Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 4 of 82
Found at i:1016502 original size:579 final size:579
Alignment explanation
Indices: 1015404--1016562 Score: 1924
Period size: 579 Copynumber: 2.0 Consensus size: 579
1015394 AGCAGCAGTT
*
1015404 TCATCTTTCTTAGCATCTTCAAGCTCCTGAAACTCTTCCTTTTCCAAGCACATCTCTATTGTTTT
1 TCATCTTTCTTAGCATCTTCAAGCTCATGAAACTCTTCCTTTTCCAAGCACATCTCTATTGTTTT
1015469 CTTTGCATCAGAAGAATCTTCCAAAATCTTGTTTTCTGGAATTTCTGCTTCCTTTATTTTCTCGT
66 CTTTGCATCAGAAGAATCTTCCAAAATCTTGTTTTCTGGAATTTCTGCTTCCTTTATTTTCTCGT
* * *
1015534 CTTCTATCTTCTCAACCCTGCTTATAACTTCTTCCTTCTGTTCCTTGGGAAGCAATTCAGAGCTT
131 CTTCTATCTTCTCAACCCTGCTGATAACTTCTTCCTCCTGTTCCTTGGGAAGAAATTCAGAGCTT
* * *
1015599 GTAGTCCCCTCCTCTGATTTATTAGCTGAGAGATTTTGCTCACCTTCATCTCCAGAAATAACATC
196 GCAGTCCCCTCCTCTGATTTATTAGCTAAGAGATTTTGCTCACCTTCATCTCCAGAAAAAACATC
* * * * *
1015664 TAGCTCTGTGTGCACTTCTTCCTTTGTTTTGTCATATTCTATATCCTCACTTATGGCTCCAGTTC
261 TAGCTCTATGGGAACTTCTTCCTTTGCTTTGTCATATTCTATATCCTCACTTATGGCTCCAGTGC
* * * *
1015729 CATGCTCCCTTTCCTCAGAAGGCAATGTAGAAGATTTATTCTGAATTTGCTCCTCAGGTTCCTCT
326 CATGCCCCCTTTCCTCAGAAGGCAATGTAGAAGATGTAGTCTGAATTTGCTCCTCAGGTTCCTCC
* *
1015794 TTTTGAAGACCTTGATCAACAATAGTTTCTTCTTCCGAGACAATGCTTGGCTCCCTTTGCTCTTC
391 TTTTGAAGACCCTGATCAACAATAGTTTCTTCTTCCGAGACAACGCTTGGCTCCCTTTGCTCTTC
*
1015859 CTTTTGCAAGCATACCTCTTCTGTTGTCTTTGTGTCAGACGAATCTTCTAGAGTCTCATGTTTTA
456 CTTTTGCAAGCATACCTCTTCTGTTGTCTTTGTGTCAGAAGAATCTTCTAGAGTCTCATGTTTTA
** *
1015924 CTATTTCAGCATCCT-TCTGTATCTCTTCTTCTATCTTCTCAATTGGGTGTGCAGTGCTG
521 CTATTTCAGCAT-CTGTCTGTATCTCTTCACCTATCTTCTCAATTGGGTGGGCAGTGCTG
*
1015983 TCATCTTTCTTAGCATCTTCAAGCTCATGAAACTCTTCCTTTTCCAAGCACGTCTCTATTGTTTT
1 TCATCTTTCTTAGCATCTTCAAGCTCATGAAACTCTTCCTTTTCCAAGCACATCTCTATTGTTTT
* * * *
1016048 CTTTGCATCGGAAGAATCTTCCGAAATCTTGTTTTCTGGAATTTCTGCTTCCTTTCTTTTCTCTT
66 CTTTGCATCAGAAGAATCTTCCAAAATCTTGTTTTCTGGAATTTCTGCTTCCTTTATTTTCTCGT
** *
1016113 CTTCTATCTTCTCAACTGTGCTGATAGCTTCTTCCTCCTGTTCCTTGGGAAGAAATTCAGAGCTT
131 CTTCTATCTTCTCAACCCTGCTGATAACTTCTTCCTCCTGTTCCTTGGGAAGAAATTCAGAGCTT
* * * *
1016178 GCAGTCCCCTCCTCTGGTTTATTCGCTAAGAGATTTTGCTCGCTTTCATCTCCAGAAAAAACATC
196 GCAGTCCCCTCCTCTGATTTATTAGCTAAGAGATTTTGCTCACCTTCATCTCCAGAAAAAACATC
* *
1016243 TAGCTCTATGGGAACTTCTTCCTTTGCTTTGTCATATTCTTTCTCCTCACTTATGGCTCCAGTGC
261 TAGCTCTATGGGAACTTCTTCCTTTGCTTTGTCATATTCTATATCCTCACTTATGGCTCCAGTGC
* **
1016308 CATGCCCCCTTTCCTCGGAAGGCAATGTAGAAGATGTAGTCTGAATTTGCTCCTTGGGTTCCTCC
326 CATGCCCCCTTTCCTCAGAAGGCAATGTAGAAGATGTAGTCTGAATTTGCTCCTCAGGTTCCTCC
* *
1016373 TTTTGAAGACCCTGATCAACAATAGTTTCTTCTTCTGAGACAGCGCTTGGCTCCCTTTGCTCTTC
391 TTTTGAAGACCCTGATCAACAATAGTTTCTTCTTCCGAGACAACGCTTGGCTCCCTTTGCTCTTC
*
1016438 CTTTTGCAAGCATACCTCTTCTTTTGTCTTTGTGTCAGAAGAATCTTCTAGAGTCTCATGTTTTA
456 CTTTTGCAAGCATACCTCTTCTGTTGTCTTTGTGTCAGAAGAATCTTCTAGAGTCTCATGTTTTA
1016503 CTATTTCAGCATCTGTCTGTATCTCTTCACCTATCTTCTCAATTGGGTGGGCAGTGCTG
521 CTATTTCAGCATCTGTCTGTATCTCTTCACCTATCTTCTCAATTGGGTGGGCAGTGCTG
1016562 T
1 T
1016563 TCTCTTCATC
Statistics
Matches: 537, Mismatches: 42, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
578 2 0.00
579 535 1.00
ACGTcount: A:0.19, C:0.26, G:0.15, T:0.40
Consensus pattern (579 bp):
TCATCTTTCTTAGCATCTTCAAGCTCATGAAACTCTTCCTTTTCCAAGCACATCTCTATTGTTTT
CTTTGCATCAGAAGAATCTTCCAAAATCTTGTTTTCTGGAATTTCTGCTTCCTTTATTTTCTCGT
CTTCTATCTTCTCAACCCTGCTGATAACTTCTTCCTCCTGTTCCTTGGGAAGAAATTCAGAGCTT
GCAGTCCCCTCCTCTGATTTATTAGCTAAGAGATTTTGCTCACCTTCATCTCCAGAAAAAACATC
TAGCTCTATGGGAACTTCTTCCTTTGCTTTGTCATATTCTATATCCTCACTTATGGCTCCAGTGC
CATGCCCCCTTTCCTCAGAAGGCAATGTAGAAGATGTAGTCTGAATTTGCTCCTCAGGTTCCTCC
TTTTGAAGACCCTGATCAACAATAGTTTCTTCTTCCGAGACAACGCTTGGCTCCCTTTGCTCTTC
CTTTTGCAAGCATACCTCTTCTGTTGTCTTTGTGTCAGAAGAATCTTCTAGAGTCTCATGTTTTA
CTATTTCAGCATCTGTCTGTATCTCTTCACCTATCTTCTCAATTGGGTGGGCAGTGCTG
Found at i:1035318 original size:27 final size:27
Alignment explanation
Indices: 1035288--1035376 Score: 108
Period size: 26 Copynumber: 3.3 Consensus size: 27
1035278 AAAAACTCAA
*
1035288 AAAAAAATATTATTATATGTCATGTTG
1 AAAAAAATATTATTAAATGTCATGTTG
* * *
1035315 AAAAAAA-ATTATTACACGTCATGTTC
1 AAAAAAATATTATTAAATGTCATGTTG
* *
1035341 AAAAAAATATTATTAAATGCCATATTG
1 AAAAAAATATTATTAAATGTCATGTTG
1035368 AACAAAAAT
1 AA-AAAAAT
1035377 GTTGTTACAC
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
26 23 0.44
27 23 0.44
28 6 0.12
ACGTcount: A:0.51, C:0.09, G:0.08, T:0.33
Consensus pattern (27 bp):
AAAAAAATATTATTAAATGTCATGTTG
Found at i:1035524 original size:117 final size:117
Alignment explanation
Indices: 1035380--1035718 Score: 325
Period size: 116 Copynumber: 2.9 Consensus size: 117
1035370 CAAAAATGTT
* ** * *
1035380 GTTA-CACGACATATTTAAAATGTTTAAC-TCTAAAAATTTATATTCTAATGAAATACAAAGATC
1 GTTATCACGCCATATTTAAGGTGTTTAACTTC-AAAAGTTTATATTCTAATGAAATACAAAGATA
* * *
1035443 GAGACAAAGTTACATGTCATGATGGAAAAAAAAATTGTTACGTTG-AAAAAAAA
65 GAGACAAAGTTACACGTCATG-TGAAAAAAAAAATTGTTACATTGAAAAAAAAA
* * * * ** * *
1035496 -TTATCGCACGCTATATTTAAGGTG-TTAACTTCAAGAGTTTATGTCCTAACAAAATATAAAAAT
1 GTTAT--CACGCCATATTTAAGGTGTTTAACTTCAAAAGTTTATATTCTAATGAAATACAAAGAT
* *
1035559 AGAGACCAAA-TTATACGTCATGT-TAAAAAAAAATTGTTACATTGAAAAAAAAA
64 AGAGA-CAAAGTTACACGTCATGTGAAAAAAAAAATTGTTACATTGAAAAAAAAA
* * * *
1035612 GTTATTACTCCATATTTAAGGTGTTTAATTTCAAAAGTTTATAATT-TAGTGAAATACAAAGATA
1 GTTATCACGCCATATTTAAGGTGTTTAACTTCAAAAGTTTAT-ATTCTAATGAAATACAAAGATA
* * *
1035676 GAGACAAAGCTACACGCCATGTTGAAAAAAAAAAGTTATTACA
65 GAGACAAAGTTACACGTCATG-TGAAAAAAAAAA-TTGTTACA
1035719 AGCCATTTTT
Statistics
Matches: 176, Mismatches: 34, Indels: 23
0.76 0.15 0.10
Matches are distributed among these distances:
115 41 0.23
116 51 0.29
117 48 0.27
118 29 0.16
119 7 0.04
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.30
Consensus pattern (117 bp):
GTTATCACGCCATATTTAAGGTGTTTAACTTCAAAAGTTTATATTCTAATGAAATACAAAGATAG
AGACAAAGTTACACGTCATGTGAAAAAAAAAATTGTTACATTGAAAAAAAAA
Found at i:1035680 original size:116 final size:113
Alignment explanation
Indices: 1035384--1035708 Score: 305
Period size: 117 Copynumber: 2.8 Consensus size: 113
1035374 AATGTTGTTA
* ** * * *
1035384 CACGACATATTTAAAATGTTTAACTCTAAAAATTTATATTCTAATGAAATACAAAGATCGAGACA
1 CACGCCATATTTAAGGTGTTTAATTC-AAAAGTTTATATT-TAATGAAATACAAAGATAGAGACA
* * *
1035449 AAGTTACATGTCATGATGGAAAAAAAAATTGTTACGTTGAAAAAAAATTATC
64 AAGTTACACGTCATG-T-TAAAAAAAAATTGTTACATTGAAAAAAAATTATC
* * * * ** * *
1035501 GCACGCTATATTTAAGGTG-TTAACTTCAAGAGTTTATGTCCTAACAAAATATAAAAATAGAGAC
1 -CACGCCATATTTAAGGTGTTTAA-TTCAAAAGTTTATAT-TTAATGAAATACAAAGATAGAGA-
*
1035565 CAAA-TTATACGTCATGTTAAAAAAAAATTGTTACATTGAAAAAAAAAGTTAT-
62 CAAAGTTACACGTCATGTTAAAAAAAAATTGTTACATTG-AAAAAAAA-TTATC
* * *
1035617 TACTCCATATTTAAGGTGTTTAATTTCAAAAGTTTATAATTTAGTGAAATACAAAGATAGAGACA
1 CACGCCATATTTAAGGTGTTTAA-TTCAAAAGTTTAT-ATTTAATGAAATACAAAGATAGAGACA
* *
1035682 AAGCTACACGCCATGTTGAAAAAAAAA
64 AAGTTACACGTCATGTT-AAAAAAAAA
1035709 AGTTATTACA
Statistics
Matches: 165, Mismatches: 33, Indels: 19
0.76 0.15 0.09
Matches are distributed among these distances:
115 38 0.23
116 53 0.32
117 54 0.33
118 20 0.12
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (113 bp):
CACGCCATATTTAAGGTGTTTAATTCAAAAGTTTATATTTAATGAAATACAAAGATAGAGACAAA
GTTACACGTCATGTTAAAAAAAAATTGTTACATTGAAAAAAAATTATC
Found at i:1035777 original size:100 final size:98
Alignment explanation
Indices: 1035599--1035807 Score: 226
Period size: 100 Copynumber: 2.1 Consensus size: 98
1035589 AAATTGTTAC
* * * *
1035599 ATTG-AAAAAAAAAGTTATTACTCCATATTTAAGGTGTTTAATTTCAAAAGTTTATAATTTAGTG
1 ATTGAAAAAAAAAAGTTATTACGCCATATTTAAGGTGTTTAACTCCAAAAGTTTATAATTTAATG
* *
1035663 AAATACAAAGATAGAGACAAAGCTACACGCCAT
66 AAATACAAAAATAGAGACAAAGCTACACGACAT
* * * *
1035696 GTTGAAAAAAAAAAGTTATTACAAGCCATTTTTAAGGTGTTTAACCTCCAACAG-TTAT-GTCTT
1 ATTGAAAAAAAAAAGTTATTAC--GCCATATTTAAGGTGTTTAA-CTCCAAAAGTTTATAAT-TT
* * * * *
1035759 AATGAAATATAAAAATAGATACCAAGTTACACGATAT
62 AATGAAATACAAAAATAGAGACAAAGCTACACGACAT
1035796 ATTGAAAAAAAA
1 ATTGAAAAAAAA
1035808 TTTGTTACAC
Statistics
Matches: 91, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
97 3 0.03
98 17 0.19
99 1 0.01
100 64 0.70
101 6 0.07
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.30
Consensus pattern (98 bp):
ATTGAAAAAAAAAAGTTATTACGCCATATTTAAGGTGTTTAACTCCAAAAGTTTATAATTTAATG
AAATACAAAAATAGAGACAAAGCTACACGACAT
Found at i:1039747 original size:10 final size:10
Alignment explanation
Indices: 1039734--1039763 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1039724 TTAAAAAATA
1039734 AAAAAAATTT
1 AAAAAAATTT
*
1039744 AAAATAATTT
1 AAAAAAATTT
1039754 AAAAAAATTT
1 AAAAAAATTT
1039764 CAAATATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAAAAATTT
Found at i:1042510 original size:161 final size:161
Alignment explanation
Indices: 1042336--1042653 Score: 555
Period size: 161 Copynumber: 2.0 Consensus size: 161
1042326 CTTGTACCGC
*
1042336 TTTAGATGTTTGAATTGAAGCTTGAAGATTATTAGAAAAGTTTTGGTTTTTGGTCATTCGAGTTT
1 TTTAGATGTTTGAATTGAAGCTTGAAGATTATAAGAAAAGTTTTGGTTTTTGGTCATTCGAGTTT
* * * **
1042401 AGTTAGAGAATCTGGTTTGTAACTTGTAATAAGGTAGAAAAGTGGTCTGCAGGTTGAGCCACTGA
66 AGCTAGAGAATCTGGTTTGTAACCTGTAATAAGGAAGAAAAGTGGTCTGCAGGCAGAGCCACTGA
*
1042466 GCTCAGTTGCCTTCAAATTCGCTCCACGACA
131 GCACAGTTGCCTTCAAATTCGCTCCACGACA
1042497 TTTAGATGTTTGAATTGAAGCTTGAAGATTATAAGAAAAGTTTTGGTTTTTGGTCATTCGAGTTT
1 TTTAGATGTTTGAATTGAAGCTTGAAGATTATAAGAAAAGTTTTGGTTTTTGGTCATTCGAGTTT
*
1042562 AGCTAGAGAATCTGGTTTGTAACCTGTAATAAGGAAGAAAAGTGGTTTGCAGGCAGAGCCACTGA
66 AGCTAGAGAATCTGGTTTGTAACCTGTAATAAGGAAGAAAAGTGGTCTGCAGGCAGAGCCACTGA
*
1042627 GCACAGTTGCCTTCAAATTTGCTCCAC
131 GCACAGTTGCCTTCAAATTCGCTCCAC
1042654 TACAGTCTAT
Statistics
Matches: 148, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
161 148 1.00
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.34
Consensus pattern (161 bp):
TTTAGATGTTTGAATTGAAGCTTGAAGATTATAAGAAAAGTTTTGGTTTTTGGTCATTCGAGTTT
AGCTAGAGAATCTGGTTTGTAACCTGTAATAAGGAAGAAAAGTGGTCTGCAGGCAGAGCCACTGA
GCACAGTTGCCTTCAAATTCGCTCCACGACA
Found at i:1047430 original size:30 final size:30
Alignment explanation
Indices: 1047394--1047467 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
1047384 CGTTAATTTT
* **
1047394 TAAAAATTTATTTGATTTAAAATAAAAATA
1 TAAAAATTTATTTAAAATAAAATAAAAATA
* *
1047424 TAAAAATTTAATTAAAATATAATAAAAATA
1 TAAAAATTTATTTAAAATAAAATAAAAATA
1047454 -AAAAA-TTATTTAAA
1 TAAAAATTTATTTAAA
1047468 TTTTATCTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 8 0.21
29 5 0.13
30 25 0.66
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (30 bp):
TAAAAATTTATTTAAAATAAAATAAAAATA
Found at i:1047432 original size:21 final size:22
Alignment explanation
Indices: 1047408--1047452 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1047398 AATTTATTTG
1047408 ATTTAAAATAAAA-AT-ATAAAA
1 ATTT-AAATAAAATATAATAAAA
*
1047429 ATTTAATTAAAATATAATAAAA
1 ATTTAAATAAAATATAATAAAA
1047451 AT
1 AT
1047453 AAAAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 6 0.29
22 8 0.38
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
ATTTAAATAAAATATAATAAAA
Found at i:1052521 original size:34 final size:34
Alignment explanation
Indices: 1052447--1052521 Score: 98
Period size: 34 Copynumber: 2.2 Consensus size: 34
1052437 TGATTTGATA
1052447 AAAATAAAAATAAAAAAAATTAATTAAATTATAT
1 AAAATAAAAATAAAAAAAATTAATTAAATTATAT
* * * *
1052481 ATAATAAAAA-AATAAAAAATTATTTAAATTTTTT
1 AAAATAAAAATAA-AAAAAATTAATTAAATTATAT
1052515 AAAATAA
1 AAAATAA
1052522 TTTTAAAACT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 2 0.06
34 33 0.94
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (34 bp):
AAAATAAAAATAAAAAAAATTAATTAAATTATAT
Found at i:1066309 original size:26 final size:26
Alignment explanation
Indices: 1066288--1066344 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
1066278 GTCATATTTT
1066288 AAAAAAA-TTGTTACATGCCATATAA
1 AAAAAAATTTGTTACATGCCATATAA
* * *
1066313 AAAAAAATTTGTTACATGTCATGTTA
1 AAAAAAATTTGTTACATGCCATATAA
1066339 AAAAAA
1 AAAAAA
1066345 TGAAAATCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 7 0.25
26 21 0.75
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.30
Consensus pattern (26 bp):
AAAAAAATTTGTTACATGCCATATAA
Found at i:1066341 original size:25 final size:25
Alignment explanation
Indices: 1066286--1066345 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
1066276 ATGTCATATT
1066286 TTAAAAAAA-TTGTTACATGCCATA
1 TTAAAAAAATTTGTTACATGCCATA
* * *
1066310 TAAAAAAAAATTTGTTACATGTCATG
1 T-TAAAAAAATTTGTTACATGCCATA
1066336 TTAAAAAAAT
1 TTAAAAAAAT
1066346 GAAAATCTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 1 0.03
25 15 0.50
26 14 0.47
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.33
Consensus pattern (25 bp):
TTAAAAAAATTTGTTACATGCCATA
Found at i:1066673 original size:19 final size:20
Alignment explanation
Indices: 1066644--1066686 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
1066634 ATTAGACGTT
1066644 AATGCCGTTTACACATTTGA
1 AATGCCGTTTACACATTTGA
*
1066664 AATG-CGTTTACACGTTTGA
1 AATGCCGTTTACACATTTGA
1066683 AATG
1 AATG
1066687 GAATATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (20 bp):
AATGCCGTTTACACATTTGA
Found at i:1066848 original size:28 final size:27
Alignment explanation
Indices: 1066772--1066850 Score: 88
Period size: 28 Copynumber: 2.9 Consensus size: 27
1066762 ATGTTGTTAT
* *
1066772 ATTGTTATACGTCATATTG-AAAAAAA
1 ATTGTTACATGTCATATTGAAAAAAAA
* * **
1066798 TTTGTTACATGCCATATAAAAAAAACAA
1 ATTGTTACATGTCATATTGAAAAAA-AA
1066826 ATTGTTACATGTCATATTGAAAAAA
1 ATTGTTACATGTCATATTGAAAAAA
1066851 TGAACCGAAT
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
26 13 0.32
27 5 0.12
28 23 0.56
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (27 bp):
ATTGTTACATGTCATATTGAAAAAAAA
Found at i:1074546 original size:11 final size:11
Alignment explanation
Indices: 1074524--1074557 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1074514 AAAAGTGCTT
*
1074524 TTGGGTTCAAA
1 TTGGCTTCAAA
*
1074535 TTGGCTTTAAA
1 TTGGCTTCAAA
1074546 TTGGCTTCAAA
1 TTGGCTTCAAA
1074557 T
1 T
1074558 AGAAGTTGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (11 bp):
TTGGCTTCAAA
Found at i:1086724 original size:2 final size:2
Alignment explanation
Indices: 1086719--1086749 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1086709 TCTCTCTCTC
1086719 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1086750 CTTTGAGTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1091418 original size:90 final size:90
Alignment explanation
Indices: 1091276--1091740 Score: 330
Period size: 90 Copynumber: 5.2 Consensus size: 90
1091266 AGGATATGAT
* * * * * ***
1091276 GGAGCTGAATTTGGTGAGTATGGAGGATATGGCAGTGGTATGGAGTTGTATAGGGAAGAGCCCTC
1 GGAGGTGAATTTGGTCACTATGGAGAATATGGTAGTGGTATGGAGCCATATAGGGAAGAGCCCTC
*
1091341 CCTTGAATACTCAGGTCATTACGGA
66 CCTTGAATACTCAGGTCATTATGGA
* ** *
1091366 GGAGGTGAATTTGGTCACTATGGAGAATATGGTAGTGGCACAGAGCCATATAGGGGAGAGCCCTC
1 GGAGGTGAATTTGGTCACTATGGAGAATATGGTAGTGGTATGGAGCCATATAGGGAAGAGCCCTC
* * * *
1091431 CCTT-ATATACTCAGCTGACCT-TGAA
66 CCTTGA-ATACTCAGGTCA-TTATGGA
*** ** ** * ** * * *
1091456 GGAGGTGAATTTGGTGGGT-TAAAGTGCTATGGTGGTCTTATGGAGCCACATAGAGATGAGCCCT
1 GGAGGTGAATTTGGTCACTATGGAG-AATATGGTAGTGGTATGGAGCCATATAGGGAAGAGCCCT
*
1091520 TCCTTGAATACTCAGGTCA-TAGTGGA
65 CCCTTGAATACTCAGGTCATTA-TGGA
* * ** *** * *
1091546 GAAGGTGAGTTTGGTCGTTATGGAGAATATGGTAGTGGTATGGAGTTGTGTAGGGGAGAGCCCTC
1 GGAGGTGAATTTGGTCACTATGGAGAATATGGTAGTGGTATGGAGCCATATAGGGAAGAGCCCTC
* *
1091611 CCTTCAATACTCAGGTCATCATGGA
66 CCTTGAATACTCAGGTCATTATGGA
* ** ** * * ** *
1091636 GGAGGTGAATTTGGTCAGT-TCAAGTACCATGGTGGTGTTATGGAGCCATATACAGAAGAGCCAT
1 GGAGGTGAATTTGGTCACTATGGAG-AATATGGTAGTGGTATGGAGCCATATAGGGAAGAGCCCT
* *
1091700 CCCTTGAATACTCCA-ATCATTGTGGA
65 CCCTTGAATACT-CAGGTCATTATGGA
* *
1091726 AGAGATGAATTTGGT
1 GGAGGTGAATTTGGT
1091741 AGTGGAATGG
Statistics
Matches: 281, Mismatches: 84, Indels: 20
0.73 0.22 0.05
Matches are distributed among these distances:
88 1 0.00
89 7 0.02
90 265 0.94
91 8 0.03
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (90 bp):
GGAGGTGAATTTGGTCACTATGGAGAATATGGTAGTGGTATGGAGCCATATAGGGAAGAGCCCTC
CCTTGAATACTCAGGTCATTATGGA
Found at i:1091583 original size:180 final size:180
Alignment explanation
Indices: 1091330--1091712 Score: 482
Period size: 180 Copynumber: 2.1 Consensus size: 180
1091320 GTTGTATAGG
*
1091330 GAAGAGCCCTCCCTTGAATACTCAGGTCATTACGGAGGAGGTGAATTTGGTCACTATGGAGAATA
1 GAAGAGCCCTCCCTTGAATACTCAGGTCATTACGGAGAAGGTGAATTTGGTCACTATGGAGAATA
* *
1091395 TGGTAGTGGCACAGAGCCATATAGGGGAGAGCCCTCCCTT-ATATACTCAGCTGACCTTGAAGGA
66 TGGTAGTGGCACAGAGCCATATAGGGGAGAGCCCTCCCTTCA-ATACTCAGCTCACCATGAAGGA
** * * *
1091459 GGTGAATTTGGTGGGTTAAAGTGCTATGGTGGTCTTATGGAGCCACATAGA
130 GGTGAATTTGGTCAGTTAAAGTACCATGGTGGTCTTATGGAGCCACATACA
* * * * **
1091510 GATGAGCCCTTCCTTGAATACTCAGGTCA-TAGTGGAGAAGGTGAGTTTGGTCGTTATGGAGAAT
1 GAAGAGCCCTCCCTTGAATACTCAGGTCATTA-CGGAGAAGGTGAATTTGGTCACTATGGAGAAT
* ** *** * * * *
1091574 ATGGTAGTGGTATGGAGTTGTGTAGGGGAGAGCCCTCCCTTCAATACTCAGGTCATCATGGAGGA
65 ATGGTAGTGGCACAGAGCCATATAGGGGAGAGCCCTCCCTTCAATACTCAGCTCACCATGAAGGA
* * *
1091639 GGTGAATTTGGTCAGTTCAAGTACCATGGTGGTGTTATGGAGCCATATACA
130 GGTGAATTTGGTCAGTTAAAGTACCATGGTGGTCTTATGGAGCCACATACA
*
1091690 GAAGAGCCATCCCTTGAATACTC
1 GAAGAGCCCTCCCTTGAATACTC
1091713 CAATCATTGT
Statistics
Matches: 171, Mismatches: 30, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
179 2 0.01
180 168 0.98
181 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (180 bp):
GAAGAGCCCTCCCTTGAATACTCAGGTCATTACGGAGAAGGTGAATTTGGTCACTATGGAGAATA
TGGTAGTGGCACAGAGCCATATAGGGGAGAGCCCTCCCTTCAATACTCAGCTCACCATGAAGGAG
GTGAATTTGGTCAGTTAAAGTACCATGGTGGTCTTATGGAGCCACATACA
Found at i:1092166 original size:3 final size:3
Alignment explanation
Indices: 1092158--1092185 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1092148 CTCTTCATTG
1092158 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1092186 ATCTGATCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1092381 original size:24 final size:24
Alignment explanation
Indices: 1092302--1092383 Score: 62
Period size: 25 Copynumber: 3.2 Consensus size: 24
1092292 TTAACGTTAT
* *
1092302 AAATTAATAATTTGTTAAAT-TTAAA
1 AAATTAATAATTTTTTATATATT--A
1092327 AAATATACATAATTTTATT-TGATA-TA
1 AAAT-TA-ATAATTTT-TTAT-ATATTA
1092353 TAAATTAATAATTTTTTATATATTA
1 -AAATTAATAATTTTTTATATATTA
1092378 AAATTA
1 AAATTA
1092384 TATATATACA
Statistics
Matches: 47, Mismatches: 2, Indels: 17
0.71 0.03 0.26
Matches are distributed among these distances:
24 11 0.23
25 15 0.32
26 5 0.11
27 11 0.23
28 5 0.11
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (24 bp):
AAATTAATAATTTTTTATATATTA
Found at i:1092813 original size:23 final size:24
Alignment explanation
Indices: 1092781--1092825 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1092771 AATTTATTAA
1092781 AAATTAATTAATGTATAAATTAGT
1 AAATTAATTAATGTATAAATTAGT
* *
1092805 AAATT-ATTAATTTATCAATTA
1 AAATTAATTAATGTATAAATTA
1092826 ATTAATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (24 bp):
AAATTAATTAATGTATAAATTAGT
Found at i:1092907 original size:16 final size:17
Alignment explanation
Indices: 1092888--1092925 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1092878 ACTAATAATT
1092888 TTTTATA-TTTAATTTA
1 TTTTATATTTTAATTTA
*
1092904 TTTTATATTTTTATTTA
1 TTTTATATTTTAATTTA
1092921 TTTTA
1 TTTTA
1092926 AAAAATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTATATTTTAATTTA
Found at i:1107564 original size:20 final size:19
Alignment explanation
Indices: 1107520--1107559 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
1107510 ATATGGATAA
1107520 TATTTAAAAAAATTTTAAAT
1 TATTTAAAAAAA-TTTAAAT
1107540 TATTTAAAAAAA-TTAAAT
1 TATTTAAAAAAATTTAAAT
1107558 TA
1 TA
1107560 AATTTTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 8 0.40
20 12 0.60
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TATTTAAAAAAATTTAAAT
Found at i:1107581 original size:17 final size:17
Alignment explanation
Indices: 1107556--1107595 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1107546 AAAAAATTAA
1107556 ATTAAATTT-TCTTTTTT
1 ATTAAATTTAT-TTTTTT
*
1107573 ATTATATTTATTTTTTT
1 ATTAAATTTATTTTTTT
1107590 ATTAAA
1 ATTAAA
1107596 ATAAATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 19 0.95
18 1 0.05
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTAAATTTATTTTTTT
Found at i:1115153 original size:20 final size:20
Alignment explanation
Indices: 1115128--1115167 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1115118 TAATAGATAA
1115128 AAAAAATTTTAAAT-TATTTT
1 AAAAAA-TTTAAATATATTTT
1115148 AAAAAATTTAAATATATTTT
1 AAAAAATTTAAATATATTTT
1115168 TTTCTTGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAAAAATTTAAATATATTTT
Found at i:1130937 original size:12 final size:11
Alignment explanation
Indices: 1130921--1130954 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1130911 AATTTTTGTG
1130921 ATTTTTTTTTC
1 ATTTTTTTTTC
*
1130932 AGTTTTTTTTTT
1 A-TTTTTTTTTC
1130944 ATTTTTTTTTC
1 ATTTTTTTTTC
1130955 TTCTTATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.09, C:0.06, G:0.03, T:0.82
Consensus pattern (11 bp):
ATTTTTTTTTC
Found at i:1133682 original size:199 final size:196
Alignment explanation
Indices: 1133343--1133738 Score: 749
Period size: 199 Copynumber: 2.0 Consensus size: 196
1133333 TATGATTTTT
1133343 TATAAGAACTTAATAATAGCTTTTAAGCAAAAAAAAAAAAAAGTTAAGCTAAACAGTCTCTAAAT
1 TATAAGAACTTAATAATAGCTTTTAAGCAAAAAAAAAAAAAAGTTAAGCTAAACAGTCTCTAAAT
1133408 CTCTAAGCCACTTCCTCCATATTATTAGTCCAATAAATTGCATTCATAGAACCGTTTTTTATCCA
66 CTCTAAGCCACTTCCTCCATATTATTAGTCCAATAAATTGCATTCATAGAACCGTTTTTTATCCA
1133473 TAAATTGTAATCATTGTTGTGCACACTATTGGTGAAAAAATACAAAACTTCTTTAATGGCCAATA
131 TAAATTGTAATCATTGTTGTGCACACTATTGGTGAAAAAATACAAAACTTCTTTAATGGCCAATA
1133538 A
196 A
1133539 TNATAAGAACTTAATAATAGTACTTTTAAG-ACAAAAAAAAAAAAAGTTAAGCTAAACAGTCTCT
1 T-ATAAGAACTTAATAATAG--CTTTTAAGCA-AAAAAAAAAAAAAGTTAAGCTAAACAGTCTCT
1133603 AAATCTCTAAGCCACTTCCTCCATATTATTAGTCCAATAAATTGCATTCATAGAACCGTTTTTTA
62 AAATCTCTAAGCCACTTCCTCCATATTATTAGTCCAATAAATTGCATTCATAGAACCGTTTTTTA
1133668 TCCATAAATTGTAATCATTGTTGTGCACACTATTGGTGAAAAAATACAAAACTTCTTTAATGGCC
127 TCCATAAATTGTAATCATTGTTGTGCACACTATTGGTGAAAAAATACAAAACTTCTTTAATGGCC
1133733 AATAA
192 AATAA
1133738 T
1 T
1133739 TCAACTTTGT
Statistics
Matches: 196, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
196 1 0.01
197 18 0.09
198 1 0.01
199 176 0.90
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (196 bp):
TATAAGAACTTAATAATAGCTTTTAAGCAAAAAAAAAAAAAAGTTAAGCTAAACAGTCTCTAAAT
CTCTAAGCCACTTCCTCCATATTATTAGTCCAATAAATTGCATTCATAGAACCGTTTTTTATCCA
TAAATTGTAATCATTGTTGTGCACACTATTGGTGAAAAAATACAAAACTTCTTTAATGGCCAATA
A
Found at i:1135218 original size:24 final size:24
Alignment explanation
Indices: 1135186--1135245 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
1135176 ATGGTGAGAA
*
1135186 TGTGACACGGCAGAGTTTAGAGTT
1 TGTGACACGACAGAGTTTAGAGTT
*
1135210 TGTGACACGACAGGGTTTAGAGTT
1 TGTGACACGACAGAGTTTAGAGTT
1135234 TGTGACACGACA
1 TGTGACACGACA
1135246 TGGTTAGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.27
Consensus pattern (24 bp):
TGTGACACGACAGAGTTTAGAGTT
Found at i:1135250 original size:24 final size:24
Alignment explanation
Indices: 1135131--1135263 Score: 98
Period size: 24 Copynumber: 5.8 Consensus size: 24
1135121 GGCAAGGTAG
* *
1135131 GGTTTAGAGTTTGTGAAACGGCAT
1 GGTTTAGAGTTTGTGACACGACAT
** * * *
1135155 -GTTGGGAATGTGTGACATGACAT
1 GGTTTAGAGTTTGTGACACGACAT
** *
1135178 GG--T-GAGAATGTGACACGGCA-
1 GGTTTAGAGTTTGTGACACGACAT
*
1135198 GAGTTTAGAGTTTGTGACACGACAG
1 G-GTTTAGAGTTTGTGACACGACAT
1135223 GGTTTAGAGTTTGTGACACGACAT
1 GGTTTAGAGTTTGTGACACGACAT
* *
1135247 GG-TTAGAATGTGTGACA
1 GGTTTAGAGTTTGTGACA
1135264 TGGCTGTGAC
Statistics
Matches: 84, Mismatches: 19, Indels: 13
0.72 0.16 0.11
Matches are distributed among these distances:
20 1 0.01
21 13 0.15
23 30 0.36
24 39 0.46
25 1 0.01
ACGTcount: A:0.27, C:0.11, G:0.34, T:0.29
Consensus pattern (24 bp):
GGTTTAGAGTTTGTGACACGACAT
Found at i:1135379 original size:24 final size:24
Alignment explanation
Indices: 1135350--1135431 Score: 71
Period size: 24 Copynumber: 3.5 Consensus size: 24
1135340 GAGAAAATCT
1135350 GTGACACACCAGAGTTTAGAGTTC
1 GTGACACACCAGAGTTTAGAGTTC
* * *
1135374 GTGACACACCATGGAG---GGAATTT
1 GTGACACACCA--GAGTTTAGAGTTC
** *
1135397 GTGACACGTCAGCGTTTAGAGTTC
1 GTGACACACCAGAGTTTAGAGTTC
1135421 GTGACACACCA
1 GTGACACACCA
1135432 TGGGAGGGAT
Statistics
Matches: 42, Mismatches: 11, Indels: 10
0.67 0.17 0.16
Matches are distributed among these distances:
21 2 0.05
23 13 0.31
24 24 0.57
26 3 0.07
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (24 bp):
GTGACACACCAGAGTTTAGAGTTC
Found at i:1135432 original size:47 final size:47
Alignment explanation
Indices: 1135302--1135595 Score: 293
Period size: 47 Copynumber: 6.3 Consensus size: 47
1135292 GTGACACGGT
* * * * * * * **
1135302 TGTGACACGCCAACATTCAGAGTTGGTGACACTCGACGGAGAAAATC
1 TGTGACACGCCAGCGTTTAGAGTTCGTGACACGCCATGGAGGGAATC
* * * *
1135349 TGTGACACACCAGAGTTTAGAGTTCGTGACACACCATGGAGGGAATT
1 TGTGACACGCCAGCGTTTAGAGTTCGTGACACGCCATGGAGGGAATC
* *
1135396 TGTGACACGTCAGCGTTTAGAGTTCGTGACACACCATGGGAGGG-ATC
1 TGTGACACGCCAGCGTTTAGAGTTCGTGACACGCCAT-GGAGGGAATC
* * * * * * * * *
1135443 TATGACATGCCAGCATTCAAAGTTCGTGATACGTCATGAAAGGAATC
1 TGTGACACGCCAGCGTTTAGAGTTCGTGACACGCCATGGAGGGAATC
*
1135490 TGTGACACGCCAGCGTTTAGAGTTCATGACACGCCATGGAGGGAATC
1 TGTGACACGCCAGCGTTTAGAGTTCGTGACACGCCATGGAGGGAATC
* * * * *
1135537 TATGACATGCCAACGTTCAGAGTTCGTGACATGCCATGGAGGGAATC
1 TGTGACACGCCAGCGTTTAGAGTTCGTGACACGCCATGGAGGGAATC
*
1135584 TGTGATACGCCA
1 TGTGACACGCCA
1135596 ACATACAGAG
Statistics
Matches: 199, Mismatches: 46, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
46 4 0.02
47 189 0.95
48 6 0.03
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (47 bp):
TGTGACACGCCAGCGTTTAGAGTTCGTGACACGCCATGGAGGGAATC
Found at i:1135621 original size:141 final size:141
Alignment explanation
Indices: 1135345--1135621 Score: 340
Period size: 141 Copynumber: 2.0 Consensus size: 141
1135335 CGACGGAGAA
* * * * *
1135345 AATCTGTGACACACCAGAGTTTAGAGTTCGTGACACACCATGGAGGGAATTTGTGACACGTCAGC
1 AATCTGTGACACACCAGAGTTTAGAGTTCATGACACACCATGGAGGGAATCTATGACACGCCAAC
* * * * * *
1135410 GTTTAGAGTTCGTGACACACCATGGGAGGGATCTATGACATGCCAGCATTCAAAGTTCGTGATAC
66 GTTCAGAGTTCGTGACACACCATGGGAGGGATCTATGACACGCCAACATACAAAGTTCGTCAGAC
1135475 GTCATGAAAGG
131 GTCATGAAAGG
* * * *
1135486 AATCTGTGACACGCCAGCGTTTAGAGTTCATGACACGCCATGGAGGGAATCTATGACATGCCAAC
1 AATCTGTGACACACCAGAGTTTAGAGTTCATGACACACCATGGAGGGAATCTATGACACGCCAAC
** * * * *
1135551 GTTCAGAGTTCGTGACATGCCAT-GGAGGGAATCTGTGATACGCCAACATACAGAGTTTGTCAGA
66 GTTCAGAGTTCGTGACACACCATGGGAGGG-ATCTATGACACGCCAACATACAAAGTTCGTCAGA
*
1135615 CTTCATG
130 CGTCATG
1135622 GAGATCTCTG
Statistics
Matches: 113, Mismatches: 22, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
140 6 0.05
141 107 0.95
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (141 bp):
AATCTGTGACACACCAGAGTTTAGAGTTCATGACACACCATGGAGGGAATCTATGACACGCCAAC
GTTCAGAGTTCGTGACACACCATGGGAGGGATCTATGACACGCCAACATACAAAGTTCGTCAGAC
GTCATGAAAGG
Found at i:1136296 original size:31 final size:31
Alignment explanation
Indices: 1136253--1136858 Score: 829
Period size: 31 Copynumber: 19.5 Consensus size: 31
1136243 GTGTCAGCGT
*
1136253 TGGCGTGTTACAACATTTGAC-TTGATATGCA
1 TGGCGTGTTACAACATTTTACGTT-ATATGCA
*
1136284 TGGCATGTTACAACATTTTACGTTATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
* * *
1136315 TGGCGTGTTGCCACATTTTACGATATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
1136346 TGGCGTGTTACAACATTTTACGTTATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
* *
1136377 TGGCGTGTTGTC-ACATTTTACGATATATGCA
1 TGGCGTGTT-ACAACATTTTACGTTATATGCA
1136408 TGGCGTGTTACAACATTTTACGTTATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
*
1136439 TGGCGTGTTACCACATTTTACGTTATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
*
1136470 TGGAGTGTTACAACATTTTACGTTATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
** *
1136501 TAACGTGTTACCACATTTTACGTTATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
* * * *
1136532 TGGCATGTTACAATATTTTACGTTCTATACA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
* *
1136563 TGGCCTGTTACAACATTTTACGATATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
* *
1136594 TGGCGTGCTACAACATTTTACGATATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
* *
1136625 TGGCGTGTTACAATATTTTACGATATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
* *
1136656 TGGCGTGTTACAATATTTTACGATATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
* * *
1136687 TGGCGTGTTACAATATTTTATGTTATCTGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
* *
1136718 TGGTGTGTTACCACATTTTACGTTATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
** * *
1136749 TAACATGTTACAACATTTTACGTTATATTCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
* * *
1136780 CGGCGTGTTACCACATTTTACGTTACATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
* *
1136811 TGGCATGTTACCACATTTTACGTTATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
*
1136842 TGGCGTGTTACCACATT
1 TGGCGTGTTACAACATT
1136859 ATAGGTTAAC
Statistics
Matches: 511, Mismatches: 61, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
30 1 0.00
31 507 0.99
32 3 0.01
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.38
Consensus pattern (31 bp):
TGGCGTGTTACAACATTTTACGTTATATGCA
Found at i:1138550 original size:145 final size:145
Alignment explanation
Indices: 1138226--1138578 Score: 363
Period size: 145 Copynumber: 2.4 Consensus size: 145
1138216 GGCAGTGAAG
* * * *
1138226 AGCCAGTAAGGACGGTTCTAA-AGGTTTGTGTTAAACAATTCCATATGCGATTATTGAATAACAT
1 AGCCAGTAAGGACAGTTCTAACA-GTTTGTGTTCAACAATTCCATATGTGATTATCGAATAACAT
* * * **
1138290 ATATGTGTTTGCAGTTGGACCATACGACGACAACTCTACAACCACTAATAGGTCCTCCTCAGACT
65 ATATGTATTTACAGTTGGACCATACGACGACAACTCTACAACCACTAATAGGTCCTCCTCAAAAG
**
1138355 CACAGTGCTAACGAGG
130 CACAGTGCTAACGACC
* * * * * *
1138371 AGCCATTAAGGACTGTTATAACGGTTTATATTCAACAATTCCATATGTGATTATCGAATAACATA
1 AGCCAGTAAGGACAGTTCTAACAGTTTGTGTTCAACAATTCCATATGTGATTATCGAATAACATA
* ** * * *
1138436 TCTGTATTTACAGTTGGACCATGTGACGACAGCTCCT-TAACCACTGAGT-GGTCCTCCTCAAAA
66 TATGTATTTACAGTTGGACCATACGACGACAACT-CTACAACCACT-AATAGGTCCTCCTCAAAA
* *
1138499 GCACTGTGTTAACGACC
129 GCACAGTGCTAACGACC
* * * * * *
1138516 AGTCGGTAA-GATCAGTTCTAACAGTTTGTGTTCAACATTTCCATATATGTTTATCGAGTAACA
1 AGCCAGTAAGGA-CAGTTCTAACAGTTTGTGTTCAACAATTCCATATGTGATTATCGAATAACA
1138579 CATTAATTTC
Statistics
Matches: 168, Mismatches: 36, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
144 2 0.01
145 162 0.96
146 4 0.02
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (145 bp):
AGCCAGTAAGGACAGTTCTAACAGTTTGTGTTCAACAATTCCATATGTGATTATCGAATAACATA
TATGTATTTACAGTTGGACCATACGACGACAACTCTACAACCACTAATAGGTCCTCCTCAAAAGC
ACAGTGCTAACGACC
Found at i:1140837 original size:118 final size:117
Alignment explanation
Indices: 1140651--1140878 Score: 312
Period size: 118 Copynumber: 1.9 Consensus size: 117
1140641 TCACACCAAG
* * * * * ** * *
1140651 TATCTGGTTCCACTTAGTGTGTCACCACAATTGGGGTGTGCTGTGTCACCCCACAATACTGTAAG
1 TATCTGCTTACACTCAGCGTGTCACCACAAATGGGGCATGCTGTGTCACCCCACAATAATGCAAG
* * * * *
1140716 AAGTCAGCATGTCATCACATAAATTTGTATGCACTCAACGTGTCACGTAAAC
66 AAGTCAGCATGCCACCACAGAAATCTGCATGCACTCAACGTGTCACGTAAAC
1140768 TATCTGCTTACACTCAGCGTGTCACCACAAGATGGGGCATGCTGTGTCACCCCACAATAATGCAA
1 TATCTGCTTACACTCAGCGTGTCACCACAA-ATGGGGCATGCTGTGTCACCCCACAATAATGCAA
*
1140833 GAAGTCATCATGCCACCACAGAAATCTGCATGCACTCAACGTGTCA
65 GAAGTCAGCATGCCACCACAGAAATCTGCATGCACTCAACGTGTCA
1140879 GCTTAGCATA
Statistics
Matches: 95, Mismatches: 15, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
117 26 0.27
118 69 0.73
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (117 bp):
TATCTGCTTACACTCAGCGTGTCACCACAAATGGGGCATGCTGTGTCACCCCACAATAATGCAAG
AAGTCAGCATGCCACCACAGAAATCTGCATGCACTCAACGTGTCACGTAAAC
Found at i:1145581 original size:2 final size:2
Alignment explanation
Indices: 1145574--1145606 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1145564 TTACTCTTTA
1145574 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1145607 TCATACATGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1149110 original size:29 final size:31
Alignment explanation
Indices: 1149078--1149149 Score: 94
Period size: 32 Copynumber: 2.4 Consensus size: 31
1149068 TTGAATATAG
*
1149078 CGTGTAACAATA-ATATTTTTTT-AACATGA
1 CGTGTAACAACAGATATTTTTTTCAACATGA
* *
1149107 CGTGTAACAACAGTATTTTTTTTTCAACATGG
1 CGTGTAACAACAG-ATATTTTTTTCAACATGA
1149139 CGTGTAACAAC
1 CGTGTAACAAC
1149150 CTTTTTAAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 11 0.30
31 9 0.24
32 17 0.46
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (31 bp):
CGTGTAACAACAGATATTTTTTTCAACATGA
Found at i:1149206 original size:30 final size:30
Alignment explanation
Indices: 1149172--1149229 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1149162 TGCTGTGTAA
** *
1149172 TATTTTTTTGTACATGGCATGTAACAACAG
1 TATTTTTTTCAACATGACATGTAACAACAG
*
1149202 TATTTTTTTCAACATGACGTGTAACAAC
1 TATTTTTTTCAACATGACATGTAACAAC
1149230 CTAACCATGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.40
Consensus pattern (30 bp):
TATTTTTTTCAACATGACATGTAACAACAG
Found at i:1149273 original size:24 final size:24
Alignment explanation
Indices: 1149241--1149316 Score: 107
Period size: 24 Copynumber: 3.2 Consensus size: 24
1149231 TAACCATGGA
*
1149241 GTGTCACATGTTTTTGTACATAAC
1 GTGTCACATGTTTCTGTACATAAC
*
1149265 GTGTCACATGTTTCTGTACATGAC
1 GTGTCACATGTTTCTGTACATAAC
* * *
1149289 GTGTCACATGTTGCTGTATATGAC
1 GTGTCACATGTTTCTGTACATAAC
1149313 GTGT
1 GTGT
1149317 AATAACTTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.39
Consensus pattern (24 bp):
GTGTCACATGTTTCTGTACATAAC
Found at i:1152680 original size:23 final size:24
Alignment explanation
Indices: 1152650--1152695 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
1152640 CATACATGGA
1152650 TTAAAATGAGG-TCAAAATGAGGG
1 TTAAAATGAGGTTCAAAATGAGGG
*
1152673 TTAAAATGAGGTTTAAAATGAGG
1 TTAAAATGAGGTTCAAAATGAGG
1152696 TTTTTTGGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.43, C:0.02, G:0.28, T:0.26
Consensus pattern (24 bp):
TTAAAATGAGGTTCAAAATGAGGG
Found at i:1152696 original size:12 final size:12
Alignment explanation
Indices: 1152650--1152698 Score: 73
Period size: 12 Copynumber: 4.2 Consensus size: 12
1152640 CATACATGGA
1152650 TTAAAATGAGG-
1 TTAAAATGAGGT
* *
1152661 TCAAAATGAGGG
1 TTAAAATGAGGT
1152673 TTAAAATGAGGT
1 TTAAAATGAGGT
1152685 TTAAAATGAGGT
1 TTAAAATGAGGT
1152697 TT
1 TT
1152699 TTTGGGGTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
11 10 0.29
12 24 0.71
ACGTcount: A:0.41, C:0.02, G:0.27, T:0.31
Consensus pattern (12 bp):
TTAAAATGAGGT
Found at i:1152897 original size:24 final size:24
Alignment explanation
Indices: 1152854--1153051 Score: 211
Period size: 24 Copynumber: 8.2 Consensus size: 24
1152844 ATAACCTTTA
* *
1152854 CATGTACAGAAACATATGACACGC
1 CATGTACAAAAACATGTGACACGC
* **
1152878 CATGTACAAAAATATGTGACATAC
1 CATGTACAAAAACATGTGACACGC
* *
1152902 CATGTA-AAGGAACATGTGACACAC
1 CATGTACAA-AAACATGTGACACGC
* * *
1152926 CATGTATAGAAACATGTAACACGC
1 CATGTACAAAAACATGTGACACGC
*
1152950 CATGTA-AAGGAACATGTGACACGC
1 CATGTACAA-AAACATGTGACACGC
* *
1152974 CATATATACAGAAACATGTGACACGC
1 C--ATGTACAAAAACATGTGACACGC
*
1153000 CATGTACAAAAACATGTGACATGC
1 CATGTACAAAAACATGTGACACGC
*
1153024 CATGTACAAAAACATGTTACACGC
1 CATGTACAAAAACATGTGACACGC
1153048 CATG
1 CATG
1153052 GTTAAAAAAG
Statistics
Matches: 145, Mismatches: 23, Indels: 12
0.81 0.13 0.07
Matches are distributed among these distances:
23 3 0.02
24 121 0.83
25 1 0.01
26 19 0.13
27 1 0.01
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (24 bp):
CATGTACAAAAACATGTGACACGC
Found at i:1153114 original size:29 final size:29
Alignment explanation
Indices: 1153063--1153157 Score: 106
Period size: 29 Copynumber: 3.3 Consensus size: 29
1153053 TTAAAAAAGG
*
1153063 TTGTTACACGCCATGTTGAAAAAAAAATTGA
1 TTGTTACACGCCATATTG-AAAAAAAATT-A
1153094 -TGTTACACGCCATATTGAAAAAAAATTA
1 TTGTTACACGCCATATTGAAAAAAAATTA
** * *
1153122 TTGTTACACAACATATT-CAAAAACATT-
1 TTGTTACACGCCATATTGAAAAAAAATTA
1153149 TTGTTACAC
1 TTGTTACAC
1153158 TTTAATGTTA
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
27 9 0.16
28 9 0.16
29 24 0.41
30 16 0.28
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (29 bp):
TTGTTACACGCCATATTGAAAAAAAATTA
Found at i:1154794 original size:2 final size:2
Alignment explanation
Indices: 1154787--1154822 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1154777 TCTTTTATTT
1154787 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1154823 TCAGACATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1154849 original size:43 final size:43
Alignment explanation
Indices: 1154797--1154879 Score: 150
Period size: 43 Copynumber: 1.9 Consensus size: 43
1154787 TATATATATA
1154797 TATATATATATATATATATATAATATTCAGACATGTCATTNTAG
1 TATATATATATATATATATATAATATTCAGACATGTCATT-TAG
1154841 TATA-ATATATATATATATATAATATTCAGACATGTCATT
1 TATATATATATATATATATATAATATTCAGACATGTCATT
1154880 GTTCAAGTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
43 35 0.90
44 4 0.10
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.43
Consensus pattern (43 bp):
TATATATATATATATATATATAATATTCAGACATGTCATTTAG
Found at i:1155425 original size:22 final size:21
Alignment explanation
Indices: 1155400--1155457 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
1155390 AACTAATTTA
*
1155400 ATTACCAACTTAAATTAACTTT
1 ATTAACAACTT-AATTAACTTT
* *
1155422 ATTAACTACTTAATTAAC-TA
1 ATTAACAACTTAATTAACTTT
1155442 ATTAACCAA-TTAATTA
1 ATTAA-CAACTTAATTA
1155458 GTTAATTAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 13 0.42
21 9 0.29
22 9 0.29
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTAACAACTTAATTAACTTT
Found at i:1155642 original size:4 final size:4
Alignment explanation
Indices: 1155611--1155653 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
1155601 TACTACTTTA
* * *
1155611 AATT AACTT AATT AACT AATT AACT AATT AATT AGTT AATT AA
1 AATT AA-TT AATT AATT AATT AATT AATT AATT AATT AATT AA
1155654 AATATCTAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
4 28 0.88
5 4 0.12
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (4 bp):
AATT
Found at i:1164705 original size:64 final size:66
Alignment explanation
Indices: 1164595--1164730 Score: 170
Period size: 64 Copynumber: 2.1 Consensus size: 66
1164585 TCCAATGGGC
* * ** *
1164595 TCTTTTTTTTCTTTTTTTTCTCTCCTTCCTTATTGCTCTTTAGTGATGGGTTCTTCTTCTTTT-T
1 TCTTTTCTTTCTTTTTTTTCTCTCCTTCCTCATTGCTCTCCAGTGATGGGCTCTTCTTCTTTTCT
1164659 T
66 T
* *
1164660 TCTTTTCTTTC-TTTTTTTCTCTCCTTCCTCCTTG-TACTCCGGTGATGGGCTCTTCTTCTTTTC
1 TCTTTTCTTTCTTTTTTTTCTCTCCTTCCTCATTGCT-CTCCAGTGATGGGCTCTTCTTCTTTTC
1164723 TT
65 TT
*
1164725 CCTTTT
1 TCTTTT
1164731 TCTCTCTCTT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
63 1 0.02
64 43 0.70
65 17 0.28
ACGTcount: A:0.04, C:0.25, G:0.10, T:0.62
Consensus pattern (66 bp):
TCTTTTCTTTCTTTTTTTTCTCTCCTTCCTCATTGCTCTCCAGTGATGGGCTCTTCTTCTTTTCT
T
Found at i:1166356 original size:42 final size:41
Alignment explanation
Indices: 1166309--1166440 Score: 149
Period size: 42 Copynumber: 3.1 Consensus size: 41
1166299 GTAATGATAT
*
1166309 TGACCCTGCTATGTACGAGTAGAAGTGTGCATAAGCCGATGA
1 TGACCC-GCTATGTGCGAGTAGAAGTGTGCATAAGCCGATGA
* * *
1166351 TGACCCGACTATGTGCAAGT-GAGAGTGTGCATAAGTCGATGC
1 TGACCCG-CTATGTGCGAGTAGA-AGTGTGCATAAGCCGATGA
* ** *
1166393 TGACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGATGT
1 TGACCC-GCTATGTGCGAGTAGAAGTGTGCATAAGCCGATGA
1166435 TGACCC
1 TGACCC
1166441 AGCCATATGC
Statistics
Matches: 76, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
41 3 0.04
42 71 0.93
43 2 0.03
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (41 bp):
TGACCCGCTATGTGCGAGTAGAAGTGTGCATAAGCCGATGA
Found at i:1166460 original size:42 final size:41
Alignment explanation
Indices: 1166338--1166463 Score: 126
Period size: 42 Copynumber: 3.0 Consensus size: 41
1166328 TAGAAGTGTG
* **
1166338 CATAAGCCGATGATGACCCGACTATGTGCAAGTGAGAGTGTG
1 CATAAGCCGATGATGACCCG-CTATGTGCAAGTGGGAGTGCA
* * * *
1166380 CATAAGTCGATGCTGACCCGGCTATGTGCGAGTAGGAGTGCA
1 CATAAGCCGATGATGACCC-GCTATGTGCAAGTGGGAGTGCA
* * * *
1166422 CATAAGCCGATGTTGACCCAGCCATATGCTAGTGGGAGTGCA
1 CATAAGCCGATGATGACCC-GCTATGTGCAAGTGGGAGTGCA
1166464 TATGAGCTAA
Statistics
Matches: 69, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
42 68 0.99
43 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.21
Consensus pattern (41 bp):
CATAAGCCGATGATGACCCGCTATGTGCAAGTGGGAGTGCA
Found at i:1166510 original size:2 final size:2
Alignment explanation
Indices: 1166503--1166530 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1166493 ATGATGATTG
1166503 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
1166531 GGTGTATGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1166815 original size:21 final size:21
Alignment explanation
Indices: 1166786--1166827 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1166776 TTGGCCAGCC
* *
1166786 AAATTTCGCTGCAGCGAGAAA
1 AAATCTCGCTGCAACGAGAAA
1166807 AAATCTCGCTGCAACGAGAAA
1 AAATCTCGCTGCAACGAGAAA
1166828 CTTTCTGTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.17
Consensus pattern (21 bp):
AAATCTCGCTGCAACGAGAAA
Found at i:1168964 original size:36 final size:36
Alignment explanation
Indices: 1168882--1169068 Score: 225
Period size: 36 Copynumber: 5.2 Consensus size: 36
1168872 AATTGTTTAA
* *
1168882 TTTAATCACTTAGGCCCAATAACTTAATTAAACAA-
1 TTTAATCAATTAAGCCCAATAACTTAATTAAACAAT
* * *
1168917 TTTAATTAATTAAGCCCAACAACTTAATTAAATAAT
1 TTTAATCAATTAAGCCCAATAACTTAATTAAACAAT
* * *
1168953 TTTAATCAATTAGGCTCAATGACTTAATTAAACAAT
1 TTTAATCAATTAAGCCCAATAACTTAATTAAACAAT
* *
1168989 TTTAATCAATTAAGCCCAATGACTTAATTAAATAA-
1 TTTAATCAATTAAGCCCAATAACTTAATTAAACAAT
* * * * *
1169024 TATAATTAATTAAGCCTAACAACTTAATTGAACAAT
1 TTTAATCAATTAAGCCCAATAACTTAATTAAACAAT
1169060 TTTAATCAA
1 TTTAATCAA
1169069 ATACTTGAGA
Statistics
Matches: 127, Mismatches: 23, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
35 58 0.46
36 69 0.54
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (36 bp):
TTTAATCAATTAAGCCCAATAACTTAATTAAACAAT
Found at i:1168978 original size:71 final size:72
Alignment explanation
Indices: 1168882--1169068 Score: 252
Period size: 71 Copynumber: 2.6 Consensus size: 72
1168872 AATTGTTTAA
* *
1168882 TTTAATCACTTAGGCCCAATAACTTAATTAAACAA-TTTAATTAATTAAGCCCAACAACTTAATT
1 TTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTTAATCAATTAAGCCCAACAACTTAATT
1168946 AAATAAT
66 AAATAAT
* * **
1168953 TTTAATCAATTAGGCTCAATGACTTAATTAAACAATTTTAATCAATTAAGCCCAATGACTTAATT
1 TTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTTAATCAATTAAGCCCAACAACTTAATT
1169018 AAATAA-
66 AAATAAT
* * * * * *
1169024 TATAATTAATTAAGCCTAACAACTTAATTGAACAATTTTAATCAA
1 TTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTTAATCAA
1169069 ATACTTGAGA
Statistics
Matches: 101, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
71 69 0.68
72 32 0.32
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (72 bp):
TTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTTAATCAATTAAGCCCAACAACTTAATT
AAATAAT
Found at i:1175756 original size:29 final size:29
Alignment explanation
Indices: 1175723--1175778 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
1175713 GAGGTGTACA
*
1175723 AGAATAGGTACGAGAGAAGAAGCTGTATG
1 AGAATAGGTACAAGAGAAGAAGCTGTATG
*
1175752 AGAATAGGTACAAGAGAATAAGCTGTA
1 AGAATAGGTACAAGAGAAGAAGCTGTA
1175779 CATGAATAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.45, C:0.07, G:0.30, T:0.18
Consensus pattern (29 bp):
AGAATAGGTACAAGAGAAGAAGCTGTATG
Found at i:1175785 original size:29 final size:28
Alignment explanation
Indices: 1175717--1175786 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 28
1175707 AGAAAAGAGG
*
1175717 TGTACAAGAATAGGTACGAGAGAAGAAGC
1 TGTAC-AGAATAGGTACAAGAGAAGAAGC
* *
1175746 TGTATGAGAATAGGTACAAGAGAATAAGC
1 TGTA-CAGAATAGGTACAAGAGAAGAAGC
1175775 TGTACATGAATA
1 TGTACA-GAATA
1175787 AGTATACGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 1 0.03
29 34 0.97
ACGTcount: A:0.44, C:0.09, G:0.27, T:0.20
Consensus pattern (28 bp):
TGTACAGAATAGGTACAAGAGAAGAAGC
Found at i:1176095 original size:26 final size:26
Alignment explanation
Indices: 1176066--1176140 Score: 132
Period size: 26 Copynumber: 2.9 Consensus size: 26
1176056 AAGTAATACT
1176066 TGAAGTAGCGCTTCACTTGTTCTGCG
1 TGAAGTAGCGCTTCACTTGTTCTGCG
1176092 TGAAGTAGCGCTTCACTTGTTCTGCG
1 TGAAGTAGCGCTTCACTTGTTCTGCG
* *
1176118 TGAAGTAACGCTTCACTTATTCT
1 TGAAGTAGCGCTTCACTTGTTCT
1176141 AGTTATTCTG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 47 1.00
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.36
Consensus pattern (26 bp):
TGAAGTAGCGCTTCACTTGTTCTGCG
Found at i:1176157 original size:35 final size:35
Alignment explanation
Indices: 1176111--1176184 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 35
1176101 GCTTCACTTG
*
1176111 TTCTGCGTGAAGTAACGCTTCACTTATTCTAGTTA
1 TTCTGCGTGAAGTAACACTTCACTTATTCTAGTTA
* * *
1176146 TTCTGCGTGAAGTAACACTTCACTTGTTCTGGTTG
1 TTCTGCGTGAAGTAACACTTCACTTATTCTAGTTA
1176181 TTCT
1 TTCT
1176185 CTATATAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.42
Consensus pattern (35 bp):
TTCTGCGTGAAGTAACACTTCACTTATTCTAGTTA
Found at i:1177419 original size:35 final size:35
Alignment explanation
Indices: 1177373--1177441 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
1177363 AATGATGATA
*
1177373 ATGCAAATGCAGCTGCTTAGGGCTTAATCTTATAT
1 ATGCAAATGCAGCTGCTTAAGGCTTAATCTTATAT
1177408 ATGCAAATGCAGCTGCTTAAGGCTTAATCTTATA
1 ATGCAAATGCAGCTGCTTAAGGCTTAATCTTATA
1177442 AAAAAAGAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (35 bp):
ATGCAAATGCAGCTGCTTAAGGCTTAATCTTATAT
Found at i:1180903 original size:2 final size:2
Alignment explanation
Indices: 1180891--1180962 Score: 101
Period size: 2 Copynumber: 36.0 Consensus size: 2
1180881 TCATTGGATG
1180891 CT CT GCT CT CT CT CT CT C- CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT -CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* * *
1180933 CT CT CT CT CC CT CC CT CT CT CT CT GT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1180963 TTCAGTTTAC
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
1 1 0.02
2 59 0.95
3 2 0.03
ACGTcount: A:0.00, C:0.51, G:0.03, T:0.46
Consensus pattern (2 bp):
CT
Found at i:1182404 original size:25 final size:26
Alignment explanation
Indices: 1182358--1182410 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
1182348 TGAACATAAA
* *
1182358 AATAATAAATATTATTTTAATT-AAT
1 AATAATAAATATTAATTAAATTCAAT
* *
1182383 AATAATTAATTTTAATTAAATTCAAT
1 AATAATAAATATTAATTAAATTCAAT
1182409 AA
1 AA
1182411 AAAATAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
AATAATAAATATTAATTAAATTCAAT
Found at i:1184100 original size:14 final size:15
Alignment explanation
Indices: 1184073--1184104 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
1184063 ATAATACAGC
1184073 TAACAAATATAATAA
1 TAACAAATATAATAA
1184088 TAACAAA-ATAATAA
1 TAACAAATATAATAA
1184102 TAA
1 TAA
1184105 AGCTAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (15 bp):
TAACAAATATAATAA
Found at i:1188761 original size:23 final size:24
Alignment explanation
Indices: 1188735--1188787 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1188725 ATTATTAATA
*
1188735 AATTT-GTTGGTTTTTAATGAAAT
1 AATTTAGTTCGTTTTTAATGAAAT
* *
1188758 AATTTATTTCTTTTTTAATGAAAT
1 AATTTAGTTCGTTTTTAATGAAAT
1188782 AATTTA
1 AATTTA
1188788 TTTCTTTCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (24 bp):
AATTTAGTTCGTTTTTAATGAAAT
Found at i:1188788 original size:24 final size:24
Alignment explanation
Indices: 1188745--1188794 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1188735 AATTTGTTGG
1188745 TTTTTAATGAAATAATTTATTTCT
1 TTTTTAATGAAATAATTTATTTCT
1188769 TTTTTAATGAAATAATTTATTTCT
1 TTTTTAATGAAATAATTTATTTCT
1188793 TT
1 TT
1188795 CTCATAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (24 bp):
TTTTTAATGAAATAATTTATTTCT
Found at i:1190345 original size:2 final size:2
Alignment explanation
Indices: 1190338--1190386 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1190328 TGCACGTATT
1190338 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1190380 TC TC TC T
1 TC TC TC T
1190387 TTAATTCTCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1197075 original size:26 final size:24
Alignment explanation
Indices: 1197037--1197106 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 24
1197027 TTTCAAAATT
*
1197037 TAAAATTTATTTATTACTAATGTAA
1 TAAAATTTATTTATTAATAATGT-A
* *
1197062 TAATATTTGATTTACTAATAATGTA
1 TAAAATTT-ATTTATTAATAATGTA
*
1197087 TAAAATTTATATATTAATAA
1 TAAAATTTATTTATTAATAA
1197107 ATACATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
24 10 0.26
25 15 0.39
26 13 0.34
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (24 bp):
TAAAATTTATTTATTAATAATGTA
Found at i:1198235 original size:3 final size:3
Alignment explanation
Indices: 1198229--1198259 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1198219 AACTTATCTT
1198229 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1198260 GTCAGTGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:1202777 original size:25 final size:27
Alignment explanation
Indices: 1202749--1202799 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 27
1202739 TCCAATTTTT
1202749 AATAAAATATTAATA-TT-AAATTATA
1 AATAAAATATTAATATTTAAAATTATA
1202774 AATAAAATATTAATATTTAAAATTAT
1 AATAAAATATTAATATTTAAAATTAT
1202800 CAATTATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 15 0.62
26 2 0.08
27 7 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
AATAAAATATTAATATTTAAAATTATA
Found at i:1202911 original size:21 final size:22
Alignment explanation
Indices: 1202851--1202935 Score: 68
Period size: 25 Copynumber: 3.8 Consensus size: 22
1202841 AACAAAATAA
1202851 ATTAA-AATTAAATAAACATAATAT
1 ATTAATAATTAAATAAAC--AAT-T
* *
1202875 CATTTA-AATTAGATAAACAA-T
1 -ATTAATAATTAAATAAACAATT
*
1202896 ATTAATAATTAAATAATCAATT
1 ATTAATAATTAAATAAACAATT
*
1202918 ATTAATATTTTAAATAAA
1 ATTAATA-ATTAAATAAA
1202936 TTATACATTA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
20 4 0.08
21 13 0.26
22 8 0.16
23 10 0.20
25 15 0.30
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.38
Consensus pattern (22 bp):
ATTAATAATTAAATAAACAATT
Found at i:1202954 original size:117 final size:110
Alignment explanation
Indices: 1202777--1203127 Score: 367
Period size: 110 Copynumber: 3.1 Consensus size: 110
1202767 AATTATAAAT
* **
1202777 AAAATATTAATATTTAAAATTATCAATTATTAATA----AAATAAATTATAAATTATTCCTATTT
1 AAAATATTAATATTT-AAATTATCAATTATTAATATTTTAAATAAATTATACATTATTAATATTT
**
1202838 AAAAACAAAATAAATTAAAATTAAATAAACATAATATCATTTAAATTAGATA
65 AAAAA-AAAATAAA-TAAAA--AAATAAACATAATAAAATTT-AATTA-ATA
* *
1202890 AACAATATTAATAATTAAATAATCAATTATTAATATTTTAAATAAATTATACATTATTAATATTT
1 AA-AATATTAATATTTAAATTATCAATTATTAATATTTTAAATAAATTATACATTATTAATATTT
* * *
1202955 AAAAAATAA-AAATAAAAAATTAATCATAATAAAATTTAATTAATA
65 AAAAAAAAATAAATAAAAAAATAAACATAATAAAATTTAATTAATA
* *
1203000 AAAATAATTAATATTTAAATTATCTATTATTAATATTTTAAATAAATAAT-CAATTATTAAT-TT
1 AAAAT-ATTAATATTTAAATTATCAATTATTAATATTTTAAATAAATTATAC-ATTATTAATATT
* * * *
1203063 TCAAAAATAAAATAAAATAAAAAATTGATCATAATAATATTTAAATTAA-A
64 T-AAAAA-AAAAT-AAATAAAAAAATAAACATAATAAAATTT-AATTAATA
*
1203113 TAAATATTAATATTT
1 AAAATATTAATATTT
1203128 TAAAAAAATA
Statistics
Matches: 208, Mismatches: 18, Indels: 25
0.83 0.07 0.10
Matches are distributed among these distances:
109 7 0.03
110 59 0.28
111 8 0.04
112 26 0.12
113 51 0.25
114 23 0.11
115 3 0.01
116 3 0.01
117 28 0.13
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (110 bp):
AAAATATTAATATTTAAATTATCAATTATTAATATTTTAAATAAATTATACATTATTAATATTTA
AAAAAAAATAAATAAAAAAATAAACATAATAAAATTTAATTAATA
Found at i:1203005 original size:20 final size:17
Alignment explanation
Indices: 1202959--1203006 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 17
1202949 ATATTTAAAA
1202959 AATAAAAATAAAAAATT
1 AATAAAAATAAAAAATT
* *
1202976 AATCATAATAAAATTTAATT
1 AATAAAAATAAAA---AATT
1202996 AATAAAAATAA
1 AATAAAAATAA
1203007 TTAATATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 11 0.46
20 13 0.54
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (17 bp):
AATAAAAATAAAAAATT
Found at i:1203131 original size:113 final size:111
Alignment explanation
Indices: 1202759--1203127 Score: 400
Period size: 113 Copynumber: 3.3 Consensus size: 111
1202749 AATAAAATAT
*
1202759 TAATA-TTAAATTATAAATAAAATATTAATATTTAAAATTATCAATTATTAATA----AAATAAA
1 TAATATTTAAATTA-ATA-AAAATATTAATATTT-AAATTATCAATTATTAATATTTTAAATAAA
** * * *
1202819 TTATAAATTATTCCTATTTAAAAACAAAATAAATTAAAATTAAATAAACATAA
63 TTAT-AATTATTAATATTTAAAAA-AAAATAAAATAAAA--AATTAATCATAA
* *
1202872 T-ATCATTTAAATTAGATAAACAATATTAATAATTAAATAATCAATTATTAATATTTTAAATAAA
1 TAAT-ATTTAAATTA-ATAAA-AATATTAATATTTAAATTATCAATTATTAATATTTTAAATAAA
*
1202936 TTATACATTATTAATATTT-AAAAAATA-AAAATAAAAAATTAATCATAA
63 TTATA-ATTATTAATATTTAAAAAAAAATAAAATAAAAAATTAATCATAA
* * *
1202984 TAAAATTT-AATTAATAAAAATAATTAATATTTAAATTATCTATTATTAATATTTTAAATAAATA
1 TAATATTTAAATTAATAAAAAT-ATTAATATTTAAATTATCAATTATTAATATTTTAAATAAATT
*
1203048 ATCAATTATTAAT-TTTCAAAAATAAAATAAAATAAAAAATTGATCATAA
65 AT-AATTATTAATATTT-AAAAA-AAAATAAAATAAAAAATTAATCATAA
*
1203097 TAATATTTAAATTAA-ATAAATATTAATATTT
1 TAATATTTAAATTAATAAAAATATTAATATTT
1203128 TAAAAAAATA
Statistics
Matches: 221, Mismatches: 19, Indels: 33
0.81 0.07 0.12
Matches are distributed among these distances:
109 6 0.03
110 54 0.24
111 10 0.05
112 30 0.14
113 55 0.25
114 36 0.16
115 3 0.01
116 5 0.02
117 22 0.10
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (111 bp):
TAATATTTAAATTAATAAAAATATTAATATTTAAATTATCAATTATTAATATTTTAAATAAATTA
TAATTATTAATATTTAAAAAAAAATAAAATAAAAAATTAATCATAA
Found at i:1203163 original size:183 final size:184
Alignment explanation
Indices: 1202970--1203311 Score: 498
Period size: 183 Copynumber: 1.9 Consensus size: 184
1202960 ATAAAAATAA
** * * *
1202970 AAAATTAATC-A-TAATAA-AATTTAATTAATAAAAATAATTAATATTTAAATTATCTATTATTA
1 AAAATTAATCAATTAATAATAATAAAAATAA-AAAAAT-ATTAATATTGAAATTATC-AATATTA
*
1203032 ATATTTTAAATAAATAATC-AATTATTAAT-TTTCAAAAATAAAATAAAATAAAAAATTGATCAT
63 ATA-TTTAAATAAATAATCAAATTATTAATATTTCAAAAATAAAATAAAAT-AAAAATTAATCAT
1203095 AATAATATTTAAATTAAATAAA-TATTAATATTTTAAAAAAATAATAAAATATTATTTT
126 AATAATATTTAAATTAAATAAAGTATTAATATTTTAAAAAAATAATAAAATATTATTTT
* * *
1203153 AAAATTAATCAATTATTAATAATAAAAANAAATAAATATTAATATTGAAATTATCAATATTAATA
1 AAAATTAATCAATTAATAATAATAAAAATAAAAAAATATTAATATTGAAATTATCAATATTAATA
* *
1203218 TTTAAATAAATTATCAAATTATTAATATTTTAAAAATAAAATAAAATAAAAATTAATCATAATAA
66 TTTAAATAAATAATCAAATTATTAATATTTCAAAAATAAAATAAAATAAAAATTAATCATAATAA
1203283 TATTTAAATTAAATAAAGTATTAATATTT
131 TATTTAAATTAAATAAAGTATTAATATTT
1203312 AAATGATTTA
Statistics
Matches: 142, Mismatches: 11, Indels: 11
0.87 0.07 0.07
Matches are distributed among these distances:
182 14 0.10
183 63 0.44
184 48 0.34
185 10 0.07
186 7 0.05
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (184 bp):
AAAATTAATCAATTAATAATAATAAAAATAAAAAAATATTAATATTGAAATTATCAATATTAATA
TTTAAATAAATAATCAAATTATTAATATTTCAAAAATAAAATAAAATAAAAATTAATCATAATAA
TATTTAAATTAAATAAAGTATTAATATTTTAAAAAAATAATAAAATATTATTTT
Found at i:1203188 original size:46 final size:45
Alignment explanation
Indices: 1203128--1203246 Score: 116
Period size: 45 Copynumber: 2.6 Consensus size: 45
1203118 ATTAATATTT
*
1203128 TAAAAAAATAATAAAATATT-ATTTTAAAATTAATCAATTATTAATAA
1 TAAAAAAATAAT-AAATATTAATATTAAAATT-ATCAA-TATTAATAA
* * *
1203175 TAAAAANA-AATAAATATTAATATTGAAATTATCAATATTAATATT
1 TAAAAAAATAATAAATATTAATATTAAAATTATCAATATTAATA-A
* *
1203220 TAAATAAATTATCAAATTATTAATATT
1 TAAAAAAATAAT-AAA-TATTAATATT
1203247 TTAAAAATAA
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
44 8 0.13
45 18 0.30
46 14 0.23
47 10 0.17
48 10 0.17
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.39
Consensus pattern (45 bp):
TAAAAAAATAATAAATATTAATATTAAAATTATCAATATTAATAA
Found at i:1205581 original size:1 final size:1
Alignment explanation
Indices: 1205570--1205611 Score: 66
Period size: 1 Copynumber: 42.0 Consensus size: 1
1205560 GACGGATTTT
* *
1205570 GGGGGGTGGGGGGGGGGGGGGGGGGGGGGAGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1205612 AAGATGTTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.02, C:0.00, G:0.95, T:0.02
Consensus pattern (1 bp):
G
Found at i:1219269 original size:3 final size:3
Alignment explanation
Indices: 1219261--1219292 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1219251 ATTTTTATTC
*
1219261 TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1219293 ATAAGATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1222238 original size:26 final size:29
Alignment explanation
Indices: 1222199--1222252 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 29
1222189 AAATACTTAT
*
1222199 TTGATTTAAAAT-A-AAAAT-ATAAAAAC
1 TTGATTGAAAATAATAAAATAATAAAAAC
*
1222225 TTGATTGAATATAATAAAATAATAAAAA
1 TTGATTGAAAATAATAAAATAATAAAAA
1222253 AATTTATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 10 0.43
27 1 0.04
28 5 0.22
29 7 0.30
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (29 bp):
TTGATTGAAAATAATAAAATAATAAAAAC
Found at i:1223344 original size:25 final size:25
Alignment explanation
Indices: 1223315--1223363 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1223305 TCGACTTAAC
1223315 TAAAA-TTTTTATTACTTCTATTTTT
1 TAAAATTTTTTATTACTT-TATTTTT
*
1223340 TAAAATTTTTTATTAGTTTATTTT
1 TAAAATTTTTTATTACTTTATTTT
1223364 GAAAAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (25 bp):
TAAAATTTTTTATTACTTTATTTTT
Found at i:1223369 original size:25 final size:26
Alignment explanation
Indices: 1223316--1223371 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
1223306 CGACTTAACT
**
1223316 AAAA-TTTTTATTACTTCTATTTTTT
1 AAAATTTTTTATTACTTCTATTTTGA
*
1223341 AAAATTTTTTATTAGTT-TATTTTGA
1 AAAATTTTTTATTACTTCTATTTTGA
1223366 AAAATT
1 AAAATT
1223372 ATTGGCATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 16 0.59
26 11 0.41
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.59
Consensus pattern (26 bp):
AAAATTTTTTATTACTTCTATTTTGA
Found at i:1227764 original size:32 final size:33
Alignment explanation
Indices: 1227728--1227797 Score: 90
Period size: 32 Copynumber: 2.1 Consensus size: 33
1227718 TTTTAATGTC
*
1227728 ATATA-TTTATTTTCATTTCTTATTATAA-TCTT
1 ATATATTTTATTTTCATTT-TTAATATAATTCTT
*
1227760 ATATATTTTATTTTTATTTTTAATATAATTTCTT
1 ATATATTTTATTTTCATTTTTAATATAA-TTCTT
1227794 ATAT
1 ATAT
1227798 TATATATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 13 0.39
33 12 0.36
34 8 0.24
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (33 bp):
ATATATTTTATTTTCATTTTTAATATAATTCTT
Found at i:1232143 original size:2 final size:2
Alignment explanation
Indices: 1232136--1232166 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1232126 NNNNNCTGCT
1232136 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1232167 TATTGCCATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1242504 original size:1 final size:1
Alignment explanation
Indices: 1242498--1242528 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
1242488 AGAGTGGAGG
1242498 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1242529 ATTGTGAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1247760 original size:4 final size:4
Alignment explanation
Indices: 1247751--1247784 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
1247741 GTACACACGG
*
1247751 TACA TACA TACA TACA TACA TACA CACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TACA TA
1247785 TATATAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
TACA
Found at i:1251653 original size:62 final size:62
Alignment explanation
Indices: 1251533--1251654 Score: 165
Period size: 62 Copynumber: 2.0 Consensus size: 62
1251523 AAACAAGAGT
* * * * *
1251533 TAAATTTAGAAAGGAGCATCTTTTAATAATTTTATTGAAAAAACTAATAGCCTGTGAGAAAA
1 TAAATTTAGAAAGGAGCATATTTGAATAATTTTATTAAAAAAACTAATAACCTATGAGAAAA
* *
1251595 TAAATTTAGAAAGGAG-AGTATTTGAATAATTTTATTAAAAAAATTAATAACTTATGAGAA
1 TAAATTTAGAAAGGAGCA-TATTTGAATAATTTTATTAAAAAAACTAATAACCTATGAGAA
1251655 TAGAATGGAT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
61 1 0.02
62 51 0.98
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.34
Consensus pattern (62 bp):
TAAATTTAGAAAGGAGCATATTTGAATAATTTTATTAAAAAAACTAATAACCTATGAGAAAA
Found at i:1267815 original size:29 final size:29
Alignment explanation
Indices: 1267760--1267815 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
1267750 AAATTCAAAA
** *
1267760 AAGTCTTTATTGTTTTATTATGTTCAATC
1 AAGTCTTTATACTTTTATTATGATCAATC
1267789 AAGTCTTTATACTTTTATT-TGGATCAA
1 AAGTCTTTATACTTTTATTAT-GATCAA
1267816 ATAAATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 1 0.04
29 22 0.96
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.52
Consensus pattern (29 bp):
AAGTCTTTATACTTTTATTATGATCAATC
Found at i:1268023 original size:33 final size:33
Alignment explanation
Indices: 1267961--1268024 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
1267951 GTATGTTATG
*
1267961 TTATCATCAATTATAATATGTTAATATACCACA
1 TTATCATCAATTATAATATGTTAACATACCACA
* * * *
1267994 TTATTATCCATTATGATATTTTAACATACCA
1 TTATCATCAATTATAATATGTTAACATACCA
1268025 TGCTAACATC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.39, C:0.16, G:0.03, T:0.42
Consensus pattern (33 bp):
TTATCATCAATTATAATATGTTAACATACCACA
Found at i:1274155 original size:13 final size:13
Alignment explanation
Indices: 1274123--1274155 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
1274113 CTAAGGATGA
1274123 GAATTTGTAGAAT
1 GAATTTGTAGAAT
1274136 GAA-TTGTAGAAT
1 GAATTTGTAGAAT
1274148 GAATTTGT
1 GAATTTGT
1274156 TCATCATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.39
Consensus pattern (13 bp):
GAATTTGTAGAAT
Found at i:1280381 original size:13 final size:13
Alignment explanation
Indices: 1280363--1280388 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1280353 ACATAGGAGA
1280363 GATAGAAGTAGGT
1 GATAGAAGTAGGT
1280376 GATAGAAGTAGGT
1 GATAGAAGTAGGT
1280389 AGAGATAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.23
Consensus pattern (13 bp):
GATAGAAGTAGGT
Found at i:1285446 original size:44 final size:44
Alignment explanation
Indices: 1285396--1285484 Score: 119
Period size: 44 Copynumber: 2.0 Consensus size: 44
1285386 TGGTAGCATC
* * *
1285396 GATCTAGCTGATAGGCTTAA-GCTTGGAAGC-AAATTCATTAATCT
1 GATCTAGCAGATAGGC-TAAGGCTTAGAAGCGAAA-TCATCAATCT
1285440 GATCTAGCAGATAGGCTAAGGCTTAGAAGCGAAATCATCAATCT
1 GATCTAGCAGATAGGCTAAGGCTTAGAAGCGAAATCATCAATCT
1285484 G
1 G
1285485 TGCCAAAGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
43 3 0.08
44 34 0.85
45 3 0.08
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (44 bp):
GATCTAGCAGATAGGCTAAGGCTTAGAAGCGAAATCATCAATCT
Found at i:1293919 original size:17 final size:16
Alignment explanation
Indices: 1293879--1293920 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
1293869 CTTGATTTTT
1293879 TTTAA-TATTTTAAAA
1 TTTAATTATTTTAAAA
*
1293894 TATATATTATTTTAAATA
1 TTTA-ATTATTTTAAA-A
1293912 TTTAATTAT
1 TTTAATTAT
1293921 AAAAATATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 3 0.14
16 1 0.05
17 14 0.64
18 4 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTAATTATTTTAAAA
Found at i:1294245 original size:16 final size:16
Alignment explanation
Indices: 1294224--1294256 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1294214 CTGGTCCTTA
1294224 ACTTAGGAAGGGATTT
1 ACTTAGGAAGGGATTT
1294240 ACTTAGGAAGGGATTT
1 ACTTAGGAAGGGATTT
1294256 A
1 A
1294257 TTTTATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (16 bp):
ACTTAGGAAGGGATTT
Found at i:1299058 original size:24 final size:24
Alignment explanation
Indices: 1299031--1299077 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
1299021 CGTATGGTCA
1299031 TGAAAGCCAGGGTTATGCACCTCG
1 TGAAAGCCAGGGTTATGCACCTCG
1299055 TGAAAGCCAGGGTTATGCACCTC
1 TGAAAGCCAGGGTTATGCACCTC
1299078 AATATAGCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.21
Consensus pattern (24 bp):
TGAAAGCCAGGGTTATGCACCTCG
Found at i:1299124 original size:27 final size:27
Alignment explanation
Indices: 1299094--1299176 Score: 139
Period size: 27 Copynumber: 3.1 Consensus size: 27
1299084 GCTACGCCTC
*
1299094 CCCACAGTATTATCCACCTACACAGGA
1 CCCACAGTATTATCCACCTACACAAGA
*
1299121 CCCACAGTATCATCCACCTACACAAGA
1 CCCACAGTATTATCCACCTACACAAGA
*
1299148 CCCACATTATTATCCACCTACACAAGA
1 CCCACAGTATTATCCACCTACACAAGA
1299175 CC
1 CC
1299177 ATGACAGGGA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.35, C:0.40, G:0.07, T:0.18
Consensus pattern (27 bp):
CCCACAGTATTATCCACCTACACAAGA
Found at i:1301111 original size:54 final size:54
Alignment explanation
Indices: 1301052--1301160 Score: 164
Period size: 54 Copynumber: 2.0 Consensus size: 54
1301042 CTCCTCCTAC
* * * *
1301052 ATATGGTGCAGCATCTTTCAACAGCTCAAAACCTTCCCATTCTACCAGTTTCCA
1 ATATGGTGCAACATCTTTCAACAGCTCAAAACCTTCCAATCCCACCAGTTTCCA
* *
1301106 ATATGGTGCAACATCTTTCAGCAGCTCAAAACCTTCTAATCCCACCAGTTTCCA
1 ATATGGTGCAACATCTTTCAACAGCTCAAAACCTTCCAATCCCACCAGTTTCCA
1301160 A
1 A
1301161 CCAAGCGTCC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.29, C:0.31, G:0.11, T:0.28
Consensus pattern (54 bp):
ATATGGTGCAACATCTTTCAACAGCTCAAAACCTTCCAATCCCACCAGTTTCCA
Found at i:1304556 original size:16 final size:17
Alignment explanation
Indices: 1304535--1304567 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1304525 TAATAAAGAT
1304535 AAATAAAATA-TTAAAA
1 AAATAAAATATTTAAAA
1304551 AAATAAAATATTTAAAA
1 AAATAAAATATTTAAAA
1304568 TATTTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATAAAATATTTAAAA
Found at i:1327427 original size:2 final size:2
Alignment explanation
Indices: 1327420--1327451 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1327410 TGCCGGCCTT
1327420 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
1327452 CATGTGTGTG
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):
TA
Found at i:1328228 original size:2 final size:2
Alignment explanation
Indices: 1328221--1328257 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1328211 TGCATGCATG
1328221 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1328258 TTACCTTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1331301 original size:2 final size:2
Alignment explanation
Indices: 1331294--1331329 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1331284 ACATACATAC
1331294 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
1331330 TTACAACAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1333338 original size:98 final size:94
Alignment explanation
Indices: 1333225--1333406 Score: 310
Period size: 98 Copynumber: 1.9 Consensus size: 94
1333215 TAAAAACTAA
*
1333225 CAAATATATGAAAAGTATGATTACTCTAATTATTAATATGATGACATTAATATATTTTAAATTAA
1 CAAATATATGAAAAGTATGATTACTCTAATTATTAATATGATGACATTAATATA--TTAAACT-A
1333290 AAAAATTATTAGATTGTTAATTATGTTTAAAT
63 AAAAATTATTAGATTGTTAATTATGTTTAAAT
*
1333322 NCAAATATATGAAAAGTATGGTTACTCTAATTATTAATATGATGACATTAATATATTAAACTAAA
1 -CAAATATATGAAAAGTATGATTACTCTAATTATTAATATGATGACATTAATATATTAAACTAAA
1333387 AAATTATTAGATTGTTAATT
65 AAATTATTAGATTGTTAATT
1333407 TGAATATTAT
Statistics
Matches: 82, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
95 23 0.28
96 6 0.07
98 53 0.65
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (94 bp):
CAAATATATGAAAAGTATGATTACTCTAATTATTAATATGATGACATTAATATATTAAACTAAAA
AATTATTAGATTGTTAATTATGTTTAAAT
Found at i:1333543 original size:24 final size:22
Alignment explanation
Indices: 1333515--1333566 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 22
1333505 AAATTATGAC
1333515 TTATAAAATTATTAATTATAATA
1 TTATAAAATTATTAA-TATAATA
** *
1333538 TATATATCATTATTTATATAATA
1 T-TATAAAATTATTAATATAATA
1333561 TTATAA
1 TTATAA
1333567 TATATATACT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
22 4 0.17
23 9 0.38
24 11 0.46
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
TTATAAAATTATTAATATAATA
Found at i:1333572 original size:17 final size:18
Alignment explanation
Indices: 1333529--1333574 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
1333519 AAAATTATTA
1333529 ATTATAATATATAT-ATC
1 ATTATAATATATATAATC
1333546 ATTAT--T-TATATAAT-
1 ATTATAATATATATAATC
1333560 ATTATAATATATATA
1 ATTATAATATATATA
1333575 CTTAAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
14 10 0.40
15 3 0.12
16 1 0.04
17 11 0.44
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTATAATATATATAATC
Found at i:1334074 original size:6 final size:6
Alignment explanation
Indices: 1334063--1334087 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1334053 TAGGAATGTA
1334063 TTAGGG TTAGGG TTAGGG TTAGGG T
1 TTAGGG TTAGGG TTAGGG TTAGGG T
1334088 AGTAATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.48, T:0.36
Consensus pattern (6 bp):
TTAGGG
Found at i:1344956 original size:29 final size:29
Alignment explanation
Indices: 1344914--1344980 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 29
1344904 AATTATGAAT
1344914 AACCCATTAAAATTGGCAGAAAATATTCA
1 AACCCATTAAAATTGGCAGAAAATATTCA
**
1344943 AACCCATTAAAATTGGCAGAATCTATTCA
1 AACCCATTAAAATTGGCAGAAAATATTCA
1344972 AACCCATTA
1 AACCCATTA
1344981 TGAAAGTTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.45, C:0.21, G:0.09, T:0.25
Consensus pattern (29 bp):
AACCCATTAAAATTGGCAGAAAATATTCA
Found at i:1345908 original size:29 final size:29
Alignment explanation
Indices: 1345861--1345916 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
1345851 TTTGATTTTA
1345861 AATAAAAGTATAAAAGTTTGA-TTGAATGT
1 AATAAAAGTATAAAAGTTT-ATTTGAATGT
* **
1345890 AATAAGAGTATAATGGTTTATTTGAAT
1 AATAAAAGTATAAAAGTTTATTTGAAT
1345917 TTTTTCAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 1 0.04
29 22 0.96
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.38
Consensus pattern (29 bp):
AATAAAAGTATAAAAGTTTATTTGAATGT
Found at i:1347290 original size:19 final size:19
Alignment explanation
Indices: 1347260--1347296 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1347250 TAAATTAATA
1347260 TATAATATATTATGTTTATC
1 TATAATATATTAT-TTTATC
1347280 TATAA-ATATTATTTTAT
1 TATAATATATTATTTTAT
1347297 ATATGTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 7 0.41
20 5 0.29
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (19 bp):
TATAATATATTATTTTATC
Found at i:1347321 original size:21 final size:21
Alignment explanation
Indices: 1347283--1347326 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1347273 GTTTATCTAT
*
1347283 AAATATTATTTTATATATGTA
1 AAATATTATTATATATATGTA
*
1347304 AAATATTATGTATA-ATATTTA
1 AAATATTAT-TATATATATGTA
1347325 AA
1 AA
1347327 GCTTATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (21 bp):
AAATATTATTATATATATGTA
Found at i:1357379 original size:30 final size:30
Alignment explanation
Indices: 1357319--1357380 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
1357309 ATCCTGGTGC
* * *
1357319 TGCTACTCAGGCACTCCTCACTACTGCTGG
1 TGCTACTCAGCCACTCCTCACAACTCCTGG
*
1357349 TGCTACTCAGCCACTCCTGAGCAAC-CCTGG
1 TGCTACTCAGCCACTCCTCA-CAACTCCTGG
1357379 TG
1 TG
1357381 TTGGTCAGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 24 0.89
31 3 0.11
ACGTcount: A:0.18, C:0.37, G:0.21, T:0.24
Consensus pattern (30 bp):
TGCTACTCAGCCACTCCTCACAACTCCTGG
Found at i:1376305 original size:14 final size:15
Alignment explanation
Indices: 1376284--1376314 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1376274 GTAATAATCA
*
1376284 ATTTTTTAATTAAAT
1 ATTTTTAAATTAAAT
1376299 ATTTTTAAATTAAAT
1 ATTTTTAAATTAAAT
1376314 A
1 A
1376315 CTGCAATGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTTTAAATTAAAT
Found at i:1383703 original size:17 final size:17
Alignment explanation
Indices: 1383681--1383721 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1383671 CTATCTCATT
1383681 AATAAATAA-ATTTAAA
1 AATAAATAATATTTAAA
*
1383697 AATTAAA-AATTTTTAAA
1 AA-TAAATAATATTTAAA
1383714 AATAAATA
1 AATAAATA
1383722 TGATTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AATAAATAATATTTAAA
Found at i:1386828 original size:16 final size:17
Alignment explanation
Indices: 1386798--1386839 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
1386788 GTTTTTTTTT
1386798 TATTTATATTATTTAAC
1 TATTTATATTATTTAAC
1386815 TATTTATA-TATTTAAC
1 TATTTATATTATTTAAC
1386831 TATTGTATA
1 TATT-TATA
1386840 AAATCTTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (17 bp):
TATTTATATTATTTAAC
Found at i:1388993 original size:17 final size:18
Alignment explanation
Indices: 1388971--1389004 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1388961 GCCTTGGTGT
*
1388971 AAAAAATGAA-AAAAAAA
1 AAAAAAAGAAGAAAAAAA
1388988 AAAAAAAGAAGAAAAAA
1 AAAAAAAGAAGAAAAAA
1389005 TTTAGAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (18 bp):
AAAAAAAGAAGAAAAAAA
Found at i:1395256 original size:70 final size:70
Alignment explanation
Indices: 1395182--1395324 Score: 250
Period size: 70 Copynumber: 2.0 Consensus size: 70
1395172 TTAGCAACTG
* * * *
1395182 AAAATTTTTAAAATTTATTTGTAATTATTGTAGTTTTAAAAGCAATCACAATTTGAGATTTTCAC
1 AAAATTTTAAAAATTTATTTGTAATTATTATAGTCTTAAAAACAATCACAATTTGAGATTTTCAC
1395247 TATCC
66 TATCC
1395252 AAAATTTTAAAAATTTATTTGTAATTATTATAGTCTTAAAAACAATCACAATTTGAGATTTTCAC
1 AAAATTTTAAAAATTTATTTGTAATTATTATAGTCTTAAAAACAATCACAATTTGAGATTTTCAC
1395317 TATCC
66 TATCC
1395322 AAA
1 AAA
1395325 TATGTAAAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.42
Consensus pattern (70 bp):
AAAATTTTAAAAATTTATTTGTAATTATTATAGTCTTAAAAACAATCACAATTTGAGATTTTCAC
TATCC
Found at i:1398423 original size:3 final size:3
Alignment explanation
Indices: 1398367--1398404 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
1398357 AAAATATGAT
*
1398367 ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1398405 TTAGACTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1399116 original size:32 final size:33
Alignment explanation
Indices: 1399066--1399132 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 33
1399056 TTCTATTAGT
* * *
1399066 TTATTATTAATAGCAATATTTGTTATTAAAGTA
1 TTATTATTAATAGCAATATTTATTATAAAAATA
*
1399099 TTATT-TTAATAGTAATATTTATTATAAAAATA
1 TTATTATTAATAGCAATATTTATTATAAAAATA
1399131 TT
1 TT
1399133 GAAAAATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 25 0.83
33 5 0.17
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.51
Consensus pattern (33 bp):
TTATTATTAATAGCAATATTTATTATAAAAATA
Found at i:1399166 original size:26 final size:24
Alignment explanation
Indices: 1399105--1399179 Score: 69
Period size: 25 Copynumber: 3.0 Consensus size: 24
1399095 AGTATTATTT
*
1399105 TAATAGTAATATTTATTATAAAAA
1 TAATAGTAATAATTATTATAAAAA
* **
1399129 TATTGAAAAATAATTATTATAAATAA
1 TAAT-AGTAATAATTATTATAAA-AA
* *
1399155 TAAATAGTAATACTTATTATTAAAA
1 T-AATAGTAATAATTATTATAAAAA
1399180 CTTAAAAATA
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
24 3 0.08
25 17 0.44
26 17 0.44
27 2 0.05
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (24 bp):
TAATAGTAATAATTATTATAAAAA
Found at i:1399222 original size:25 final size:25
Alignment explanation
Indices: 1399169--1399224 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
1399159 TAGTAATACT
* *
1399169 TATTATTAAAACTTAAAAATATTTA
1 TATTATTAAAACATAAAAATATATA
*
1399194 TATTATTAAAATCATAAAAAT-TATC
1 TATTATTAAAA-CATAAAAATATATA
1399219 TATTAT
1 TATTAT
1399225 AGATAGTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 19 0.70
26 8 0.30
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (25 bp):
TATTATTAAAACATAAAAATATATA
Found at i:1400307 original size:22 final size:22
Alignment explanation
Indices: 1400240--1400313 Score: 58
Period size: 26 Copynumber: 3.1 Consensus size: 22
1400230 GAGCCAAAAA
*
1400240 ATATATAAATAAATAATTTTAGTT
1 ATATAT-AATTAATAA-TTTAGTT
* *
1400264 AATTTAATAATATTATATATTTAGTT
1 -ATAT-ATAAT-TAATA-ATTTAGTT
*
1400290 ATATATAATTAATAATTTAATT
1 ATATATAATTAATAATTTAGTT
1400312 AT
1 AT
1400314 CAATGATATT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
22 9 0.22
23 4 0.10
24 5 0.12
25 9 0.22
26 12 0.30
27 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (22 bp):
ATATATAATTAATAATTTAGTT
Found at i:1412414 original size:17 final size:17
Alignment explanation
Indices: 1412385--1412428 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
1412375 CCAAACTAAA
* *
1412385 TAAATAAAATAAAATCC
1 TAAATAAATTAAAATAC
*
1412402 TAAATTAATTAAAATAC
1 TAAATAAATTAAAATAC
1412419 TAAATAAATT
1 TAAATAAATT
1412429 TTCATATGCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAATAAATTAAAATAC
Found at i:1415730 original size:2 final size:2
Alignment explanation
Indices: 1415723--1415760 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1415713 TTTCATAACA
1415723 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
1415761 TATTTANACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1418781 original size:3 final size:3
Alignment explanation
Indices: 1418775--1418802 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1418765 TTCTTCTCCC
1418775 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1418803 CATTAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Done.