i:24289286 original size:30 final size:29
Alignment explanation
Indices: 24289247--24289405 Score: 194
Period size: 30 Copynumber: 5.4 Consensus size: 29
24289237 CTCTAAGTTG
24289247 TCCAGAAATTACATTTTGACCCCAAAACTT
1 TCCA-AAATTACATTTTGACCCCAAAACTT
* *
24289277 TCTGAAAATTACATTTTGACCCTAAAACTT
1 TC-CAAAATTACATTTTGACCCCAAAACTT
* *
24289307 TCCCAAAATTATATTTTGACCCCGAAACTT
1 T-CCAAAATTACATTTTGACCCCAAAACTT
* *
24289337 TCAAAAATTACATTTTGACTCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAAC-TT
* * *
24289367 TCCAAAATTATACTTTGACCCCGAAACTT
1 TCCAAAATTACATTTTGACCCCAAAACTT
24289396 T-CAAAATTAC
1 TCCAAAATTAC
24289406 CATATTTACC
Statistics
Matches: 110, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
28 8 0.07
29 25 0.23
30 75 0.68
31 2 0.02
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (29 bp):
TCCAAAATTACATTTTGACCCCAAAACTT
Found at i:24289373 original size:59 final size:58
Alignment explanation
Indices: 24289247--24289424 Score: 234
Period size: 59 Copynumber: 3.0 Consensus size: 58
24289237 CTCTAAGTTG
* *
24289247 TCCAGAAATTACATTTTGACCCCAAAACTTTCTGAAAATTACATTTTGACCCTAAAACTTT
1 TCCA-AAATTATATTTTGACCCCGAAACTTTC--AAAATTACATTTTGACCCTAAAACTTT
*
24289308 CCCAAAATTATATTTTGACCCCGAAACTTTCAAAAATTACATTTTGACTCC-AAAACTTT
1 TCCAAAATTATATTTTGACCCCGAAACTTTC-AAAATTACATTTTGAC-CCTAAAACTTT
* *
24289367 TCCAAAATTATACTTTGACCCCGAAACTTTCAAAATTACCATATTT-ACCCTCAAACTT
1 TCCAAAATTATATTTTGACCCCGAAACTTTCAAAATTA-CAT-TTTGACCCTAAAACTT
24289425 CCCTAAATCC
Statistics
Matches: 106, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
58 9 0.08
59 64 0.60
60 30 0.28
61 3 0.03
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.34
Consensus pattern (58 bp):
TCCAAAATTATATTTTGACCCCGAAACTTTCAAAATTACATTTTGACCCTAAAACTTT
Found at i:24289460 original size:59 final size:58
Alignment explanation
Indices: 24289397--24289592 Score: 168
Period size: 59 Copynumber: 3.3 Consensus size: 58
24289387 CCGAAACTTT
* *
24289397 CAAAA-TTACCATATTTACCCTCAAACTTCCCTAAATCCCATTTTTAACCCCGATTTCAC
1 CAAAACTTACCAT-TTTACCCTCAAACTTTCC-AAATTCCATTTTTAACCCCGATTTCAC
* * * * * ** **
24289456 CAAAACTTACCGTTTT-GCCTCCGAACTTTCCAAAATTTCATTTTTGA-CCTTATTTTTGC
1 CAAAACTTACCATTTTACCCT-CAAACTTTCC-AAATTCCATTTTTAACCCCGA-TTTCAC
* *
24289515 CAAAATTTACCATTTTATTCCC-CAAACTTTCCAAATTCCATTTTTAGCCCCGATTTCA-
1 CAAAACTTACCATTTTA--CCCTCAAACTTTCCAAATTCCATTTTTAACCCCGATTTCAC
*
24289573 CAAAAATTACCATTTTACCC
1 CAAAACTTACCATTTTACCC
24289593 CTAAAACCCA
Statistics
Matches: 106, Mismatches: 24, Indels: 17
0.72 0.16 0.12
Matches are distributed among these distances:
56 3 0.03
58 22 0.21
59 61 0.58
60 18 0.17
62 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.04, T:0.37
Consensus pattern (58 bp):
CAAAACTTACCATTTTACCCTCAAACTTTCCAAATTCCATTTTTAACCCCGATTTCAC
Found at i:24291327 original size:6 final size:6
Alignment explanation
Indices: 24291318--24291353 Score: 63
Period size: 6 Copynumber: 5.8 Consensus size: 6
24291308 TGAAATATAC
24291318 AAAATA AAAATA AAAATA AAAATA AAAATA AGAAAT
1 AAAATA AAAATA AAAATA AAAATA AAAATA A-AAAT
24291354 GTGTTTGGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 25 0.86
7 4 0.14
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:24292004 original size:18 final size:17
Alignment explanation
Indices: 24291962--24291998 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
24291952 TAAATGGACT
*
24291962 TTTAAATTAAAATTTAA
1 TTTAATTTAAAATTTAA
*
24291979 TTTAATTTAAAATTTTA
1 TTTAATTTAAAATTTAA
24291996 TTT
1 TTT
24291999 TTATTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAATTTAAAATTTAA
Found at i:24298071 original size:24 final size:24
Alignment explanation
Indices: 24298018--24298074 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
24298008 TCTTTAGCTC
* * * *
24298018 TATTTAATTGTTTCAATTAAATTC
1 TATTTATTTATTTCAATTAAACTA
*
24298042 TGTTTATTTATTTCAATTAAACTA
1 TATTTATTTATTTCAATTAAACTA
24298066 TATTTATTT
1 TATTTATTT
24298075 GTTTGAGTCA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.58
Consensus pattern (24 bp):
TATTTATTTATTTCAATTAAACTA
Found at i:24298964 original size:75 final size:75
Alignment explanation
Indices: 24298841--24298988 Score: 278
Period size: 75 Copynumber: 2.0 Consensus size: 75
24298831 GTGAGCTTCA
24298841 TAGAGATCACATCAGTCAATTCATTACTCTTTTGAATGATTTAAATAATGTTGAGGTTCATATTG
1 TAGAGATCACATCAGTCAATTCATTACTCTTTTGAATGATTTAAATAATGTTGAGGTTCATATTG
24298906 ATGATGAGCT
66 ATGATGAGCT
* *
24298916 TAGAGATTACATTAGTCAATTCATTACTCTTTTGAATGATTTAAATAATGTTGAGGTTCATATTG
1 TAGAGATCACATCAGTCAATTCATTACTCTTTTGAATGATTTAAATAATGTTGAGGTTCATATTG
24298981 ATGATGAG
66 ATGATGAG
24298989 GATCAAGCTA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (75 bp):
TAGAGATCACATCAGTCAATTCATTACTCTTTTGAATGATTTAAATAATGTTGAGGTTCATATTG
ATGATGAGCT
Found at i:24300173 original size:24 final size:24
Alignment explanation
Indices: 24300089--24300163 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
24300079 AGAAATAATC
* *
24300089 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTATTTG
24300113 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
*
24300137 TTTCAATTAAACTATGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
24300161 TTT
1 TTT
24300164 GAGTCAAACT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.25, C:0.11, G:0.09, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:24303877 original size:27 final size:27
Alignment explanation
Indices: 24303837--24303891 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
24303827 GTTGGAAGAA
*
24303837 AGATGTGTTTCTATCAGATAATCGAAT
1 AGATGTGTTCCTATCAGATAATCGAAT
24303864 AGATGTGTTCCTATCAGATAATCGAAT
1 AGATGTGTTCCTATCAGATAATCGAAT
24303891 A
1 A
24303892 TCTAATTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.35
Consensus pattern (27 bp):
AGATGTGTTCCTATCAGATAATCGAAT
Found at i:24319064 original size:22 final size:22
Alignment explanation
Indices: 24319039--24319097 Score: 57
Period size: 25 Copynumber: 2.6 Consensus size: 22
24319029 ATTTAATTAT
*
24319039 TTATATTTAATCATATAATAAA
1 TTATATTTAATAATATAATAAA
* *
24319061 TTATTAATATAATTAATATAATTAA
1 TTA-T-ATTTAA-TAATATAATAAA
24319086 TTAT-TTTAATAA
1 TTATATTTAATAA
24319098 ATTATTTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
21 3 0.10
22 7 0.23
23 1 0.03
24 6 0.20
25 13 0.43
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
TTATATTTAATAATATAATAAA
Found at i:24319137 original size:14 final size:15
Alignment explanation
Indices: 24319118--24319158 Score: 66
Period size: 14 Copynumber: 2.8 Consensus size: 15
24319108 ATTTCAATTT
24319118 TTTTAAATAATAA-A
1 TTTTAAATAATAATA
*
24319132 TTTTAAAAAATAATA
1 TTTTAAATAATAATA
24319147 TTTTAAATAATA
1 TTTTAAATAATA
24319159 TTCTTCACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TTTTAAATAATAATA
Found at i:24319211 original size:15 final size:15
Alignment explanation
Indices: 24319191--24319248 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
24319181 ATTCAATATT
24319191 AATATTTTAATAATA
1 AATATTTTAATAATA
*
24319206 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
* *
24319225 AATATATTCATAATA
1 AATATTTTAATAATA
24319240 AATATTTTA
1 AATATTTTA
24319249 TAGTATAAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:24320010 original size:7 final size:7
Alignment explanation
Indices: 24320000--24320128 Score: 141
Period size: 7 Copynumber: 18.4 Consensus size: 7
24319990 TGTTTTGGGG
24320000 TTTGAAT
1 TTTGAAT
*
24320007 TTTGGAT
1 TTTGAAT
**
24320014 TTCAAAT
1 TTTGAAT
24320021 TTTGAAT
1 TTTGAAT
*
24320028 TTCGAAT
1 TTTGAAT
24320035 TTTGAAT
1 TTTGAAT
24320042 TTTGAAT
1 TTTGAAT
24320049 TTTGAAT
1 TTTGAAT
*
24320056 TTCGAAT
1 TTTGAAT
**
24320063 TTCAAAT
1 TTTGAAT
**
24320070 TTTTTAT
1 TTTGAAT
24320077 TTTGAAT
1 TTTGAAT
24320084 TTTGAAT
1 TTTGAAT
24320091 TTTGAAT
1 TTTGAAT
*
24320098 TTCGAAT
1 TTTGAAT
**
24320105 TTTTTAT
1 TTTGAAT
*
24320112 TTTAAAT
1 TTTGAAT
24320119 TTTGAAT
1 TTTGAAT
24320126 TTT
1 TTT
24320129 TGATGTTTTA
Statistics
Matches: 100, Mismatches: 22, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 100 1.00
ACGTcount: A:0.28, C:0.04, G:0.11, T:0.57
Consensus pattern (7 bp):
TTTGAAT
Found at i:24320108 original size:35 final size:35
Alignment explanation
Indices: 24320018--24320128 Score: 177
Period size: 35 Copynumber: 3.2 Consensus size: 35
24320008 TTGGATTTCA
**
24320018 AATTTTGAATTTCGAATTTTGAATTTTGAATTTTG
1 AATTTTGAATTTCGAATTTTTTATTTTGAATTTTG
* *
24320053 AATTTCGAATTTCAAATTTTTTATTTTGAATTTTG
1 AATTTTGAATTTCGAATTTTTTATTTTGAATTTTG
*
24320088 AATTTTGAATTTCGAATTTTTTATTTTAAATTTTG
1 AATTTTGAATTTCGAATTTTTTATTTTGAATTTTG
24320123 AATTTT
1 AATTTT
24320129 TGATGTTTTA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 69 1.00
ACGTcount: A:0.29, C:0.04, G:0.10, T:0.58
Consensus pattern (35 bp):
AATTTTGAATTTCGAATTTTTTATTTTGAATTTTG
Found at i:24320137 original size:28 final size:28
Alignment explanation
Indices: 24320082--24320147 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
24320072 TTTATTTTGA
* *
24320082 ATTTTGAATTTTGAATTTCGAATTTTTT
1 ATTTTAAATTTTGAATTTCGAATGTTTT
*
24320110 ATTTTAAATTTTGAATTTTTG-ATGTTTT
1 ATTTTAAATTTTGAA-TTTCGAATGTTTT
24320138 ATATTTAAAT
1 AT-TTTAAAT
24320148 ATAATTAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 22 0.67
29 11 0.33
ACGTcount: A:0.29, C:0.02, G:0.09, T:0.61
Consensus pattern (28 bp):
ATTTTAAATTTTGAATTTCGAATGTTTT
Found at i:24323184 original size:18 final size:18
Alignment explanation
Indices: 24323157--24323217 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
24323147 GAAATAATTG
*
24323157 TATTATTTAATTTAAAAT
1 TATTAGTTAATTTAAAAT
*
24323175 TATTAGTT-A---AAATT
1 TATTAGTTAATTTAAAAT
*
24323189 GTATTATTTAATTTAAAAT
1 -TATTAGTTAATTTAAAAT
24323208 TATTAGTTAA
1 TATTAGTTAA
24323218 AACAAAAAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
14 4 0.12
15 7 0.21
16 1 0.03
17 1 0.03
18 16 0.48
19 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (18 bp):
TATTAGTTAATTTAAAAT
Found at i:24323194 original size:33 final size:33
Alignment explanation
Indices: 24323152--24323219 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
24323142 ATTTAGAAAT
24323152 AATTGTATTATTTAATTTAAAATTATTAGTTAA
1 AATTGTATTATTTAATTTAAAATTATTAGTTAA
24323185 AATTGTATTATTTAATTTAAAATTATTAGTTAA
1 AATTGTATTATTTAATTTAAAATTATTAGTTAA
24323218 AA
1 AA
24323220 CAAAAAAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (33 bp):
AATTGTATTATTTAATTTAAAATTATTAGTTAA
Found at i:24329192 original size:33 final size:33
Alignment explanation
Indices: 24329154--24329267 Score: 140
Period size: 41 Copynumber: 3.2 Consensus size: 33
24329144 AGAGAACGAC
*
24329154 AATTTTGATTTTGCATTAAGGAAGGGCATGACA
1 AATTTTGATTTTACATTAAGGAAGGGCATGACA
24329187 AATTTTGATTTTACATTAAGGAAGGGCAGAAGGGCATGACA
1 AATTTTGATTTTACATT----AA--G--GAAGGGCATGACA
24329228 AATTTTGATTTTACATTAAGGAAGGGCATGAC-
1 AATTTTGATTTTACATTAAGGAAGGGCATGACA
24329260 AATTTTGA
1 AATTTTGA
24329268 ATCAATCAGA
Statistics
Matches: 72, Mismatches: 1, Indels: 17
0.80 0.01 0.19
Matches are distributed among these distances:
32 8 0.11
33 28 0.39
35 1 0.01
37 4 0.06
39 1 0.01
41 30 0.42
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.32
Consensus pattern (33 bp):
AATTTTGATTTTACATTAAGGAAGGGCATGACA
Found at i:24329219 original size:41 final size:41
Alignment explanation
Indices: 24329174--24329255 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
24329164 TTGCATTAAG
24329174 GAAGGGCATGACAAATTTTGATTTTACATTAAGGAAGGGCA
1 GAAGGGCATGACAAATTTTGATTTTACATTAAGGAAGGGCA
24329215 GAAGGGCATGACAAATTTTGATTTTACATTAAGGAAGGGCA
1 GAAGGGCATGACAAATTTTGATTTTACATTAAGGAAGGGCA
24329256 TGACAATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.37, C:0.10, G:0.27, T:0.27
Consensus pattern (41 bp):
GAAGGGCATGACAAATTTTGATTTTACATTAAGGAAGGGCA
Found at i:24329959 original size:6 final size:6
Alignment explanation
Indices: 24329938--24330003 Score: 52
Period size: 6 Copynumber: 11.5 Consensus size: 6
24329928 AACAGTAGCC
* * *
24329938 ATCAAA ATC-CA ATCAAA ATCAAA AT---A ATCTTAA ATCAAAA ATAAAA
1 ATCAAA ATCAAA ATCAAA ATCAAA ATCAAA ATC-AAA ATC-AAA ATCAAA
24329984 AT-AAA ATCAAA ATCAAA ATC
1 ATCAAA ATCAAA ATCAAA ATC
24330004 GATTAGAACC
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
3 3 0.06
5 9 0.18
6 29 0.59
7 8 0.16
ACGTcount: A:0.64, C:0.15, G:0.00, T:0.21
Consensus pattern (6 bp):
ATCAAA
Found at i:24330413 original size:25 final size:27
Alignment explanation
Indices: 24330368--24330421 Score: 78
Period size: 25 Copynumber: 2.1 Consensus size: 27
24330358 TCACTTTTCA
24330368 ATAATTTTAATTTGAAGTGTCTAAATT
1 ATAATTTTAATTTGAAGTGTCTAAATT
24330395 ATAA-TTTAA-TTG-AGCTGTCTAAATT
1 ATAATTTTAATTTGAAG-TGTCTAAATT
24330420 AT
1 AT
24330422 TAGTTAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 2 0.08
25 15 0.58
26 5 0.19
27 4 0.15
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (27 bp):
ATAATTTTAATTTGAAGTGTCTAAATT
Found at i:24332148 original size:19 final size:19
Alignment explanation
Indices: 24332103--24332141 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
24332093 TGTCTTTAGT
24332103 TCTATTTTGATCACCCAAA
1 TCTATTTTGATCACCCAAA
24332122 TCTATTTTGATCACCCAAA
1 TCTATTTTGATCACCCAAA
24332141 T
1 T
24332142 TAATTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.38
Consensus pattern (19 bp):
TCTATTTTGATCACCCAAA
Found at i:24338119 original size:88 final size:88
Alignment explanation
Indices: 24337970--24338145 Score: 316
Period size: 88 Copynumber: 2.0 Consensus size: 88
24337960 CATAATGCAT
*
24337970 TAGCTAAAAATAATTGCACCAGCTATTTCAAAGATTGCAATAAAGCTGGTTAATTTCTCTAGACC
1 TAGCTAAAAATAATTGCACCAGCTATTTCAAAGATTGCAATAAAGCTGCTTAATTTCTCTAGACC
24338035 ATGATTACTTTCAACCATGCAAA
66 ATGATTACTTTCAACCATGCAAA
*
24338058 TAGCTAAAAATAATTGCACCAGCTATTTCAAAGATTGCAATAAAGCTTCTTAATTTCTCTAGACC
1 TAGCTAAAAATAATTGCACCAGCTATTTCAAAGATTGCAATAAAGCTGCTTAATTTCTCTAGACC
* *
24338123 ATGATTAGTTTCAAGCATGCAAA
66 ATGATTACTTTCAACCATGCAAA
24338146 CCCCATATAC
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 84 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (88 bp):
TAGCTAAAAATAATTGCACCAGCTATTTCAAAGATTGCAATAAAGCTGCTTAATTTCTCTAGACC
ATGATTACTTTCAACCATGCAAA
Found at i:24339505 original size:15 final size:15
Alignment explanation
Indices: 24339485--24339518 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
24339475 ATTGATTTTT
24339485 TTAATATTAAAATTG
1 TTAATATTAAAATTG
* *
24339500 TTAATATTCAAATTT
1 TTAATATTAAAATTG
24339515 TTAA
1 TTAA
24339519 ATTTTAAATT
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:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (15 bp):
TTAATATTAAAATTG
Found at i:24340157 original size:16 final size:15
Alignment explanation
Indices: 24340131--24340172 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
24340121 TGTAAGTTAT
24340131 TTAACATGAATCGAGC
1 TTAA-ATGAATCGAGC
24340147 TGTAAATGAATCGAGC
1 T-TAAATGAATCGAGC
*
24340163 TTAAACGAAT
1 TTAAATGAAT
24340173 AAATTTCTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 8 0.33
16 13 0.54
17 3 0.12
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.26
Consensus pattern (15 bp):
TTAAATGAATCGAGC
Found at i:24340328 original size:23 final size:25
Alignment explanation
Indices: 24340301--24340360 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 25
24340291 TCGTATGTTT
*
24340301 AATGTTCGTGAACAT-TAAACGAAC
1 AATGTTCATGAACATGTAAACGAAC
* *
24340325 -ATGTTTATGAACATGTTAACGAAC
1 AATGTTCATGAACATGTAAACGAAC
*
24340349 AATGTTAATGAA
1 AATGTTCATGAA
24340361 TAATAAACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 12 0.40
24 8 0.27
25 10 0.33
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.30
Consensus pattern (25 bp):
AATGTTCATGAACATGTAAACGAAC
Found at i:24340338 original size:12 final size:12
Alignment explanation
Indices: 24340321--24340360 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
24340311 AACATTAAAC
*
24340321 GAACATGTTTAT
1 GAACATGTTAAT
*
24340333 GAACATGTTAAC
1 GAACATGTTAAT
24340345 GAACAATGTTAAT
1 GAAC-ATGTTAAT
24340358 GAA
1 GAA
24340361 TAATAAACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.30
Consensus pattern (12 bp):
GAACATGTTAAT
Found at i:24340353 original size:25 final size:23
Alignment explanation
Indices: 24340309--24340360 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 23
24340299 TTAATGTTCG
*
24340309 TGAACATTAAACGAACATGTTTA
1 TGAACATTAAACGAACATGTTAA
*
24340332 TGAACATGTTAACGAACAATGTTAA
1 TGAACAT-TAAACGAAC-ATGTTAA
24340357 TGAA
1 TGAA
24340361 TAATAAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 7 0.28
24 8 0.32
25 10 0.40
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (23 bp):
TGAACATTAAACGAACATGTTAA
Found at i:24341107 original size:4 final size:4
Alignment explanation
Indices: 24341098--24341161 Score: 83
Period size: 4 Copynumber: 15.2 Consensus size: 4
24341088 TATTGTTGGC
* *
24341098 TATT TATT TATGCT TGTT TATT TATT TCATA TATT TATT TATT TATT TATT
1 TATT TATT TAT--T TATT TATT TATT T-ATT TATT TATT TATT TATT TATT
24341149 TATT TATT TATT T
1 TATT TATT TATT T
24341162 TCAAATAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
4 47 0.89
5 3 0.06
6 3 0.06
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.70
Consensus pattern (4 bp):
TATT
Found at i:24341976 original size:2 final size:2
Alignment explanation
Indices: 24341971--24342016 Score: 65
Period size: 2 Copynumber: 22.5 Consensus size: 2
24341961 GCTTATTGTT
* *
24341971 TA TA TA TA GTA TG TG 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
24342014 TA T
1 TA T
24342017 TATTCTGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (2 bp):
TA
Found at i:24342177 original size:2 final size:2
Alignment explanation
Indices: 24342172--24342211 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
24342162 ATTTTTTACT
*
24342172 TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA T
24342212 TCATCATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Done.