Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009267.1 Hibiscus syriacus cultivar Beakdansim tig00112925_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1725308
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 10
Found at i:1212495 original size:41 final size:40
Alignment explanation
Indices: 1212429--1212514 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 40
1212419 TTCTATTTCG
1212429 CGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCAAATT
* *
1212469 TGTTGCGATAGTCT-ACAATT-GTCGTTGTGATTTTCCAAATT
1 CGTTGCGATAGT-TGA-AATTCG-CGTTGCGATTTTCCAAATT
1212510 CGTTG
1 CGTTG
1212515 AAAAAAAAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
40 13 0.32
41 27 0.68
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.41
Consensus pattern (40 bp):
CGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCAAATT
Found at i:1212601 original size:6 final size:6
Alignment explanation
Indices: 1212590--1212671 Score: 143
Period size: 6 Copynumber: 14.2 Consensus size: 6
1212580 GACACGTATT
1212590 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1212638 ACCACG ACCACG ACCACG ---ACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1212672 GACGAGACGA
Statistics
Matches: 73, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.04
6 70 0.96
ACGTcount: A:0.34, C:0.49, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1213197 original size:6 final size:6
Alignment explanation
Indices: 1213176--1213272 Score: 180
Period size: 6 Copynumber: 16.5 Consensus size: 6
1213166 TCTCGTCTCG
1213176 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1213222 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1213270 GGT
1 GGT
1213273 AATACGTGTC
Statistics
Matches: 91, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 10 0.11
6 81 0.89
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:1213438 original size:41 final size:41
Alignment explanation
Indices: 1213393--1213692 Score: 555
Period size: 41 Copynumber: 7.3 Consensus size: 41
1213383 ACTGTAGACT
1213393 ATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAA
1213434 ATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAA
1213475 ATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAA
* *
1213516 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATAGAAA
1 ATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAA
* *
1213557 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAGTGGAAA
1 ATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAA
1213598 ATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAA
1213639 ATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAA
*
1213680 ATCGCAACACGAA
1 ATCGCAACGCGAA
1213693 ATGGAAAATC
Statistics
Matches: 252, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 252 1.00
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.17
Consensus pattern (41 bp):
ATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAA
Found at i:1213767 original size:61 final size:61
Alignment explanation
Indices: 1213393--1213736 Score: 350
Period size: 61 Copynumber: 5.6 Consensus size: 61
1213383 ACTGTAGACT
* * ** *
1213393 ATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGAATTTCAACT
1 ATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAAATCGCAACACGAAATGGAA-A
* ** * * ** * *
1213455 ATCGCAACGCGAAATGGAA-AATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAA-AATCGCAACACGAAATGGAAA
* * * ** ** *
1213516 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATAGAAAATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAAATCGCAACACGAAATGGAA-A
* ** * * ** * *
1213578 ATCGCAACGCGAAGTGGAA-AATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAA-AATCGCAACACGAAATGGAAA
1213639 ATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAAATCGCAACACGAAATGGAAA
1 ATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAAATCGCAACACGAAATGGAAA
*
1213700 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATG
1 ATCGCAACGCGAATTTCAACTATCGCAACGCGAAATG
1213737 CAACGCGAAT
Statistics
Matches: 227, Mismatches: 50, Indels: 11
0.79 0.17 0.04
Matches are distributed among these distances:
61 133 0.59
62 94 0.41
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.18
Consensus pattern (61 bp):
ATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAAATCGCAACACGAAATGGAAA
Found at i:1222765 original size:15 final size:15
Alignment explanation
Indices: 1222744--1222781 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1222734 TTGAGACATT
*
1222744 ACCCGCCCCGCATCC
1 ACCCGCCCCACATCC
*
1222759 GCCCGCCCCACATCC
1 ACCCGCCCCACATCC
1222774 ACCCGCCC
1 ACCCGCCC
1222782 AGCTAAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.13, C:0.68, G:0.13, T:0.05
Consensus pattern (15 bp):
ACCCGCCCCACATCC
Found at i:1224246 original size:3 final size:3
Alignment explanation
Indices: 1224233--1224281 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
1224223 GTTTTTATCG
*
1224233 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1224279 TTA
1 TTA
1224282 CATATTACAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 4 0.10
3 38 0.90
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1226334 original size:22 final size:22
Alignment explanation
Indices: 1226309--1226352 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1226299 TCAAACGATG
*
1226309 CAATGTGTGTTATTTTAAGTGA
1 CAATGTATGTTATTTTAAGTGA
* * *
1226331 CAATTTATTTTATTTTATGTGA
1 CAATGTATGTTATTTTAAGTGA
1226353 ATGTAAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (22 bp):
CAATGTATGTTATTTTAAGTGA
Found at i:1231070 original size:11 final size:11
Alignment explanation
Indices: 1231042--1231079 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
1231032 AAGAGCAAAG
1231042 AGAAAAATCAA
1 AGAAAAATCAA
1231053 AGCAAAAATCAA
1 AG-AAAAATCAA
*
1231065 AGAAAAAGCAA
1 AGAAAAATCAA
1231076 AGAA
1 AGAA
1231080 CAAAAGAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.71, C:0.11, G:0.13, T:0.05
Consensus pattern (11 bp):
AGAAAAATCAA
Found at i:1232714 original size:36 final size:35
Alignment explanation
Indices: 1232659--1232796 Score: 170
Period size: 36 Copynumber: 3.9 Consensus size: 35
1232649 TTTTGAGAAT
1232659 TTTAAAACAAATTTTTGTCTCGCTTGAGACAATTTC
1 TTTAAAACAAA-TTTTGTCTCGCTTGAGACAATTTC
* *
1232695 TTTCAAAGCAAATTTTGTCTCGCTTGAGACAGCTTTC
1 TTT-AAAACAAATTTTGTCTCGCTTGAGACA-ATTTC
* * *
1232732 -TAAAAACAAATTTTGTCTCGTTTGAGACAAATTC
1 TTTAAAACAAATTTTGTCTCGCTTGAGACAATTTC
* *
1232766 TCTTAAAACAAACTTCGTCTCGCTTGAGACA
1 T-TTAAAACAAATTTTGTCTCGCTTGAGACA
1232797 TTTTTCCTTT
Statistics
Matches: 87, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
34 3 0.03
35 25 0.29
36 48 0.55
37 11 0.13
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (35 bp):
TTTAAAACAAATTTTGTCTCGCTTGAGACAATTTC
Found at i:1232748 original size:71 final size:72
Alignment explanation
Indices: 1232662--1232796 Score: 202
Period size: 71 Copynumber: 1.9 Consensus size: 72
1232652 TGAGAATTTT
* * * *
1232662 AAAACAAATTTTTGTCTCGCTTGAGACAATTTCT-TTCAAAGCAAATTTTGTCTCGCTTGAGACA
1 AAAACAAATTTTTGTCTCGCTTGAGACAAATTCTCTT-AAAACAAACTTCGTCTCGCTTGAGACA
1232726 GCTTTCTA
65 GCTTTCTA
*
1232734 AAAACAAA-TTTTGTCTCGTTTGAGACAAATTCTCTTAAAACAAACTTCGTCTCGCTTGAGACA
1 AAAACAAATTTTTGTCTCGCTTGAGACAAATTCTCTTAAAACAAACTTCGTCTCGCTTGAGACA
1232797 TTTTTCCTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
71 47 0.82
72 10 0.18
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (72 bp):
AAAACAAATTTTTGTCTCGCTTGAGACAAATTCTCTTAAAACAAACTTCGTCTCGCTTGAGACAG
CTTTCTA
Found at i:1232893 original size:105 final size:101
Alignment explanation
Indices: 1232770--1233007 Score: 284
Period size: 105 Copynumber: 2.3 Consensus size: 101
1232760 AAATTCTCTT
* * *
1232770 AAAACAAACTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCAC-
1 AAAACAAACTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
*
1232834 TTAAAACAAAATTAATCTCACCTT-AGATTGTTGTTTCTTTC-
66 TT-AAACAAAATTAATCTCA-CTTGAGA---TCGTTTC--TCA
* * * * *
1232875 AAAACAAATTTTGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGGATTTGTTTCACA
1 AAAACAAACTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
* *
1232940 TTAAACAAAGTTGATCTCACTTGAGATCGTTTCTCA
66 TTAAACAAAATTAATCTCACTTGAGATCGTTTCTCA
*
1232976 AAAACAAACTTTGTCTCGCTTGAGACAATTTC
1 AAAACAAACTTTGTCTCGCTTGAGACATTTTC
1233008 TCTAAAAACA
Statistics
Matches: 116, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
100 2 0.02
101 29 0.25
102 6 0.05
104 3 0.03
105 74 0.64
106 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (101 bp):
AAAACAAACTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
TTAAACAAAATTAATCTCACTTGAGATCGTTTCTCA
Found at i:1233025 original size:36 final size:35
Alignment explanation
Indices: 1232954--1233073 Score: 127
Period size: 34 Copynumber: 3.4 Consensus size: 35
1232944 ACAAAGTTGA
* * *
1232954 TCTCACTTGAGATCGTTTCTC-AAAAACAAACTTTG
1 TCTCGCTTGAGA-CATTTCTCTAAAAACAAATTTTG
1232989 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCGCTTGAGAC-ATTTCTCTAAAAACAAATTTTG
** * * * *
1233025 TCTCATTTGAGAC-TATATCTAAAAGCAAATTTCG
1 TCTCGCTTGAGACATTTCTCTAAAAACAAATTTTG
1233059 TCTCGCTTGAGACAT
1 TCTCGCTTGAGACAT
1233074 CATTTTCTCT
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
34 29 0.41
35 18 0.25
36 24 0.34
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (35 bp):
TCTCGCTTGAGACATTTCTCTAAAAACAAATTTTG
Found at i:1233364 original size:29 final size:28
Alignment explanation
Indices: 1233326--1233574 Score: 184
Period size: 29 Copynumber: 8.6 Consensus size: 28
1233316 TTTCTCTTGG
1233326 AAAAAATCTTTGAGTTTGTTCCTTTTGA
1 AAAAAATCTTTGAGTTTGTTCCTTTTGA
*
1233354 ATAAAAATCTTGGAGTTTGTTCCTTTTGA
1 A-AAAAATCTTTGAGTTTGTTCCTTTTGA
* *
1233383 ATAAATATCTTTGAG-TTGTTTCTTTTG-
1 A-AAAAATCTTTGAGTTTGTTCCTTTTGA
* * **
1233410 AAAAAATCTTTGAGTCTATTTATTTTGA
1 AAAAAATCTTTGAGTTTGTTCCTTTTGA
* *** * *
1233438 AACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGA
1 AA-AAA-------ATCT-TTGAGTTTGTTCCTTTTGA
*
1233475 AAAAAATCTTTGAGTTTGTTCCTCTTGA
1 AAAAAATCTTTGAGTTTGTTCCTTTTGA
* *
1233503 ATAAAAATCTTGGAGTTTGTTCCTTTTTA
1 A-AAAAATCTTTGAGTTTGTTCCTTTTGA
* *
1233532 ATAAATATCTTTGAG-TTGTTTCTTTTG-
1 A-AAAAATCTTTGAGTTTGTTCCTTTTGA
1233559 -AAAAATCTTTGAGTTT
1 AAAAAATCTTTGAGTTT
1233575 ATTTATTTTG
Statistics
Matches: 180, Mismatches: 27, Indels: 30
0.76 0.11 0.13
Matches are distributed among these distances:
25 12 0.07
26 14 0.08
27 10 0.06
28 40 0.22
29 82 0.46
36 6 0.03
37 16 0.09
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (28 bp):
AAAAAATCTTTGAGTTTGTTCCTTTTGA
Found at i:1233460 original size:149 final size:148
Alignment explanation
Indices: 1233296--1233616 Score: 588
Period size: 149 Copynumber: 2.2 Consensus size: 148
1233286 ACGATTTTTT
* *
1233296 TTTTGTCTCTCTTGAGACAGTTTCTCTTGGAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTCCTCTTGAATAAAAA
1233361 TCTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAAATCTTTGAGTC
66 TCTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTG-AAAAATCTTTGAGTC
1233426 TATTTATTTTGAAACAAAG
130 TATTTATTTTGAAACAAAG
1233445 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTCCTCTTGAATAAAAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTCCTCTTGAATAAAAA
* *
1233510 TCTTGGAGTTTGTTCCTTTTTAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATCTTTGAGTTT
66 TCTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATCTTTGAGTCT
1233575 ATTTATTTTGAAACAAAG
131 ATTTATTTTGAAACAAAG
*
1233593 TTTTGTCTCTCTTGAGACAATTTC
1 TTTTGTCTCTCTTGAGACAGTTTC
1233617 GTGAAAAATC
Statistics
Matches: 167, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
148 56 0.34
149 111 0.66
ACGTcount: A:0.26, C:0.12, G:0.15, T:0.47
Consensus pattern (148 bp):
TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTCCTCTTGAATAAAAA
TCTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATCTTTGAGTCT
ATTTATTTTGAAACAAAG
Found at i:1233661 original size:52 final size:53
Alignment explanation
Indices: 1233583--1233686 Score: 176
Period size: 52 Copynumber: 2.0 Consensus size: 53
1233573 TTATTTATTT
1233583 TGAAACAAAGTTTTGTCTCTCTTGAGACAAT-TTCGTG-AAAAATCTTTGAGTC
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATGTT-GTGAAAAAATCTTTGAGTC
1233635 TGAAACAAAGTTTTGTCTCTCTTGAGACAATGTTGTGAAAAAAATCTTTGAG
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATGTTGTG-AAAAAATCTTTGAG
1233687 ATTGTTTCTT
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
52 34 0.69
53 2 0.04
54 13 0.27
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (53 bp):
TGAAACAAAGTTTTGTCTCTCTTGAGACAATGTTGTGAAAAAATCTTTGAGTC
Found at i:1233726 original size:27 final size:28
Alignment explanation
Indices: 1233670--1233740 Score: 108
Period size: 28 Copynumber: 2.5 Consensus size: 28
1233660 GACAATGTTG
1233670 TGAAAAAAATCTTTGAGATTGTTTCTTT
1 TGAAAAAAATCTTTGAGATTGTTTCTTT
*
1233698 TGAAAAAAATCTTTGAGTTTGTTTCTTT
1 TGAAAAAAATCTTTGAGATTGTTTCTTT
*
1233726 GGAAACAAAAT-TTTG
1 TGAAA-AAAATCTTTG
1233741 TCTCTCTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 35 0.88
29 5 0.12
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (28 bp):
TGAAAAAAATCTTTGAGATTGTTTCTTT
Found at i:1233824 original size:64 final size:64
Alignment explanation
Indices: 1233690--1233849 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 64
1233680 CTTTGAGATT
* * * *
1233690 GTTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTTGAAAAAAATCTTTGAATATGTTTCTTT-GAAACAAAATTTTGTATCTCTTAAGACA
* * * *
1233755 ATTTCTTTTGAAAAAAATCTTTGAATCTGTTTCTCTT-AAA-ATGAATTTTGTATCTCTTGAGAC
1 GTTTCTTTTGAAAAAAATCTTTGAATATGTTTCT-TTGAAACA-AAATTTTGTATCTCTTAAGAC
1233818 A
64 A
* **
1233819 GTTTCTCTTGAAGTAAATCTTTGAATATGTT
1 GTTTCTTTTGAAAAAAATCTTTGAATATGTT
1233850 CATTTTGGAA
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
63 1 0.01
64 47 0.58
65 31 0.38
66 2 0.02
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.46
Consensus pattern (64 bp):
GTTTCTTTTGAAAAAAATCTTTGAATATGTTTCTTTGAAACAAAATTTTGTATCTCTTAAGACA
Found at i:1234057 original size:120 final size:118
Alignment explanation
Indices: 1233889--1234110 Score: 272
Period size: 120 Copynumber: 1.9 Consensus size: 118
1233879 TTAACAAAAT
* * *
1233889 CATCTTTGAGTCTATTTCTTTAAAAACAAATGTTGTCTCTCTTGAGACAGTTTCTAATTAAAAAC
1 CATCTTTGAGTCTATTTCTTTAAAAACAAATGTTGTATCTCTTAAGACAATTTCT-ATTAAAAA-
1233954 TAA-CTTTTGAGATTGTTTCATTTGAAAC-AAATTTGGTCTTACTTAAGATGTAATC
64 -AATC-TTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTTACTTAAGATGTAATC
** * *
1234009 CATCTTTGAGTCTATTTCTTTTGAAACAAAAT-TT-TATCTCTTAAAGACAATTTCTTTTGAAAA
1 CATCTTTGAGTCTATTTCTTTAAAAAC-AAATGTTGTATCTCTT-AAGACAATTTCTATTAAAAA
* * *
1234072 AATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCT
64 AATCTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCT
1234111 CTCGAGATAA
Statistics
Matches: 88, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
117 23 0.26
118 11 0.12
119 13 0.15
120 37 0.42
121 4 0.05
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (118 bp):
CATCTTTGAGTCTATTTCTTTAAAAACAAATGTTGTATCTCTTAAGACAATTTCTATTAAAAAAA
TCTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTTACTTAAGATGTAATC
Found at i:1234313 original size:15 final size:15
Alignment explanation
Indices: 1234290--1234333 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
1234280 TTTTGAGTCG
*
1234290 TTTCACTTGAAACAT
1 TTTCTCTTGAAACAT
*
1234305 TTTCTCTTGTAACAT
1 TTTCTCTTGAAACAT
*
1234320 TTTCTCTTAAAACA
1 TTTCTCTTGAAACA
1234334 AGATCATCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (15 bp):
TTTCTCTTGAAACAT
Found at i:1234802 original size:43 final size:44
Alignment explanation
Indices: 1234744--1235214 Score: 283
Period size: 46 Copynumber: 10.7 Consensus size: 44
1234734 TCATCCCCAG
* * *
1234744 ACCAGATCTCTTCATCACGTATGAGCCGTGTCA-ACCATAGATA
1 ACCAGACCTCTTCATCACGTAGGAGCCGTGTCATACCTTAGATA
* * * *
1234787 ACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATG
1 ACCAGACC-TCTTCATCACGTAGGAGCCGTGTCAT-ACC-TTAGATA
* * * * **
1234833 GCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCC-CCG---
1 ACCAGACCTCTTCATCACGTAGGAGCCGTGTCATACCTTAGATA
* *
1234873 ACCAGATCTCTTCATCACGTAGGAGCCGTGTCA-CCCTTAGATA
1 ACCAGACCTCTTCATCACGTAGGAGCCGTGTCATACCTTAGATA
* * * *
1234916 ACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATG
1 ACCAGACC-TCTTCATCACGTAGGAGCCGTGTCAT-ACC-TTAGATA
* * * * **
1234962 GCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCC-CCG---
1 ACCAGACCTCTTCATCACGTAGGAGCCGTGTCATACCTTAGATA
* *
1235002 ACCAGATCTCTTCATCACGTAGGAGCCGTGTCA-CCCTTAGATA
1 ACCAGACCTCTTCATCACGTAGGAGCCGTGTCATACCTTAGATA
* * * *
1235045 ACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATG
1 ACCAGACC-TCTTCATCACGTAGGAGCCGTGTCAT-ACC-TTAGATA
* * * * **
1235091 GCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCAG---
1 ACCAGACCTCTTCATCACGTAGGAGCCGTGTCATACCTTAGATA
* * * *
1235132 ACCAGAACTCTTCATCACGTAGGAACCGAGTTATCATCCACCCTTAGATTC
1 ACCAGACCTCTTCATCACGTAGGAGCC--G-TGTCAT--A-CCTTAGA-TA
* * *
1235183 CCCAGACCTCTTCATCACGTATGAGCAGTGTC
1 ACCAGACCTCTTCATCACGTAGGAGCCGTGTC
1235215 GTCCCCACCA
Statistics
Matches: 324, Mismatches: 71, Indels: 61
0.71 0.16 0.13
Matches are distributed among these distances:
39 4 0.01
40 62 0.19
41 24 0.07
42 3 0.01
43 83 0.26
44 7 0.02
45 13 0.04
46 95 0.29
47 7 0.02
48 3 0.01
49 1 0.00
51 22 0.07
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.25
Consensus pattern (44 bp):
ACCAGACCTCTTCATCACGTAGGAGCCGTGTCATACCTTAGATA
Found at i:1234857 original size:89 final size:90
Alignment explanation
Indices: 1234745--1235214 Score: 345
Period size: 89 Copynumber: 5.3 Consensus size: 90
1234735 CATCCCCAGA
* *
1234745 CCAGATCTCTTCATCACGTATGAGCCGTGTCA-ACCATAGATAACCAG-CCGTCCTCATCACGTA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCATACCTTAGATAACCAGACC-TCCTCATCACGTA
1234808 GGAACCGTGTTATCACCTTTAGATGG
65 GGAACCGTGTTATCACCTTTAGATGG
* ** * *
1234834 CCAGAACTCTTCATCACGTATGAGCCGTGTCATTCC-CCG---ACCAGATCTCTTCATCACGTAG
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCATACCTTAGATAACCAGACCTCCTCATCACGTAG
* * **
1234895 GAGCCGTG---TCACCCTTAGATAA
66 GAACCGTGTTATCACCTTTAGATGG
* * * * * ** * *
1234917 CCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACG
1 CCAGAAC-TCTTCATCACGTATGAGCCGTGTCAT-ACC-TTAGATAACCAGACCTCCTCATCACG
* * * *
1234981 TATGAGCCGTGTCATTC-CC---CGA---
63 TAGGAACCGTGTTA-TCACCTTTAGATGG
* * *
1235003 CCAGATCTCTTCATCACGTAGGAGCCGTGTCA-CCCTTAGATAACCAG-CCGTCCTCATCACGTA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCATACCTTAGATAACCAGACC-TCCTCATCACGTA
1235066 GGAACCGTGTTATCACCTTTAGATGG
65 GGAACCGTGTTATCACCTTTAGATGG
* ** * *
1235092 CCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCAG---ACCAGAACTCTTCATCACGTAG
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCATACCTTAGATAACCAGACCTCCTCATCACGTAG
* * **
1235154 GAACCGAGTTATCATCCACCCTTAGATTCC
66 GAACCGTG-T-T-AT-CACCTTTAGA-TGG
* *
1235184 CCAGACCTCTTCATCACGTATGAGCAGTGTC
1 CCAGAACTCTTCATCACGTATGAGCCGTGTC
1235215 GTCCCCACCA
Statistics
Matches: 304, Mismatches: 48, Indels: 55
0.75 0.12 0.14
Matches are distributed among these distances:
82 4 0.01
83 70 0.23
84 4 0.01
86 54 0.18
87 27 0.09
88 2 0.01
89 92 0.30
90 8 0.03
91 9 0.03
92 32 0.11
93 2 0.01
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.26
Consensus pattern (90 bp):
CCAGAACTCTTCATCACGTATGAGCCGTGTCATACCTTAGATAACCAGACCTCCTCATCACGTAG
GAACCGTGTTATCACCTTTAGATGG
Found at i:1234929 original size:129 final size:130
Alignment explanation
Indices: 1234699--1235155 Score: 803
Period size: 129 Copynumber: 3.5 Consensus size: 130
1234689 TTATCCCTAG
* * * * * *
1234699 AGATGGCCAGTAGTCCTCATCATGTAGGAACCGTGTCA-TCCCCAGACCAGATCTCTTCATCACG
1 AGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCAGACCAGATCTCTTCATCACG
* * *
1234763 TATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTT
66 TAGGAGCCGTGTCACCCTTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTT
1234828 AGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCC-GACCAGATCTCTTCATCACG
1 AGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCAGACCAGATCTCTTCATCACG
1234892 TAGGAGCCGTGTCACCCTTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTT
66 TAGGAGCCGTGTCACCCTTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTT
1234957 AGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCC-GACCAGATCTCTTCATCACG
1 AGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCAGACCAGATCTCTTCATCACG
1235021 TAGGAGCCGTGTCACCCTTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTT
66 TAGGAGCCGTGTCACCCTTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTT
*
1235086 AGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCAGACCAGAACTCTTCATCACG
1 AGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCAGACCAGATCTCTTCATCACG
1235151 TAGGA
66 TAGGA
1235156 ACCGAGTTAT
Statistics
Matches: 316, Mismatches: 10, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
129 287 0.91
130 29 0.09
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (130 bp):
AGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCAGACCAGATCTCTTCATCACG
TAGGAGCCGTGTCACCCTTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTT
Found at i:1235380 original size:3 final size:3
Alignment explanation
Indices: 1235367--1235413 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
1235357 GTTTTTATCG
*
1235367 TTA TT- TTA TTA TTA TTA TTA TTA TTTA TTA TTA -TA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
1235411 TTA
1 TTA
1235414 CATATTACAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 4 0.10
3 32 0.82
4 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1235395 original size:19 final size:18
Alignment explanation
Indices: 1235371--1235407 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
1235361 TTATCGTTAT
1235371 TTTATTATTATTATTATTA
1 TTTATTATTA-TATTATTA
1235390 TTTATTATTATATTATTA
1 TTTATTATTATATTATTA
1235408 ATATTACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTATTATTATATTATTA
Found at i:1235419 original size:24 final size:25
Alignment explanation
Indices: 1235368--1235420 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
1235358 TTTTTATCGT
* **
1235368 TATT-TTATTATTATTATTATTATT
1 TATTATTATTATTATTAATATTACA
1235392 TATTATTA-TATTATTAATATTACA
1 TATTATTATTATTATTAATATTACA
1235416 TATTA
1 TATTA
1235421 CAATTTTTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (25 bp):
TATTATTATTATTATTAATATTACA
Found at i:1240889 original size:45 final size:46
Alignment explanation
Indices: 1240820--1240914 Score: 113
Period size: 45 Copynumber: 2.1 Consensus size: 46
1240810 CACAGACGCA
* * *
1240820 ACTACTCAAACTTAGAACTTCAAGAGAGTAACACT-TTC-ATTAATC
1 ACTACTCAAACCTAGAACTCCAAGAGAG-AACAATATTCTATTAATC
* *
1240865 ACTACTCGAACCTAGAGCTCCAAGAGAGAACAATACTTCTATTAATC
1 ACTACTCAAACCTAGAACTCCAAGAGAGAACAATA-TTCTATTAATC
1240912 ACT
1 ACT
1240915 GAGTCCACCC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
44 5 0.12
45 24 0.57
46 3 0.07
47 10 0.24
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (46 bp):
ACTACTCAAACCTAGAACTCCAAGAGAGAACAATATTCTATTAATC
Found at i:1249649 original size:16 final size:16
Alignment explanation
Indices: 1249628--1249659 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1249618 CACCCAGTGG
1249628 CTAAGAAGGGACACCC
1 CTAAGAAGGGACACCC
1249644 CTAAGAAGGGACACCC
1 CTAAGAAGGGACACCC
1249660 AAGATAATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.31, G:0.25, T:0.06
Consensus pattern (16 bp):
CTAAGAAGGGACACCC
Found at i:1267206 original size:2 final size:2
Alignment explanation
Indices: 1267201--1267265 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
1267191 TGTGTGTGTG
1267201 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
1267243 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
1267266 CTTCTAATTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1275089 original size:14 final size:15
Alignment explanation
Indices: 1275070--1275102 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1275060 AATAATATAA
1275070 TTTTAAAATTATT-T
1 TTTTAAAATTATTAT
*
1275084 TTTTAATATTATTAT
1 TTTTAAAATTATTAT
1275099 TTTT
1 TTTT
1275103 TTGAGTTACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTAAAATTATTAT
Found at i:1275914 original size:20 final size:20
Alignment explanation
Indices: 1275875--1275914 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1275865 GTTAAAATAA
* **
1275875 CCGGTTTAAAAAAATTCGAT
1 CCGGTTAAAAAAAACCCGAT
1275895 CCGGTTAAAAAAAACCCGAT
1 CCGGTTAAAAAAAACCCGAT
1275915 TTTTCTCAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (20 bp):
CCGGTTAAAAAAAACCCGAT
Found at i:1281944 original size:29 final size:29
Alignment explanation
Indices: 1281887--1281944 Score: 91
Period size: 28 Copynumber: 2.0 Consensus size: 29
1281877 TGAAAAAGTA
*
1281887 ATTTTGAATCAAAAAATAATTTTGAACTT
1 ATTTTGAATCAAAAAATAATTTAGAACTT
1281916 ATTTT-AATCAAAAAATAATTTAGAGACTT
1 ATTTTGAATCAAAAAATAATTTAGA-ACTT
1281945 CAAGGGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (29 bp):
ATTTTGAATCAAAAAATAATTTAGAACTT
Found at i:1282044 original size:21 final size:20
Alignment explanation
Indices: 1282003--1282043 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1281993 TTCTCTACCG
1282003 TCTTTTCATTTTTAAATTTT
1 TCTTTTCATTTTTAAATTTT
*
1282023 TCTTTTC-TTTTATTAATTTT
1 TCTTTTCATTTT-TAAATTTT
1282043 T
1 T
1282044 TAGGCAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.73
Consensus pattern (20 bp):
TCTTTTCATTTTTAAATTTT
Found at i:1287119 original size:2 final size:2
Alignment explanation
Indices: 1287114--1287183 Score: 131
Period size: 2 Copynumber: 35.0 Consensus size: 2
1287104 TTGTGTGGAC
1287114 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1287156 AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1287184 GTAAGAGTAT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1303170 original size:98 final size:99
Alignment explanation
Indices: 1303057--1303338 Score: 265
Period size: 103 Copynumber: 2.8 Consensus size: 99
1303047 TTTGACAAAG
*
1303057 TATAATATATAGTTTTCAGAAAACGGT-TTTTCAAAATATATAT-TGTATA-TTTTGAAAACATT
1 TATAATATATAGTTTT--GAAAA--GTATTTTCAAAATATATATATATATAGTTTTGAAAACATT
*
1303119 TTTAAAAAT-TATATA-ATATAGTTTCGAAAACATTTA
62 TTGAAAAATATATATAGATATAGTTTCGAAAACATTTA
* * * *
1303155 TATATTATATAGTTTTTAAAAGTCATTTTGAAAATATATATAATATATAGTTTTTAAAACATTTT
1 TATAATATATAGTTTTGAAAAGT-ATTTTCAAAATATATAT-ATATATAGTTTTGAAAACATTTT
* *
1303220 GAAAATTATATATAGTATATAGTTTTGAAAACATTTTGAAAA
64 GAAAAATATATATAG-ATATAGTTTCGAAAACA-TTT----A
* * *
1303262 TTATAATATATAGTTTTGAAAA-CATTTTGAAAAT-TGTA-ATATATAGTTTTGAAAACATTTTT
1 -TATAATATATAGTTTTGAAAAGTATTTTCAAAATATATATATATATAGTTTTGAAAACA-TTTT
*
1303324 GAAAATATTTATATA
64 GAAAA-ATATATATA
1303339 TTATATAAGA
Statistics
Matches: 153, Mismatches: 15, Indels: 25
0.79 0.08 0.13
Matches are distributed among these distances:
94 2 0.01
96 19 0.12
98 20 0.13
99 19 0.12
100 6 0.04
102 16 0.10
103 21 0.14
104 9 0.06
105 10 0.07
106 11 0.07
107 1 0.01
108 19 0.12
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (99 bp):
TATAATATATAGTTTTGAAAAGTATTTTCAAAATATATATATATATAGTTTTGAAAACATTTTGA
AAAATATATATAGATATAGTTTCGAAAACATTTA
Found at i:1303175 original size:27 final size:23
Alignment explanation
Indices: 1303117--1303175 Score: 64
Period size: 27 Copynumber: 2.4 Consensus size: 23
1303107 TTTGAAAACA
1303117 TTTTTAAAAATTATATAATATAG
1 TTTTTAAAAATTATATAATATAG
**
1303140 TTTCGAAAACATTTATATATTATATAG
1 TTTTTAAAA-A-TTATATA--ATATAG
1303167 TTTTTAAAA
1 TTTTTAAAA
1303176 GTCATTTTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 7 0.25
24 1 0.04
25 7 0.25
27 13 0.46
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (23 bp):
TTTTTAAAAATTATATAATATAG
Found at i:1303214 original size:65 final size:60
Alignment explanation
Indices: 1303093--1303288 Score: 155
Period size: 73 Copynumber: 3.0 Consensus size: 60
1303083 TTTTTCAAAA
* *
1303093 TATATATTGTATATTTTGAAAACATTTTTAAAAATTATATAATATAGTTTCGAAAACATT
1 TATATATTATATATTTTGAAAACATTTTGAAAAATTATATAATATAGTTTCGAAAACATT
* **
1303153 TATATATTATATAGTTTTTAAAAGTCATTTTG-AAAATATATATAATATATAGTTTTTAAAACAT
1 TATATATTATATA-TTTTGAAAA--CATTTTGAAAAAT-TATAT-A-ATATAGTTTCGAAAACA-
1303217 TTTGAAAAT
59 --T-----T
*
1303226 TATATATAGTATATAGTTTTGAAAACATTTTG-AAAATTATA-ATATATAGTTTTGAAAACATT
1 TATATAT--TATATA-TTTTGAAAACATTTTGAAAAATTATATA-ATATAGTTTCGAAAACATT
1303288 T
1 T
1303289 TGAAAATTGT
Statistics
Matches: 113, Mismatches: 7, Indels: 30
0.75 0.05 0.20
Matches are distributed among these distances:
60 12 0.11
61 8 0.07
62 7 0.06
63 11 0.10
64 1 0.01
65 15 0.13
67 1 0.01
68 1 0.01
70 18 0.16
72 4 0.04
73 20 0.18
75 15 0.13
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (60 bp):
TATATATTATATATTTTGAAAACATTTTGAAAAATTATATAATATAGTTTCGAAAACATT
Found at i:1303239 original size:37 final size:35
Alignment explanation
Indices: 1303153--1303462 Score: 289
Period size: 33 Copynumber: 8.7 Consensus size: 35
1303143 CGAAAACATT
1303153 TATATAT-TATATAGTTTTTAAAAGTCATTTTGAAAA
1 TATATATATATATAGTTTTTAAAA--CATTTTGAAAA
1303189 TATATATAATATATAGTTTTTAAAACATTTTGAAAA
1 TATATAT-ATATATAGTTTTTAAAACATTTTGAAAA
*
1303225 TTATATATAGTATATAGTTTTGAAAACATTTTGAAAA
1 -TATATATA-TATATAGTTTTTAAAACATTTTGAAAA
*
1303262 T-TATA-ATATATAGTTTTGAAAACATTTTGAAAA
1 TATATATATATATAGTTTTTAAAACATTTTGAAAA
* *
1303295 T-TGTA-ATATATAGTTTTGAAAACATTTTTGAAAA
1 TATATATATATATAGTTTTTAAAACA-TTTTGAAAA
* * *
1303329 TAT-T-TATATAT--TATATAAGACATTTTGAAAA
1 TATATATATATATAGTTTTTAAAACATTTTGAAAA
* **
1303360 TATATATAATATATAGTTTTTAAAAAATATTTTTGAAGT
1 TATATAT-ATATATAGTTTTT--AAAACA-TTTTGAAAA
* *
1303399 TATATATATTGTATATGTTTTTAAAAACGTTTCTGAAAA
1 TATATATA-TATATA-GTTTTT-AAAACATTT-TGAAAA
*
1303438 TACGTATA-ATATATAGTTTTAAAAA
1 TA--TATATATATATAGTTTTTAAAA
1303463 AAAAAGCATT
Statistics
Matches: 235, Mismatches: 19, Indels: 39
0.80 0.06 0.13
Matches are distributed among these distances:
31 12 0.05
32 8 0.03
33 51 0.22
34 24 0.10
35 5 0.02
36 23 0.10
37 37 0.16
38 29 0.12
39 35 0.15
40 7 0.03
41 4 0.02
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.45
Consensus pattern (35 bp):
TATATATATATATAGTTTTTAAAACATTTTGAAAA
Found at i:1303277 original size:33 final size:33
Alignment explanation
Indices: 1303046--1303384 Score: 261
Period size: 33 Copynumber: 9.9 Consensus size: 33
1303036 CTCAAAACGT
* *
1303046 TTTTGACAAAGTATAATATATAGTTTTCAGAAAACGGT
1 TTTTGA-AAATTATAATATATAGTTTT--GAAAAC--A
* * *
1303084 TTTTCAAAATATATATTGTATA-TTTTGAAAACA
1 TTTTGAAAAT-TATAATATATAGTTTTGAAAACA
* *
1303117 TTTTTAAAAATTAT-ATAATATAGTTTCGAAAACA
1 -TTTTGAAAATTATAAT-ATATAGTTTTGAAAACA
* *
1303151 -TTT----A-TATATTATATAGTTTTTAAAAGTCA
1 TTTTGAAAATTATAATATATAGTTTTGAAAA--CA
*
1303180 TTTTGAAAATATATATAATATATAGTTTTTAAAACA
1 TTTTG-AAA-AT-TATAATATATAGTTTTGAAAACA
1303216 TTTTGAAAATTATATATAGTATATAGTTTTGAAAACA
1 TTTTGAAAA-T-TATA-A-TATATAGTTTTGAAAACA
1303253 TTTTGAAAATTATAATATATAGTTTTGAAAACA
1 TTTTGAAAATTATAATATATAGTTTTGAAAACA
*
1303286 TTTTGAAAATTGTAATATATAGTTTTGAAAACA
1 TTTTGAAAATTATAATATATAGTTTTGAAAACA
* *
1303319 TTTTTGAAAA-TAT-TTATATA-TTATAT-AAGACA
1 -TTTTGAAAATTATAATATATAGTT-T-TGAAAACA
*
1303351 TTTTGAAAATATATATAATATATAGTTTTTAAAA
1 TTTTG-AAA-AT-TATAATATATAGTTTTGAAAA
1303385 AATATTTTTG
Statistics
Matches: 252, Mismatches: 20, Indels: 60
0.76 0.06 0.18
Matches are distributed among these distances:
27 16 0.06
28 2 0.01
29 2 0.01
30 3 0.01
31 7 0.03
32 19 0.08
33 61 0.24
34 30 0.12
35 23 0.09
36 20 0.08
37 35 0.14
38 34 0.13
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.44
Consensus pattern (33 bp):
TTTTGAAAATTATAATATATAGTTTTGAAAACA
Found at i:1303337 original size:135 final size:133
Alignment explanation
Indices: 1303084--1303384 Score: 318
Period size: 135 Copynumber: 2.3 Consensus size: 133
1303074 AGAAAACGGT
* *
1303084 TTTTCAAAATATATAT--TGTATA-TTTTGAAAACATTTTTAAAAATTATATAATATAGTTTCGA
1 TTTTGAAAATATATATAATATATAGTTTTGAAAACATTTTTAAAAATTATATAATATAGTTTCGA
* * *
1303146 AAACATTTATATATTATATAGTTTTTAAAAGTCATTTTGAAAATATATATAATATATAGTT-TTT
66 AAACATTTATATAATATATAGTTTTGAAAAG-CATTTTGAAAATATATAT-ATATATA-TTATAT
1303210 AAAACA
128 AAAACA
* * *
1303216 TTTTGAAAATTATATATAGTATATAGTTTTGAAAACA-TTTTGAAAATTATA-ATATATAGTTTT
1 TTTTGAAAA-TATATATAATATATAGTTTTGAAAACATTTTTAAAAATTATATA-ATATAGTTTC
*
1303279 GAAAACATTTTGAAAATTGTAATATATAGTTTTGAAAA-CATTTTTG-AAA-ATAT-T-TATATA
64 GAAAACA-TTT----A-TATAATATATAGTTTTGAAAAGCA-TTTTGAAAATATATATATATATA
*
1303339 TTATATAAGACA
122 TTATATAAAACA
*
1303351 TTTTGAAAATATATATAATATATAGTTTTTAAAA
1 TTTTGAAAATATATATAATATATAGTTTTGAAAA
1303385 AATATTTTTG
Statistics
Matches: 145, Mismatches: 11, Indels: 24
0.81 0.06 0.13
Matches are distributed among these distances:
132 8 0.06
133 7 0.05
134 26 0.18
135 56 0.39
136 14 0.10
137 1 0.01
138 4 0.03
139 5 0.03
140 6 0.04
141 18 0.12
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (133 bp):
TTTTGAAAATATATATAATATATAGTTTTGAAAACATTTTTAAAAATTATATAATATAGTTTCGA
AAACATTTATATAATATATAGTTTTGAAAAGCATTTTGAAAATATATATATATATATTATATAAA
ACA
Found at i:1303396 original size:70 final size:66
Alignment explanation
Indices: 1303153--1303462 Score: 232
Period size: 70 Copynumber: 4.3 Consensus size: 66
1303143 CGAAAACATT
* *
1303153 TATATATTATATAGTTTTTAAAAGTCATTTTGAAAATATATATAATATATAGTTTTTAAAACATT
1 TATATAATATATAG-TTTTAAAA-ACATTTTG-AAA-ATATAT--TATATA--TTTTAAAACATT
1303218 TTGAAAATTA
58 TTGAAAA-TA
* * *
1303228 TATATAGTATATAGTTTTGAAAACATTTTGAAAATTATAATATATAGTTTTGAAAACATTTTG-A
1 TATATAATATATAGTTTTAAAAACATTTTGAAAA-TATATTATATA-TTTT-AAAACATTTTGAA
1303292 AA-A
63 AATA
* * *
1303295 T-TGTAATATATAGTTTTGAAAACATTTTTGAAAATAT-TTATATATTATATAAGACATTTTGAA
1 TATATAATATATAGTTTTAAAAACA-TTTTGAAAATATATTATATATT-T-TAAAACATTTTGAA
1303358 AATA
63 AATA
* *
1303362 TATATAATATATAGTTTTTAAAAAATATTTTTGAAGTTATATATATTGTATATGTTTTTAAAAAC
1 TATATAATATATAG-TTTT-AAAAACA-TTTTGAA---A-ATATA-T-TATAT-ATTTT-AAAAC
*
1303427 GTTTCTGAAAATA
55 ATTT-TGAAAATA
**
1303440 CGTATAATATATAGTTTTAAAAA
1 TATATAATATATAGTTTTAAAAA
1303463 AAAAAGCATT
Statistics
Matches: 198, Mismatches: 17, Indels: 39
0.78 0.07 0.15
Matches are distributed among these distances:
64 2 0.01
65 17 0.09
66 28 0.14
67 13 0.07
68 11 0.06
69 11 0.06
70 30 0.15
71 1 0.01
72 7 0.04
73 8 0.04
74 11 0.06
75 13 0.07
76 7 0.04
77 17 0.09
78 22 0.11
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.45
Consensus pattern (66 bp):
TATATAATATATAGTTTTAAAAACATTTTGAAAATATATTATATATTTTAAAACATTTTGAAAAT
A
Found at i:1303525 original size:3 final size:3
Alignment explanation
Indices: 1303517--1303566 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
1303507 TTTTATATAG
* *
1303517 ATT ATT ATT ATTT ATT ATT ATT ACT ATT ATT ATT ATT -TT -TT TTT
1 ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1303561 ATT ATT
1 ATT ATT
1303567 TCCTATTTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
2 4 0.10
3 35 0.83
4 3 0.07
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (3 bp):
ATT
Found at i:1303545 original size:25 final size:25
Alignment explanation
Indices: 1303517--1303564 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
1303507 TTTTATATAG
1303517 ATTATTATTATTTATTATTATTACT
1 ATTATTATTATTTATTATTATTACT
* *
1303542 ATTATTATTATTTTTTTTTATTA
1 ATTATTATTATTTATTATTATTA
1303565 TTTCCTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (25 bp):
ATTATTATTATTTATTATTATTACT
Found at i:1303562 original size:28 final size:30
Alignment explanation
Indices: 1303517--1303593 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 30
1303507 TTTTATATAG
* *
1303517 ATTATTATTATTTATTATTA-TTACTA-TT
1 ATTATTATTTTTTTTTATTATTTACTATTT
*
1303545 ATTATTATTTTTTTTTATTATTTCCTATTT
1 ATTATTATTTTTTTTTATTATTTACTATTT
1303575 ATTTATTTATTTATTTTTT
1 A-TTA-TTATTT-TTTTTT
1303594 CTTTTCTCTC
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 18 0.44
29 5 0.12
30 3 0.07
31 3 0.07
32 6 0.15
33 6 0.15
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (30 bp):
ATTATTATTTTTTTTTATTATTTACTATTT
Found at i:1303588 original size:23 final size:20
Alignment explanation
Indices: 1303550--1303590 Score: 55
Period size: 23 Copynumber: 1.9 Consensus size: 20
1303540 CTATTATTAT
1303550 TATTTTTTTTTATTATTTCC
1 TATTTTTTTTTATTATTTCC
1303570 TATTTATTTATTTATTTATTT
1 TATTT-TTT-TTTA-TTATTT
1303591 TTTCTTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 3 0.17
22 4 0.22
23 6 0.33
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (20 bp):
TATTTTTTTTTATTATTTCC
Found at i:1304620 original size:23 final size:22
Alignment explanation
Indices: 1304587--1304642 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
1304577 CCTAAATTCT
* *
1304587 TATTTTATTTATTTATTATTA-
1 TATTTTTTTTAATTATTATTAG
1304608 TCATGTTTTTTTAATTATTATTAG
1 T-AT-TTTTTTTAATTATTATTAG
1304632 TATTTTTTTTA
1 TATTTTTTTTA
1304643 CCTCATATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 1 0.03
22 10 0.33
23 18 0.60
24 1 0.03
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (22 bp):
TATTTTTTTTAATTATTATTAG
Found at i:1304637 original size:20 final size:20
Alignment explanation
Indices: 1304592--1304639 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
1304582 ATTCTTATTT
1304592 TATTTATTTATTATTATCATG
1 TATTT-TTTATTATTATCATG
*
1304613 T-TTTTTTAATTATTATTA-G
1 TATTTTTT-ATTATTATCATG
1304632 TATTTTTT
1 TATTTTTT
1304640 TTACCTCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 5 0.21
20 18 0.75
21 1 0.04
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (20 bp):
TATTTTTTATTATTATCATG
Found at i:1305907 original size:21 final size:21
Alignment explanation
Indices: 1305881--1305924 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1305871 CCGCAGGCGG
1305881 ATGGAAAGTTCGAATGAATCT
1 ATGGAAAGTTCGAATGAATCT
1305902 ATGGAAAGTTCGAATGAATCT
1 ATGGAAAGTTCGAATGAATCT
1305923 AT
1 AT
1305925 CTTAAATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.30
Consensus pattern (21 bp):
ATGGAAAGTTCGAATGAATCT
Found at i:1307747 original size:5 final size:5
Alignment explanation
Indices: 1307745--1308345 Score: 676
Period size: 5 Copynumber: 121.2 Consensus size: 5
1307735 TTTTATATTA
1307745 TATAT TATAT TATAT TATAT TATA- TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1307794 TATA- TATTAT TATAT TATA- TATAT TAT-T TATA- TATAT TATAT TATAT
1 TATAT TA-TAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1307841 TATAT TATAT TATAT TATAT TATAT TATAT TATA- T-TAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1307889 TATAT TATAT TATAT TATA- TATAT TATAT TATAT TATAT TATAT ATATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT -TATAT
1307939 TATAT TATTAT ATATAT TATAT TATA- T-TAT TATAT TATA- TAT-T TATAT
1 TATAT TA-TAT -TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
* * * * *
1307987 TATAT TATAT TATTT ATATAT TATAT CTATAT TCTAT TCTAT TCTAT TCTAT
1 TATAT TATAT TATAT -TATAT TATAT -TATAT TATAT TATAT TATAT TATAT
* * * * * * * * * *
1308039 TCTAT TCTAT TCTAT TCTAT TCTAT TCTAT TCTAT TCTAT TCTAT TCTAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
* * * * * * * * * *
1308089 TCTAT TCTAT TCTAT TCTAT TCTAT TCTAT TCTAT TCTAT TCTAT TCTA-
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
* * * * * * * *
1308138 TCTAT TCTAT TCTAT TCTAT TCTAT TCTAT TCTAT TCTAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1308188 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1308238 TATAT TATAT TATAT TATAT TATA- TATA- TATAT TATAT TATAT TATA-
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
*
1308285 TATAT TATTAT ATATAT TATAT TATAT TATATT TATAT ATATAT TACTTT
1 TATAT TA-TAT -TATAT TATAT TATAT TATA-T TATAT -TATAT TA-TAT
*
1308335 TATAA TATAT T
1 TATAT TATAT T
1308346 TTTATTCATT
Statistics
Matches: 562, Mismatches: 8, Indels: 52
0.90 0.01 0.08
Matches are distributed among these distances:
3 4 0.01
4 48 0.09
5 464 0.83
6 42 0.07
7 4 0.01
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:1312494 original size:95 final size:95
Alignment explanation
Indices: 1312327--1312502 Score: 246
Period size: 95 Copynumber: 1.9 Consensus size: 95
1312317 ATATATATAA
* * * * * *
1312327 TAAAGCTTGAGTTGTCCCTCTAGAGCATTTTGTTAAACGCCCCGGCTTTATGGATAATATTTGGC
1 TAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGGATAAGATTTAGC
*
1312392 TAGCCTGATAAAGGTGATTATACTATACAT
66 TAACCTGATAAAGGTGATTATACTATACAT
* * *
1312422 TAAAGCTTGAGCTGTCTCTCTA-AGGTAATTGGTTAAACTCCCCGACTTTATGGATAAGATTTAG
1 TAAAGCTTGAGCTGTCCCTCTAGA-GCAATTGGTTAAACGCCCCGACTTTATGGATAAGATTTAG
1312486 CTAACCTGATAAAGGTG
65 CTAACCTGATAAAGGTG
1312503 TTTACATATT
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
94 1 0.01
95 69 0.99
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (95 bp):
TAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGGATAAGATTTAGC
TAACCTGATAAAGGTGATTATACTATACAT
Found at i:1314014 original size:84 final size:82
Alignment explanation
Indices: 1313655--1314758 Score: 973
Period size: 84 Copynumber: 13.4 Consensus size: 82
1313645 AATTTTTTCT
* * *
1313655 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGACTAAG
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATC-TGC-ACCAAAGACCTTCGAGTTCGACTACG
* *
1313720 CTCAGCTTCGAGGGCACATC
64 CTCAGC-TCCAAGGCACATC
* * * *
1313740 ATTTACAGCATAACTCAAGGCTAAAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCAACTACGC
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTG-CACCAAAGACCTTCGAGTTCGACTACGC
*
1313805 TCAACTCCAAGGCACATC
65 TCAGCTCCAAGGCACATC
* * * * * * *
1313823 ATTTGCAACATAGCTTAAGTCGAGAAGGGCTATCTG--CCAAAGACCTTCGAGTTCGATTACACT
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCT
* * *
1313886 CAACTCAAAGGCACCAAC
66 CAGCTCCAAGGCA-CATC
* * *
1313904 ATTTGCAGCATAACTTAAGGCAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTATG
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTG-C-ACCAAAGACCTTCGAGTTCGACTACG
*
1313969 CTCAGCTCCAAGGCATATC
64 CTCAGCTCCAAGGCACATC
* * * * * * * **
1313988 ATTTACAGCATAACTTAAGTCGAGAAGGG----CTG--TCAAAGACCCTCAAGTTCGATTATACT
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCT
* * *
1314047 TAGCTTCGAGGGCACATC
66 CAGC-TCCAAGGCACATC
* * ** * * * *
1314065 AATTACAATATAACTCAAGGCTAGAAGGGTTATCTGTCACTAAA-ACCTTCAAGTTCAACTACGC
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTG-CACCAAAGACCTTCGAGTTCGACTACGC
* *
1314129 TCAGCTCCAAGGCATATA
65 TCAGCTCCAAGGCACATC
* * * * * *
1314147 ATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTTGACTACG
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTG-C-ACCAAAGACCTTCGAGTTCGACTACG
*
1314212 CTCAGCT-CAATGACACATC
64 CTCAGCTCCAA-GGCACATC
* * * * * * **
1314231 ATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTG--CCAAAGACCCTCAAGTTCGATTATACT
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCT
* *
1314294 CAGCTTCGAGGGCACATC
66 CAGC-TCCAAGGCACATC
* * *
1314312 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGGACCTTCGAGTTTGACTACG
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTG-CACCAAA-GACCTTCGAGTTCGACTACG
* *
1314377 CTCAGCTCTAAGGCATATC
64 CTCAGCTCCAAGGCACATC
* * * * *
1314396 ATTTGCAGCATAACTTAAGTCAAAAAGGGTTATCTGCCAACCAAAGACCTTAGAGTTCGACTACA
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTG-C-ACCAAAGACCTTCGAGTTCGACTACG
* *
1314461 CTCAGTTCTAAGGCACATC
64 CTCAGCTCCAAGGCACATC
* * * * * * * *
1314480 ATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTG--CCAAAGACCCTCGAGTTCGATTACACT
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCT
* *
1314543 CAGCTTCGAGGCACATC
66 CAGCTCCAAGGCACATC
* * * * * *
1314560 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTTGGGTTCGATTACAC
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTG-CACCAAAGACCTTCGAGTTCGACTACGC
*
1314625 TCAGCT-CAACGACACATC
65 TCAGCTCCAA-GGCACATC
* * * * *
1314643 ATTTGCGGTATAACTCAAGGCTAGAAGGGTTATTTG--CCAAAGACCTTTGAGTTCGACTACGCT
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCT
*
1314706 CAGCTCCAAGGCACGTC
66 CAGCTCCAAGGCACATC
* * * * * * *
1314723 ATCTACAACATAGCTCAAGGCAAGAAGGGCTATCTG
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTG
1314759 TCAATAAAAT
Statistics
Matches: 830, Mismatches: 160, Indels: 63
0.79 0.15 0.06
Matches are distributed among these distances:
76 24 0.03
77 33 0.04
80 190 0.23
81 79 0.10
82 43 0.05
83 134 0.16
84 234 0.28
85 93 0.11
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (82 bp):
ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCT
CAGCTCCAAGGCACATC
Found at i:1314483 original size:249 final size:247
Alignment explanation
Indices: 1313655--1314758 Score: 1221
Period size: 249 Copynumber: 4.5 Consensus size: 247
1313645 AATTTTTTCT
* * * *
1313655 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGACTAAG
1 ATTTGCAGCATAACTTAAGGCAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* * * * * * * *
1313720 CTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAAAAGGGTTATCTGTCACCAAAG
66 CTCAGC-TCCAAGGCACATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAG
* * * * * * * * * * * * *
1313785 ACCTTCGAGTTCAACTACGCTCAAC-TCCAAGGCACATCATTTGCAACATAGCTTAAGTCGAGAA
127 ACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAA
* * * *
1313849 GGGCTATCTG---CCAAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCACCAAC
192 GGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACACTCAGCTC-AAGGCA-CATC
* *
1313904 ATTTGCAGCATAACTTAAGGCAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTATG
1 ATTTGCAGCATAACTTAAGGCAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* * *
1313969 CTCAGCTCCAAGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGG----CTGTCAAAGACCC
66 CTCAGCTCCAAGGCACATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
* * * *
1314030 TCAAGTTCGATTATACTTAGCTTCGAGGGCACATCAATTACAATATAACTCAAGGCTAGAAGGGT
131 TCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGT
* * * * * *
1314095 TATCTGTCACTAAA-ACCTTCAAGTTCAACTACGCTCAGCTCCAAGGCATATA
196 TATCTGTCACCAAAGACCTTCGAGTTCGACTACACTCAGCT-CAAGGCACATC
* * * * * *
1314147 ATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTTGACTACG
1 ATTTGCAGCATAACTTAAGGCAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* * *
1314212 CTCAGCT-CAATGACACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACC
66 CTCAGCTCCAA-GGCACATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
* *
1314276 CTCAAGTTCGATTATACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGG
130 CTCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGG
* * *
1314341 TTATCTGTCACCAAAGGACCTTCGAGTTTGACTACGCTCAGCTCTAAGGCATATC
195 TTATCTGTCACCAAA-GACCTTCGAGTTCGACTACACTCAGCTC-AAGGCACATC
* * * *
1314396 ATTTGCAGCATAACTTAAGTCAAAAAGGGTTATCTGCCAACCAAAGACCTTAGAGTTCGACTACA
1 ATTTGCAGCATAACTTAAGGCAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* * **
1314461 CTCAGTTCTAAGGCACATCATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
66 CTCAGCTCCAAGGCACATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
* * *
1314526 TCGAGTTCGATTACACTCAGCTTCGA-GGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGT
131 TCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGT
* * * * * *
1314590 TATCTGCCAACAAAGACCTTTGGGTTCGATTACACTCAGCTCAACGACACATC
196 TATCTGTCACCAAAGACCTTCGAGTTCGACTACACTCAGCTCAA-GGCACATC
* * * * * *
1314643 ATTTGCGGTATAACTCAAGGCTAGAAGGGTTATTTG----CCAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGGCAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* * * * * *
1314704 CTCAGCTCCAAGGCACGTCATCTACAACATAGCTCAAGGCAAGAAGGGCTATCTG
66 CTCAGCTCCAAGGCACATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTG
1314759 TCAATAAAAT
Statistics
Matches: 737, Mismatches: 103, Indels: 36
0.84 0.12 0.04
Matches are distributed among these distances:
241 22 0.03
242 42 0.06
243 168 0.23
244 30 0.04
245 5 0.01
246 2 0.00
247 144 0.20
248 85 0.12
249 237 0.32
250 2 0.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (247 bp):
ATTTGCAGCATAACTTAAGGCAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
TCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGT
TATCTGTCACCAAAGACCTTCGAGTTCGACTACACTCAGCTCAAGGCACATC
Found at i:1315436 original size:36 final size:34
Alignment explanation
Indices: 1315361--1315600 Score: 206
Period size: 36 Copynumber: 6.8 Consensus size: 34
1315351 TTAAAGTATG
*
1315361 TATATAATATATAGCTTT-AAAACATTTTGAAAATA
1 TATATAATATATAG-TTTAAAAACATTTTGAAAA-C
*
1315396 TATATAATATATAGTTAAAAAAACATTTTTGAAAAC
1 TATATAATATATAGTT-TAAAAACA-TTTTGAAAAC
* *
1315432 TATATACTATATAGTTTTTAAAACATTTTGAAAA-
1 TATATAATATATAG-TTTAAAAACATTTTGAAAAC
*
1315466 -ATAT-ATA-GT--TTTAAAAACATTTTTGAAAAC
1 TATATAATATATAGTTTAAAAACA-TTTTGAAAAC
* *
1315496 TATATAATATATAGTTTTTAAAACATTTTGAAAATAAA
1 TATATAATATATAG-TTTAAAAACATTTTG--AA-AAC
*
1315534 TATATAATATATAGTTTTTGAAAAACATTTTGAAGAC
1 TATATAATATATAG--TTT-AAAAACATTTTGAAAAC
* *
1315571 ATATATAATATATAATTTTTAAAACATTTT
1 -TATATAATATAT-AGTTTAAAAACATTTT
1315601 TTAAAATCAT
Statistics
Matches: 170, Mismatches: 16, Indels: 37
0.76 0.07 0.17
Matches are distributed among these distances:
28 9 0.05
29 9 0.05
31 5 0.03
32 5 0.03
33 5 0.03
34 2 0.01
35 28 0.16
36 44 0.26
37 17 0.10
38 30 0.18
39 5 0.03
40 11 0.06
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (34 bp):
TATATAATATATAGTTTAAAAACATTTTGAAAAC
Found at i:1315470 original size:64 final size:64
Alignment explanation
Indices: 1315401--1315529 Score: 231
Period size: 64 Copynumber: 2.0 Consensus size: 64
1315391 AAATATATAT
*
1315401 AATATATAGTTAAAAAAACATTTTTGAAAACTATATACTATATAGTTTTTAAAACATTTTGAAA
1 AATATATAGTTAAAAAAACATTTTTGAAAACTATATAATATATAGTTTTTAAAACATTTTGAAA
**
1315465 AATATATAGTTTTAAAAACATTTTTGAAAACTATATAATATATAGTTTTTAAAACATTTTGAAA
1 AATATATAGTTAAAAAAACATTTTTGAAAACTATATAATATATAGTTTTTAAAACATTTTGAAA
1315529 A
1 A
1315530 TAAATATATA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.40
Consensus pattern (64 bp):
AATATATAGTTAAAAAAACATTTTTGAAAACTATATAATATATAGTTTTTAAAACATTTTGAAA
Found at i:1315499 original size:29 final size:28
Alignment explanation
Indices: 1315437--1315501 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
1315427 AAAACTATAT
*
1315437 ACTATATAGTTTTTAAAACATTTTGAAA
1 ACTATATAGTTTTAAAAACATTTTGAAA
*
1315465 AATATATAGTTTTAAAAACATTTTTGAAA
1 ACTATATAGTTTTAAAAACA-TTTTGAAA
1315494 ACTATATA
1 ACTATATA
1315502 ATATATAGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 18 0.55
29 15 0.45
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (28 bp):
ACTATATAGTTTTAAAAACATTTTGAAA
Found at i:1315538 original size:38 final size:35
Alignment explanation
Indices: 1315465--1315600 Score: 173
Period size: 38 Copynumber: 3.7 Consensus size: 35
1315455 CATTTTGAAA
* *
1315465 AATATATAGTTTTAAAAACATTTTTGAAAACTATAT
1 AATATATAGTTTTTAAAACA-TTTTGAAAAATATAT
1315501 AATATATAGTTTTTAAAACATTTTGAAAATAAATATAT
1 AATATATAGTTTTTAAAACATTTTG--AA-AAATATAT
*
1315539 AATATATAGTTTTTGAAAAACATTTTGAAGACATATAT
1 AATATATAGTTTTT--AAAACATTTTGAA-AAATATAT
*
1315577 AATATATAATTTTTAAAACATTTT
1 AATATATAGTTTTTAAAACATTTT
1315601 TTAAAATCAT
Statistics
Matches: 90, Mismatches: 5, Indels: 10
0.86 0.05 0.10
Matches are distributed among these distances:
35 5 0.06
36 29 0.32
37 2 0.02
38 43 0.48
40 11 0.12
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (35 bp):
AATATATAGTTTTTAAAACATTTTGAAAAATATAT
Found at i:1315590 original size:140 final size:136
Alignment explanation
Indices: 1315361--1315692 Score: 412
Period size: 140 Copynumber: 2.4 Consensus size: 136
1315351 TTAAAGTATG
* **
1315361 TATATAATATATAG-CTTTAAAACATTTTGAAAATATATATAATATATAG-TTAAAAAAACATTT
1 TATATAATATATAGTTTTTAAAACATTTTGAAAATATATATAATATATAGTTTTTAAAAACATTT
* * *
1315424 TTGAAAACTATATACTATATAGTTTTTAAAACATTTTGAAAAATATATAG-TTTTAAAAACATTT
66 TTGAAAACTATATAATATATAATTTTTAAAACATTTTGAAAAAT-CATAGTTTTTAAAAACATTT
1315488 TTGAAAA
130 TTGAAAA
1315495 CTATATAATATATAGTTTTTAAAACATTTTGAAAATAAATATATAATATATAGTTTTTGAAAAAC
1 -TATATAATATATAGTTTTTAAAACATTTTGAAAAT--ATATATAATATATAGTTTTT-AAAAAC
* **
1315560 A-TTTTGAAGACATATATAATATATAATTTTTAAAACATTTTTTAAAATCATAGTTTTTAAAAAC
62 ATTTTTGAAAAC-TATATAATATATAATTTTTAAAACATTTTGAAAAATCATAGTTTTTAAAAAC
1315624 ATTTTTGAAAA
126 ATTTTTGAAAA
* *
1315635 T-TAT-ATAGT-T--TTTTAAAAATATTTTTGAAAATGTATATATAATATATAGTTTTTAAAA
1 TATATAATA-TATAGTTTTTAAAACA-TTTTGAAAA--TATATATAATATATAGTTTTTAAAA
1315693 GAAACAATTT
Statistics
Matches: 175, Mismatches: 11, Indels: 22
0.84 0.05 0.11
Matches are distributed among these distances:
135 27 0.15
136 48 0.27
137 4 0.02
138 20 0.11
139 16 0.09
140 60 0.34
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (136 bp):
TATATAATATATAGTTTTTAAAACATTTTGAAAATATATATAATATATAGTTTTTAAAAACATTT
TTGAAAACTATATAATATATAATTTTTAAAACATTTTGAAAAATCATAGTTTTTAAAAACATTTT
TGAAAA
Found at i:1315625 original size:28 final size:30
Alignment explanation
Indices: 1315586--1315666 Score: 105
Period size: 31 Copynumber: 2.8 Consensus size: 30
1315576 TAATATATAA
*
1315586 TTTTT-AAAACATTTTTTAAAAT-CATAG-
1 TTTTTAAAAACATTTTTGAAAATACATAGT
*
1315613 TTTTTAAAAACATTTTTGAAAATTATATAGT
1 TTTTTAAAAACATTTTTGAAAA-TACATAGT
*
1315644 TTTTTAAAAATATTTTTGAAAAT
1 TTTTTAAAAACATTTTTGAAAAT
1315667 GTATATATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
27 5 0.11
28 15 0.32
29 1 0.02
30 5 0.11
31 21 0.45
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (30 bp):
TTTTTAAAAACATTTTTGAAAATACATAGT
Found at i:1315634 original size:13 final size:13
Alignment explanation
Indices: 1315586--1315634 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
1315576 TAATATATAA
1315586 TTTTT-AAAACAT
1 TTTTTAAAAACAT
*
1315598 TTTTTAAAATCAT
1 TTTTTAAAAACAT
1315611 AGTTTTTAAAAACAT
1 --TTTTTAAAAACAT
*
1315626 TTTTGAAAA
1 TTTTTAAAA
1315635 TTATATAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 5 0.16
13 14 0.45
15 12 0.39
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (13 bp):
TTTTTAAAAACAT
Found at i:1315680 original size:39 final size:41
Alignment explanation
Indices: 1315636--1315721 Score: 104
Period size: 43 Copynumber: 2.1 Consensus size: 41
1315626 TTTTGAAAAT
* * * *
1315636 TATATAGTTTTT-TAA-AAATATTTTTGAAAATGTATATATAA
1 TATATAGTTTTTAAAAGAAACAATTTTAAAAATGTATAT-T-A
1315677 TATATAGTTTTTAAAAGAAACAATTTTAAAAATGTATATTA
1 TATATAGTTTTTAAAAGAAACAATTTTAAAAATGTATATTA
1315718 TATA
1 TATA
1315722 GTTTTTGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
41 17 0.44
42 3 0.08
43 19 0.49
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.45
Consensus pattern (41 bp):
TATATAGTTTTTAAAAGAAACAATTTTAAAAATGTATATTA
Found at i:1315715 original size:41 final size:38
Alignment explanation
Indices: 1315634--1315727 Score: 100
Period size: 41 Copynumber: 2.4 Consensus size: 38
1315624 ATTTTTGAAA
* * * *
1315634 ATTATATAGTTTTTTAAAAATATTTTTGAAAATGTATAT
1 ATTATATAGTTTTTAAAAAACAATTTTAAAAATG-ATAT
1315673 ATAATATATAGTTTTTAAAAGAAACAATTTTAAAAATG-TAT
1 AT--TATATAGTTTTT-AAA-AAACAATTTTAAAAATGATAT
1315714 ATTATATAGTTTTT
1 ATTATATAGTTTTT
1315728 GTTTTTATGT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
39 14 0.30
41 17 0.36
42 2 0.04
43 14 0.30
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.48
Consensus pattern (38 bp):
ATTATATAGTTTTTAAAAAACAATTTTAAAAATGATAT
Found at i:1316741 original size:5 final size:5
Alignment explanation
Indices: 1316726--1316961 Score: 305
Period size: 5 Copynumber: 47.8 Consensus size: 5
1316716 TCCTTTTGTT
1316726 TTATA TATATA TTATA TATATA TTATA -TATA TTATA TTATA TTATA TTATA
1 TTATA T-TATA TTATA T-TATA TTATA TTATA TTATA TTATA TTATA TTATA
1316777 TTATA -TATA -TATA TTATA TTATA TTATA TTATA TTATA TTATA -T-TA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
1316823 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
1316873 TTATA -TATA TTATTA TTATTA TTATATA TTATA TTATA -TATA TATATA
1 TTATA TTATA TTA-TA TTA-TA -T-TATA TTATA TTATA TTATA T-TATA
* *
1316921 TT-TA TTATA -T-TA TTATT TTCTA TTATA -TATA TTTATA TTAT
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA -TTATA TTAT
1316962 TTAATCATTT
Statistics
Matches: 210, Mismatches: 4, Indels: 34
0.85 0.02 0.14
Matches are distributed among these distances:
3 4 0.02
4 32 0.15
5 141 0.67
6 28 0.13
7 3 0.01
8 2 0.01
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:1316786 original size:33 final size:33
Alignment explanation
Indices: 1316726--1316961 Score: 310
Period size: 33 Copynumber: 7.1 Consensus size: 33
1316716 TCCTTTTGTT
1316726 TTATATATATATTATATATATATTATATATATTATA
1 TTATAT-TATATTATAT-TATA-TATATATATTATA
1316762 TTATATTATATTATATTATATATATATATTATA
1 TTATATTATATTATATTATATATATATATTATA
1316795 TTATATTATATTATATTATAT-TATATTATTATA
1 TTATATTATATTATATTATATATATA-TATTATA
1316828 TTATATTATATTATA-T-TATAT-TATATTATA
1 TTATATTATATTATATTATATATATATATTATA
1316858 TTATATTATATTATATTATATATAT-TATTATTA
1 TTATATTATATTATATTATATATATATATTA-TA
*
1316891 TTAT-TATATATTATATTATATATATATATATTTA
1 TTATAT-TATATTATATTATATATATATAT-TATA
1316925 TTATATTATTATT-T-TCTAT-TATATATATTTATA
1 TTATATTA-TATTATAT-TATATATATATA-TTATA
1316958 TTAT
1 TTAT
1316962 TTAATCATTT
Statistics
Matches: 185, Mismatches: 2, Indels: 29
0.86 0.01 0.13
Matches are distributed among these distances:
30 22 0.12
31 6 0.03
32 17 0.09
33 98 0.53
34 20 0.11
35 16 0.09
36 6 0.03
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (33 bp):
TTATATTATATTATATTATATATATATATTATA
Found at i:1323088 original size:24 final size:26
Alignment explanation
Indices: 1323041--1323102 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 26
1323031 TAGTAATTTA
1323041 ATTTTTATA--TTAATTTTTTAAAAT
1 ATTTTTATATTTTAATTTTTTAAAAT
*
1323065 CTTTTTATATTTTAA-TTTTT-AAAT
1 ATTTTTATATTTTAATTTTTTAAAAT
*
1323089 AATTTTAT-TTTTAA
1 ATTTTTATATTTTAA
1323103 AATATTAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
23 6 0.18
24 18 0.55
25 5 0.15
26 4 0.12
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (26 bp):
ATTTTTATATTTTAATTTTTTAAAAT
Found at i:1323950 original size:59 final size:59
Alignment explanation
Indices: 1323881--1324076 Score: 162
Period size: 59 Copynumber: 3.2 Consensus size: 59
1323871 TTTTGAAGTG
1323881 ATAAAATTATAGTTAAAATTAAAATTAAATATGACTCTAATTAATTTAATTTTGATTAA
1 ATAAAATTATAGTTAAAATTAAAATTAAATATGACTCTAATTAATTTAATTTTGATTAA
* * * * * * *
1323940 ATAGAATTATAATTAAAATTATATTTAATAAAATTAT-ATTTTTTCT-CTTAGTATAAGATTTTG
1 ATAAAATTATAGTTAAAATTA-A---AATTAAA-TATGA----CTCTAATTAAT-TTA-ATTTTG
**
1324003 AAGAGA
55 ATTA-A
* * *
1324009 AAAAAATTATAGTTAAATTTAAAATTAAATAGGACTCTAATTAATTTAATTTTGATTAA
1 ATAAAATTATAGTTAAAATTAAAATTAAATATGACTCTAATTAATTTAATTTTGATTAA
1324068 ATAAAATTA
1 ATAAAATTA
1324077 AACTAAATTC
Statistics
Matches: 101, Mismatches: 22, Indels: 28
0.67 0.15 0.19
Matches are distributed among these distances:
59 28 0.28
60 9 0.09
61 5 0.05
62 4 0.04
63 7 0.07
64 5 0.05
65 7 0.07
66 4 0.04
67 5 0.05
68 9 0.09
69 18 0.18
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.42
Consensus pattern (59 bp):
ATAAAATTATAGTTAAAATTAAAATTAAATATGACTCTAATTAATTTAATTTTGATTAA
Found at i:1325896 original size:24 final size:24
Alignment explanation
Indices: 1325846--1325904 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
1325836 AATTTTATAT
* *
1325846 GGCACTACGGTG-TAATTCTACAC
1 GGCACTTCGGTGCAAATTCTACAC
* **
1325869 GGCAGTTCGGTGCAAATTCTACGT
1 GGCACTTCGGTGCAAATTCTACAC
1325893 GGCACTTCGGTG
1 GGCACTTCGGTG
1325905 TGACAACATA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
23 10 0.34
24 19 0.66
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (24 bp):
GGCACTTCGGTGCAAATTCTACAC
Found at i:1332402 original size:24 final size:24
Alignment explanation
Indices: 1332357--1332427 Score: 85
Period size: 23 Copynumber: 3.0 Consensus size: 24
1332347 AATTTTATAT
1332357 GGCACTAT-GGTGC-AATTCTACGA
1 GGCACT-TCGGTGCAAATTCTACGA
*
1332380 GGCACTTCGGTGCAAATTCTACGT
1 GGCACTTCGGTGCAAATTCTACGA
* *
1332404 GGCACTTCGGT-CAATTTATACGA
1 GGCACTTCGGTGCAAATTCTACGA
1332427 G
1 G
1332428 CTGTGGTGAC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
22 1 0.02
23 21 0.50
24 20 0.48
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28
Consensus pattern (24 bp):
GGCACTTCGGTGCAAATTCTACGA
Found at i:1336318 original size:2 final size:2
Alignment explanation
Indices: 1336313--1336338 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1336303 TAAATAAAAA
1336313 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
1336339 TGTCGGAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1336797 original size:13 final size:14
Alignment explanation
Indices: 1336765--1336798 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1336755 TAAATAGGAT
1336765 AAATAAAGGAAAAG
1 AAATAAAGGAAAAG
*
1336779 AAATAAAGGGAAA-
1 AAATAAAGGAAAAG
1336792 AAATAAA
1 AAATAAA
1336799 AATAAAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.09
Consensus pattern (14 bp):
AAATAAAGGAAAAG
Found at i:1336904 original size:25 final size:25
Alignment explanation
Indices: 1336876--1336944 Score: 120
Period size: 25 Copynumber: 2.8 Consensus size: 25
1336866 AAGCAAACAT
1336876 AAAACAAAGAAATGAAAATTATTTA
1 AAAACAAAGAAATGAAAATTATTTA
*
1336901 AAAACAAAGAAATGAAAATTGTTTA
1 AAAACAAAGAAATGAAAATTATTTA
*
1336926 AAAACAAAGAAATAAAAAT
1 AAAACAAAGAAATGAAAAT
1336945 AAAACATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.67, C:0.04, G:0.09, T:0.20
Consensus pattern (25 bp):
AAAACAAAGAAATGAAAATTATTTA
Found at i:1337047 original size:2 final size:2
Alignment explanation
Indices: 1337040--1337199 Score: 100
Period size: 2 Copynumber: 87.5 Consensus size: 2
1337030 AATCAAAGGA
** *
1337040 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GC AT AT AG
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1337082 GT -T A- AT A- AT A- AT A- AT A- AT A- AT A- AT A- AT AG AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
1337115 A- AT A- AT AG CT AT AT AT AT AT A- AT A- AT A- AT AA AT GAC GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
1337153 A- AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1337193 AT AT AT A
1 AT AT AT A
1337200 AGGGAATAAA
Statistics
Matches: 121, Mismatches: 20, Indels: 34
0.69 0.11 0.19
Matches are distributed among these distances:
1 16 0.13
2 104 0.86
3 1 0.01
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (2 bp):
AT
Found at i:1337092 original size:3 final size:3
Alignment explanation
Indices: 1337084--1337145 Score: 65
Period size: 3 Copynumber: 20.0 Consensus size: 3
1337074 GCATATAGGT
*
1337084 TAA TAA TAA TAA TAA TAA TAA TAA TAGA -AA TAA TAA TAGC T-A TATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TA-A
1337130 TATA TAA TAA TAA TAA
1 TA-A TAA TAA TAA TAA
1337146 ATGACGTAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
2 2 0.04
3 41 0.79
4 9 0.17
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1339291 original size:110 final size:110
Alignment explanation
Indices: 1339143--1339346 Score: 293
Period size: 110 Copynumber: 1.9 Consensus size: 110
1339133 TGGGAAATTG
* * ** * *
1339143 TTTGTTGACAGTCAGCTGCCCCTTCGCTGTGAAGTTGAGCTTGTACTGTCTCGAGTCTAATATCC
1 TTTGTTGACAATCAACCACCCCTTCGCTGTGAAGTTGAGCTTGTACTGTCTCGAGTCCAATATCA
*
1339208 TTCGTTGTGAAGTTGAAATTGACTTTGAATGAAACTAAAAAGTTA
66 TTCGCTGTGAAGTTGAAATTGACTTTGAATGAAACTAAAAAGTTA
** *
1339253 TTTGTTGACAATCAACCACCCCTTCG-TCGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATATC
1 TTTGTTGACAATCAACCACCCCTTCGCT-GTGAAGTTGAGCTTGTACTGTCTCGAGTCCAATATC
*
1339317 ATTCGCTGTGAAGTTGAAATTGCCTTTGAA
65 ATTCGCTGTGAAGTTGAAATTGACTTTGAA
1339347 ATTGGGAAGC
Statistics
Matches: 82, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
109 1 0.01
110 81 0.99
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.36
Consensus pattern (110 bp):
TTTGTTGACAATCAACCACCCCTTCGCTGTGAAGTTGAGCTTGTACTGTCTCGAGTCCAATATCA
TTCGCTGTGAAGTTGAAATTGACTTTGAATGAAACTAAAAAGTTA
Found at i:1342833 original size:18 final size:18
Alignment explanation
Indices: 1342810--1342848 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1342800 ACCGGTCACA
*
1342810 ACCCGACCTAACCCGTTG
1 ACCCGACCCAACCCGTTG
*
1342828 ACCCGACCCGACCCGTTG
1 ACCCGACCCAACCCGTTG
1342846 ACC
1 ACC
1342849 GTTGACCCGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.49, G:0.18, T:0.13
Consensus pattern (18 bp):
ACCCGACCCAACCCGTTG
Found at i:1342857 original size:15 final size:15
Alignment explanation
Indices: 1342837--1342880 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 15
1342827 GACCCGACCC
1342837 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
*
1342852 GACCCGTTAACCGTT
1 GACCCGTTGACCGTT
1342867 GACCGGCGTTGACC
1 GACC--CGTTGACC
1342881 ACTGTTGACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 18 0.72
17 7 0.28
ACGTcount: A:0.16, C:0.34, G:0.27, T:0.23
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:1344196 original size:18 final size:18
Alignment explanation
Indices: 1344170--1344204 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1344160 GGACTGAAGG
* *
1344170 AAATGATAAGATTGGATT
1 AAATAATAAGATCGGATT
1344188 AAATAATAAGATCGGAT
1 AAATAATAAGATCGGAT
1344205 GGAAGGAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.03, G:0.20, T:0.29
Consensus pattern (18 bp):
AAATAATAAGATCGGATT
Found at i:1345420 original size:24 final size:24
Alignment explanation
Indices: 1345393--1345460 Score: 109
Period size: 24 Copynumber: 2.8 Consensus size: 24
1345383 TTCAATTTGA
* *
1345393 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATATGATACTTGACCTGG
1345417 ATTCTGATATGATACTTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
*
1345441 ATTTTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
1345461 ATGAATTATG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:1345477 original size:24 final size:24
Alignment explanation
Indices: 1345397--1345470 Score: 94
Period size: 24 Copynumber: 3.1 Consensus size: 24
1345387 ATTTGAATTC
* * *
1345397 TGATCTGATACTTGACTTGGATTC
1 TGATATGATACTTGACATGGATTA
* *
1345421 TGATATGATACTTGACCTGGATTT
1 TGATATGATACTTGACATGGATTA
*
1345445 TGATATGATACTTGACATGAATTA
1 TGATATGATACTTGACATGGATTA
1345469 TG
1 TG
1345471 TTTTGATTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (24 bp):
TGATATGATACTTGACATGGATTA
Found at i:1345640 original size:43 final size:43
Alignment explanation
Indices: 1345579--1345670 Score: 166
Period size: 43 Copynumber: 2.1 Consensus size: 43
1345569 GGGCTTTACT
* *
1345579 TGGTGTGTTGGTGGGTGTATGGTTCTGGGGAACCTACACATTA
1 TGGTGTATTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
1345622 TGGTGTATTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
1 TGGTGTATTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
1345665 TGGTGT
1 TGGTGT
1345671 GTTCGGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.17, C:0.11, G:0.36, T:0.36
Consensus pattern (43 bp):
TGGTGTATTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
Found at i:1355426 original size:14 final size:14
Alignment explanation
Indices: 1355407--1355441 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
1355397 TAAATAGGAT
1355407 AAATAAAGGGAAAA
1 AAATAAAGGGAAAA
1355421 AAATAAAGGGAAAA
1 AAATAAAGGGAAAA
1355435 AAATAAA
1 AAATAAA
1355442 AAATAAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (14 bp):
AAATAAAGGGAAAA
Found at i:1355461 original size:23 final size:25
Alignment explanation
Indices: 1355435--1355495 Score: 72
Period size: 26 Copynumber: 2.5 Consensus size: 25
1355425 AAAGGGAAAA
1355435 AAATAAA-AAATAAA-ACATATATT
1 AAATAAATAAATAAATACATATATT
*
1355458 AAATAAATAAATAAATATATATATAT
1 AAATAAATAAATAAATACATATAT-T
* *
1355484 ATATATATAAAT
1 AAATAAATAAAT
1355496 GCGTGAATAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.22
24 7 0.22
25 7 0.22
26 11 0.34
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (25 bp):
AAATAAATAAATAAATACATATATT
Found at i:1358938 original size:19 final size:19
Alignment explanation
Indices: 1358897--1358940 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
1358887 TTTTAAAAAT
1358897 TAAAATAATTATGTATTAC
1 TAAAATAATTATGTATTAC
1358916 TAAAA-AATATATAGTATTA-
1 TAAAATAAT-TAT-GTATTAC
1358935 TAAAAT
1 TAAAAT
1358941 CATCAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 3 0.14
19 13 0.59
20 6 0.27
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (19 bp):
TAAAATAATTATGTATTAC
Found at i:1359960 original size:7 final size:7
Alignment explanation
Indices: 1359948--1359979 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
1359938 TATAAGGGAC
1359948 AAAATAT
1 AAAATAT
1359955 AAAATAT
1 AAAATAT
1359962 AAAATAT
1 AAAATAT
1359969 AAAATAT
1 AAAATAT
1359976 AAAA
1 AAAA
1359980 AACCTCTCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (7 bp):
AAAATAT
Found at i:1362205 original size:3 final size:3
Alignment explanation
Indices: 1362197--1362225 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1362187 TGCTTAATTC
1362197 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1362226 GTTTAAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1363133 original size:182 final size:182
Alignment explanation
Indices: 1362784--1363627 Score: 1189
Period size: 182 Copynumber: 4.6 Consensus size: 182
1362774 GTCGATCCAA
* * * * * *
1362784 ATAAAAATTGTATCGATCCATATCAATATAACAAGTAAAAATATGATAAAATCGGT-T-TAATTA
1 ATAAAAA-TGTATCGATCCATAACGATATAACAGGTAAAAATATGACAAAACCGGTCTCGAA--A
* * * * * *
1362847 TGAC--AACCGGTAAAGCGCTACCGAATATGTTGAAAGTATCGATTAGATTGAA-ATAAGTATCG
63 TGACAAAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGA-TA-CTTTAATATAAGTATCG
* ** * *
1362909 ACACTTTGTGAATTTAAAAGAGAAGCAGTAATATCACCTATAAAGTGTCGATACTTT
126 ACACTTTGAGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTT
* *
1362966 ATAAAAATGTATCAATCCATAACGATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGA
1 ATAAAAATGTATCGATCCATAACGATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGA
* *
1363031 CAAAATCGGTAAAGAGCTACCGGATATATTGAAAGTGTTGATACTTTAATATAAGTATCGACACT
66 CAAAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACT
* * *
1363096 TTGATAATTTAAAAGAGAAGTAATTTTAGCGCCTATAAAGTGTCGATACTTT
131 TTGAGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTT
* *
1363148 ATAAAAATGTATCGATCCATAACGATACAACAGGTAAAAATATGACAAAACTGGTCTCGGAAA-G
1 ATAAAAATGTATCGATCCATAACGATATAACAGGTAAAAATATGACAAAACCGGTCTC-GAAATG
* * *
1363212 ATAAAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATTGACAC
65 ACAAAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACAC
* *
1363277 TTTGGGAATTTAAAAGAGAAGCAGTTTTAGTGCCTATAAAGTGTCGATACTTT
130 TTTGAGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTT
* *
1363330 ATGATAATGTATCGATCCATAACGATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGA
1 ATAAAAATGTATCGATCCATAACGATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGA
* *
1363395 CAAAACTGGTAAAGAGCTACCGAATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACT
66 CAAAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACT
*
1363460 TT-AGGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCTATACTTT
131 TTGA-GAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTT
* * * * *
1363512 ATGATAATGCATCAATCCATAACGATATAGCAGGTAAAAATATGACAAAACCGGTCTCGAAATGA
1 ATAAAAATGTATCGATCCATAACGATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGA
* *
1363577 CAAAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGAAATTTTAATA
66 CAAAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATA
1363628 AGTACAAGTA
Statistics
Matches: 598, Mismatches: 56, Indels: 16
0.89 0.08 0.02
Matches are distributed among these distances:
181 55 0.09
182 505 0.84
183 38 0.06
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (182 bp):
ATAAAAATGTATCGATCCATAACGATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGA
CAAAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACT
TTGAGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTT
Found at i:1366064 original size:33 final size:33
Alignment explanation
Indices: 1366027--1366093 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
1366017 AAATAGATGG
* *
1366027 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAAAAGTTGAGGTGTTAAGGGGTGA
1366060 AGTGGTGAAAAAAGTTGAGGTGTTAAGGGGTGA
1 AGTGGTGAAAAAAGTTGAGGTGTTAAGGGGTGA
1366093 A
1 A
1366094 CTTAAGATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAAAAGTTGAGGTGTTAAGGGGTGA
Found at i:1366303 original size:18 final size:18
Alignment explanation
Indices: 1366280--1366318 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1366270 GAAAAAATAT
*
1366280 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGAAG
1366298 GAAGAAGAAAAGATGAAG
1 GAAGAAGAAAAGATGAAG
1366316 GAA
1 GAA
1366319 ATGAGGAGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.36, T:0.05
Consensus pattern (18 bp):
GAAGAAGAAAAGATGAAG
Found at i:1367898 original size:19 final size:19
Alignment explanation
Indices: 1367874--1367922 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1367864 AATGTGGGGT
1367874 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1367893 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
1367912 TAATTTTGTAT
1 TAATTTTGTAT
1367923 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1368714 original size:200 final size:200
Alignment explanation
Indices: 1368366--1368834 Score: 778
Period size: 200 Copynumber: 2.3 Consensus size: 200
1368356 GTAAGTAGAT
* ** *
1368366 GTGTTGATACATTTATAAAAAGTATTTATCCCAAAAACATCGAAACCCATAATTATATTGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* *
1368431 GGTAAATTTACAATGTAACCGGTATAACTATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACATAATGT
*
1368496 ATCGACACTTTTGGAATTTGTGTCGATACTTTTTGTCCAGAA-TGAATGCCCAAAAGGGTGCACG
131 ATCGACAATTTTGGAATTTGTGTCGATACTTTTTGTCCAGAACT-AATGCCCAAAAGGGTGCACG
1368560 CATAAA
195 CATAAA
* *
1368566 GTGTCGATACATTTATAAAAAGTATCGATCTCAAAAACATCGAAACTCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* *
1368631 GGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTATATAGTGT
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACATAATGT
*
1368696 ATCGACAATTTTGGAATTTGTGTCGATACTTTTTGTCCATAACTAATGCCCAAAAGGGTGCACGC
131 ATCGACAATTTTGGAATTTGTGTCGATACTTTTTGTCCAGAACTAATGCCCAAAAGGGTGCACGC
1368761 ATAAA
196 ATAAA
* * *
1368766 GTGTCGATACATTTATAAAGAAATATCGATCCCAAAAACATCGAAACCCATATTTGTAATGTAAT
1 GTGTCGATACATTTATAAA-AAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAAT
1368831 AGGT
65 AGGT
1368835 CTACATAATG
Statistics
Matches: 250, Mismatches: 17, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
200 205 0.82
201 45 0.18
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (200 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
GGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACATAATGT
ATCGACAATTTTGGAATTTGTGTCGATACTTTTTGTCCAGAACTAATGCCCAAAAGGGTGCACGC
ATAAA
Found at i:1371578 original size:24 final size:24
Alignment explanation
Indices: 1371551--1371606 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
1371541 TTTCAAATTC
1371551 ATTTCATATGT-AATTGGAGTTTGA
1 ATTTCA-ATGTCAATTGGAGTTTGA
* *
1371575 ATTTCAATTTCAATTTGAGTTTGA
1 ATTTCAATGTCAATTGGAGTTTGA
*
1371599 GTTTCAAT
1 ATTTCAAT
1371607 ATAAATTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 3 0.11
24 25 0.89
ACGTcount: A:0.29, C:0.07, G:0.16, T:0.48
Consensus pattern (24 bp):
ATTTCAATGTCAATTGGAGTTTGA
Found at i:1371613 original size:24 final size:24
Alignment explanation
Indices: 1371562--1371614 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1371552 TTTCATATGT
* * *
1371562 AATTGGAGTTTGAATTTCAATTTC
1 AATTTGAGTTTGAATTTCAATATA
*
1371586 AATTTGAGTTTGAGTTTCAATATA
1 AATTTGAGTTTGAATTTCAATATA
1371610 AATTT
1 AATTT
1371615 TGGATCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTCAATATA
Found at i:1372397 original size:203 final size:203
Alignment explanation
Indices: 1371865--1372574 Score: 1201
Period size: 203 Copynumber: 3.5 Consensus size: 203
1371855 GTGCATGCAT
*
1371865 AAAGTGTCGATCCAAAAAACATCGAAACCGAAAATTATAATGTAATAGGTAAATTTACAATGTAA
1 AAAGTGTCGATCCAAAAAACATCGAAACCAAAAATTATAATGTAATAGGTAAATTTACAATGTAA
* *
1371930 CCGGTATAAATATATCGATTTTATAAGAAAATAGGTATACATAATGTATCGACACCTTTTAAATT
66 CCGGTATAAATATACCGGTTTTATAAGAAAATAGGTATACATAATGTATCGACACCTTTTAAATT
* *
1371995 TGGGTCGATACTTTTTGTGCGAGGCTTTGTTTTCTCAACAAGGTGCACGCATAAAGTGTCGATAC
131 TGTGTCGATACTTTTTGTGCGAGGCTTTGTTTCCTCAACAAGGTGCACGCATAAAGTGTCGATAC
1372060 ATTTATTA
196 ATTTATTA
*
1372068 AAAGTGTCGATCCAAAAAACATCGAAA-CAAAAATTATAATGTAATAGGTAAACTTACAATGTAA
1 AAAGTGTCGATCCAAAAAACATCGAAACCAAAAATTATAATGTAATAGGTAAATTTACAATGTAA
*
1372132 CCGGTATAAATATACCGGTTTTATAAGAAAATAGGTATACATAATGTATCGTCACCTTTTAAATT
66 CCGGTATAAATATACCGGTTTTATAAGAAAATAGGTATACATAATGTATCGACACCTTTTAAATT
* * *
1372197 TGTGTCGATACTTTTTGTGCGAGGCTTTGTTTCCTCAATAAGGAGCACACATAAAGAT-TCGATA
131 TGTGTCGATACTTTTTGTGCGAGGCTTTGTTTCCTCAACAAGGTGCACGCATAAAG-TGTCGATA
1372261 CATTTATTA
195 CATTTATTA
*
1372270 AAAGTGTCGATCCAAAAAACATCGAAACCGAAAATTATAATGTAATAGGTAAATTTACAATGTAA
1 AAAGTGTCGATCCAAAAAACATCGAAACCAAAAATTATAATGTAATAGGTAAATTTACAATGTAA
* *
1372335 CTGGTATAAATATACCGGTTTTATAAGAAAATATGTATACATAATGTATCGACACCTTTTAAATT
66 CCGGTATAAATATACCGGTTTTATAAGAAAATAGGTATACATAATGTATCGACACCTTTTAAATT
* *
1372400 TGTGTCGATACTTTTTGTGCGAGGCTTTGTTTGCTCAACAAGGTGCACGCATAATGTGTCGATAC
131 TGTGTCGATACTTTTTGTGCGAGGCTTTGTTTCCTCAACAAGGTGCACGCATAAAGTGTCGATAC
1372465 ATTTATTA
196 ATTTATTA
* * * *
1372473 AAAGTTTCGATCCACAAAACATCGAAACCAAAAATTCTAATGTAAGAGGTAAATTTACAATGTAA
1 AAAGTGTCGATCCAAAAAACATCGAAACCAAAAATTATAATGTAATAGGTAAATTTACAATGTAA
* *
1372538 CCAGTATAAATATATCGGTTTTAT-AGAAAATAGGTAT
66 CCGGTATAAATATACCGGTTTTATAAGAAAATAGGTAT
1372575 GCGTAATTAT
Statistics
Matches: 475, Mismatches: 29, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
202 203 0.43
203 272 0.57
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (203 bp):
AAAGTGTCGATCCAAAAAACATCGAAACCAAAAATTATAATGTAATAGGTAAATTTACAATGTAA
CCGGTATAAATATACCGGTTTTATAAGAAAATAGGTATACATAATGTATCGACACCTTTTAAATT
TGTGTCGATACTTTTTGTGCGAGGCTTTGTTTCCTCAACAAGGTGCACGCATAAAGTGTCGATAC
ATTTATTA
Found at i:1373278 original size:19 final size:19
Alignment explanation
Indices: 1373254--1373302 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1373244 AATGTAGGGT
1373254 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1373273 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
1373292 TAATTTTGTAT
1 TAATTTTGTAT
1373303 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1375872 original size:20 final size:19
Alignment explanation
Indices: 1375834--1375872 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1375824 CGAAACCAAT
*
1375834 AATTATAATGTAATAGGTA
1 AATTATAATGTAACAGGTA
*
1375853 AATTAATAATGTAACCGGTA
1 AATT-ATAATGTAACAGGTA
1375873 TAAATATACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.33
Consensus pattern (19 bp):
AATTATAATGTAACAGGTA
Found at i:1376152 original size:201 final size:199
Alignment explanation
Indices: 1375783--1376502 Score: 875
Period size: 200 Copynumber: 3.6 Consensus size: 199
1375773 ACCTAAATAT
*
1375783 GTGTCGATACATTT-TCCAAAAGTATCGATCCAAAAAAACATCGAAACCAATAATTATAATGTAA
1 GTGTCGATACATTTAT-TAAAAGTATCGATCC-AAAAAACATCGAAACCAATAATTATAATGTAA
* * * * * * *
1375847 TAGGTAAATTAATAATGTAACCGGTATAAATATACC-AGTTAATTAGAAAACATGTCAACATAAT
64 TAGGTAAATTTACAATGTAACCGATATAAATATACCGAGTTTATGAGAAAATAGGTC-ACATAAT
**
1375911 GTATCGACACTTGTGGAATTTGTGTCGATACTTATTGTCCAGAATGAATGCCCAAACGAGGTGCA
128 GTATCGACACTTGTTAAATTTGTGTCGATACTT-TTGTCCAGAATGAATGCCCAAACGAGGTGCA
1375976 CACATAAA
192 CACATAAA
*
1375984 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAATA
1 GTGTCGATACATTTATTAAAAGTATCGATCCAAAAAACATCGAAACCAATAATTATAATGTAATA
* * *
1376049 GGTAAATTTACAATGTAACCGATATAAATATATCGATTTTATGAGAAAATAGGTCAGCATAAAGT
66 GGTAAATTTACAATGTAACCGATATAAATATACCGAGTTTATGAGAAAATAGGTCA-CATAATGT
* *
1376114 ATCGACACTTGTTAAATTTGTGTCGATACATTTTGTCCATAATGAATG-TCAAACG-GGTTGCAC
130 ATCGACACTTGTTAAATTTGTGTCGATAC-TTTTGTCCAGAATGAATGCCCAAACGAGG-TGCAC
*
1376177 ACATAGA
193 ACATAAA
* * * * *
1376184 GTGTCGATACATTTATTAAAAGTATTGATCCCAAAAACATCGAAACCGATAATTACAATGTGATA
1 GTGTCGATACATTTATTAAAAGTATCGATCCAAAAAACATCGAAACCAATAATTATAATGTAATA
* * * *
1376249 GGAAAATTTACAATGTACCCGATAGAAATATACCG-GTTTTATGAGAAAATAGGTCTAAATAATG
66 GGTAAATTTACAATGTAACCGATATAAATATACCGAG-TTTATGAGAAAATAGGTC-ACATAATG
* ** *
1376313 TATCGACACTTTTTACGTTTGTGTCGATACGTTTT-TCTAGAATGAATGCCC-AACGAGGTGCAC
129 TATCGACACTTGTTAAATTTGTGTCGATAC-TTTTGTCCAGAATGAATGCCCAAACGAGGTGCAC
1376376 ACATAAA
193 ACATAAA
* * * * * * * *
1376383 GTGTCGGTACATTTA--AAATTGTATTGATCAAAAAAATATCAAAACCGATAATTATAATGTATT
1 GTGTCGATACATTTATTAAA-AGTATCGATCCAAAAAACATCGAAACCAATAATTATAATGTAAT
* * * * *
1376446 AGGTAAATTTGCAATGTTATCGGTATAAATATACCG-GTTTACTTAGAAAATAGGTCA
65 AGGTAAATTTACAATGTAACCGATATAAATATACCGAGTTTA-TGAGAAAATAGGTCA
1376503 ATATAAGCGC
Statistics
Matches: 455, Mismatches: 53, Indels: 26
0.85 0.10 0.05
Matches are distributed among these distances:
197 8 0.02
198 79 0.17
199 42 0.09
200 230 0.51
201 93 0.20
202 3 0.01
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (199 bp):
GTGTCGATACATTTATTAAAAGTATCGATCCAAAAAACATCGAAACCAATAATTATAATGTAATA
GGTAAATTTACAATGTAACCGATATAAATATACCGAGTTTATGAGAAAATAGGTCACATAATGTA
TCGACACTTGTTAAATTTGTGTCGATACTTTTGTCCAGAATGAATGCCCAAACGAGGTGCACACA
TAAA
Found at i:1376604 original size:87 final size:87
Alignment explanation
Indices: 1376504--1376665 Score: 281
Period size: 87 Copynumber: 1.9 Consensus size: 87
1376494 AATAGGTCAA
*
1376504 TATAAGCGCTACCTATTACATTATATAAGCACTACCTAATATGTTATTGTACTTGATAATATTT-
1 TATAAGCGATACCTATTACATTATATAAGCACTACCTAATATGTTATTGTACTTGATAATATTTC
1376568 TCGGTTAAATGCCTATTTTATTT
66 T-GGTTAAATGCCTATTTTATTT
* *
1376591 TATAAGCGATACCTATTACATTATATAAGCGCTACCTAATTTGTTATTGTACTTGATAATATTTC
1 TATAAGCGATACCTATTACATTATATAAGCACTACCTAATATGTTATTGTACTTGATAATATTTC
1376656 TGGTTAAATG
66 TGGTTAAATG
1376666 ATATAACATA
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
87 70 0.99
88 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (87 bp):
TATAAGCGATACCTATTACATTATATAAGCACTACCTAATATGTTATTGTACTTGATAATATTTC
TGGTTAAATGCCTATTTTATTT
Found at i:1379224 original size:2 final size:2
Alignment explanation
Indices: 1379219--1379277 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1379209 ACATATATCG
1379219 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
1379261 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
1379278 TATGTTAACA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1382524 original size:13 final size:13
Alignment explanation
Indices: 1382506--1382543 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1382496 GTCCGACCCT
1382506 ACCCGACCCGTTG
1 ACCCGACCCGTTG
**
1382519 ACCCGACTTGTTG
1 ACCCGACCCGTTG
1382532 ACCCGACCCGTT
1 ACCCGACCCGTT
1382544 AACCGTTTAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.16, C:0.42, G:0.21, T:0.21
Consensus pattern (13 bp):
ACCCGACCCGTTG
Found at i:1393203 original size:50 final size:49
Alignment explanation
Indices: 1393139--1393259 Score: 161
Period size: 50 Copynumber: 2.4 Consensus size: 49
1393129 ATTTAACGCA
*
1393139 CAACACTAACTTACACCAGTGTAAGTTAGTTATTTCATTTACTAAACTAT
1 CAACACTAACTTACA-CAGTGTAAGTTAGTCATTTCATTTACTAAACTAT
* ** *
1393189 CAACACTAATTTACATTGGTATAAGTTAGTCATTTCATTTACTAAACTAT
1 CAACACTAACTTACA-CAGTGTAAGTTAGTCATTTCATTTACTAAACTAT
* *
1393239 CAATACTGACTTACACAGTGT
1 CAACACTAACTTACACAGTGT
1393260 TATCATAGCT
Statistics
Matches: 59, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
49 3 0.05
50 56 0.95
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (49 bp):
CAACACTAACTTACACAGTGTAAGTTAGTCATTTCATTTACTAAACTAT
Found at i:1398383 original size:25 final size:25
Alignment explanation
Indices: 1398349--1398407 Score: 91
Period size: 25 Copynumber: 2.3 Consensus size: 25
1398339 CAAAGAGAGA
1398349 AAAATGAGACAATGGAAAATCATAGC
1 AAAA-GAGACAATGGAAAATCATAGC
*
1398375 AAAAGAGACCATGGAAAATCATAGC
1 AAAAGAGACAATGGAAAATCATAGC
*
1398400 AAATGAGA
1 AAAAGAGA
1398408 TAATCCAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 27 0.87
26 4 0.13
ACGTcount: A:0.54, C:0.12, G:0.20, T:0.14
Consensus pattern (25 bp):
AAAAGAGACAATGGAAAATCATAGC
Found at i:1399723 original size:20 final size:19
Alignment explanation
Indices: 1399670--1399724 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
1399660 TTCCATATTC
*
1399670 TTCCACACTCTTCCATAAGG
1 TTCCACACTC-TCCACAAGG
*
1399690 ATCCACACTACTCCACAAGG
1 TTCCACACT-CTCCACAAGG
1399710 TTCCACACATCTCCA
1 TTCCACAC-TCTCCA
1399725 GAATATTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 28 0.93
21 2 0.07
ACGTcount: A:0.29, C:0.40, G:0.07, T:0.24
Consensus pattern (19 bp):
TTCCACACTCTCCACAAGG
Found at i:1407586 original size:2 final size:2
Alignment explanation
Indices: 1407579--1407610 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1407569 CATAAAAGCA
1407579 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
1407611 TAGATTGAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1409297 original size:20 final size:20
Alignment explanation
Indices: 1409272--1409422 Score: 153
Period size: 20 Copynumber: 7.5 Consensus size: 20
1409262 GGGAAAATCA
1409272 CAATGCGATACTGACTATCG
1 CAATGCGATACTGACTATCG
1409292 CAATGCGATACTGACTATCG
1 CAATGCGATACTGACTATCG
*
1409312 CAATGCGATACTTACTATCG
1 CAATGCGATACTGACTATCG
* *
1409332 CAATGCGATAAT-ACAAAATCG
1 CAATGCGATACTGAC--TATCG
* * *
1409353 CAACGAGATACTGACTTTCG
1 CAATGCGATACTGACTATCG
* * *
1409373 CAACGCGATTCTGACTTTCG
1 CAATGCGATACTGACTATCG
* *
1409393 CAACGCGATAAT-ACATAATCG
1 CAATGCGATACTGAC-T-ATCG
1409414 CAATGCGAT
1 CAATGCGAT
1409423 TTTCAAAGCG
Statistics
Matches: 112, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
19 4 0.04
20 82 0.73
21 24 0.21
22 2 0.02
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
CAATGCGATACTGACTATCG
Found at i:1409350 original size:81 final size:82
Alignment explanation
Indices: 1409265--1409422 Score: 212
Period size: 81 Copynumber: 1.9 Consensus size: 82
1409255 GCGAATTGGG
* * * * *
1409265 AAAATCACAATGCGATACTGACTATCGCAATGCGATACTGACTATCGCAATGCGATACTTAC-T-
1 AAAATCACAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATA-ATACATA
1409328 ATCGCAATGCGATAATAC
65 ATCGCAATGCGATAATAC
* * * *
1409346 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATACATAA
1 AAAATCACAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATACATAA
1409411 TCGCAATGCGAT
66 TCGCAATGCGAT
1409423 TTTCAAAGCG
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
80 3 0.05
81 50 0.76
82 13 0.20
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (82 bp):
AAAATCACAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATACATAA
TCGCAATGCGATAATAC
Found at i:1409353 original size:61 final size:61
Alignment explanation
Indices: 1409288--1409422 Score: 189
Period size: 61 Copynumber: 2.2 Consensus size: 61
1409278 GATACTGACT
* * *
1409288 ATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATACAAA
1 ATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATACAAA
* * * * * *
1409349 ATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATACATA
1 ATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATACAAA
1409410 ATCGCAATGCGAT
1 ATCGCAATGCGAT
1409423 TTTCAAAGCG
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (61 bp):
ATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATACAAA
Found at i:1409381 original size:41 final size:40
Alignment explanation
Indices: 1409278--1409422 Score: 123
Period size: 41 Copynumber: 3.6 Consensus size: 40
1409268 ATCACAATGC
* * * *
1409278 GATACTGACTATCGCAATGCGATACTGACTATCGCAATGC
1 GATACTGACTATCGCAATGCGATAATGACAATCGCAACGA
*
1409318 GATACTTACTATCGCAATGCGATAAT-ACAAAATCGCAACGA
1 GATACTGACTATCGCAATGCGATAATGAC--AATCGCAACGA
* * ** ** *
1409359 GATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGC
1 GATACTGACTATCGCAATGCGATAATGACAATCGCAACGA
*
1409399 GATAAT-ACATAATCGCAATGCGAT
1 GATACTGAC-T-ATCGCAATGCGAT
1409423 TTTCAAAGCG
Statistics
Matches: 84, Mismatches: 16, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
39 4 0.05
40 38 0.45
41 40 0.48
42 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (40 bp):
GATACTGACTATCGCAATGCGATAATGACAATCGCAACGA
Found at i:1409950 original size:20 final size:20
Alignment explanation
Indices: 1409896--1409954 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1409886 GCAATTCTCT
**
1409896 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
1409916 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
1409936 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
1409955 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1411300 original size:18 final size:18
Alignment explanation
Indices: 1411274--1411318 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1411264 TCCACTTCGG
*
1411274 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1411292 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1411310 GAGCCATCA
1 GAGCCATCA
1411319 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1411854 original size:19 final size:20
Alignment explanation
Indices: 1411811--1411855 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1411801 AGCAACACGA
1411811 AAATGACTATCGCAATGCGG
1 AAATGACTATCGCAATGCGG
*
1411831 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAATGCGG
1411850 AAATGA
1 AAATGA
1411856 AAATCGCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (20 bp):
AAATGACTATCGCAATGCGG
Found at i:1411878 original size:14 final size:14
Alignment explanation
Indices: 1411855--1411912 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1411845 ATGCGAAATG
1411855 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
1411869 AAAATTGCAATGCGAA
1 AAAATCGCAA--CGAC
1411885 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1411901 AAAATCGCAACG
1 AAAATCGCAACG
1411913 CGAAACACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1411897 original size:32 final size:33
Alignment explanation
Indices: 1411839--1411917 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
1411829 GGAAATGGCT
1411839 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1411872 ATTGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1411904 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
1411918 CACAAATCGC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 28 0.65
33 15 0.35
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1412053 original size:27 final size:28
Alignment explanation
Indices: 1411987--1412055 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 28
1411977 AGTAAACTAT
*
1411987 TCTTCTTCTGGAATGTTTATATATGTTG
1 TCTTCTTCTGGAATGTTTATATAAGTTG
*
1412015 TCTT-TT-T-AAATGTTTATATAAG-TG
1 TCTTCTTCTGGAATGTTTATATAAGTTG
1412039 -CTTACTTCTGGAATGTT
1 TCTT-CTTCTGGAATGTT
1412056 ATCTGAGCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
23 3 0.09
24 2 0.06
25 15 0.44
26 2 0.06
27 8 0.24
28 4 0.12
ACGTcount: A:0.22, C:0.10, G:0.16, T:0.52
Consensus pattern (28 bp):
TCTTCTTCTGGAATGTTTATATAAGTTG
Found at i:1412418 original size:41 final size:42
Alignment explanation
Indices: 1412322--1412409 Score: 124
Period size: 41 Copynumber: 2.1 Consensus size: 42
1412312 GACTCACCTG
* *
1412322 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
* * *
1412364 TCCTCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
1412405 TCATC
1 TCATC
1412410 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 22 0.55
42 18 0.45
ACGTcount: A:0.22, C:0.43, G:0.15, T:0.20
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
Found at i:1413944 original size:297 final size:297
Alignment explanation
Indices: 1413410--1414004 Score: 1172
Period size: 297 Copynumber: 2.0 Consensus size: 297
1413400 CTTGTGCTTG
*
1413410 GCGCGTTTGATGACGGGAAGCACAGAGTTTCTACCTCCCACCGATAGAGATAGAGCTGCAGTAGG
1 GCGCGTTTGACGACGGGAAGCACAGAGTTTCTACCTCCCACCGATAGAGATAGAGCTGCAGTAGG
*
1413475 CTTGTGGTTTCGGCATTATATGGCTAGAGCAATATATTCGAGACGCTGCCTACCTGCATCCGCCT
66 CTTGTGGTTTCGGCATTATATGGCTAGAGCAATATATTCGAGACGCTGCCTACCTGCATCCGCAT
1413540 TATGAAAGTGTCCATTGTTAATTGGTAAGTCAAATGCAAGTTTTGTTAACATATATACTCCTTTT
131 TATGAAAGTGTCCATTGTTAATTGGTAAGTCAAATGCAAGTTTTGTTAACATATATACTCCTTTT
1413605 GGTTTGAAAATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTG
196 GGTTTGAAAATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTG
1413670 TAGGAAGTCTTGTTTGAGCAAATGTTTGGTTTCTGTA
261 TAGGAAGTCTTGTTTGAGCAAATGTTTGGTTTCTGTA
1413707 GCGCGTTTGACGACGGGAAGCACAGAGTTTCTACCTCCCACCGATAGAGATAGAGCTGCAGTAGG
1 GCGCGTTTGACGACGGGAAGCACAGAGTTTCTACCTCCCACCGATAGAGATAGAGCTGCAGTAGG
1413772 CTTGTGGTTTCGGCATTATATGGCTAGAGCAATATATTCGAGACGCTGCCTACCTGCATCCGCAT
66 CTTGTGGTTTCGGCATTATATGGCTAGAGCAATATATTCGAGACGCTGCCTACCTGCATCCGCAT
1413837 TATGAAAGTGTCCATTGTTAATTGGTAAGTCAAATGCAAGTTTTGTTAACATATATACTCCTTTT
131 TATGAAAGTGTCCATTGTTAATTGGTAAGTCAAATGCAAGTTTTGTTAACATATATACTCCTTTT
1413902 GGTTTGAAAATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTG
196 GGTTTGAAAATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTG
1413967 TAGGAAGTCTTGTTTGAGCAAATGTTTGGTTTCTGTA
261 TAGGAAGTCTTGTTTGAGCAAATGTTTGGTTTCTGTA
1414004 G
1 G
1414005 GTTAATCCTT
Statistics
Matches: 296, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
297 296 1.00
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (297 bp):
GCGCGTTTGACGACGGGAAGCACAGAGTTTCTACCTCCCACCGATAGAGATAGAGCTGCAGTAGG
CTTGTGGTTTCGGCATTATATGGCTAGAGCAATATATTCGAGACGCTGCCTACCTGCATCCGCAT
TATGAAAGTGTCCATTGTTAATTGGTAAGTCAAATGCAAGTTTTGTTAACATATATACTCCTTTT
GGTTTGAAAATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTG
TAGGAAGTCTTGTTTGAGCAAATGTTTGGTTTCTGTA
Found at i:1414139 original size:14 final size:14
Alignment explanation
Indices: 1414120--1414155 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1414110 ATTGTTTAAT
1414120 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1414134 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1414148 TGATTTGT
1 TGATTTGT
1414156 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1414316 original size:19 final size:19
Alignment explanation
Indices: 1414292--1414359 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
1414282 ATCGTAACGA
1414292 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
1414311 GAAAATCGTAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1414330 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
1414344 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
1414360 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
19 28 0.64
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1414377 original size:19 final size:19
Alignment explanation
Indices: 1414349--1414436 Score: 87
Period size: 19 Copynumber: 4.8 Consensus size: 19
1414339 AACGAGAAAA
*
1414349 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1414368 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
* ***
1414384 TAG--TTGCGATAGCCATTT
1 TCGCATTGCGATTTTCA-TT
1414402 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1414421 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
1414437 TCGTTGCGAT
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
14 8 0.15
16 2 0.04
18 2 0.04
19 33 0.61
20 9 0.17
ACGTcount: A:0.17, C:0.22, G:0.18, T:0.43
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1414410 original size:20 final size:20
Alignment explanation
Indices: 1414387--1414466 Score: 59
Period size: 19 Copynumber: 4.3 Consensus size: 20
1414377 GATTTTCTAG
1414387 TTGCGATAGCCATTTTCGCA
1 TTGCGATAGCCATTTTCGCA
***
1414407 TTGCGATTTTCA-TTTCGCA
1 TTGCGATAGCCATTTTCGCA
1414426 TTGCGAT-----TTTCTCG--
1 TTGCGATAGCCATTT-TCGCA
*
1414440 TTGCGATAGCCATTTTCGCG
1 TTGCGATAGCCATTTTCGCA
1414460 TTGCGAT
1 TTGCGAT
1414467 TTCCCCGTTG
Statistics
Matches: 48, Mismatches: 3, Indels: 18
0.70 0.04 0.26
Matches are distributed among these distances:
14 7 0.15
15 2 0.04
16 3 0.06
18 3 0.06
19 17 0.35
20 16 0.33
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.41
Consensus pattern (20 bp):
TTGCGATAGCCATTTTCGCA
Found at i:1414413 original size:53 final size:53
Alignment explanation
Indices: 1414349--1414468 Score: 213
Period size: 53 Copynumber: 2.3 Consensus size: 53
1414339 AACGAGAAAA
*
1414349 TCGCAATGCGATTTTCATTTCGCATTGCGATTTTCTAGTTGCGATAGCCATTT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTAGTTGCGATAGCCATTT
*
1414402 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAGCCATTT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTAGTTGCGATAGCCATTT
*
1414455 TCGCGTTGCGATTT
1 TCGCATTGCGATTT
1414469 CCCCGTTGCG
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 64 1.00
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.42
Consensus pattern (53 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTAGTTGCGATAGCCATTT
Found at i:1414705 original size:20 final size:20
Alignment explanation
Indices: 1414680--1414729 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1414670 TTGAAGATGA
1414680 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
1414700 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
1414720 TTGCGATTTT
1 TTGCGATTTT
1414730 GTATTATCTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Done.