Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chrUn_random
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: 10571689
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.28
Warning! 1662808 characters in sequence are not A, C, G, or T
File 16 of 30
Found at i:5533893 original size:23 final size:25
Alignment explanation
Indices: 5533867--5533928 Score: 92
Period size: 24 Copynumber: 2.5 Consensus size: 25
5533857 TATTTTTCCC
5533867 TTTTTCTTTTTTTTCTTT-TCTTTT
1 TTTTTCTTTTTTTTCTTTGTCTTTT
5533891 TTTTTCTTTTTTTT-TTTGTCTTTT
1 TTTTTCTTTTTTTTCTTTGTCTTTT
5533915 TCTTCTTCTTTTTT
1 T-TT-TTCTTTTTT
5533929 CCTTCACTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
23 3 0.09
24 21 0.60
25 2 0.06
26 9 0.26
ACGTcount: A:0.00, C:0.13, G:0.02, T:0.85
Consensus pattern (25 bp):
TTTTTCTTTTTTTTCTTTGTCTTTT
Found at i:5533915 original size:14 final size:14
Alignment explanation
Indices: 5533866--5533915 Score: 73
Period size: 15 Copynumber: 3.4 Consensus size: 14
5533856 TTATTTTTCC
5533866 CTTTTTCTTTTTTTT
1 CTTTTT-TTTTTTTT
5533881 CTTTTCTTTTTTTTT
1 CTTTT-TTTTTTTTT
*
5533896 CTTTTTTTTTTTGT
1 CTTTTTTTTTTTTT
5533910 CTTTTT
1 CTTTTT
5533916 CTTCTTCTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
14 14 0.42
15 18 0.55
16 1 0.03
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.86
Consensus pattern (14 bp):
CTTTTTTTTTTTTT
Found at i:5533928 original size:14 final size:14
Alignment explanation
Indices: 5533874--5533933 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 14
5533864 CCCTTTTTCT
5533874 TTTTTTTCTT-TTC
1 TTTTTTTCTTCTTC
5533887 TTTTTTT-TTCTT-
1 TTTTTTTCTTCTTC
*
5533899 TTTTTTT-TT-GTC
1 TTTTTTTCTTCTTC
5533911 --TTTTTCTTCTTC
1 TTTTTTTCTTCTTC
*
5533923 TTTTTTCCTTC
1 TTTTTTTCTTC
5533934 ACTTACCCCT
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
10 5 0.13
11 3 0.08
12 13 0.34
13 9 0.24
14 8 0.21
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.82
Consensus pattern (14 bp):
TTTTTTTCTTCTTC
Found at i:5535585 original size:19 final size:19
Alignment explanation
Indices: 5535561--5535598 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5535551 CCATTTGACT
*
5535561 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
5535580 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
5535599 GGTTTGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:5540152 original size:15 final size:15
Alignment explanation
Indices: 5540129--5540169 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
5540119 GATCAAAGAT
5540129 TTTGG-TTTTAAAGC
1 TTTGGATTTTAAAGC
*
5540143 TTTGGATTTTAAAGT
1 TTTGGATTTTAAAGC
*
5540158 TTTTGATTTTAA
1 TTTGGATTTTAA
5540170 GGTTGTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 5 0.21
15 19 0.79
ACGTcount: A:0.24, C:0.02, G:0.17, T:0.56
Consensus pattern (15 bp):
TTTGGATTTTAAAGC
Found at i:5544267 original size:20 final size:20
Alignment explanation
Indices: 5544222--5544259 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5544212 TTTTGGCTCC
5544222 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
5544242 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTGGAGTA
5544260 AGATTTGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:5550058 original size:110 final size:111
Alignment explanation
Indices: 5549934--5550210 Score: 294
Period size: 110 Copynumber: 2.5 Consensus size: 111
5549924 TTAATATTAT
* * * *
5549934 ATTATAAATAAAATATTAATATTTAAATTATCAATTATTAATA-AACTAAATCATAAATTATTAC
1 ATTAT-AATAAAATATTAATATTTAAATTATCAATTATTAATATAAATAAATCACAAATCATTAA
*
5549998 TAT-T-TATAAAAAT-AAATTAAAAATAAATAAGCATAATAACATTTAA
65 TATATATAAAAAAATGAAA-T-AAAATAAATAAGCATAATAACATTTAA
* * * *
5550044 ATTATATATAAAATATTAATAATTAAATCATCAATTATTAATATTTTAAATAAATTACCAATCAT
1 ATTATA-ATAAAATATTAATATTTAAATTATCAATTATTAATA---TAAATAAATCACAAATCAT
* * *
5550109 TAATATATATAAAAAAATGAAATAAAATAATTAATCATAATAATATTTAA
62 TAATATATATAAAAAAATGAAATAAAATAAATAAGCATAATAACATTTAA
* * *
5550159 ATTA-AATAAAATATTAATATTTTAAAATATTAATGATTAAATTATAAATAAA
1 ATTATAATAAAATATTAATA-TTTAAATTATCAATTATT-AA-TATAAATAAA
5550211 ATATTAATAT
Statistics
Matches: 139, Mismatches: 17, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
109 1 0.01
110 39 0.28
113 22 0.16
114 32 0.23
115 31 0.22
116 11 0.08
117 3 0.02
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.38
Consensus pattern (111 bp):
ATTATAATAAAATATTAATATTTAAATTATCAATTATTAATATAAATAAATCACAAATCATTAAT
ATATATAAAAAAATGAAATAAAATAAATAAGCATAATAACATTTAA
Found at i:5550097 original size:42 final size:38
Alignment explanation
Indices: 5550040--5550552 Score: 170
Period size: 42 Copynumber: 13.2 Consensus size: 38
5550030 ATAATAACAT
*
5550040 TTAAATTATATATAAAATATTAATAATTAAATCATCAATTA
1 TTAAATT-TAAATAAAATATTAATAATTAAAT-AT-AATTA
* ** *
5550081 TTAATATTTTAAATAAATTACCAATCATT-AATAT-A-TA
1 TTAA-A-TTTAAATAAAATATTAATAATTAAATATAATTA
* * *
5550118 -TAAA--AAAATGAAATA-AAATAATT-AATCATAATAATA
1 TTAAATTTAAATAAAATATTAATAATTAAAT-ATAAT--TA
* *
5550154 TTTAAA-TTAAATAAAATATTAATATTTTAAAATATTAATGA
1 -TTAAATTTAAATAAAATATTAATA-ATT-AAATA-TAATTA
* *
5550195 TTAAATTATAAATAAAATATTAAT-ATTATATGATCAATAA
1 TTAAATT-TAAATAAAATATTAATAATTAAAT-AT-AATTA
* *
5550235 TTAATAATTTAAA-AAAATTATCAATCATTAAA-AT--TTA
1 TT-A-AATTTAAATAAAA-TATTAATAATTAAATATAATTA
** *
5550272 ACAAA-TAAAATAAAATA--AA-AATT-AATCATAATAATA
1 TTAAATTTAAATAAAATATTAATAATTAAAT-ATAAT--TA
* *
5550308 TTTAAA-TTAAATAAAATATTAATATTTAAAATATTAATGA
1 -TTAAATTTAAATAAAATATTAATAATT-AAATA-TAATTA
*
5550348 TTAAATTATAAATAAAATATTAATATTTAAATTATTAATTA
1 TTAAATT-TAAATAAAATATTAATAATTAAA-TA-TAATTA
* * * *
5550389 TTAATATTTTAATTAAAT-TTTA-AATT--AT-TAATNA
1 TTAA-ATTTAAATAAAATATTAATAATTAAATATAATTA
* *
5550423 TTTAACAATAAAATAAAATA--AA-AATT-AATCATAATAATA
1 -TTAA-ATTTAAATAAAATATTAATAATTAAAT-ATAAT--TA
* *
5550462 TTTAAA-TTAAATAAAATATTAATATTTAAAATATTAATGA
1 -TTAAATTTAAATAAAATATTAATAATT-AAATA-TAATTA
*
5550502 TTAAAATTATAAATTAAAATA-TAATATTTAAATTATTAATTA
1 TT-AAATT-TAAA-TAAAATATTAATAATTAAA-TA-TAATTA
5550544 TTAATATTT
1 TTAA-ATTT
5550553 TATAAATTAA
Statistics
Matches: 365, Mismatches: 47, Indels: 120
0.69 0.09 0.23
Matches are distributed among these distances:
30 2 0.01
31 12 0.03
32 14 0.04
33 1 0.00
34 17 0.05
35 22 0.06
36 9 0.02
37 34 0.09
38 6 0.02
39 33 0.09
40 44 0.12
41 71 0.19
42 84 0.23
43 16 0.04
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.41
Consensus pattern (38 bp):
TTAAATTTAAATAAAATATTAATAATTAAATATAATTA
Found at i:5550233 original size:25 final size:26
Alignment explanation
Indices: 5550181--5550234 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
5550171 ATTAATATTT
*
5550181 TAAAATATTAATGATTAAATTATAAA
1 TAAAATATTAATGATTAAATGATAAA
* *
5550207 TAAAATATTAAT-ATTATATGATCAA
1 TAAAATATTAATGATTAAATGATAAA
5550232 TAA
1 TAA
5550235 TTAATAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.39
Consensus pattern (26 bp):
TAAAATATTAATGATTAAATGATAAA
Found at i:5550254 original size:154 final size:151
Alignment explanation
Indices: 5550040--5550593 Score: 753
Period size: 154 Copynumber: 3.6 Consensus size: 151
5550030 ATAATAACAT
* *
5550040 TTAAATTATATATAAAATATTAATAATTAAATCATCAATTATTAATATTTTAAATAAATTACCAA
1 TTAAATTATAAATAAAATATTAAT-ATTAAATCATCAATTATTAATATTTTAAATAAATTATCAA
* *
5550105 TCATTAATATATATAAA-AAAATGAAATAAAATAATTAATCATAATAATATTTAAATTAAATAAA
65 TCATTAATATTTA-AAATAAAATAAAAT-AAA-AATTAATCATAATAATATTTAAATTAAATAAA
5550169 ATATTAATATTTTAAAATATTAATGA
127 ATATTAATA-TTTAAAATATTAATGA
* * * * *
5550195 TTAAATTATAAATAAAATATTAATATTATATGATCAATAATTAATAATTTAAAAAAATTATCAAT
1 TTAAATTATAAATAAAATATTAATATTAAATCATCAATTATTAATATTTTAAATAAATTATCAAT
*
5550260 CATTAAAATTTAACAAATAAAATAAAATAAAAATTAATCATAATAATATTTAAATTAAATAAAAT
66 CATTAATATTT-A-AAATAAAATAAAATAAAAATTAATCATAATAATATTTAAATTAAATAAAAT
5550325 ATTAATATTTAAAATATTAATGA
129 ATTAATATTTAAAATATTAATGA
* * * * *
5550348 TTAAATTATAAATAAAATATTAATATTTAAATTATTAATTATTAATATTTTAATTAAATTTTAAA
1 TTAAATTATAAATAAAATATTAATA-TTAAATCATCAATTATTAATATTTTAAATAAATTATCAA
*
5550413 TTATTAATNATTTAACAATAAAATAAAATAAAAATTAATCATAATAATATTTAAATTAAATAAAA
65 TCATTAAT-ATTTAA-AATAAAATAAAATAAAAATTAATCATAATAATATTTAAATTAAATAAAA
5550478 TATTAATATTTAAAATATTAATGA
128 TATTAATATTTAAAATATTAATGA
* *
5550502 TTAAAATTATAAATTAAAATA-TAATATTTAAATTATTAATTATTAATATTTT--ATAAATTA--
1 TT-AAATTATAAA-TAAAATATTAATA-TTAAATCATCAATTATTAATATTTTAAATAAATTATC
* *
5550562 AATTATTAATATTTAAAA-ATTAATAAAATAAA
63 AATCATTAATATTTAAAATA-AAATAAAATAAA
5550594 TAATCATATA
Statistics
Matches: 366, Mismatches: 25, Indels: 22
0.89 0.06 0.05
Matches are distributed among these distances:
148 1 0.00
149 13 0.04
150 6 0.02
151 10 0.03
153 48 0.13
154 197 0.54
155 75 0.20
156 16 0.04
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (151 bp):
TTAAATTATAAATAAAATATTAATATTAAATCATCAATTATTAATATTTTAAATAAATTATCAAT
CATTAATATTTAAAATAAAATAAAATAAAAATTAATCATAATAATATTTAAATTAAATAAAATAT
TAATATTTAAAATATTAATGA
Found at i:5550325 original size:21 final size:21
Alignment explanation
Indices: 5550274--5550325 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
5550264 AAAATTTAAC
5550274 AAATAAAATAAAATAAAAATT
1 AAATAAAATAAAATAAAAATT
* * **
5550295 -AATCATAATAATATTTAAATT
1 AAAT-AAAATAAAATAAAAATT
5550316 AAATAAAATA
1 AAATAAAATA
5550326 TTAATATTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
20 3 0.12
21 18 0.75
22 3 0.12
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATAAAATAAAATAAAAATT
Found at i:5550339 original size:15 final size:15
Alignment explanation
Indices: 5550319--5550586 Score: 115
Period size: 15 Copynumber: 17.9 Consensus size: 15
5550309 TTAAATTAAA
5550319 TAAAATATTAATATT
1 TAAAATATTAATATT
5550334 TAAAATATTAATGA-T
1 TAAAATATTAAT-ATT
*
5550349 TAAATTA-TAA-A--
1 TAAAATATTAATATT
5550360 TAAAATATTAATATT
1 TAAAATATTAATATT
*
5550375 TAAATTATTAAT-TAT
1 TAAAATATTAATAT-T
* *
5550390 TAATATTTTAATTAAATTT
1 TAAAATATTAA-T--A-TT
*
5550409 TAAATTATTAATNATT
1 TAAAATATTAAT-ATT
* **
5550425 TAACAATA-AAATAAAA
1 TAA-AATATTAAT-ATT
5550441 TAAAA-ATTAATCA--
1 TAAAATATTAAT-ATT
5550454 TAATAATATTTAA-ATT
1 TAA-AATA-TTAATATT
5550470 AAATAAAATATTAATATT
1 ---TAAAATATTAATATT
5550488 TAAAATATTAATGA-T
1 TAAAATATTAAT-ATT
5550503 TAAAAT-TATAA-A-T
1 TAAAATAT-TAATATT
5550516 TAAAATA-TAATATT
1 TAAAATATTAATATT
*
5550530 TAAATTATTAAT-TAT
1 TAAAATATTAATAT-T
* * *
5550545 TAATAT-TTTATAAAT
1 TAAAATATTAAT-ATT
*
5550560 TAAATTATTAATATT
1 TAAAATATTAATATT
5550575 TAAAA-ATTAATA
1 TAAAATATTAATA
5550587 AAATAAATAA
Statistics
Matches: 194, Mismatches: 27, Indels: 65
0.68 0.09 0.23
Matches are distributed among these distances:
11 6 0.03
12 7 0.04
13 13 0.07
14 28 0.14
15 88 0.45
16 23 0.12
17 8 0.04
18 8 0.04
19 12 0.06
20 1 0.01
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (15 bp):
TAAAATATTAATATT
Found at i:5550517 original size:13 final size:13
Alignment explanation
Indices: 5550501--5550543 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
5550491 AATATTAATG
5550501 ATTAAAATTATAA
1 ATTAAAATTATAA
5550514 ATTAAAA-TATAA
1 ATTAAAATTATAA
* *
5550526 TATTTAAATTATTA
1 -ATTAAAATTATAA
5550540 ATTA
1 ATTA
5550544 TTAATATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
12 5 0.20
13 16 0.64
14 4 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTAAAATTATAA
Found at i:5550542 original size:26 final size:28
Alignment explanation
Indices: 5550487--5550543 Score: 82
Period size: 26 Copynumber: 2.1 Consensus size: 28
5550477 ATATTAATAT
5550487 TTAAAATATTAATGATTAAAATTATAAA
1 TTAAAATATTAATGATTAAAATTATAAA
* *
5550515 TTAAAATA-TAAT-ATTTAAATTATTAA
1 TTAAAATATTAATGATTAAAATTATAAA
5550541 TTA
1 TTA
5550544 TTAATATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 15 0.56
27 4 0.15
28 8 0.30
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (28 bp):
TTAAAATATTAATGATTAAAATTATAAA
Found at i:5553947 original size:16 final size:17
Alignment explanation
Indices: 5553922--5553960 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
5553912 TAAAAAAGAA
*
5553922 AAATTTTATAT-TTATG
1 AAATTATATATATTATG
5553938 AAATTATATATATTATG
1 AAATTATATATATTATG
5553955 AAATTA
1 AAATTA
5553961 GGTCATGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (17 bp):
AAATTATATATATTATG
Found at i:5564797 original size:11 final size:11
Alignment explanation
Indices: 5564781--5564811 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
5564771 TTATGCTCCT
5564781 CAAGATGGCAA
1 CAAGATGGCAA
5564792 CAAGATGGCAA
1 CAAGATGGCAA
*
5564803 CAAGTTGGC
1 CAAGATGGC
5564812 TGACCGCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.39, C:0.19, G:0.29, T:0.13
Consensus pattern (11 bp):
CAAGATGGCAA
Found at i:5565586 original size:31 final size:31
Alignment explanation
Indices: 5565548--5565656 Score: 200
Period size: 31 Copynumber: 3.5 Consensus size: 31
5565538 GTGTCAGCAT
*
5565548 TGGCGTGTTACAACATTTTACGTTATATGCC
1 TGGCGTGTTACAACATTTTACGTTATATGCA
5565579 TGGCGTGTTACAACATTTTACGTTATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
*
5565610 TGGCGTGTTACAACATTTTACATTATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
5565641 TGGCGTGTTACAACAT
1 TGGCGTGTTACAACAT
5565657 AACTAACAAA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 76 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (31 bp):
TGGCGTGTTACAACATTTTACGTTATATGCA
Found at i:5579854 original size:28 final size:29
Alignment explanation
Indices: 5579813--5579872 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
5579803 GTCTATGGGC
*
5579813 AATTTTTCAGTTTT-TGGGGAAAAAATGT
1 AATTTTTCACTTTTATGGGGAAAAAATGT
* * *
5579841 AATTTTTGACTTTTACTGGGGCAAAAGTGT
1 AATTTTTCACTTTTA-TGGGGAAAAAATGT
5579871 AA
1 AA
5579873 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.07, G:0.22, T:0.40
Consensus pattern (29 bp):
AATTTTTCACTTTTATGGGGAAAAAATGT
Found at i:5583458 original size:43 final size:43
Alignment explanation
Indices: 5583397--5583480 Score: 168
Period size: 43 Copynumber: 2.0 Consensus size: 43
5583387 AGCTTCCAAA
5583397 GGAAGCTTTGACTCTTCATCCTTATCCCATGGCCAGTTCTTTT
1 GGAAGCTTTGACTCTTCATCCTTATCCCATGGCCAGTTCTTTT
5583440 GGAAGCTTTGACTCTTCATCCTTATCCCATGGCCAGTTCTT
1 GGAAGCTTTGACTCTTCATCCTTATCCCATGGCCAGTTCTT
5583481 ATCTTCACCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.17, C:0.29, G:0.17, T:0.38
Consensus pattern (43 bp):
GGAAGCTTTGACTCTTCATCCTTATCCCATGGCCAGTTCTTTT
Found at i:5583537 original size:19 final size:19
Alignment explanation
Indices: 5583513--5583554 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
5583503 CTTCTTCACC
*
5583513 TTCATGCTCCCATGCCATT
1 TTCATGCTCACATGCCATT
*
5583532 TTCATGCTTACATGCCATT
1 TTCATGCTCACATGCCATT
5583551 TTCA
1 TTCA
5583555 CCTTGCCACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.19, C:0.31, G:0.10, T:0.40
Consensus pattern (19 bp):
TTCATGCTCACATGCCATT
Found at i:5583674 original size:11 final size:10
Alignment explanation
Indices: 5583647--5583690 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
5583637 CGTTGGAAGA
5583647 AAAGAGAAAG
1 AAAGAGAAAG
*
5583657 GAA-AGAAAG
1 AAAGAGAAAG
5583666 AAAGTAGAAAG
1 AAAG-AGAAAG
*
5583677 AAAGAGAGAG
1 AAAGAGAAAG
5583687 AAAG
1 AAAG
5583691 GAAGAAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 8 0.28
10 11 0.38
11 10 0.34
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (10 bp):
AAAGAGAAAG
Found at i:5608565 original size:19 final size:20
Alignment explanation
Indices: 5608543--5608583 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
5608533 ACAAAAGGAA
5608543 ATTTTTA-GAATAAAATAAT
1 ATTTTTATGAATAAAATAAT
*
5608562 A-TTTTATTAATAAAATAAT
1 ATTTTTATGAATAAAATAAT
5608581 ATT
1 ATT
5608584 AAAATATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
18 5 0.26
19 13 0.68
20 1 0.05
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
ATTTTTATGAATAAAATAAT
Found at i:5608955 original size:13 final size:12
Alignment explanation
Indices: 5608934--5608985 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
5608924 ATATAGTAAA
*
5608934 ATAATAATAGTAT
1 ATAAAAATA-TAT
5608947 ATAAAAATATAT
1 ATAAAAATATAT
* *
5608959 ATATATATATAT
1 ATAAAAATATAT
* *
5608971 ATATATATATAT
1 ATAAAAATATAT
5608983 ATA
1 ATA
5608986 TAGATAAAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
12 28 0.78
13 8 0.22
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (12 bp):
ATAAAAATATAT
Found at i:5608958 original size:2 final size:2
Alignment explanation
Indices: 5608953--5608987 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5608943 GTATATAAAA
5608953 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5608988 GATAAAGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5612690 original size:20 final size:20
Alignment explanation
Indices: 5612665--5612710 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
5612655 TTTTGGCCCC
5612665 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
*
5612685 ATTTGACTTATTGGAGTATG
1 ATTTGACTTATTGGAGTATA
5612705 ATTTGA
1 ATTTGA
5612711 GGTTTAGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:5614170 original size:13 final size:13
Alignment explanation
Indices: 5614152--5614176 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5614142 AGAGAAATTG
5614152 TGATTTTATAAAA
1 TGATTTTATAAAA
5614165 TGATTTTATAAA
1 TGATTTTATAAA
5614177 TTTTCTGGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:5617358 original size:20 final size:20
Alignment explanation
Indices: 5617341--5617378 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5617331 CCTCAAATCT
5617341 TACTCCAATAAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
5617361 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
5617379 GGGGCCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:5624784 original size:15 final size:14
Alignment explanation
Indices: 5624751--5624793 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
5624741 CTTAAAACAA
* *
5624751 CTTTAAAACCAAAAA
1 CTTTAAAATC-AAAG
5624766 CTTTAAAATTCAAAG
1 CTTTAAAA-TCAAAG
5624781 CTTTAAAATCAAA
1 CTTTAAAATCAAA
5624794 ATCTCTGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 5 0.20
15 19 0.76
16 1 0.04
ACGTcount: A:0.53, C:0.16, G:0.02, T:0.28
Consensus pattern (14 bp):
CTTTAAAATCAAAG
Found at i:5630886 original size:5 final size:5
Alignment explanation
Indices: 5630876--5630925 Score: 79
Period size: 5 Copynumber: 10.6 Consensus size: 5
5630866 TTCCTTATTA
5630876 TTTTC TTTTC TTTTC -TTTC TTTTC TTTTC TTTTC TTTTC -TTTC -TTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
5630923 TTT
1 TTT
5630926 CTCTCCCACC
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
4 12 0.28
5 31 0.72
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:5630896 original size:14 final size:14
Alignment explanation
Indices: 5630877--5630925 Score: 82
Period size: 14 Copynumber: 3.5 Consensus size: 14
5630867 TCCTTATTAT
5630877 TTTCTTTTCTTTTC
1 TTTCTTTTCTTTTC
5630891 TTTCTTTTCTTTTC
1 TTTCTTTTCTTTTC
5630905 TTTTCTTTTC-TTTC
1 -TTTCTTTTCTTTTC
5630919 TTTCTTT
1 TTTCTTT
5630926 CTCTCCCACC
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
13 7 0.21
14 18 0.53
15 9 0.26
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTCTTTTCTTTTC
Found at i:5630900 original size:19 final size:18
Alignment explanation
Indices: 5630876--5630925 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 18
5630866 TTCCTTATTA
5630876 TTTTCTTTTCTTTTCTTT
1 TTTTCTTTTCTTTTCTTT
5630894 CTTTTCTTTTCTTTTCTTT
1 -TTTTCTTTTCTTTTCTTT
5630913 TCTTTC-TTTCTTT
1 T-TTTCTTTTCTTT
5630926 CTCTCCCACC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 8 0.27
19 22 0.73
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTCTTTTCTTTTCTTT
Found at i:5630904 original size:24 final size:23
Alignment explanation
Indices: 5630876--5630925 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 23
5630866 TTCCTTATTA
5630876 TTTTCTTTTCTTTTCTTTCTTTTC
1 TTTTCTTTTCTTTTCTTTC-TTTC
5630900 TTTTCTTTTCTTTTCTTTCTTTC
1 TTTTCTTTTCTTTTCTTTCTTTC
5630923 TTT
1 TTT
5630926 CTCTCCCACC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTCTTTTCTTTTCTTTCTTTC
Found at i:5631139 original size:35 final size:34
Alignment explanation
Indices: 5631047--5631139 Score: 118
Period size: 34 Copynumber: 2.7 Consensus size: 34
5631037 CTTTCAACTT
* *
5631047 TTAAATTTTCAGCAGCTAAGGCTGCTTATTTTTGC
1 TTAAAATTTCAGCAGCTAA-GCTGCTTATTTTTCC
*
5631082 TTCAAAA--TCAGCAGCTATGCTGCTCTATTTTTCC
1 TT-AAAATTTCAGCAGCTAAGCTGCT-TATTTTTCC
5631116 TTAAAATTTCAGCAGCTAAGCTGC
1 TTAAAATTTCAGCAGCTAAGCTGC
5631140 ACCTTTCCCT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
33 10 0.20
34 20 0.40
35 17 0.34
36 3 0.06
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.38
Consensus pattern (34 bp):
TTAAAATTTCAGCAGCTAAGCTGCTTATTTTTCC
Found at i:5632383 original size:21 final size:20
Alignment explanation
Indices: 5632343--5632383 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
5632333 TGAGCTGATT
5632343 TTGGTGATTTTAGTGAGTTA
1 TTGGTGATTTTAGTGAGTTA
5632363 TTGGCTGATATTTAGTG-GTTA
1 TTGG-TGAT-TTTAGTGAGTTA
5632384 GAAATGTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 8 0.42
22 7 0.37
ACGTcount: A:0.20, C:0.02, G:0.29, T:0.49
Consensus pattern (20 bp):
TTGGTGATTTTAGTGAGTTA
Found at i:5634219 original size:67 final size:66
Alignment explanation
Indices: 5634111--5634243 Score: 205
Period size: 67 Copynumber: 2.0 Consensus size: 66
5634101 GCATATAGAG
* * *
5634111 TCTTAAGTCATCTAAACCAATTCTATTCTTTTTGTAGATCATTATGCCTCCTCGATGTGAGCTAC
1 TCTTAAGTCATCTAAACCAATTCCATTCTTCTTGTAGATCATTATGCCTCCTCGACGTGAGCTAC
5634176 C
66 C
*
5634177 NTCTTAAGT-AGTCTAAACCAATTCCGTTCTTCTTGTAGATCATTATGCCTCCTCGACGTGAGCT
1 -TCTTAAGTCA-TCTAAACCAATTCCATTCTTCTTGTAGATCATTATGCCTCCTCGACGTGAGCT
5634241 ACC
64 ACC
5634244 ATCTATCACT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
66 1 0.02
67 60 0.98
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (66 bp):
TCTTAAGTCATCTAAACCAATTCCATTCTTCTTGTAGATCATTATGCCTCCTCGACGTGAGCTAC
C
Found at i:5651624 original size:28 final size:29
Alignment explanation
Indices: 5651583--5651642 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
5651573 GTCAATGGGC
* *
5651583 AATTTTTCAGTTTT-TGGGGCAAAAATGT
1 AATTTTTCACTTTTAGGGGGCAAAAATGT
* *
5651611 AATTTTTGACTTTTAAGGGGGCAAAAGTGT
1 AATTTTTCACTTTT-AGGGGGCAAAAATGT
5651641 AA
1 AA
5651643 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.07, G:0.23, T:0.38
Consensus pattern (29 bp):
AATTTTTCACTTTTAGGGGGCAAAAATGT
Found at i:5669502 original size:13 final size:13
Alignment explanation
Indices: 5669484--5669508 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5669474 ATTTTCAAAA
5669484 ATTTTATAAAATT
1 ATTTTATAAAATT
5669497 ATTTTATAAAAT
1 ATTTTATAAAAT
5669509 CCCATTTTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTATAAAATT
Found at i:5672132 original size:29 final size:31
Alignment explanation
Indices: 5672080--5672142 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
5672070 TTATTATTAT
* * **
5672080 TATTTATATTTGTTTAT-TTTTTTTCATTTC
1 TATTTATATTTGTTCATATGTTTTAAATTTC
5672110 TATTT-TATTTGTTCATATGTTTTAAATTTC
1 TATTTATATTTGTTCATATGTTTTAAATTTC
5672140 TAT
1 TAT
5672143 AGATTTTCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 10 0.36
30 18 0.64
ACGTcount: A:0.21, C:0.06, G:0.05, T:0.68
Consensus pattern (31 bp):
TATTTATATTTGTTCATATGTTTTAAATTTC
Found at i:5673662 original size:38 final size:39
Alignment explanation
Indices: 5673600--5673687 Score: 124
Period size: 38 Copynumber: 2.3 Consensus size: 39
5673590 TCCTTCCAAA
* *
5673600 TCTCTAAATAGTTTTGTATAGTCTTAGCAATAAAAGC-T
1 TCTCTAAATAGCTTCGTATAGTCTTAGCAATAAAAGCTT
* * *
5673638 TCTCTAAATAGCTTCGTATGGTCTTAGGAATGAAAGCTT
1 TCTCTAAATAGCTTCGTATAGTCTTAGCAATAAAAGCTT
5673677 TCTCTAAATAG
1 TCTCTAAATAG
5673688 TTTTGTCCAA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
38 32 0.73
39 12 0.27
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.38
Consensus pattern (39 bp):
TCTCTAAATAGCTTCGTATAGTCTTAGCAATAAAAGCTT
Found at i:5678210 original size:21 final size:21
Alignment explanation
Indices: 5678184--5678226 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5678174 TTGGTGGTTC
5678184 GATAAAGATGAGGTATAATTT
1 GATAAAGATGAGGTATAATTT
5678205 GATAAAGATGAGGTATAATTT
1 GATAAAGATGAGGTATAATTT
5678226 G
1 G
5678227 GAGTATAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.33
Consensus pattern (21 bp):
GATAAAGATGAGGTATAATTT
Found at i:5685293 original size:17 final size:18
Alignment explanation
Indices: 5685243--5685282 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
5685233 TATTAAGGTA
*
5685243 TAAAAAAT-CAAATGTTTT
1 TAAAAAATAAAAAT-TTTT
5685261 TAAAAAATAAAAATTTTT
1 TAAAAAATAAAAATTTTT
5685279 TAAA
1 TAAA
5685283 TAAAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
TAAAAAATAAAAATTTTT
Found at i:5685419 original size:17 final size:18
Alignment explanation
Indices: 5685379--5685426 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
5685369 ATATTTCCAA
*
5685379 ATTTAATTTATAA-TATT
1 ATTTAATTTAAAATTATT
*
5685396 ATGTAATTTAAAATTATT
1 ATTTAATTTAAAATTATT
*
5685414 -TTTAATTAAAAAT
1 ATTTAATTTAAAAT
5685427 ACACCCACGC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 22 0.85
18 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
ATTTAATTTAAAATTATT
Found at i:5688986 original size:26 final size:26
Alignment explanation
Indices: 5688957--5689009 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
5688947 CTGGTCTTTG
*
5688957 CATGTTCATTATT-TAAATACTTAGTC
1 CATGTTAATTATTAT-AATACTTAGTC
5688983 CATGTTAATTATTATAATACTTAGTC
1 CATGTTAATTATTATAATACTTAGTC
5689009 C
1 C
5689010 CATATTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.32, C:0.15, G:0.08, T:0.45
Consensus pattern (26 bp):
CATGTTAATTATTATAATACTTAGTC
Found at i:5698010 original size:56 final size:56
Alignment explanation
Indices: 5697873--5698010 Score: 140
Period size: 56 Copynumber: 2.5 Consensus size: 56
5697863 TTATTGAAGG
* * * * *
5697873 AATTCCGTTGGTAA-TTCCAACA-AAATCCGTAGATAATGATTAAATTACCGATAA
1 AATTTCGTTGGTAATTTCCAATAGAAATCCATAGATAATGAATAAATTACCGACAA
* * *
5697927 AATTTTGTTGGTAATTTCCAATGGAAATCCATAGATAATGAATAAA-TCCCTGACAA
1 AATTTCGTTGGTAATTTCCAATAGAAATCCATAGATAATGAATAAATTACC-GACAA
**
5697983 AATTTCGTTAGG-AATTTTTAATAGAAAT
1 AATTTCGTT-GGTAATTTCCAATAGAAAT
5698011 ATATAAGTAA
Statistics
Matches: 68, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
54 12 0.18
55 9 0.13
56 45 0.66
57 2 0.03
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (56 bp):
AATTTCGTTGGTAATTTCCAATAGAAATCCATAGATAATGAATAAATTACCGACAA
Found at i:5705229 original size:10 final size:10
Alignment explanation
Indices: 5705194--5705232 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
5705184 TTGTGGCTGA
5705194 ATTTGATGAT
1 ATTTGATGAT
*
5705204 ATTTCATGAT
1 ATTTGATGAT
*
5705214 ATTTTGGTGAT
1 A-TTTGATGAT
5705225 ATTTGATG
1 ATTTGATG
5705233 TTTGGTGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.26, C:0.03, G:0.21, T:0.51
Consensus pattern (10 bp):
ATTTGATGAT
Found at i:5711513 original size:16 final size:15
Alignment explanation
Indices: 5711488--5711517 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5711478 AAAACCCTGT
5711488 GGACTATTTGGTTTA
1 GGACTATTTGGTTTA
5711503 GGACTTATTTGGTTT
1 GGAC-TATTTGGTTT
5711518 CAACATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.17, C:0.07, G:0.27, T:0.50
Consensus pattern (15 bp):
GGACTATTTGGTTTA
Found at i:5712672 original size:14 final size:14
Alignment explanation
Indices: 5712653--5712679 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5712643 TTGACATTTA
5712653 AAATACATAATAAC
1 AAATACATAATAAC
5712667 AAATACATAATAA
1 AAATACATAATAA
5712680 TTATAATCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (14 bp):
AAATACATAATAAC
Found at i:5716608 original size:28 final size:30
Alignment explanation
Indices: 5716550--5716609 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 30
5716540 TTTTTGAAAT
* *
5716550 TTACACTTTTGCCCCCGTAAAAGTGAAAAA
1 TTACACTTTTGCCCCCGAAAAACTGAAAAA
*
5716580 TTACATTTTTG-CCCC-AAAAACTGAAAAA
1 TTACACTTTTGCCCCCGAAAAACTGAAAAA
5716608 TT
1 TT
5716610 GCCCATAGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 13 0.48
29 4 0.15
30 10 0.37
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.30
Consensus pattern (30 bp):
TTACACTTTTGCCCCCGAAAAACTGAAAAA
Found at i:5725080 original size:251 final size:248
Alignment explanation
Indices: 5724620--5725236 Score: 708
Period size: 251 Copynumber: 2.5 Consensus size: 248
5724610 TTATTCTACG
* * * *
5724620 TTTATAATTTTTTACGTTAATT-TTAACAAGTTTACGTCAAGGTTTTTTAGTTGCTAATTCTCAC
1 TTTATTATTTTTTACATTAATTCTT-ACAAGTTTACGTCAAGG-TTTTTAATTGCTAATTTTCAC
* * * * ** *
5724684 TATAATTATTTTAATTCTTATTATTA-TTCATTTATAAACTAAAATTTGTAAACTGTACTTTATA
64 TATAAGTATTTTTA-TCTTATTATTATTTCA-TTATAAA-TTAAATTTGT-AACAGTA-TAAAAA
* * *
5724748 CTTTTAGCTCGACAATACAAATTTAATTGTTTAATATTTTTAAAAAAAATTATTTTGACTTAATT
124 CTTTTAGCTCGACAATACAAATTTAAATATTTAATATTTTCAAAAAAAATTATTTTGACTTAATT
* ** * *
5724813 GACTTGTTATATTAAATCTCATGCATTTACGTCAACATTTTGACAATGCTAGTTCCACT-
189 GACTTGTTACATTAAATCTCACACATTTACATCAACACTTTGACAATGCTAGTTCCACTC
* * *
5724872 TTTATTATTTTTTACATTACTTCTTACAAGTTTACGTCAAGATCTTTTAATTGCTAATTTTCATT
1 TTTATTATTTTTTACATTAATTCTTACAAGTTTACGTCAAGGT-TTTTAATTGCTAATTTTCACT
* *
5724937 ATATA-TATTTTTATCCTTATTGTTATTTCAGTATAAATTAAATTTGTAACAGT-TAAAAACTTT
65 ATA-AGTATTTTTAT-CTTATTATTATTTCATTATAAATTAAATTTGTAACAGTATAAAAACTTT
* * *
5725000 TAGCTCGACAATATAAATTTAAATATTTAAT-TTTTCCAAAAATGATATTTATTTTGATTTAATT
128 TAGCTCGACAATACAAATTTAAATATTTAATATTTT-CAAAAA--A-AATTATTTTGACTTAATT
* * * * *
5725064 GACTTGTTACATTAAATTTCACACATTTATATCAATACTTTGACAATGCTTGTTCGACTC
189 GACTTGTTACATTAAATCTCACACATTTACATCAACACTTTGACAATGCTAGTTCCACTC
* *
5725124 TTT-TTTTTTTTTACATTAATTCTTACAAGTTTACATCAAGGTTTTTCAATTGCTAATTTTCACT
1 TTTATTATTTTTTACATTAATTCTTACAAGTTTACGTCAAGGTTTTT-AATTGCTAATTTTCACT
* * *
5725188 ATAAGTATTTTTATATTATTATTATTCCTTTATAAATTAAAATTTGTAA
65 ATAAGTATTTTTATCTTATTATTATTTCATTATAAATT-AAATTTGTAA
5725237 ACCATTAAAT
Statistics
Matches: 311, Mismatches: 41, Indels: 27
0.82 0.11 0.07
Matches are distributed among these distances:
247 4 0.01
248 40 0.13
250 30 0.10
251 149 0.48
252 81 0.26
253 7 0.02
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.48
Consensus pattern (248 bp):
TTTATTATTTTTTACATTAATTCTTACAAGTTTACGTCAAGGTTTTTAATTGCTAATTTTCACTA
TAAGTATTTTTATCTTATTATTATTTCATTATAAATTAAATTTGTAACAGTATAAAAACTTTTAG
CTCGACAATACAAATTTAAATATTTAATATTTTCAAAAAAAATTATTTTGACTTAATTGACTTGT
TACATTAAATCTCACACATTTACATCAACACTTTGACAATGCTAGTTCCACTC
Found at i:5725437 original size:219 final size:220
Alignment explanation
Indices: 5725047--5725470 Score: 568
Period size: 219 Copynumber: 1.9 Consensus size: 220
5725037 AAAAATGATA
* * *
5725047 TTTATTTTGATTTAATTGACTTGTTACATTAAATTTCACACATTTATATCAATACTTTGACAATG
1 TTTATTTTGACTTAATTGACTTGTTACATTAAATCTCACACATTTAAATCAATACTTTGACAATG
* * ** * *
5725112 CTTGTTCGACTCTTTTTTTTTTTTACATTAATTCTTACAAGTTTACATCAAGGTTTTTCAATTGC
66 CGTGTTCGACTCTTTATAATTTTTACATTAACTCTTACAAGTTTACATCAAGGTATTTCAATTGC
*
5725177 TAATTTTCACTATAAGTATTTTTATATTATTATTATTCCTTTATAAATTAAAATTTGTAAACCAT
131 TAATTTTCACTATAAGTATTTTAATATTATTATTATTCCTTTATAAATTAAAATTTGTAAACCAT
5725242 TAAATACTTTAAACGTGAGAATATT
196 TAAATACTTTAAACGTGAGAATATT
* ** * * *
5725267 TTTA-TTTGACTTAATTGGCTTGTTATGTTAAATCTCACATATTTAAATCAATATTTTGACAATT
1 TTTATTTTGACTTAATTGACTTGTTACATTAAATCTCACACATTTAAATCAATACTTTGACAATG
*
5725331 CGTGTTTC-AC-CTTTATAATTTTTA-AGTTAACTCTTGCAAGTTTACATCAAGGTATTTCAATT
66 CGTG-TTCGACTCTTTATAATTTTTACA-TTAACTCTTACAAGTTTACATCAAGGTATTTCAATT
* * * * * *
5725393 GCTAATTTTGATTATAATTATTTTAATCCTTGTTATTATTCCTTTATAAATTAAAATTTGTAAAT
129 GCTAATTTTCACTATAAGTATTTTAAT-ATTATTATTATTCCTTTATAAATTAAAATTTGTAAAC
**
5725458 TGTTAAATACTTT
193 CATTAAATACTTT
5725471 TCGCTCGATA
Statistics
Matches: 176, Mismatches: 25, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
217 1 0.01
218 67 0.38
219 101 0.57
220 7 0.04
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.49
Consensus pattern (220 bp):
TTTATTTTGACTTAATTGACTTGTTACATTAAATCTCACACATTTAAATCAATACTTTGACAATG
CGTGTTCGACTCTTTATAATTTTTACATTAACTCTTACAAGTTTACATCAAGGTATTTCAATTGC
TAATTTTCACTATAAGTATTTTAATATTATTATTATTCCTTTATAAATTAAAATTTGTAAACCAT
TAAATACTTTAAACGTGAGAATATT
Found at i:5725666 original size:17 final size:18
Alignment explanation
Indices: 5725641--5725678 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
5725631 AATTTCTACA
5725641 TTTTATTATAATTATT-T
1 TTTTATTATAATTATTCT
* *
5725658 TTTTCTTATTATTATTCT
1 TTTTATTATAATTATTCT
5725676 TTT
1 TTT
5725679 ATAATTTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTATTATAATTATTCT
Found at i:5727010 original size:20 final size:20
Alignment explanation
Indices: 5726985--5727030 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
5726975 TTTTGACCCC
5726985 ATTTGACTTATT-AGAGTATA
1 ATTTGACTTATTGA-AGTATA
*
5727005 ATTTGACTTATTGAAGTATG
1 ATTTGACTTATTGAAGTATA
5727025 ATTTGA
1 ATTTGA
5727031 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGAAGTATA
Found at i:5727106 original size:28 final size:27
Alignment explanation
Indices: 5727075--5727127 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
5727065 TTTGGAGTAT
*
5727075 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTT-CCACCTC
*
5727103 AGGGGCAAAATTGTAATTTTCCACC
1 AGGGGCAAAATGGTAATTTTCCACC
5727128 ACCAGGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (27 bp):
AGGGGCAAAATGGTAATTTTCCACCTC
Found at i:5727133 original size:28 final size:28
Alignment explanation
Indices: 5727075--5727133 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
5727065 TTTGGAGTAT
* *
5727075 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTTGCCACCCC
*
5727103 AGGGGCAAAATTGTAATTTT-CCACCACC
1 AGGGGCAAAATGGTAATTTTGCCACC-CC
5727131 AGG
1 AGG
5727134 ATATTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (28 bp):
AGGGGCAAAATGGTAATTTTGCCACCCC
Found at i:5732237 original size:19 final size:19
Alignment explanation
Indices: 5732213--5732250 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5732203 CTGCCAAACC
*
5732213 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
5732232 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
5732251 AGTTAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:5733356 original size:14 final size:14
Alignment explanation
Indices: 5733339--5733380 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
5733329 TTTAGAATAA
5733339 AATAATATTATATT
1 AATAATATTATATT
* *
5733353 AATAAAATAATATT
1 AATAATATTATATT
5733367 AA-AATATTAATATT
1 AATAATATT-ATATT
5733381 TAGTCGGATG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 4 0.17
14 19 0.83
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATAATATTATATT
Found at i:5740352 original size:2 final size:2
Alignment explanation
Indices: 5740341--5740374 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5740331 ACACTTTACG
5740341 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5740375 TCCAAATGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5740876 original size:31 final size:33
Alignment explanation
Indices: 5740835--5740898 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 33
5740825 CTCCATTTTC
* *
5740835 CTTATTTGGGCTAAGCCCATTTATTTTC-ATTT
1 CTTATTTGGGCCAAGCCCACTTATTTTCTATTT
*
5740867 CTTA-TTGGGCCATGCCCACTTATTTTCTATTT
1 CTTATTTGGGCCAAGCCCACTTATTTTCTATTT
5740899 GGCCATGCCC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 20 0.71
32 8 0.29
ACGTcount: A:0.17, C:0.22, G:0.12, T:0.48
Consensus pattern (33 bp):
CTTATTTGGGCCAAGCCCACTTATTTTCTATTT
Found at i:5740918 original size:26 final size:26
Alignment explanation
Indices: 5740864--5740917 Score: 92
Period size: 25 Copynumber: 2.1 Consensus size: 26
5740854 TTTATTTTCA
5740864 TTTCTTATTGGGCCATGCCCACTTAT
1 TTTCTTATTGGGCCATGCCCACTTAT
*
5740890 TTTC-TATTTGGCCATGCCCACTTAT
1 TTTCTTATTGGGCCATGCCCACTTAT
5740915 TTT
1 TTT
5740918 TTTTTCATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 23 0.85
26 4 0.15
ACGTcount: A:0.15, C:0.26, G:0.13, T:0.46
Consensus pattern (26 bp):
TTTCTTATTGGGCCATGCCCACTTAT
Found at i:5740930 original size:9 final size:9
Alignment explanation
Indices: 5740916--5740941 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
5740906 CCCACTTATT
5740916 TTTTTTTCA
1 TTTTTTTCA
5740925 TTTTTTTCA
1 TTTTTTTCA
5740934 TTTTTTTC
1 TTTTTTTC
5740942 TCTCTTCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:5741021 original size:22 final size:22
Alignment explanation
Indices: 5740993--5741062 Score: 113
Period size: 22 Copynumber: 3.2 Consensus size: 22
5740983 CGTGGCTTCC
5740993 CTTCACCACTGTGGCTTCCTCT
1 CTTCACCACTGTGGCTTCCTCT
**
5741015 CTTCACCACCATGGCTTCCTCT
1 CTTCACCACTGTGGCTTCCTCT
*
5741037 CTTCATCACTGTGGCTTCCTCT
1 CTTCACCACTGTGGCTTCCTCT
5741059 CTTC
1 CTTC
5741063 CTTTCCTCTC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.10, C:0.41, G:0.11, T:0.37
Consensus pattern (22 bp):
CTTCACCACTGTGGCTTCCTCT
Found at i:5741244 original size:34 final size:34
Alignment explanation
Indices: 5741183--5741288 Score: 164
Period size: 34 Copynumber: 3.2 Consensus size: 34
5741173 TCAATTTTGG
5741183 TGGCA-CAAAGTAG-TCCAA-TTTTTTGCACAAAT
1 TGGCAGCAAA-TAGCTCCAATTTTTTTGCACAAAT
5741215 TGGCAGCAAATAGCTCCAATTTTTTTGCACAAAT
1 TGGCAGCAAATAGCTCCAATTTTTTTGCACAAAT
* *
5741249 TGGCAGCAAGTAGCTCTAATTTTTTTGCACAAAT
1 TGGCAGCAAATAGCTCCAATTTTTTTGCACAAAT
5741283 TGGCAG
1 TGGCAG
5741289 TACTTTGATG
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
32 8 0.12
33 9 0.13
34 52 0.75
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (34 bp):
TGGCAGCAAATAGCTCCAATTTTTTTGCACAAAT
Found at i:5741583 original size:26 final size:26
Alignment explanation
Indices: 5741553--5741602 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
5741543 TCTCTCGCGG
5741553 TTCTTTCACTCCTTT-TTTCTCTTCAT
1 TTCTTTC-CTCCTTTATTTCTCTTCAT
* *
5741579 TTCTTTCTTCCTTTATTTTTCTTC
1 TTCTTTCCTCCTTTATTTCTCTTC
5741603 TCTTTTTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.06, C:0.28, G:0.00, T:0.66
Consensus pattern (26 bp):
TTCTTTCCTCCTTTATTTCTCTTCAT
Found at i:5743032 original size:252 final size:253
Alignment explanation
Indices: 5742573--5743076 Score: 579
Period size: 252 Copynumber: 2.0 Consensus size: 253
5742563 TTACATAAGC
* * * * *
5742573 TGTTAAATACTTTTAGCTTAATCATATAAATTTAAATGTTTAATTTTCTCAAAAATTATATTTAT
1 TGTTAAATACTTTTAGCTCAATAATACAAATTTAAAGGTTTAATTTTCACAAAAATTATATTTAT
* * * *
5742638 TTTGACTTAATTGACTTGTTACACTAAATCTCACATGTTTGCATCAACATTTTAGCAACACTTGT
66 TTTGACTTAATTGACTAGTTACACTAAATCTCACATATTTACATCAACATTTTAGCAACACTTAT
** * * * * * *
5742703 TCCACTTGTATAATTTTTTACATTTGCTCTTATAAGTGTGCGTCAATGTTTTTCAGTTGCTAGTT
131 TCCACTTGTATAATTTTTTACATTAACTCTTACAAGTGTACGTCAAGGATATTCAATTGCTAGTT
* * *
5742768 TTCACCATAATTATTTTTATTCATATTATTATTCCTTTTATAAATT-AAATTTGTAAAT
196 TTCACCATAATTATTTTTATCCATATTATTATTCATTTT-TAAATTAAAATTTATAAAT
* *
5742826 TGTTAAATACTTTTAGCTCAATAATACAAATTTATAGGTTTAATTTTCAC-AAAATTATGTTTAT
1 TGTTAAATACTTTTAGCTCAATAATACAAATTTAAAGGTTTAATTTTCACAAAAATTATATTTAT
** * ** * * **
5742890 TTTGACTTAATTGACTAGTTACTTTAAATCTCATATATTTATGTTAATATTTT-GACAATGCTTA
66 TTTGACTTAATTGACTAGTTACACTAAATCTCACATATTTACATCAACATTTTAG-CAACACTTA
* * * * *
5742954 TTCCTCCTT-TATTAA-TTTTTACATTAATTCTTACAAGTTTATGTTAAGGATATTCAATTGCTA
130 TTCC-ACTTGTA-TAATTTTTTACATTAACTCTTACAAGTGTACGTCAAGGATATTCAATTGCTA
* *
5743017 -TTTTCCCCTATAATTATTTTTATCCTTATTATTATTCATTTTTAAATTAAAATTTATAAA
193 GTTTTCACC-ATAATTATTTTTATCCATATTATTATTCATTTTTAAATTAAAATTTATAAA
5743077 CCATTATGTT
Statistics
Matches: 208, Mismatches: 38, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
251 14 0.07
252 144 0.69
253 50 0.24
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (253 bp):
TGTTAAATACTTTTAGCTCAATAATACAAATTTAAAGGTTTAATTTTCACAAAAATTATATTTAT
TTTGACTTAATTGACTAGTTACACTAAATCTCACATATTTACATCAACATTTTAGCAACACTTAT
TCCACTTGTATAATTTTTTACATTAACTCTTACAAGTGTACGTCAAGGATATTCAATTGCTAGTT
TTCACCATAATTATTTTTATCCATATTATTATTCATTTTTAAATTAAAATTTATAAAT
Found at i:5743651 original size:21 final size:21
Alignment explanation
Indices: 5743609--5743652 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5743599 CAAAATACTT
* *
5743609 CTAGGGATTGACCTTCCTTGC
1 CTAGGGATCGACCTTCCATGC
5743630 CTAGGGATCGACCCTT-CATGC
1 CTAGGGATCGA-CCTTCCATGC
5743651 CT
1 CT
5743653 TAACATGCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.16, C:0.32, G:0.23, T:0.30
Consensus pattern (21 bp):
CTAGGGATCGACCTTCCATGC
Found at i:5747729 original size:54 final size:54
Alignment explanation
Indices: 5747667--5747815 Score: 244
Period size: 54 Copynumber: 2.8 Consensus size: 54
5747657 TAAACCACCA
* * * *
5747667 TCTCACCCAGCTCATGTTCATCCCCCCACATCGTGCACATAGACGGACACCCCG
1 TCTCACCCAACTCATGTGCATCCCCCCACATCATGCACATAGACAGACACCCCG
*
5747721 TCTCACCCAACTCATGTGCATCCCCCCACATCATGCACATAGCCAGACACCCCG
1 TCTCACCCAACTCATGTGCATCCCCCCACATCATGCACATAGACAGACACCCCG
*
5747775 TCTCACCAAACTCATGTGCATCCCCCCACATCATGCACATA
1 TCTCACCCAACTCATGTGCATCCCCCCACATCATGCACATA
5747816 ACCGGAGTCA
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 89 1.00
ACGTcount: A:0.26, C:0.44, G:0.11, T:0.19
Consensus pattern (54 bp):
TCTCACCCAACTCATGTGCATCCCCCCACATCATGCACATAGACAGACACCCCG
Found at i:5750802 original size:20 final size:20
Alignment explanation
Indices: 5750777--5750822 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
5750767 TTTTAGTCCC
5750777 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
*
5750797 ATTTGACTTATTGGAGTATG
1 ATTTGACTTATTGGAGTATA
5750817 ATTTGA
1 ATTTGA
5750823 GGTTTAGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:5762366 original size:20 final size:20
Alignment explanation
Indices: 5762341--5762386 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
5762331 TTTTGGCCCC
5762341 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
*
5762361 ATTTGACTTATTGGAGTATG
1 ATTTGACTTATTGGAGTATA
5762381 ATTTGA
1 ATTTGA
5762387 GCTTTAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:5762461 original size:28 final size:27
Alignment explanation
Indices: 5762430--5762483 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
5762420 ATTTGGAGTA
*
5762430 TAGGGGTAAAAAGGTAATTTTGCCACCC
1 TAGGGGCAAAAAGGTAATTTT-CCACCC
**
5762458 TAGGGGCAAAATTGTAATTTTCCACC
1 TAGGGGCAAAAAGGTAATTTTCCACC
5762484 ACCAGGATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (27 bp):
TAGGGGCAAAAAGGTAATTTTCCACCC
Found at i:5765514 original size:13 final size:13
Alignment explanation
Indices: 5765496--5765520 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5765486 GGAGAAATTG
5765496 TGATTTTATAAAA
1 TGATTTTATAAAA
5765509 TGATTTTATAAA
1 TGATTTTATAAA
5765521 TTTTCTGGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:5779751 original size:17 final size:19
Alignment explanation
Indices: 5779713--5779752 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
5779703 GATTATTTAT
5779713 TATATTTACAAGTATGTAAA
1 TATATTTACAAGTA-GTAAA
5779733 TATATTTACAA-TA-TAAA
1 TATATTTACAAGTAGTAAA
5779750 TAT
1 TAT
5779753 TTCTTCCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
19 2 0.10
20 11 0.55
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (19 bp):
TATATTTACAAGTAGTAAA
Found at i:5784441 original size:19 final size:19
Alignment explanation
Indices: 5784417--5784454 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5784407 CTGCCAAACC
*
5784417 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
5784436 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
5784455 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:5791523 original size:19 final size:19
Alignment explanation
Indices: 5791499--5791536 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5791489 CTGCCAAACC
*
5791499 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
5791518 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
5791537 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:5792270 original size:43 final size:43
Alignment explanation
Indices: 5792222--5792358 Score: 184
Period size: 43 Copynumber: 3.2 Consensus size: 43
5792212 GTTATGTGAT
**
5792222 GATGATGACCCGACTATGTGCAAGTAGGGAGTGTTCATAAGCC
1 GATGATGACCCGACTATGTGCAAGTAGGGAGTGCACATAAGCC
* * *
5792265 GATGATGACCCGACTATGTACAAGCAAGGAGTGCACATAAGCC
1 GATGATGACCCGACTATGTGCAAGTAGGGAGTGCACATAAGCC
* * * * *
5792308 GATGATGACCCAACTATGTGCGAGTAGAGAGTGCACATGAGCT
1 GATGATGACCCGACTATGTGCAAGTAGGGAGTGCACATAAGCC
5792351 GATGATGA
1 GATGATGA
5792359 TGATAAGGCT
Statistics
Matches: 81, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 81 1.00
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.20
Consensus pattern (43 bp):
GATGATGACCCGACTATGTGCAAGTAGGGAGTGCACATAAGCC
Found at i:5793584 original size:135 final size:135
Alignment explanation
Indices: 5793389--5793636 Score: 363
Period size: 135 Copynumber: 1.8 Consensus size: 135
5793379 ACCGGTGTCT
* * *
5793389 CACCCAAATCGGATTCTCCCTTTTTTCCATTAATACTCAAGCCGACGATTGCTCCTTTCTTCTCT
1 CACCCAAATCAGATTCT-CCTTTTTTCCATTAATACTCAAGCCGACGATTGCACCATTCTTCTCT
*
5793454 CCTTTGCTAGCAAGCTACCCAAAAGCTGAGTTTGTTTCCCTCCCTACCGTCGGCGCACAGAACAA
65 CCTTCGCTAGCAAGCTACCCAAAAGCTGAGTTTGTTTCCCTCCCTACCGTCGGCGCACAGAACAA
5793519 GCACCA
130 GCACCA
** *
5793525 CACCCAAATCAGATTCT-CTTTTTGTCCATTAATACTCTGGCCGATGATTGCACCATTCTTCTCT
1 CACCCAAATCAGATTCTCCTTTTT-TCCATTAATACTCAAGCCGACGATTGCACCATTCTTCTCT
* * ** *
5793589 CCTTCGTTTGCTGGCTACTCAAAAGCTGAGTTTGTTTCCCTCCCTACC
65 CCTTCGCTAGCAAGCTACCCAAAAGCTGAGTTTGTTTCCCTCCCTACC
5793637 ACCAACGCGC
Statistics
Matches: 99, Mismatches: 12, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
134 6 0.06
135 77 0.78
136 16 0.16
ACGTcount: A:0.21, C:0.33, G:0.14, T:0.32
Consensus pattern (135 bp):
CACCCAAATCAGATTCTCCTTTTTTCCATTAATACTCAAGCCGACGATTGCACCATTCTTCTCTC
CTTCGCTAGCAAGCTACCCAAAAGCTGAGTTTGTTTCCCTCCCTACCGTCGGCGCACAGAACAAG
CACCA
Found at i:5799097 original size:28 final size:29
Alignment explanation
Indices: 5799056--5799115 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
5799046 GTCTATGGGC
* *
5799056 AATTTTTCAGTTTT-TGGGGCAAAAATGT
1 AATTTTTCACTTTTAGGGGGCAAAAATGT
* *
5799084 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCACTTTTA-GGGGGCAAAAATGT
5799114 AA
1 AA
5799116 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.30, C:0.08, G:0.23, T:0.38
Consensus pattern (29 bp):
AATTTTTCACTTTTAGGGGGCAAAAATGT
Found at i:5804231 original size:13 final size:13
Alignment explanation
Indices: 5804213--5804237 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5804203 TTTCAGAAAA
5804213 TTTATAAAATCAT
1 TTTATAAAATCAT
5804226 TTTATAAAATCA
1 TTTATAAAATCA
5804238 CAATTTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:5807068 original size:29 final size:30
Alignment explanation
Indices: 5807025--5807083 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
5807015 CTTGATTGAG
5807025 GATGAAGAAGATGACATGCAAAGAGATGAA
1 GATGAAGAAGATGACATGCAAAGAGATGAA
* *
5807055 GATG-AGAAGATGACATGGAAGGAGATGAA
1 GATGAAGAAGATGACATGCAAAGAGATGAA
5807084 AATAAAGATG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 23 0.85
30 4 0.15
ACGTcount: A:0.47, C:0.05, G:0.34, T:0.14
Consensus pattern (30 bp):
GATGAAGAAGATGACATGCAAAGAGATGAA
Found at i:5812588 original size:18 final size:17
Alignment explanation
Indices: 5812552--5812594 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
5812542 GTAACTAAGG
*
5812552 ATAAAATCATATAATTA
1 ATAAAATTATATAATTA
*
5812569 ATAAAATTATGATTATTA
1 ATAAAATTAT-ATAATTA
*
5812587 ATTAAATT
1 ATAAAATT
5812595 GTAAGGTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
ATAAAATTATATAATTA
Found at i:5812740 original size:15 final size:17
Alignment explanation
Indices: 5812712--5812746 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
5812702 TATTTTATAT
5812712 TAATATTATAAAAATTA
1 TAATATTATAAAAATTA
5812729 TAAT-TTAT-AAAATTA
1 TAATATTATAAAAATTA
5812744 TAA
1 TAA
5812747 AATTCATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
16 4 0.22
17 4 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAATATTATAAAAATTA
Found at i:5815238 original size:86 final size:86
Alignment explanation
Indices: 5815076--5815239 Score: 229
Period size: 86 Copynumber: 1.9 Consensus size: 86
5815066 TTGAAGAAAA
* * * *
5815076 GTTGTTACATGTCATGTTTAAGGTGTTTAACTCCAAAACTTTATATTATAGTGAAATACAAGGAT
1 GTTGTTACATATCATATTTAAGGTGTTTAACTCCAAAACTTTATATTATACTGAAATACAAAGAT
* * *
5815141 AGAGATCAAGTTACACGTCAT
66 AAAAATAAAGTTACACGTCAT
* * * *
5815162 GTTGTTACATATCATATTTAAGGTGTTTAACTCCAAGAGTTTATATTTTTCTGAAATACAAAGAT
1 GTTGTTACATATCATATTTAAGGTGTTTAACTCCAAAACTTTATATTATACTGAAATACAAAGAT
5815227 AAAAATAAAGTTA
66 AAAAATAAAGTTA
5815240 TACGCCGTAT
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
86 67 1.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (86 bp):
GTTGTTACATATCATATTTAAGGTGTTTAACTCCAAAACTTTATATTATACTGAAATACAAAGAT
AAAAATAAAGTTACACGTCAT
Found at i:5819483 original size:19 final size:19
Alignment explanation
Indices: 5819455--5819512 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
5819445 ACTAAAAAAT
*
5819455 AATAATAAATAAATAATAA
1 AATAAAAAATAAATAATAA
5819474 AATAAAAAATAAATATATAA
1 AATAAAAAATAAATA-ATAA
* *
5819494 ATATAAAATATAAAAAATA
1 A-ATAAAAAATAAATAATA
5819513 TGTAAATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 14 0.41
20 8 0.24
21 12 0.35
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (19 bp):
AATAAAAAATAAATAATAA
Found at i:5821544 original size:25 final size:25
Alignment explanation
Indices: 5821515--5821562 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
5821505 TGCTTACAAA
*
5821515 AAATA-AAATAATATAATAATAATCG
1 AAATATAAA-AATATAAAAATAATCG
5821540 AAATATAAAAATATAAAAATAAT
1 AAATATAAAAATATAAAAATAAT
5821563 AAATAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (25 bp):
AAATATAAAAATATAAAAATAATCG
Found at i:5824598 original size:2 final size:2
Alignment explanation
Indices: 5824591--5824639 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
5824581 GAATATGCAA
5824591 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5824632 AT AT AT AT
1 AT AT AT AT
5824640 TTATCTTGAN
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5824724 original size:2 final size:2
Alignment explanation
Indices: 5824717--5824769 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
5824707 GGGAATATGC
5824717 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
5824759 TA TA TA TA TA T
1 TA TA TA TA TA T
5824770 TTATCTTGAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5826752 original size:26 final size:27
Alignment explanation
Indices: 5826701--5826762 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
5826691 AATAGTTTTT
*
5826701 TATTTTTTTATTATATTTAATCAAATA
1 TATTTATTTATTATATTTAATCAAATA
*
5826728 TATTTATTT-TTAT-TTTAAATTAAATA
1 TATTTATTTATTATATTT-AATCAAATA
5826754 -ATTT-TTTAT
1 TATTTATTTAT
5826763 AATTAATTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
24 3 0.10
25 8 0.26
26 12 0.39
27 8 0.26
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (27 bp):
TATTTATTTATTATATTTAATCAAATA
Found at i:5832542 original size:16 final size:15
Alignment explanation
Indices: 5832517--5832546 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5832507 TGCTTTTTTA
5832517 TTTTTTAATATCTTT
1 TTTTTTAATATCTTT
5832532 TTTTATTAATATCTT
1 TTTT-TTAATATCTT
5832547 AAAGAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTTTAATATCTTT
Found at i:5833834 original size:15 final size:16
Alignment explanation
Indices: 5833814--5833845 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
5833804 GCATTGCTTG
5833814 TGCTTTTTTT-TTTGT
1 TGCTTTTTTTGTTTGT
5833829 TGCTTTTTTTGTTTGT
1 TGCTTTTTTTGTTTGT
5833845 T
1 T
5833846 TTTGTGGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.00, C:0.06, G:0.16, T:0.78
Consensus pattern (16 bp):
TGCTTTTTTTGTTTGT
Found at i:5837019 original size:31 final size:31
Alignment explanation
Indices: 5836983--5837056 Score: 96
Period size: 33 Copynumber: 2.4 Consensus size: 31
5836973 GAGAAGAATC
*
5836983 CTAGCAAC-CAAAAATACCTAGCCACAGTTTT
1 CTAGCAACAAAAAAATACCTAGCCACAG-TTT
*
5837014 CTAGCAATCAAAAAAATCCCTAGCCACAGTTT
1 CTAGCAA-CAAAAAAATACCTAGCCACAGTTT
*
5837046 CTACCAACAAA
1 CTAGCAACAAA
5837057 GAGAAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 11 0.29
32 10 0.26
33 17 0.45
ACGTcount: A:0.42, C:0.30, G:0.08, T:0.20
Consensus pattern (31 bp):
CTAGCAACAAAAAAATACCTAGCCACAGTTT
Found at i:5849168 original size:2 final size:2
Alignment explanation
Indices: 5849161--5849207 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
5849151 AAGTTGTCAA
* * *
5849161 AT AT AT AT AT AT AT AT AT AT -T TT AT AT TT AT AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5849202 AT AT AT
1 AT AT AT
5849208 TCTCTCTACC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
AT
Found at i:5849450 original size:21 final size:20
Alignment explanation
Indices: 5849421--5849461 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
5849411 TTGATTTTTC
5849421 CAATTTTATAATATTTTAAT
1 CAATTTTATAATATTTTAAT
*
5849441 CAATCTTTATATTATTTTAAT
1 CAAT-TTTATAATATTTTAAT
5849462 AAGGAATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (20 bp):
CAATTTTATAATATTTTAAT
Found at i:5851837 original size:19 final size:19
Alignment explanation
Indices: 5851779--5851839 Score: 68
Period size: 19 Copynumber: 3.0 Consensus size: 19
5851769 TATTTTTTAT
5851779 TAATTTTTAAAATTATTATTATA
1 TAATTTTTAAAATTA--A-TA-A
* *
5851802 TAATTTTAAAAAATAATAA
1 TAATTTTTAAAATTAATAA
5851821 TAATTTTTAAAATTAATAA
1 TAATTTTTAAAATTAATAA
5851840 AAAAATAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 18 0.53
20 2 0.06
21 1 0.03
23 13 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TAATTTTTAAAATTAATAA
Found at i:5856963 original size:16 final size:16
Alignment explanation
Indices: 5856942--5856973 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5856932 ACTGTTATAC
5856942 TTAAAATAAAAAATAT
1 TTAAAATAAAAAATAT
*
5856958 TTAAAATAAAATATAT
1 TTAAAATAAAAAATAT
5856974 AATATAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TTAAAATAAAAAATAT
Found at i:5857103 original size:34 final size:33
Alignment explanation
Indices: 5857042--5857128 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 33
5857032 AAAGAAATTA
* * *
5857042 AAATAAAATATATAATATAAAAAATTATATTAAAG
1 AAATAAAA-ATAAAATATATAAAATTATAAT-AAG
*
5857077 AAATAAAAATAAAATATATAAGATTATAATAAG
1 AAATAAAAATAAAATATATAAAATTATAATAAG
*
5857110 AAATGAAAATAAAATATAT
1 AAATAAAAATAAAATATAT
5857129 TGCATTAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 21 0.45
34 18 0.38
35 8 0.17
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (33 bp):
AAATAAAAATAAAATATATAAAATTATAATAAG
Found at i:5858285 original size:16 final size:17
Alignment explanation
Indices: 5858260--5858296 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
5858250 AATTTCACAC
*
5858260 AATAATTAAAT-ATATA
1 AATAACTAAATAATATA
5858276 AATAACTAAATAATATA
1 AATAACTAAATAATATA
5858293 AATA
1 AATA
5858297 GAAAGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
AATAACTAAATAATATA
Found at i:5859232 original size:20 final size:20
Alignment explanation
Indices: 5859188--5859234 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
5859178 ACTTCTAAAC
* *
5859188 CTCAAATCATACTTCAATTA
1 CTCAAATCATACTCCAATAA
5859208 CTCAAATCATACTCCAATAA
1 CTCAAATCATACTCCAATAA
*
5859228 GTCAAAT
1 CTCAAAT
5859235 GGGGCCAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.43, C:0.26, G:0.02, T:0.30
Consensus pattern (20 bp):
CTCAAATCATACTCCAATAA
Found at i:5860343 original size:35 final size:34
Alignment explanation
Indices: 5860291--5860428 Score: 124
Period size: 35 Copynumber: 4.1 Consensus size: 34
5860281 TTTCACAAAG
** * *
5860291 CTTTACAATGGCCTTTACCAGGCTTAGCCAAAAC
1 CTTTACAATGGTTTTTACCAGGCTCAACCAAAAC
*
5860325 CTTTCACAATGGTTTTTACC-GAGATCAACCAAAAC
1 CTTT-ACAATGGTTTTTACCAG-GCTCAACCAAAAC
* *
5860360 C--TAAAATGGTTTTT-CCAAGGCTCAACCACAAC
1 CTTTACAATGGTTTTTACC-AGGCTCAACCAAAAC
*
5860392 CTTTCACAATGGTTTTT-CACGGGCTCAACCAAAAC
1 CTTT-ACAATGGTTTTTAC-CAGGCTCAACCAAAAC
5860427 CT
1 CT
5860429 AAAGTGGTTT
Statistics
Matches: 85, Mismatches: 11, Indels: 15
0.77 0.10 0.14
Matches are distributed among these distances:
31 2 0.02
32 23 0.27
33 2 0.02
34 6 0.07
35 51 0.60
36 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (34 bp):
CTTTACAATGGTTTTTACCAGGCTCAACCAAAAC
Found at i:5860373 original size:32 final size:31
Alignment explanation
Indices: 5860332--5860441 Score: 112
Period size: 32 Copynumber: 3.4 Consensus size: 31
5860322 AACCTTTCAC
*
5860332 AATGGTTTTTACCGAGATCAACCAAAACCTAA
1 AATGGTTTTT-CCGAGCTCAACCAAAACCTAA
* * *
5860364 AATGGTTTTTCCAAGGCTCAACCACAACCTTTCAC
1 AATGGTTTTTCCGA-GCTCAACCAAAACC--T-AA
*
5860399 AATGGTTTTTCACGGGCTCAACCAAAACCTAA
1 AATGGTTTTTC-CGAGCTCAACCAAAACCTAA
*
5860431 AGTGGTTTTTC
1 AATGGTTTTTC
5860442 AAAGGATCAA
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
31 3 0.05
32 33 0.52
33 1 0.02
34 1 0.02
35 25 0.39
36 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.29
Consensus pattern (31 bp):
AATGGTTTTTCCGAGCTCAACCAAAACCTAA
Found at i:5860405 original size:67 final size:67
Alignment explanation
Indices: 5860322--5860492 Score: 238
Period size: 67 Copynumber: 2.5 Consensus size: 67
5860312 GCTTAGCCAA
* * *
5860322 AACCTTTCACAATGGTTTTTACCGAGATCAACCAAAACCTAAAATGGTTTTTCCAAGGCTCAACC
1 AACCTTTCACAATGGTTTTTACCGGGATCAACCAAAACCTAAAATGGTTTTTCAAAGGATCAACC
5860387 AC
66 AC
* *
5860389 AACCTTTCACAATGGTTTTT-CACGGGCTCAACCAAAACCTAAAGTGGTTTTTCAAAGGATCAAC
1 AACCTTTCACAATGGTTTTTAC-CGGGATCAACCAAAACCTAAAATGGTTTTTCAAAGGATCAAC
5860453 CAC
65 CAC
* *
5860456 AA-CTTACAACAATGGTTTTTCACGGGGATCAACCAAA
1 AACCTTTC-ACAATGGTTTTT-ACCGGGATCAACCAAA
5860493 TCCCAACAAC
Statistics
Matches: 92, Mismatches: 8, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
66 5 0.05
67 74 0.80
68 12 0.13
69 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (67 bp):
AACCTTTCACAATGGTTTTTACCGGGATCAACCAAAACCTAAAATGGTTTTTCAAAGGATCAACC
AC
Found at i:5860442 original size:32 final size:34
Alignment explanation
Indices: 5860347--5860492 Score: 131
Period size: 32 Copynumber: 4.3 Consensus size: 34
5860337 TTTTTACCGA
5860347 GATCAACCAAAACCT-AAAATGGTTTTTC-CAAG
1 GATCAACCAAAACCTCAAAATGGTTTTTCACAAG
* * * *
5860379 GCTCAACCACAACCTTTCACAATGGTTTTTCAC-GG
1 GATCAACCAAAACC--TCAAAATGGTTTTTCACAAG
* *
5860414 GCTCAACCAAAACCT-AAAGTGGTTTTTCA-AAG
1 GATCAACCAAAACCTCAAAATGGTTTTTCACAAG
* * **
5860446 GATCAACCACAACTTACAACAATGGTTTTTCACGGG
1 GATCAACCAAAACCT-CAA-AATGGTTTTTCACAAG
5860482 GATCAACCAAA
1 GATCAACCAAA
5860493 TCCCAACAAC
Statistics
Matches: 90, Mismatches: 15, Indels: 14
0.76 0.13 0.12
Matches are distributed among these distances:
32 37 0.41
33 1 0.01
34 3 0.03
35 37 0.41
36 12 0.13
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (34 bp):
GATCAACCAAAACCTCAAAATGGTTTTTCACAAG
Found at i:5860474 original size:35 final size:34
Alignment explanation
Indices: 5860364--5860477 Score: 117
Period size: 35 Copynumber: 3.4 Consensus size: 34
5860354 CAAAACCTAA
*
5860364 AATGGTTTTTCCAAGGCTCAACCACAACCTTTC-AC
1 AATGGTTTTTCAAAGGCTCAACCACAA-C-TTCAAC
** * *
5860399 AATGGTTTTTCACGGGCTCAACCAAAACCT-AA-
1 AATGGTTTTTCAAAGGCTCAACCACAACTTCAAC
* *
5860431 AGTGGTTTTTCAAAGGATCAACCACAACTTACAAC
1 AATGGTTTTTCAAAGGCTCAACCACAACTT-CAAC
5860466 AATGGTTTTTCA
1 AATGGTTTTTCA
5860478 CGGGGATCAA
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
32 24 0.38
33 2 0.03
34 3 0.05
35 34 0.54
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (34 bp):
AATGGTTTTTCAAAGGCTCAACCACAACTTCAAC
Found at i:5865523 original size:19 final size:19
Alignment explanation
Indices: 5865499--5865538 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
5865489 TTCTGATTTA
5865499 TGTTTTT-TATTTATGTTTT
1 TGTTTTTATATTTAT-TTTT
*
5865518 TGTTTTTATTTTTATTTTT
1 TGTTTTTATATTTATTTTT
5865537 TG
1 TG
5865539 CATCATTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.80
Consensus pattern (19 bp):
TGTTTTTATATTTATTTTT
Found at i:5865530 original size:13 final size:13
Alignment explanation
Indices: 5865494--5865518 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5865484 GTTAATTCTG
5865494 ATTTATGTTTTTT
1 ATTTATGTTTTTT
5865507 ATTTATGTTTTT
1 ATTTATGTTTTT
5865519 GTTTTTATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (13 bp):
ATTTATGTTTTTT
Found at i:5865535 original size:18 final size:18
Alignment explanation
Indices: 5865502--5865536 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5865492 TGATTTATGT
*
5865502 TTTTTATTTATGTTTTTG
1 TTTTTATTTATATTTTTG
*
5865520 TTTTTATTTTTATTTTT
1 TTTTTATTTATATTTTT
5865537 TGCATCATTT
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:0.11, C:0.00, G:0.06, T:0.83
Consensus pattern (18 bp):
TTTTTATTTATATTTTTG
Found at i:5868703 original size:37 final size:37
Alignment explanation
Indices: 5868653--5868726 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
5868643 ACGTTAATAG
* *
5868653 CACAAATACAGCTGGTTAAATATGTTTATTAGTCTCA
1 CACAAATACAGCTGGTTAAATATATTTATTAATCTCA
5868690 CACAAATACAGCTGGTTAAATATATTTATTAATCTCA
1 CACAAATACAGCTGGTTAAATATATTTATTAATCTCA
5868727 TTAAATCCCC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (37 bp):
CACAAATACAGCTGGTTAAATATATTTATTAATCTCA
Found at i:5879394 original size:195 final size:189
Alignment explanation
Indices: 5879065--5879440 Score: 475
Period size: 195 Copynumber: 2.0 Consensus size: 189
5879055 GTTTGGAGAA
* * * *
5879065 TTTTTTCAAGTATTATATCTTACAATATTATCAAGTTTGGATCTTTACGAATAAAAAGTAAGATT
1 TTTTTTCAAGAATTATACCTTACAATATTATCAAATTTGGATCTTTAAGAATAAAAAGTAAGATT
* * * * * **
5879130 TATAATATGAAAGAGTTACCCCTTTCATATAATCCAAGGCTTATTGAGTCTTGATATGCGTCAAG
66 TATAATATAAAAGAGCTAACCCTTTCATATAATCCAAGGCCTATTGAGTCCTGATATGCACCAAG
*
5879195 AAAAAAAAAAACATTTTTATCCCATAAAAAGTTAAAAAAGTGTTAAAATTTATAGATTAGGGAT
131 ----AAAAAAACATTTTTATCCAATAAAAAGTT-AAAAAGTGTTAAAATTTATAGATTAGGGAT
* * * *
5879259 TTTTTTCAAGAATTATGCCTTATAATATTATCAAATTTGGGTC-TTAAGAATAAAGAGTAAGATT
1 TTTTTTCAAGAATTATACCTTACAATATTATCAAATTTGGATCTTTAAGAATAAAAAGTAAGATT
* * *
5879323 TATAATATTAAAGAGAGCTAACCCTTTCATATAATCCGAGGCCTATTGCGTCCTGATATGTACCA
66 TATAATA-TAAA-AGAGCTAACCCTTTCATATAATCCAAGGCCTATTGAGTCCTGATATGCACCA
* * **
5879388 AGAAAAAACCCTTTTTATCCAATAAAAAGTTAAAAAGTGTTGCAATTTATAGA
129 AGAAAAAAACATTTTTATCCAATAAAAAGTTAAAAAGTGTTAAAATTTATAGA
5879441 CTTTCAACTA
Statistics
Matches: 157, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
190 20 0.13
191 26 0.17
193 26 0.17
194 40 0.25
195 45 0.29
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (189 bp):
TTTTTTCAAGAATTATACCTTACAATATTATCAAATTTGGATCTTTAAGAATAAAAAGTAAGATT
TATAATATAAAAGAGCTAACCCTTTCATATAATCCAAGGCCTATTGAGTCCTGATATGCACCAAG
AAAAAAACATTTTTATCCAATAAAAAGTTAAAAAGTGTTAAAATTTATAGATTAGGGAT
Found at i:5882779 original size:2 final size:2
Alignment explanation
Indices: 5882774--5882806 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5882764 CTCCTTTTTA
5882774 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5882807 ATAAAGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5882865 original size:2 final size:2
Alignment explanation
Indices: 5882858--5882891 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5882848 NTTAATAAAT
5882858 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
5882892 AAAGAGAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5883560 original size:29 final size:29
Alignment explanation
Indices: 5883528--5883583 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
5883518 TTTAAAAAAA
5883528 ATTTAAAT-AAATCCTTATATTTTTATTAT
1 ATTT-AATCAAATCCTTATATTTTTATTAT
*
5883557 ATTTAATCAAATCTTTATATTTTTATT
1 ATTTAATCAAATCCTTATATTTTTATT
5883584 TTGAATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (29 bp):
ATTTAATCAAATCCTTATATTTTTATTAT
Found at i:5890729 original size:36 final size:36
Alignment explanation
Indices: 5890689--5890777 Score: 117
Period size: 36 Copynumber: 2.5 Consensus size: 36
5890679 AGGGTTATCA
* *
5890689 CTTAATCCCGTTAAAAAATCGGTGTAAGGATTATTG
1 CTTAATCCCGTTAAAAAATCGATATAAGGATTATTG
* * *
5890725 CTTAATCCCATTAAAAAGTCGATATAAGGGTTATTG
1 CTTAATCCCGTTAAAAAATCGATATAAGGATTATTG
*
5890761 CTTGATCCCG-TAAAAAA
1 CTTAATCCCGTTAAAAAA
5890778 GCTATTATGA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
35 6 0.13
36 39 0.87
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (36 bp):
CTTAATCCCGTTAAAAAATCGATATAAGGATTATTG
Found at i:5890778 original size:36 final size:36
Alignment explanation
Indices: 5890679--5890778 Score: 112
Period size: 36 Copynumber: 2.8 Consensus size: 36
5890669 AACTACTGTG
** * *
5890679 AGGGTTATCACTTAATCCCGTTAAAAAA-TCGGTGTA
1 AGGGTTATTGCTTAATCCCG-TAAAAAAGTCGATATA
* * *
5890715 AGGATTATTGCTTAATCCCATTAAAAAGTCGATATA
1 AGGGTTATTGCTTAATCCCGTAAAAAAGTCGATATA
*
5890751 AGGGTTATTGCTTGATCCCGTAAAAAAG
1 AGGGTTATTGCTTAATCCCGTAAAAAAG
5890779 CTATTATGAG
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
35 6 0.12
36 46 0.88
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (36 bp):
AGGGTTATTGCTTAATCCCGTAAAAAAGTCGATATA
Found at i:5895966 original size:15 final size:15
Alignment explanation
Indices: 5895946--5896004 Score: 100
Period size: 15 Copynumber: 3.9 Consensus size: 15
5895936 TTTACAATGT
5895946 AATGTGATTGCAAGC
1 AATGTGATTGCAAGC
*
5895961 AATGTGATTGCAAAC
1 AATGTGATTGCAAGC
*
5895976 AATATGATTGCAAGC
1 AATGTGATTGCAAGC
5895991 AATGTGATTGCAAG
1 AATGTGATTGCAAG
5896005 GAAGATAACA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (15 bp):
AATGTGATTGCAAGC
Found at i:5896080 original size:20 final size:20
Alignment explanation
Indices: 5896055--5896094 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5896045 GATTAAAATG
5896055 CAGCGAAGATAACATTGCAA
1 CAGCGAAGATAACATTGCAA
5896075 CAGCGAAGATAACATTGCAA
1 CAGCGAAGATAACATTGCAA
5896095 TGTTTGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.15
Consensus pattern (20 bp):
CAGCGAAGATAACATTGCAA
Found at i:5896284 original size:71 final size:73
Alignment explanation
Indices: 5896209--5896360 Score: 181
Period size: 71 Copynumber: 2.1 Consensus size: 73
5896199 ATATAATGTC
**
5896209 ATTTTTAAATATA-TTT-TTA-ATTAAATATATTTTATTTTTCATTTTTT-TCTACAAG-TATAT
1 ATTTTTAAATATAGTTTCTTATATT--ATATATTTTATTTTAAATTTTTTCTCTACAAGATA-AT
5896269 ATTTTATTTTT
63 ATTTTATTTTT
* * *
5896280 ATTTTT-AATATAGTTTCTTATATTGTATATTTTATTTTAAATTTTTTCTTTAGAAGATAATATT
1 ATTTTTAAATATAGTTTCTTATATTATATATTTTATTTTAAATTTTTTCTCTACAAGATAATATT
5896344 TTATTTTT
66 TTATTTTT
5896352 ATTTCTTAA
1 ATTT-TTAA
5896361 TACGTTTTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
70 6 0.09
71 29 0.42
72 26 0.38
73 7 0.10
74 1 0.01
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.62
Consensus pattern (73 bp):
ATTTTTAAATATAGTTTCTTATATTATATATTTTATTTTAAATTTTTTCTCTACAAGATAATATT
TTATTTTT
Found at i:5897907 original size:23 final size:23
Alignment explanation
Indices: 5897877--5897989 Score: 106
Period size: 23 Copynumber: 4.9 Consensus size: 23
5897867 ATAACATTCT
5897877 TTACTAACTAGTCACGTAATGCC
1 TTACTAACTAGTCACGTAATGCC
* *
5897900 TTACTAACAAGTCACGCAATGCC
1 TTACTAACTAGTCACGTAATGCC
* * *
5897923 TTAATAACAAGTTACGTAATGCC
1 TTACTAACTAGTCACGTAATGCC
*
5897946 -TA-TCAACTAGT-ACGCAATGCC
1 TTACT-AACTAGTCACGTAATGCC
*
5897967 TTATCAAAAACTAGTCACGTAAT
1 TTA-C--TAACTAGTCACGTAAT
5897990 TTTCAAAGTC
Statistics
Matches: 74, Mismatches: 9, Indels: 11
0.79 0.10 0.12
Matches are distributed among these distances:
21 10 0.14
22 10 0.14
23 41 0.55
25 7 0.09
26 6 0.08
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.27
Consensus pattern (23 bp):
TTACTAACTAGTCACGTAATGCC
Found at i:5897967 original size:44 final size:46
Alignment explanation
Indices: 5897881--5897969 Score: 121
Period size: 46 Copynumber: 2.0 Consensus size: 46
5897871 CATTCTTTAC
*
5897881 TAACTAGTCACGTAATGCCTTACTAACAAGTCACGCAATGCCTTAA
1 TAACAAGTCACGTAATGCCTTACTAACAAGTCACGCAATGCCTTAA
* *
5897927 TAACAAGTTACGTAATGCC-TA-TCAACTAGT-ACGCAATGCCTTA
1 TAACAAGTCACGTAATGCCTTACT-AACAAGTCACGCAATGCCTTA
5897970 TCAAAAACTA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
44 14 0.36
45 8 0.21
46 17 0.44
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (46 bp):
TAACAAGTCACGTAATGCCTTACTAACAAGTCACGCAATGCCTTAA
Found at i:5898006 original size:21 final size:21
Alignment explanation
Indices: 5897979--5898031 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
5897969 ATCAAAAACT
**
5897979 AGTCACGTAATTTTCAAAGTCA
1 AGTCACGTAATTCCCAAAGT-A
*
5898001 A-TCACGCAATTCCCAAAGTA
1 AGTCACGTAATTCCCAAAGTA
5898021 AGTCACGTAAT
1 AGTCACGTAAT
5898032 GCCTTATCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 2 0.08
21 23 0.88
22 1 0.04
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (21 bp):
AGTCACGTAATTCCCAAAGTA
Found at i:5898058 original size:26 final size:26
Alignment explanation
Indices: 5898021--5898253 Score: 240
Period size: 26 Copynumber: 9.5 Consensus size: 26
5898011 TCCCAAAGTA
* *
5898021 AGTCACGTAATGCCTTATCAGAAACT
1 AGTCACGCAATGCCTTATCAAAAACT
5898047 AGTCACGCAATGCCTTATCAAAAACT
1 AGTCACGCAATGCCTTATCAAAAACT
* *
5898073 AGTCATGCAATGCC-CATC---AACT
1 AGTCACGCAATGCCTTATCAAAAACT
*
5898095 AGTCACGCAATGCCTTATCAGAAACT
1 AGTCACGCAATGCCTTATCAAAAACT
* *
5898121 AGTCATGCAATGTCTTATCAAAAACT
1 AGTCACGCAATGCCTTATCAAAAACT
* **
5898147 AGTCACGCAATG---T-CCAAAGTC-
1 AGTCACGCAATGCCTTATCAAAAACT
* * *
5898168 AATCACACAATGCC-TAT---TAACT
1 AGTCACGCAATGCCTTATCAAAAACT
*
5898190 AGTCACGCAATGCCTTATCAGAAACT
1 AGTCACGCAATGCCTTATCAAAAACT
*
5898216 AGTCACGCAATGACTTATCAAAAACT
1 AGTCACGCAATGCCTTATCAAAAACT
5898242 AGTCACGCAATG
1 AGTCACGCAATG
5898254 TCCAAAGTTA
Statistics
Matches: 171, Mismatches: 24, Indels: 24
0.78 0.11 0.11
Matches are distributed among these distances:
21 11 0.06
22 34 0.20
23 8 0.05
25 3 0.02
26 115 0.67
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.24
Consensus pattern (26 bp):
AGTCACGCAATGCCTTATCAAAAACT
Found at i:5898101 original size:48 final size:48
Alignment explanation
Indices: 5897882--5898253 Score: 224
Period size: 48 Copynumber: 7.8 Consensus size: 48
5897872 ATTCTTTACT
* * *
5897882 AACTAGTCACGTAATGCCT-TACTAACAAGTCACGCAATGCC-T-T-AAT
1 AACTAGTCACGCAATGCCTAT-C-AACTAGTCACGCAATGCCTTATCAAA
* * *
5897928 AACAAGTTACGTAATGCCTATCAACTAGT-ACGCAATGCCTTATCAAA
1 AACTAGTCACGCAATGCCTATCAACTAGTCACGCAATGCCTTATCAAA
* * * * *
5897975 AACTAGTCACGTAAT---TTTCAAAGTCAATCACGCAATTCC----C--A
1 AACTAGTCACGCAATGCCTATC-AACT-AGTCACGCAATGCCTTATCAAA
* *
5898016 AAGTAAGTCACGTAATGCCTTATCAGAAACTAGTCACGCAATGCCTTATCAAA
1 AACT-AGTCACGCAATGCC-TATC---AACTAGTCACGCAATGCCTTATCAAA
* * *
5898069 AACTAGTCATGCAATGCCCATCAACTAGTCACGCAATGCCTTATCAGA
1 AACTAGTCACGCAATGCCTATCAACTAGTCACGCAATGCCTTATCAAA
* * *
5898117 AACTAGTCATGCAATGTCTTATCAAAAACTAGTCACGCAATG---T-CCAAA
1 AACTAGTCACGCAATG-CCTATC---AACTAGTCACGCAATGCCTTATCAAA
** * * * *
5898165 GTC-AATCACACAATGCCTATTAACTAGTCACGCAATGCCTTATCAGA
1 AACTAGTCACGCAATGCCTATCAACTAGTCACGCAATGCCTTATCAAA
*
5898212 AACTAGTCACGCAATGACTTATCAAAAACTAGTCACGCAATG
1 AACTAGTCACGCAATG-CCTATC---AACTAGTCACGCAATG
5898254 TCCAAAGTTA
Statistics
Matches: 254, Mismatches: 39, Indels: 60
0.72 0.11 0.17
Matches are distributed among these distances:
41 4 0.02
42 11 0.04
43 17 0.07
44 13 0.05
45 10 0.04
46 29 0.11
47 50 0.20
48 59 0.23
49 9 0.04
51 4 0.02
52 44 0.17
53 4 0.02
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (48 bp):
AACTAGTCACGCAATGCCTATCAACTAGTCACGCAATGCCTTATCAAA
Found at i:5898108 original size:74 final size:71
Alignment explanation
Indices: 5897882--5898227 Score: 297
Period size: 74 Copynumber: 4.9 Consensus size: 71
5897872 ATTCTTTACT
* * * * * * *
5897882 AACTAGTCACGTAATGCCTTA-C-TAACAAGTCACGCAATGCC-T-T-AATAACAAGTTACGTAA
1 AACTAGTCACGCAATGCCTTATCAAAACTAGTCACGCAATGCCTTATCAAAAACTAGTCACGCAA
*
5897942 TGCCTA
66 TGCCCA
* ** *
5897948 TCAACTAGT-ACGCAATGCCTTATCAAAAACTAGTCACGTAAT---TT-TCAAAGTC-AATCACG
1 --AACTAGTCACGCAATGCCTTATC-AAAACTAGTCACGCAATGCCTTATCAAAAACTAGTCACG
*
5898007 CAATTCCCA
63 CAATGCCCA
* * *
5898016 AAGTAAGTCACGTAATGCCTTATCAGAAACTAGTCACGCAATGCCTTATCAAAAACTAGTCATGC
1 AACT-AGTCACGCAATGCCTTATCA-AAACTAGTCACGCAATGCCTTATCAAAAACTAGTCACGC
5898081 AATGCCCA
64 AATGCCCA
* *
5898089 TCAACTAGTCACGCAATGCCTTATCAGAAACTAGTCATGCAATGTCTTATCAAAAACTAGTCACG
1 --AACTAGTCACGCAATGCCTTATCA-AAACTAGTCACGCAATGCCTTATCAAAAACTAGTCACG
*
5898154 CAATGTCCA
63 CAATGCCCA
* * * * *
5898163 AAGTCAATCACACAATGCC-TAT--TAACTAGTCACGCAATGCCTTATCAGAAACTAGTCACGCA
1 AACT-AGTCACGCAATGCCTTATCAAAACTAGTCACGCAATGCCTTATCAAAAACTAGTCACGCA
5898225 ATG
65 ATG
5898228 ACTTATCAAA
Statistics
Matches: 229, Mismatches: 33, Indels: 31
0.78 0.11 0.11
Matches are distributed among these distances:
66 3 0.01
67 16 0.07
68 50 0.22
69 42 0.18
70 13 0.06
71 2 0.01
72 12 0.05
73 25 0.11
74 63 0.28
75 3 0.01
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.25
Consensus pattern (71 bp):
AACTAGTCACGCAATGCCTTATCAAAACTAGTCACGCAATGCCTTATCAAAAACTAGTCACGCAA
TGCCCA
Done.