Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold286
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: 607008
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 16077 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:4181 original size:16 final size:16
Alignment explanation
Indices: 4144--4183 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
4134 TTAATAAAAT
* *
4144 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
4160 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
4176 TAAAATTA
1 TAAAATTA
4184 TTAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:4211 original size:16 final size:16
Alignment explanation
Indices: 4190--4232 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
4180 ATTATTAAAT
4190 TATTAATTGTTAATTG
1 TATTAATTGTTAATTG
*
4206 TATTAATTATTAATTG
1 TATTAATTGTTAATTG
4222 TATTAATTGTT
1 TATTAATTGTT
4233 GTAATAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (16 bp):
TATTAATTGTTAATTG
Found at i:4215 original size:23 final size:25
Alignment explanation
Indices: 4182--4231 Score: 77
Period size: 23 Copynumber: 2.0 Consensus size: 25
4172 TTAGTAAAAT
4182 TATTAAATTATTAATTG-TTAATTG
1 TATTAAATTATTAATTGATTAATTG
4206 TATT-AATTATTAATTGTATTAATTG
1 TATTAAATTATTAATTG-ATTAATTG
4231 T
1 T
4232 TGTAATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 12 0.50
24 4 0.17
25 8 0.33
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (25 bp):
TATTAAATTATTAATTGATTAATTG
Found at i:4237 original size:9 final size:9
Alignment explanation
Indices: 4190--4231 Score: 56
Period size: 9 Copynumber: 5.1 Consensus size: 9
4180 ATTATTAAAT
4190 TATTAATTG
1 TATTAATTG
4199 --TTAATTG
1 TATTAATTG
4206 TATTAA-T-
1 TATTAATTG
4213 TATTAATTG
1 TATTAATTG
4222 TATTAATTG
1 TATTAATTG
4231 T
1 T
4232 TGTAATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
7 13 0.45
8 2 0.07
9 14 0.48
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:4284 original size:9 final size:9
Alignment explanation
Indices: 4272--4299 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
4262 TTTATCAAAT
4272 TATTAATTG
1 TATTAATTG
4281 TATTAATTG
1 TATTAATTG
4290 TATTAATTG
1 TATTAATTG
4299 T
1 T
4300 TGTAAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:10370 original size:30 final size:30
Alignment explanation
Indices: 10336--10414 Score: 122
Period size: 30 Copynumber: 2.5 Consensus size: 30
10326 AGGAAATAGT
10336 TAAAATTTAAATTTAATAAAATAAATTTAA
1 TAAAATTTAAATTTAATAAAATAAATTTAA
10366 TAAAATTTAAATTTAATAAAATAAATTTAA
1 TAAAATTTAAATTTAATAAAATAAATTTAA
*
10396 TGATAATAATTAAATTTAA
1 T-A-AA-ATTTAAATTTAA
10415 ATTTTTAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
30 31 0.69
31 1 0.02
32 2 0.04
33 11 0.24
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (30 bp):
TAAAATTTAAATTTAATAAAATAAATTTAA
Found at i:10391 original size:20 final size:19
Alignment explanation
Indices: 10338--10418 Score: 63
Period size: 14 Copynumber: 4.6 Consensus size: 19
10328 GAAATAGTTA
10338 AAATTTAAATTTAAT--A-
1 AAATTTAAATTTAATAAAT
10354 AAA--TAAATTTAAT--A-
1 AAATTTAAATTTAATAAAT
10368 AAATTTAAATTTAATAAAAT
1 AAATTTAAATTTAAT-AAAT
* *
10388 AAATTT-AATGATAATAATT
1 AAATTTAAAT-TTAATAAAT
10407 AAATTTAAATTT
1 AAATTTAAATTT
10419 TTAATTTTGA
Statistics
Matches: 54, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
14 14 0.26
16 13 0.24
19 14 0.26
20 13 0.24
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (19 bp):
AAATTTAAATTTAATAAAT
Found at i:10406 original size:14 final size:14
Alignment explanation
Indices: 10343--10396 Score: 90
Period size: 14 Copynumber: 3.7 Consensus size: 14
10333 AGTTAAAATT
10343 TAAATTTAATAAAA
1 TAAATTTAATAAAA
10357 TAAATTTAATAAAA
1 TAAATTTAATAAAA
10371 TTTAAATTTAATAAAA
1 --TAAATTTAATAAAA
10387 TAAATTTAAT
1 TAAATTTAAT
10397 GATAATAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
14 24 0.63
16 14 0.37
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAATTTAATAAAA
Found at i:17809 original size:13 final size:14
Alignment explanation
Indices: 17764--17816 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
17754 AAAAATAATC
17764 AATACTTTTTATAT
1 AATACTTTTTATAT
* * *
17778 AATATTTTTTCAAAA
1 AATACTTTTT-ATAT
17793 AATA-TTTTTATAT
1 AATACTTTTTATAT
17806 AATA-TTTTTAT
1 AATACTTTTTAT
17817 TATTTTAGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
13 13 0.39
14 14 0.42
15 6 0.18
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.57
Consensus pattern (14 bp):
AATACTTTTTATAT
Found at i:18616 original size:22 final size:22
Alignment explanation
Indices: 18591--18632 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
18581 TTTTAACACA
* *
18591 AATTTTTTTAGCTTTATCTCTC
1 AATTTTATAAGCTTTATCTCTC
*
18613 AATTTTATAATCTTTATCTC
1 AATTTTATAAGCTTTATCTC
18633 GTTTCTCTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.17, G:0.02, T:0.57
Consensus pattern (22 bp):
AATTTTATAAGCTTTATCTCTC
Found at i:21340 original size:17 final size:19
Alignment explanation
Indices: 21317--21365 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
21307 CCTATCCCGA
21317 AATATTAAATAATTTTT-T
1 AATATTAAATAATTTTTAT
*
21335 -ATATTACATTAATTTTTAT
1 AATATTA-AATAATTTTTAT
*
21354 AAAATTAAATAA
1 AATATTAAATAA
21366 AATACATGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 6 0.24
18 9 0.36
19 5 0.20
20 5 0.20
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
AATATTAAATAATTTTTAT
Found at i:24612 original size:105 final size:104
Alignment explanation
Indices: 24423--24625 Score: 291
Period size: 105 Copynumber: 1.9 Consensus size: 104
24413 ATTCAAAAAA
* *
24423 AAAAATGGAATCGATGAGCAAAAGGCGATCAATGGACCTTAGAGCAGCGACAAAGGCATCGATAA
1 AAAAATGGAATCGATGAGCAAAAAGCGATCAAGGGACCTTAGAGCAGCGACAAAGGCATCGATAA
*
24488 ACAACGTAAACTCAAAAACAAATACAAGAAAAAAAAATT
66 ACAACGTAAACACAAAAACAAATACAAGAAAAAAAAATT
* * * * *
24527 AAAAATGGAATTGATTAGCGAAAAAGTGATCAAGGGAGCTTAGATCAGCGACAAAGGCATCGATA
1 AAAAATGGAATCGATGAGC-AAAAAGCGATCAAGGGACCTTAGAGCAGCGACAAAGGCATCGATA
* *
24592 AACAACGTAAA-ACACGAAACAAATTCAAGAAAAA
65 AACAACGTAAACACA-AAAACAAATACAAGAAAAA
24626 TAATAAAATT
Statistics
Matches: 87, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
104 19 0.22
105 68 0.78
ACGTcount: A:0.51, C:0.15, G:0.19, T:0.14
Consensus pattern (104 bp):
AAAAATGGAATCGATGAGCAAAAAGCGATCAAGGGACCTTAGAGCAGCGACAAAGGCATCGATAA
ACAACGTAAACACAAAAACAAATACAAGAAAAAAAAATT
Found at i:25055 original size:15 final size:15
Alignment explanation
Indices: 25018--25056 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
25008 AAATTAGGAT
25018 GATGGAAAATTGAAG
1 GATGGAAAATTGAAG
*
25033 GGTGGAAAACTTGAAG
1 GATGGAAAA-TTGAAG
25049 GAT-GAAAA
1 GATGGAAAA
25057 ACATAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.46, C:0.03, G:0.33, T:0.18
Consensus pattern (15 bp):
GATGGAAAATTGAAG
Found at i:25057 original size:16 final size:16
Alignment explanation
Indices: 25018--25058 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
25008 AAATTAGGAT
25018 GATGGAAAA-TTGAAG
1 GATGGAAAACTTGAAG
*
25033 GGTGGAAAACTTGAAG
1 GATGGAAAACTTGAAG
*
25049 GATGAAAAAC
1 GATGGAAAAC
25059 ATAAATTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.46, C:0.05, G:0.32, T:0.17
Consensus pattern (16 bp):
GATGGAAAACTTGAAG
Found at i:26124 original size:21 final size:21
Alignment explanation
Indices: 26094--26141 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 21
26084 ATGGCATTCA
*
26094 TAAAATAATAATATTTAATAT
1 TAAAAAAATAATATTTAATAT
26115 T--AAAAA-AATATTTAATAT
1 TAAAAAAATAATATTTAATAT
26133 TAAAAAAAT
1 TAAAAAAAT
26142 TTAAAGCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
18 13 0.57
19 4 0.17
20 5 0.22
21 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAAAAAATAATATTTAATAT
Found at i:26145 original size:16 final size:18
Alignment explanation
Indices: 26103--26141 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
26093 ATAAAATAAT
26103 AATATTTAATATTAAAAA
1 AATATTTAATATTAAAAA
26121 AATATTTAATATTAAAAA
1 AATATTTAATATTAAAAA
26139 AAT
1 AAT
26142 TTAAAGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATATTTAATATTAAAAA
Found at i:26774 original size:21 final size:21
Alignment explanation
Indices: 26744--26783 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
26734 TCCATGTAGA
*
26744 TATTAGATTAAACATTAAATT
1 TATTAAATTAAACATTAAATT
*
26765 TATTAAATTAAATATTAAA
1 TATTAAATTAAACATTAAA
26784 ATTAAACTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (21 bp):
TATTAAATTAAACATTAAATT
Found at i:26798 original size:13 final size:12
Alignment explanation
Indices: 26743--26808 Score: 50
Period size: 12 Copynumber: 5.6 Consensus size: 12
26733 TTCCATGTAG
*
26743 ATATTAGATTAA
1 ATATTAAATTAA
*
26755 ACATTAAATT--
1 ATATTAAATTAA
26765 -TATTAAATTAA
1 ATATTAAATTAA
26776 ATATTAAAATTAA
1 ATATT-AAATTAA
*
26789 ACTGTTAAA-TAA
1 A-TATTAAATTAA
26801 TATATTAA
1 -ATATTAA
26809 TACTTAATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
9 8 0.19
12 20 0.47
13 12 0.28
14 3 0.07
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (12 bp):
ATATTAAATTAA
Found at i:26898 original size:117 final size:119
Alignment explanation
Indices: 26755--27008 Score: 460
Period size: 117 Copynumber: 2.1 Consensus size: 119
26745 ATTAGATTAA
26755 ACATTAAATTTATTAAATTAAATATTAAAATTAAACTGTTAAATAATATATTAATACTTAATTTG
1 ACATTAAATTTATTAAATTAAATATTAAAATTAAACTGTTAAATAATATATTAATACTTAATTTG
26820 AAAATTTTCATTAAAAAAAATTGATGGTTTGTAATTTTTAGTCATTTCTATGTC
66 AAAATTTTCATTAAAAAAAATTGATGGTTTGTAATTTTTAGTCATTTCTATGTC
26874 ACATTAAA-TT-TTAAATTAAATATTAAAATTAAACTGTTAAATAATATATTAATACTTAATTTG
1 ACATTAAATTTATTAAATTAAATATTAAAATTAAACTGTTAAATAATATATTAATACTTAATTTG
26937 AAAATTTTCATTAAAAAAAATTGATGGTTTGTAATTTTTAGTCATTTCTATGTC
66 AAAATTTTCATTAAAAAAAATTGATGGTTTGTAATTTTTAGTCATTTCTATGTC
*
26991 AGCA-TCAATTTATATAAA
1 A-CATTAAATTTAT-TAAA
27009 ATTTTGTACT
Statistics
Matches: 130, Mismatches: 1, Indels: 7
0.94 0.01 0.05
Matches are distributed among these distances:
117 111 0.85
118 6 0.05
119 9 0.07
120 4 0.03
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (119 bp):
ACATTAAATTTATTAAATTAAATATTAAAATTAAACTGTTAAATAATATATTAATACTTAATTTG
AAAATTTTCATTAAAAAAAATTGATGGTTTGTAATTTTTAGTCATTTCTATGTC
Found at i:26915 original size:26 final size:25
Alignment explanation
Indices: 26876--26925 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
26866 TCTATGTCAC
*
26876 ATTAAATTTTAAATTAA-ATATTAAA
1 ATTAAATGTTAAA-TAATATATTAAA
26901 ATTAAACTGTTAAATAATATATTAA
1 ATTAAA-TGTTAAATAATATATTAA
26926 TACTTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (25 bp):
ATTAAATGTTAAATAATATATTAAA
Found at i:29141 original size:2 final size:2
Alignment explanation
Indices: 29134--29161 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29124 CAATTAAATA
29134 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
29162 TAGAAATTTG
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:31545 original size:15 final size:15
Alignment explanation
Indices: 31525--31558 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
31515 GAATTAGTTC
31525 TATTCTATGTTCAAA
1 TATTCTATGTTCAAA
*
31540 TATTCTATGTTCATA
1 TATTCTATGTTCAAA
31555 TATT
1 TATT
31559 GCACACACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.53
Consensus pattern (15 bp):
TATTCTATGTTCAAA
Found at i:33588 original size:46 final size:47
Alignment explanation
Indices: 33522--33614 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 47
33512 TGGCTTTTTT
* * *
33522 TTGTTGTTTGTGGGGGGGGGGGG-TTTGATTCTTTTTTTTTCTTTGG
1 TTGTTGTTTGTGGGGGGGGGGGGATTAGATCCTTTTTTTCTCTTTGG
33568 TTGTTGTTTGTGGGGGGGGGGGGATTAGATCCTTTTTTTCTCTTTGG
1 TTGTTGTTTGTGGGGGGGGGGGGATTAGATCCTTTTTTTCTCTTTGG
33615 CTTTGAGTTG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
46 23 0.53
47 20 0.47
ACGTcount: A:0.04, C:0.06, G:0.39, T:0.51
Consensus pattern (47 bp):
TTGTTGTTTGTGGGGGGGGGGGGATTAGATCCTTTTTTTCTCTTTGG
Found at i:33760 original size:2 final size:2
Alignment explanation
Indices: 33755--33779 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
33745 TGTTTTTTTT
33755 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
33780 TAAGCTGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:39027 original size:174 final size:173
Alignment explanation
Indices: 38689--39067 Score: 514
Period size: 174 Copynumber: 2.2 Consensus size: 173
38679 AGGTTTTTTT
* *
38689 ATTTTAGAAATAAATTTTAATTATTAAGCTAATGCTAATTAGTATAATTCTTGATTAATCCTCTG
1 ATTTTAGAAAGAAATTTTAATTATTAAGCT-ATGCTAATTAGTATAAATCTTGATTAATCCTCTG
* *
38754 AAATGTAATTTGCGGAAGTATTGTTTAGCTGTAAAAAGTTTTTGATCGGGTAATGGAAGTAATGC
65 AAATGTAATTTGCGGAAGTATTATTTAGCTGTAAAAAGTTTTTGATCGAGTAATGGAAGTAATGC
* * * * *
38819 TTAATGAGCTTGTTATGAATTTGGATTTGTTCACAAAACGGTGAATAG
130 TTAATGACCTTATTATGAATTTGGATTAGTTCAC--AA--GTGAACAA
* * *
38867 ATTTTAGAAAGAAAGTTTAATT-TTAAGCTAT-TTGATTAGTATAAATCTTGATTAATCCTCTGA
1 ATTTTAGAAAGAAATTTTAATTATTAAGCTATGCTAATTAGTATAAATCTTGATTAATCCTCTGA
* * * * *
38930 AATTTAATTTGC-GATGTATTATTTAGCTGTAAAAAGTTTTTGATTGAGTGATGGAATTAATGCT
66 AATGTAATTTGCGGAAGTATTATTTAGCTGTAAAAAGTTTTTGATCGAGTAATGGAAGTAATGCT
*
38994 TAATGACCTTATTATGCATTT-GAGTTAGTTCACAAGTGAACAA
131 TAATGACCTTATTATGAATTTGGA-TTAGTTCACAAGTGAACAA
39037 ATTTTAGAAAGAAATTTTAATTATTAAGCTA
1 ATTTTAGAAAGAAATTTTAATTATTAAGCTA
39068 GTAATGATTA
Statistics
Matches: 180, Mismatches: 19, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
170 27 0.15
171 8 0.04
172 2 0.01
173 2 0.01
174 72 0.40
175 40 0.22
176 2 0.01
177 7 0.04
178 20 0.11
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (173 bp):
ATTTTAGAAAGAAATTTTAATTATTAAGCTATGCTAATTAGTATAAATCTTGATTAATCCTCTGA
AATGTAATTTGCGGAAGTATTATTTAGCTGTAAAAAGTTTTTGATCGAGTAATGGAAGTAATGCT
TAATGACCTTATTATGAATTTGGATTAGTTCACAAGTGAACAA
Found at i:39090 original size:52 final size:52
Alignment explanation
Indices: 39034--39136 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 52
39024 CACAAGTGAA
39034 CAAATTTTAGAAAGAAATTTT-AATTATTAAGCTAGTAATGATTAATATAATC
1 CAAATTTTAGAAAG-AATTTTCAATTATTAAGCTAGTAATGATTAATATAATC
*
39086 CAAATTTTGGAAAGAATTTTCAATTATTAAGCTAGTAATGATTAATATAAT
1 CAAATTTTAGAAAGAATTTTCAATTATTAAGCTAGTAATGATTAATATAAT
39137 TTTTGATTAA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
51 6 0.12
52 43 0.88
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.39
Consensus pattern (52 bp):
CAAATTTTAGAAAGAATTTTCAATTATTAAGCTAGTAATGATTAATATAATC
Found at i:39707 original size:24 final size:25
Alignment explanation
Indices: 39666--39714 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
39656 AAAGTTAACA
*
39666 AAAAATTTAAATACAATAAATTTAT
1 AAAAATTTAAATACAATAAAATTAT
39691 AAAAATATTAAA-A-AATAAAATTAT
1 AAAAAT-TTAAATACAATAAAATTAT
39715 CATGGAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 10 0.45
25 7 0.32
26 5 0.23
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (25 bp):
AAAAATTTAAATACAATAAAATTAT
Found at i:49652 original size:153 final size:149
Alignment explanation
Indices: 49238--49884 Score: 870
Period size: 153 Copynumber: 4.3 Consensus size: 149
49228 ATTTTAGTCA
* * * *
49238 TTTGTTCGTATTTTTTTCGGAATTTATTACTTTTAAAAAATATACTATTTTTTAATTTTTTTTAT
1 TTTGTTCGTATTTTTTCCGGATTTTATTACTTTAAAAAAATATACTATTTTTTAA-TTTTATTAT
49303 TTTACATTATTTTAGTACATTATGTTTGAAATATATTAATTTACTGTGTTTTTTAAATAAATTAA
65 TTTACATTATTTTAGTACATTATGTTTGAAATATATTAATTTACTGTGTTTTTTAAATAAATTAA
**
49368 AAAAACCCTTATTTCGGCCC
130 AAAAAATCTTATTTCGGCCC
* ** *
49388 TTTATTCGTATTTTTTTAGGATTTTATTACTTTTAAAAAATATACTATTTTTTAATTTT-TTATT
1 TTTGTTCGTATTTTTTCCGGATTTTATTACTTTAAAAAAATATACTATTTTTTAATTTTATTATT
* * * * *
49452 TTACATTATTTCAGTACGTTATATTTGAAATGTATTAATTTAGTGTGTTTTTTTAAATAAATTAA
66 TTACATTATTTTAGTACATTATGTTTGAAATATATTAATTTACTGTG-TTTTTTAAATAAATTAA
49517 AAAAAATCTTATTTCGGCCC
130 AAAAAATCTTATTTCGGCCC
*
49537 TTTGTTCGTATTTTTTCCCGGATTTTATTACTTTCAATAAAAATATATTATTTTTGT-ATTTTAT
1 TTTGTTCGTATTTTTT-CCGGATTTTATTACTTT-AA-AAAAATATACTATTTTT-TAATTTTAT
* *
49601 TAGTTTACATTATTTTAGTACATCATGTTTGAAATATATTAATTTACTGTGTTTTTTTAAATAAA
62 TATTTTACATTATTTTAGTACATTATGTTTGAAATATATTAATTTACTGTG-TTTTTTAAATAAA
* *
49666 TTTAAAAAAATCCTTATTTCGGCCA
126 TTAAAAAAAAT-CTTATTTCGGCCC
* * *
49691 TTTGTTCGTATTTTTTTCCCCAGAGTTTATTACTTT-AAAAAACATACTATTTTTTAATTTTATT
1 TTTGTTCGTA-TTTTTT--CCGGATTTTATTACTTTAAAAAAATATACTATTTTTTAATTTTATT
* * *
49755 ATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTAAAT-AATT
63 ATTTTACATTATTTTAGTACATTATGTTTGAAATATATTAATTTACTGTGTTTTTTAAATAAATT
*
49819 AAAATAAAACTCTTATTTCGGCCT
128 AAAA-AAAA-TCTTATTTCGGCCC
* *
49843 TTTGTTCGTATTTTTTCTGAATTTTATTACTTTCAATAAAAA
1 TTTGTTCGTATTTTTTCCGGATTTTATTACTTT-AA-AAAAA
49885 ACACACTAAA
Statistics
Matches: 443, Mismatches: 39, Indels: 28
0.87 0.08 0.05
Matches are distributed among these distances:
148 47 0.11
149 67 0.15
150 67 0.15
151 15 0.03
152 63 0.14
153 139 0.31
154 23 0.05
155 6 0.01
156 16 0.04
ACGTcount: A:0.30, C:0.09, G:0.08, T:0.52
Consensus pattern (149 bp):
TTTGTTCGTATTTTTTCCGGATTTTATTACTTTAAAAAAATATACTATTTTTTAATTTTATTATT
TTACATTATTTTAGTACATTATGTTTGAAATATATTAATTTACTGTGTTTTTTAAATAAATTAAA
AAAAATCTTATTTCGGCCC
Found at i:49835 original size:306 final size:301
Alignment explanation
Indices: 49238--49884 Score: 968
Period size: 306 Copynumber: 2.1 Consensus size: 301
49228 ATTTTAGTCA
* * * *
49238 TTTGTTCGTATTTTTTTCGGAATTTATTACTTT-TA-AAAAATATACTATTTTTTAATTTTTTTT
1 TTTGTTCGTATTTTTTCCGGATTTTATTACTTTCAATAAAAATATACTATTTTTTAATTTTTATT
* *
49301 ATTTTACATTATTTTAGTACATTATGTTTGAAATATATTAATTTACTGTGTTTTTTAAATAAATT
66 AGTTTACATTATTTTAGTACATCATGTTTGAAATATATTAATTTACTGTGTTTTTTAAATAAATT
* * *
49366 AAAAAAACCCTTATTTCGGCCCTTTATTCGTATTTTTTTAGGATTTTATTACTTTTAAAAAATAT
131 AAAAAAACCCTTATTTCGGCCATTTATTCGTATTTTTTTAGGAGTTTATTACTTTTAAAAAACAT
*
49431 ACTATTTTTTAATTTTTTATTTTACATTATTTCAGTACGTTATATTTGAAATGTATTAATTTAGT
196 ACTATTTTTTAATTTTTTATTTTACATTATTTCAGTACATTATATTTGAAATGTATTAATTTAGT
49496 GTGTTTTTTTAAATAAATTAAAAAAAATCTTATTTCGGCCC
261 GTGTTTTTTTAAATAAATTAAAAAAAATCTTATTTCGGCCC
*
49537 TTTGTTCGTATTTTTTCCCGGATTTTATTACTTTCAATAAAAATATATTATTTTTGT-A-TTTTA
1 TTTGTTCGTATTTTTT-CCGGATTTTATTACTTTCAATAAAAATATACTATTTTT-TAATTTTTA
49600 TTAGTTTACATTATTTTAGTACATCATGTTTGAAATATATTAATTTACTGTGTTTTTTTAAATAA
64 TTAGTTTACATTATTTTAGTACATCATGTTTGAAATATATTAATTTACTGTG-TTTTTTAAATAA
* *
49665 ATTTAAAAAAATCCTTATTTCGGCCATTTGTTCGTATTTTTTTCCCCA-GAGTTTATTAC-TTTA
128 A-TTAAAAAAACCCTTATTTCGGCCATTTATTCGTATTTTTTT----AGGAGTTTATTACTTTTA
* *
49728 AAAAACATACTATTTTTTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTAT
188 AAAAACATACTATTTTTTAATTTT-TTATTTTACATTATTTCAGTACATTATATTTGAAATGTAT
* *
49793 TCATTTAGTGTG-TTTTTTAAAT-AATTAAAATAAAACTCTTATTTCGGCCT
252 TAATTTAGTGTGTTTTTTTAAATAAATTAAAA-AAAA-TCTTATTTCGGCCC
* *
49843 TTTGTTCGTATTTTTTCTGAATTTTATTACTTTCAATAAAAA
1 TTTGTTCGTATTTTTTCCGGATTTTATTACTTTCAATAAAAA
49885 ACACACTAAA
Statistics
Matches: 316, Mismatches: 19, Indels: 20
0.89 0.05 0.06
Matches are distributed among these distances:
299 16 0.05
300 15 0.05
301 55 0.17
302 30 0.09
303 39 0.12
304 8 0.03
305 65 0.21
306 87 0.28
307 1 0.00
ACGTcount: A:0.30, C:0.09, G:0.08, T:0.52
Consensus pattern (301 bp):
TTTGTTCGTATTTTTTCCGGATTTTATTACTTTCAATAAAAATATACTATTTTTTAATTTTTATT
AGTTTACATTATTTTAGTACATCATGTTTGAAATATATTAATTTACTGTGTTTTTTAAATAAATT
AAAAAAACCCTTATTTCGGCCATTTATTCGTATTTTTTTAGGAGTTTATTACTTTTAAAAAACAT
ACTATTTTTTAATTTTTTATTTTACATTATTTCAGTACATTATATTTGAAATGTATTAATTTAGT
GTGTTTTTTTAAATAAATTAAAAAAAATCTTATTTCGGCCC
Found at i:49966 original size:306 final size:300
Alignment explanation
Indices: 49352--49967 Score: 690
Period size: 306 Copynumber: 2.0 Consensus size: 300
49342 TTTACTGTGT
* *
49352 TTTTTAAATAAATTAAAAAAACCCTTATTTCGGCCCTTTATTCGTATTTTTTTAGGATTTTATTA
1 TTTTTAAATAAATTAAAAAAACCCTTATTTCGGCCATTTATTCGTATTTTTTTAGGAGTTTATTA
* *
49417 CTTTTAAAAAATATACTATTTTTTAATTTTTTATTTTACATTATTTCAGTACGTTATATTTGAAA
66 CTTTTAAAAAACATACTATTTTTTAATTTTTTATTTTACATTATTTCAGTACATTATATTTGAAA
49482 TGTATTAATTTAGTGTGTTTTTTTAAATAAATTAAAAAAAATCTTATTTCGGCCCTTTGTTCGTA
131 TGTATTAATTTAGTGTGTTTTTTTAAATAAATTAAAAAAAATCTTATTTCGGCCCTTTGTTCGTA
* * * * ** ** ** * *
49547 TTTTTTCCCGGATTTTATTACTTTCAATAAAAATATATTATTTTTGTATTTTATTAGTTTACATT
196 TTTTTTCCCGAATTTTATTACTTTCAATAAAAACACACTAAATTAATACATTATCA--TAACATT
* * * * * *** * ** * * * *
49612 ATTTTAGTACATCATGTTTGAAATATATTAATTTACTGTGTT
259 AATGTACTAAATAATGTAAAAAATAAATTAAAATAATATATA
* *
49654 TTTTTAAATAAATTTAAAAAAATCCTTATTTCGGCCATTTGTTCGTATTTTTTTCCCCA-GAGTT
1 TTTTTAAATAAA-TTAAAAAAACCCTTATTTCGGCCATTTATTCGTATTTTTTT----AGGAGTT
* *
49718 TATTAC-TTTAAAAAACATACTATTTTTTAATTTTATTATTTTACATTATTTTAGTACATTATGT
61 TATTACTTTTAAAAAACATACTATTTTTTAATTTT-TTATTTTACATTATTTCAGTACATTATAT
* *
49782 TTGAAATGTATTCATTTAGTGTG-TTTTTTAAAT-AATTAAAATAAAACTCTTATTTCGGCCTTT
125 TTGAAATGTATTAATTTAGTGTGTTTTTTTAAATAAATTAAAA-AAAA-TCTTATTTCGGCCCTT
*
49845 TGTTCGTATTTTTT-CTGAATTTTATTACTTTCAATAAAAAACACACTAAATTAATACATT-TCA
188 TGTTCGTATTTTTTCCCGAATTTTATTACTTTCAAT-AAAAACACACTAAATTAATACATTATCA
49908 -AACA-TAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATATA
252 TAACATTAATGTACT-AAATAATGTAAAA-AAT-AAATT--AAAATAATATATA
49960 TTTTTAAA
1 TTTTTAAA
49968 AGTAATAAAA
Statistics
Matches: 262, Mismatches: 38, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
301 6 0.02
302 23 0.09
303 41 0.16
304 12 0.05
305 62 0.24
306 117 0.45
307 1 0.00
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.49
Consensus pattern (300 bp):
TTTTTAAATAAATTAAAAAAACCCTTATTTCGGCCATTTATTCGTATTTTTTTAGGAGTTTATTA
CTTTTAAAAAACATACTATTTTTTAATTTTTTATTTTACATTATTTCAGTACATTATATTTGAAA
TGTATTAATTTAGTGTGTTTTTTTAAATAAATTAAAAAAAATCTTATTTCGGCCCTTTGTTCGTA
TTTTTTCCCGAATTTTATTACTTTCAATAAAAACACACTAAATTAATACATTATCATAACATTAA
TGTACTAAATAATGTAAAAAATAAATTAAAATAATATATA
Found at i:55347 original size:27 final size:27
Alignment explanation
Indices: 55309--55371 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
55299 TTTTAGTCTT
*
55309 GTGCCACCAATGAGAATGACACCATTG
1 GTGCCGCCAATGAGAATGACACCATTG
*
55336 GTGCCGCCAATGAGAATGGCACCATTG
1 GTGCCGCCAATGAGAATGACACCATTG
55363 GTGCCGCCA
1 GTGCCGCCA
55372 TTCAGCCCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (27 bp):
GTGCCGCCAATGAGAATGACACCATTG
Found at i:56492 original size:12 final size:12
Alignment explanation
Indices: 56477--56514 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
56467 GCCCGAGCAG
*
56477 GAGCCTCAGCCA
1 GAGCCACAGCCA
56489 GAGCCACAGCCA
1 GAGCCACAGCCA
*
56501 GAGCCCCAGCCA
1 GAGCCACAGCCA
56513 GA
1 GA
56515 TTCGGAGCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.29, C:0.42, G:0.26, T:0.03
Consensus pattern (12 bp):
GAGCCACAGCCA
Found at i:61109 original size:4 final size:4
Alignment explanation
Indices: 61095--61185 Score: 69
Period size: 4 Copynumber: 20.8 Consensus size: 4
61085 TCTTCTTCTC
*
61095 CTTT TTTT CTTT CTTCT ACTTT CATTTT CTTT CTTCT CATTT CCTTTT CTTT
1 CTTT CTTT CTTT CTT-T -CTTT C--TTT CTTT CTT-T C-TTT -C-TTT CTTT
61147 CTTT CTTCT CCTTT C-TT -TTT CTTT CTTT CTTT CTTT CTT
1 CTTT CTT-T -CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTT
61186 CTCCTTTCCT
Statistics
Matches: 73, Mismatches: 3, Indels: 22
0.74 0.03 0.22
Matches are distributed among these distances:
3 4 0.05
4 45 0.62
5 8 0.11
6 16 0.22
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.70
Consensus pattern (4 bp):
CTTT
Found at i:61109 original size:24 final size:24
Alignment explanation
Indices: 61082--61209 Score: 106
Period size: 24 Copynumber: 5.4 Consensus size: 24
61072 CTTCATTCCC
61082 TCTTCTTCTTCTCCTTTT-TTTCTT
1 TCTTCTTCTT-TCCTTTTCTTTCTT
* *
61106 TCTTCTACTTTCATTTTCTTTC-T
1 TCTTCTTCTTTCCTTTTCTTTCTT
*
61129 TC-TC--ATTTCCTTTTCTTTCTT
1 TCTTCTTCTTTCCTTTTCTTTCTT
* *
61150 TCTTCTCCTTTCTTTTTCTTTCTT
1 TCTTCTTCTTTCCTTTTCTTTCTT
* *
61174 TCTTTCTTTCTTCTCCTTTCCTTCTCCT
1 TC-TTC-TTCTT-TCCTTTTCTT-TCTT
61202 T-TTCTTCT
1 TCTTCTTCT
61210 CCACCCACCA
Statistics
Matches: 85, Mismatches: 10, Indels: 17
0.76 0.09 0.15
Matches are distributed among these distances:
20 13 0.15
21 3 0.04
22 4 0.05
23 9 0.11
24 30 0.35
25 7 0.08
26 7 0.08
27 8 0.09
28 4 0.05
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.67
Consensus pattern (24 bp):
TCTTCTTCTTTCCTTTTCTTTCTT
Found at i:61122 original size:20 final size:18
Alignment explanation
Indices: 61087--61193 Score: 96
Period size: 18 Copynumber: 5.7 Consensus size: 18
61077 TTCCCTCTTC
61087 TTCTTCTCCTTT-TTTTCT
1 TTCTTCT-CTTTCTTTTCT
61105 TTCTTCTACTTTCATTTTCT
1 TTCTTCT-CTTTC-TTTTCT
61125 TTCTTCTCATTTCCTTTTCT
1 TTCTTCTC-TTT-CTTTTCT
*
61145 TTCTT-TCTTCTCCTTTCT
1 TTCTTCTCTT-TCTTTTCT
61163 TT-TTCTTTCTTTC-TTTCT
1 TTCTTC--TCTTTCTTTTCT
61181 TTCTTCTCCTTTC
1 TTCTTCT-CTTTC
61194 CTTCTCCTTT
Statistics
Matches: 77, Mismatches: 2, Indels: 20
0.78 0.02 0.20
Matches are distributed among these distances:
17 3 0.04
18 33 0.43
19 9 0.12
20 31 0.40
21 1 0.01
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (18 bp):
TTCTTCTCTTTCTTTTCT
Found at i:61197 original size:11 final size:10
Alignment explanation
Indices: 61087--61211 Score: 79
Period size: 10 Copynumber: 12.9 Consensus size: 10
61077 TTCCCTCTTC
61087 TTCTTCTCCT
1 TTCTTCTCCT
*
61097 TT-TT-TTCT
1 TTCTTCTCCT
*
61105 TTCTTCTACT
1 TTCTTCTCCT
*
61115 TTCATT-TTCT
1 TTC-TTCTCCT
*
61125 TTCTTCTCAT
1 TTCTTCTCCT
61135 TTC--CT--T
1 TTCTTCTCCT
61141 TTCTT-T-CT
1 TTCTTCTCCT
61149 TTCTTCTCCT
1 TTCTTCTCCT
* *
61159 TTCTTTTTCT
1 TTCTTCTCCT
*
61169 TTCTTTCTTTCT
1 TTC-TTC-TCCT
61181 TTCTTCTCCT
1 TTCTTCTCCT
61191 TTCCTTCTCCTT
1 TT-CTTCTCC-T
61203 TTCTTCTCC
1 TTCTTCTCC
61212 ACCCACCAGC
Statistics
Matches: 93, Mismatches: 9, Indels: 25
0.73 0.07 0.20
Matches are distributed among these distances:
6 4 0.04
7 1 0.01
8 13 0.14
9 7 0.08
10 37 0.40
11 21 0.23
12 10 0.11
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.66
Consensus pattern (10 bp):
TTCTTCTCCT
Found at i:62518 original size:69 final size:69
Alignment explanation
Indices: 62436--62611 Score: 199
Period size: 69 Copynumber: 2.6 Consensus size: 69
62426 CCTTAGAAAT
* * * * *
62436 AGTTGGCGTGAGCTCAAGCTCCCATCTGTCATCTTAAGCTTGCAGGTTCAACACCACATCCTCCA
1 AGTTAGCGCGAGCTCAAGCTCCCAACTGTAATCTTAAGCTTGCAGGTTCAACACCACAACCTCCA
*
62501 AAAT
66 AAAC
* * * * * *
62505 AGTTAGTGCGAGCTTAAGCTCCTAACTGTAATCTTAGGCTTGTAGGTTCAACACCGCAACCTCCA
1 AGTTAGCGCGAGCTCAAGCTCCCAACTGTAATCTTAAGCTTGCAGGTTCAACACCACAACCTCCA
*
62570 ACAC
66 AAAC
* * * *
62574 AGTTAGCGCGAACTCAAGCTCCTAGCTGCAATCTTAAG
1 AGTTAGCGCGAGCTCAAGCTCCCAACTGTAATCTTAAG
62612 GCTCGTTATT
Statistics
Matches: 88, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
69 88 1.00
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (69 bp):
AGTTAGCGCGAGCTCAAGCTCCCAACTGTAATCTTAAGCTTGCAGGTTCAACACCACAACCTCCA
AAAC
Found at i:62666 original size:31 final size:32
Alignment explanation
Indices: 62631--62706 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 32
62621 TTGAGTTAGT
* * * *
62631 TGATTTAAGATCACAGCTTC-ATATAGCTCGC
1 TGATTTAAGATCACAACCTCTAAACAGCTCGC
*
62662 TGATTTAAGATCGCAACCTCTAAACAGCTCGC
1 TGATTTAAGATCACAACCTCTAAACAGCTCGC
62694 TGATTTAAGATCA
1 TGATTTAAGATCA
62707 AAACTGATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
31 17 0.45
32 21 0.55
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (32 bp):
TGATTTAAGATCACAACCTCTAAACAGCTCGC
Found at i:63680 original size:15 final size:15
Alignment explanation
Indices: 63660--63692 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
63650 AAAATAGACT
63660 TAAGTTAGTCATTTA
1 TAAGTTAGTCATTTA
63675 TAAGTTAGTCATTTA
1 TAAGTTAGTCATTTA
63690 TAA
1 TAA
63693 CTATAAGCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (15 bp):
TAAGTTAGTCATTTA
Found at i:63754 original size:198 final size:199
Alignment explanation
Indices: 63517--63917 Score: 795
Period size: 198 Copynumber: 2.0 Consensus size: 199
63507 TCTATAGTAA
63517 TATATAATACTACAATAATGTAAACATTAAAAAATATTATATAAAATCTTAATGAATAAAAATAT
1 TATATAATACTACAATAATGTAAACATTAAAAAATATTATATAAAATCTTAATGAATAAAAATAT
63582 ATAAATATAATAAAAATTAAATTAAAAATAATGTAATATAATTTTTAAAAAATAATATGGACGGA
66 ATAAATATAATAAAAATTAAATTAAAAATAATGTAATATAATTTTTAAAAAATAATATGGACGGA
63647 CCTAAAATAGACTTAAGTTAGTCATTTATAAGTTAGTCATTTATAACTATAAGCGGATTTGAGAA
131 CCTAAAATAGACTTAAGTTAGTCATTTATAAGTTAGTCATTTATAACTATAAGCGGATTTGAGAA
63712 AATT
196 AATT
63716 TATATAATACT-CAATAATGTAAACATTAAAAAATATTATATAAAATCTTAATGAATAAAAATAT
1 TATATAATACTACAATAATGTAAACATTAAAAAATATTATATAAAATCTTAATGAATAAAAATAT
63780 ATAAATATAATAAAAATTAAATTAAAAATAATGTAATATAATTTTTAAAAAATAATATGGACGGA
66 ATAAATATAATAAAAATTAAATTAAAAATAATGTAATATAATTTTTAAAAAATAATATGGACGGA
63845 CCTAAAATAGACTTAAGTTAGTCATTTATAAGTTAGTCATTTATAACTATAAGCGGATTTGAGAA
131 CCTAAAATAGACTTAAGTTAGTCATTTATAAGTTAGTCATTTATAACTATAAGCGGATTTGAGAA
63910 AATT
196 AATT
63914 TATA
1 TATA
63918 CTCATATTTC
Statistics
Matches: 202, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
198 191 0.95
199 11 0.05
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.34
Consensus pattern (199 bp):
TATATAATACTACAATAATGTAAACATTAAAAAATATTATATAAAATCTTAATGAATAAAAATAT
ATAAATATAATAAAAATTAAATTAAAAATAATGTAATATAATTTTTAAAAAATAATATGGACGGA
CCTAAAATAGACTTAAGTTAGTCATTTATAAGTTAGTCATTTATAACTATAAGCGGATTTGAGAA
AATT
Found at i:63878 original size:15 final size:15
Alignment explanation
Indices: 63858--63890 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
63848 AAAATAGACT
63858 TAAGTTAGTCATTTA
1 TAAGTTAGTCATTTA
63873 TAAGTTAGTCATTTA
1 TAAGTTAGTCATTTA
63888 TAA
1 TAA
63891 CTATAAGCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (15 bp):
TAAGTTAGTCATTTA
Found at i:68152 original size:15 final size:15
Alignment explanation
Indices: 68125--68172 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
68115 TTTTCGTTTG
*
68125 TTTT-AACTTTTTTT
1 TTTTCAACTCTTTTT
68139 TTTTCAACTCTTTTT
1 TTTTCAACTCTTTTT
*
68154 TTTGTCAAGCACTTTTT
1 TTT-TCAA-CTCTTTTT
68171 TT
1 TT
68173 AAAAAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 4 0.14
15 12 0.41
16 4 0.14
17 9 0.31
ACGTcount: A:0.15, C:0.15, G:0.04, T:0.67
Consensus pattern (15 bp):
TTTTCAACTCTTTTT
Found at i:68154 original size:16 final size:16
Alignment explanation
Indices: 68125--68172 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
68115 TTTTCGTTTG
68125 TTTT-AACT-TTTTTT
1 TTTTCAACTCTTTTTT
68139 TTTTCAACTCTTTTTT
1 TTTTCAACTCTTTTTT
* *
68155 TTGTCAAGCACTTTTTT
1 TTTTCAA-CTCTTTTTT
68172 T
1 T
68173 AAAAAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 4 0.14
15 4 0.14
16 12 0.41
17 9 0.31
ACGTcount: A:0.15, C:0.15, G:0.04, T:0.67
Consensus pattern (16 bp):
TTTTCAACTCTTTTTT
Found at i:73832 original size:25 final size:25
Alignment explanation
Indices: 73804--73896 Score: 91
Period size: 25 Copynumber: 3.7 Consensus size: 25
73794 ATACACGCAT
73804 TGTTTTTATATAATATATATATGCA
1 TGTTTTTATATAATATATATATGCA
* * *
73829 TGTTTTTATATAGTATA-CTCT-CA
1 TGTTTTTATATAATATATATATGCA
*
73852 TGGTTTTTTTTATAATATATATATGCA
1 T-G-TTTTTATATAATATATATATGCA
* * *
73879 TCTTTTTATGTAGTATAT
1 TGTTTTTATATAATATAT
73897 GTATACCTGT
Statistics
Matches: 53, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
23 3 0.06
24 3 0.06
25 42 0.79
26 2 0.04
27 3 0.06
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.55
Consensus pattern (25 bp):
TGTTTTTATATAATATATATATGCA
Found at i:76381 original size:3 final size:3
Alignment explanation
Indices: 76373--76402 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
76363 TCAATACAAG
*
76373 TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
76403 CACCACGAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:76392 original size:15 final size:15
Alignment explanation
Indices: 76374--76403 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
76364 CAATACAAGT
76374 TATTATTATTATTAC
1 TATTATTATTATTAC
76389 TATTATTATTATTAC
1 TATTATTATTATTAC
76404 ACCACGAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTATTATTATTAC
Found at i:87696 original size:31 final size:32
Alignment explanation
Indices: 87651--87718 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 32
87641 TCATTTAATA
*
87651 TTAAAGTTTGATTTT-GATGTTCGATTTGGTAC
1 TTAAAGTTTAATTTTAG-TGTTCGATTTGGTAC
87683 TTAAA-TTTAATTTTAGTGTTCGATTTGGTAC
1 TTAAAGTTTAATTTTAGTGTTCGATTTGGTAC
87714 TTAAA
1 TTAAA
87719 CGAAAAGTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
31 28 0.82
32 6 0.18
ACGTcount: A:0.26, C:0.06, G:0.18, T:0.50
Consensus pattern (32 bp):
TTAAAGTTTAATTTTAGTGTTCGATTTGGTAC
Found at i:91758 original size:16 final size:16
Alignment explanation
Indices: 91732--91774 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
91722 CATACTCCAT
* *
91732 TATACATATATGAATG
1 TATATATATATGAACG
* *
91748 TGTATATATATGTACG
1 TATATATATATGAACG
91764 TATATATATAT
1 TATATATATAT
91775 ATATATTTGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.44
Consensus pattern (16 bp):
TATATATATATGAACG
Found at i:95070 original size:60 final size:57
Alignment explanation
Indices: 94971--95095 Score: 169
Period size: 60 Copynumber: 2.1 Consensus size: 57
94961 TAGTCAGCAG
* * *
94971 CCAACTATTAGTATTTTTTTTTTGTCACCAAATTATGAAAAGTTACAAAATAATCAC
1 CCAACTATTAGTATTTTTTTATGGTCACCAAACTATGAAAAGTTACAAAATAATCAC
* *
95028 CCAACTATTAGTAAATTTCTTTTATGGTCACCCAACTATGAAAAGTTACAAAATAGTCAC
1 CCAACTATTAGT--ATTT-TTTTATGGTCACCAAACTATGAAAAGTTACAAAATAATCAC
95088 CCGAACTA
1 CC-AACTA
95096 CTCAATTTCG
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
57 12 0.20
59 4 0.07
60 38 0.64
61 5 0.08
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (57 bp):
CCAACTATTAGTATTTTTTTATGGTCACCAAACTATGAAAAGTTACAAAATAATCAC
Found at i:95123 original size:60 final size:57
Alignment explanation
Indices: 94983--95123 Score: 142
Period size: 60 Copynumber: 2.4 Consensus size: 57
94973 AACTATTAGT
* * *
94983 ATTT-TTTTTTTGTCACCAAATTATGAAAAGTTACAAAATAATCACCCAACTATTAGTAA
1 ATTTCTTTTTTGGTCACC-AACTATGAAAAGTTACAAAATAATCACCCAAC--TTACTAA
* * *
95042 ATTTCTTTTATGGTCACCCAACTATGAAAAGTTACAAAATAGTCACCCGAAC-TACTCA
1 ATTTCTTTTTTGGTCA-CCAACTATGAAAAGTTACAAAATAATCACCC-AACTTACTAA
95100 ATTTCGTCTCTTTTGGTCACCAAC
1 ATTTC-T-T-TTTTGGTCACCAAC
95124 CGACTAATGT
Statistics
Matches: 69, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
58 9 0.13
59 5 0.07
60 42 0.61
61 13 0.19
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (57 bp):
ATTTCTTTTTTGGTCACCAACTATGAAAAGTTACAAAATAATCACCCAACTTACTAA
Found at i:97252 original size:23 final size:22
Alignment explanation
Indices: 97201--97252 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 22
97191 AATACATGAT
*
97201 AAGATTATATTTTGATCTCTCAA
1 AAGATT-TATTTCGATCTCTCAA
97224 AA-ATTTATTTCGATC-CTTCTAA
1 AAGATTTATTTCGATCTC-TC-AA
97246 AAGATTT
1 AAGATTT
97253 CTAGATTCCC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 1 0.04
21 11 0.44
22 7 0.28
23 6 0.24
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (22 bp):
AAGATTTATTTCGATCTCTCAA
Found at i:98457 original size:386 final size:385
Alignment explanation
Indices: 97739--98457 Score: 1129
Period size: 386 Copynumber: 1.9 Consensus size: 385
97729 TTCTATCCGT
* *
97739 ATTGAGTTCCACCATTTCCAAACCTCTTAACAAGAACAAAGGCTCCATCAATGGTTCTGAGTTTT
1 ATTGAATTCCACCATTTCCAAACCTCTTAACAAGAAAAAAGGCTCCATCAATGGTTCTGAGTTTT
*
97804 GAAACCATCCTATCAATACATAAGAACCAATATAAATGAGGATCCAATGAGCTTTTATTAGATTT
66 GAAACCATCCGATCAATACATAAGAACCAATATAAATGAGGATCCAATGAGCTTTTATTAGATTT
* *
97869 GTCATGCACACACTTCATACTAAATAGAAATGGAAGTACTGGAACAAATGTTTTCATGGCATTGG
131 GTCATACACACACTTCATACTAAATAGAAATGGAAGTACTGGAACAAATGTTTTCATAGCATTGG
* *
97934 TTTAGAGTTCTCACCTATGTTGCTCTGAGTCTTCATTTTTCTTCAACTATCCATGTTTGACATAT
196 GTTAGAGTTCTCACCTATGTTGCTCTGAGTCTTCATTTTTCTTCAACAATCCATGTTTGACATAT
* * * * *
97999 ATCTGAACACAAATACGATGATATGAGTCTCTAAATACATGAACAACAAAACATACCCATATATA
261 AGCCGAACACAAATACGAGGATAT-ACTCTCTAAATACATGAACAACAAAACATACCCATATAAA
98064 CTAACACCTGACCGCAAGTAAAACTTATTCTCACCCTTCTACACCATCCTTCACAATCTGC
325 CTAACACCTGACCGCAAGTAAAACTTATTCTCACCCTTCTACACCATCCTTCACAATCTGC
* *
98125 ATTGAATTCCACCATTTCCGAACCTCTTAACAAGAAAAAAGGCTCCATCAATGGTTTTGAGTTCT
1 ATTGAATTCCACCATTTCCAAACCTCTTAACAAGAAAAAAGGCTCCATCAATGGTTCTGAGTT-T
*
98190 TGAAACCATCCGATCAATACATAAGAACCAATGTAAATGAGGATCCAATGAGCTTTTATTAGATT
65 TGAAACCATCCGATCAATACATAAGAACCAATATAAATGAGGATCCAATGAGCTTTTATTAGATT
* * * * *
98255 TGTCATACACACGCTTCATACTAAATAGAAATGGAAGTATTGTAAGAGATG-TTTCATAGCATTG
130 TGTCATACACACACTTCATACTAAATAGAAATGGAAGTACTGGAACAAATGTTTTCATAGCATTG
* * *
98319 GGTTGGAGTTCTCACCTATGTTGCTCTGAGTCTTCATTTTTCTTTAACAATCCGTGTTTGACATA
195 GGTTAGAGTTCTCACCTATGTTGCTCTGAGTCTTCATTTTTCTTCAACAATCCATGTTTGACATA
* * * *
98384 TAGCCGAACACGAGTATC-AGGATAT-CTCTCTAAATACATGAACAACAGAACATTCCCATATAA
260 TAGCCGAACACAAATA-CGAGGATATACTCTCTAAATACATGAACAACAAAACATACCCATATAA
98447 ACATTAACACC
324 AC--TAACACC
98458 CATGTGCGAA
Statistics
Matches: 302, Mismatches: 27, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
384 36 0.12
386 156 0.52
387 110 0.36
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.31
Consensus pattern (385 bp):
ATTGAATTCCACCATTTCCAAACCTCTTAACAAGAAAAAAGGCTCCATCAATGGTTCTGAGTTTT
GAAACCATCCGATCAATACATAAGAACCAATATAAATGAGGATCCAATGAGCTTTTATTAGATTT
GTCATACACACACTTCATACTAAATAGAAATGGAAGTACTGGAACAAATGTTTTCATAGCATTGG
GTTAGAGTTCTCACCTATGTTGCTCTGAGTCTTCATTTTTCTTCAACAATCCATGTTTGACATAT
AGCCGAACACAAATACGAGGATATACTCTCTAAATACATGAACAACAAAACATACCCATATAAAC
TAACACCTGACCGCAAGTAAAACTTATTCTCACCCTTCTACACCATCCTTCACAATCTGC
Found at i:103269 original size:17 final size:16
Alignment explanation
Indices: 103247--103278 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
103237 TGAATAAAAA
103247 ACAAACAAACAATAAAT
1 ACAAACAAAC-ATAAAT
103264 ACAAACAAACATAAA
1 ACAAACAAACATAAA
103279 AATTTTGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.72, C:0.19, G:0.00, T:0.09
Consensus pattern (16 bp):
ACAAACAAACATAAAT
Found at i:116818 original size:12 final size:12
Alignment explanation
Indices: 116801--116827 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
116791 TATTAAGTAT
116801 ATAATTTTTTAA
1 ATAATTTTTTAA
116813 ATAATTTTTTAA
1 ATAATTTTTTAA
116825 ATA
1 ATA
116828 TATAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATAATTTTTTAA
Found at i:129428 original size:18 final size:18
Alignment explanation
Indices: 129405--129439 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
129395 CATTGTTGGG
*
129405 TTATTCTATTCAGTCATA
1 TTATTCTATTCACTCATA
129423 TTATTCTATTCACTCAT
1 TTATTCTATTCACTCAT
129440 CAGTTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.20, G:0.03, T:0.51
Consensus pattern (18 bp):
TTATTCTATTCACTCATA
Found at i:135589 original size:200 final size:199
Alignment explanation
Indices: 135241--135766 Score: 748
Period size: 200 Copynumber: 2.6 Consensus size: 199
135231 GAGTCTTCAT
* * * * * *
135241 TTTTAATGAAATACATTTGTCCGAAACATATTTGAACACGGGTATCTAACGCTTAGACCCAAGTC
1 TTTTCATGAAATACATTTGTCCTATACATATTCGAACAC-GGTATCTAACACTTAGACCCAAATC
* *
135306 CGAGCAACATAGATATCAAGCACTAGATTCATAGCAACTAGGCAAAGCAATCAACCTAGAAGGGA
65 CGAGCAATATAGATATCAAGCACTAGATTCATAGCAACTAGGCCAAGCAATCAACCTAGAAGGGA
* * * *
135371 TTTCACTCCTTTTCCTTAGTAATCACTACTCAACCTATTGTTAATATCAAAGATTGCTAAGACTC
130 TTTCACTCCTTTTCCTTAGTAATCACAACTCAACCTATAGTTAACATCAAAGATAGCTAAGACTC
*
135436 TTTGA
195 TTCGA
* * * *
135441 TTTTCATGAAATACATTTGTCCTATACAAATTCAAACACAGGTATCTAAAAATTAGACCCAAATC
1 TTTTCATGAAATACATTTGTCCTATACATATTCGAACAC-GGTATCTAACACTTAGACCCAAATC
* * *
135506 CGAGCAATACAGATATCAAGCACAAGATTCATGGCAACTAGGCCAAGCAATCAACCTAGAAGGGA
65 CGAGCAATATAGATATCAAGCACTAGATTCATAGCAACTAGGCCAAGCAATCAACCTAGAAGGGA
* * **
135571 TTTCACTCCTTTTCCTTAGTAATCACAACTCACCCTATAGTTAACATCATAGATAGCTCTGACTC
130 TTTCACTCCTTTTCCTTAGTAATCACAACTCAACCTATAGTTAACATCAAAGATAGCTAAGACTC
*
135636 TTCGG
195 TTCGA
*
135641 TTTTCATGAAATACATTTGTCCTATACATATTCGAACACGAGTATCTAACACTTAGACCCAAATA
1 TTTTCATGAAATACATTTGTCCTATACATATTCGAACACG-GTATCTAACACTTAGACCCAAATC
* * *
135706 CAAGCAATATAGATATCAAACACTAGATTCGA-AACAACTAGGCCAAGCAATCAACCTAGAA
65 CGAGCAATATAGATATCAAGCACTAGATTC-ATAGCAACTAGGCCAAGCAATCAACCTAGAA
135767 ATCCCATAAT
Statistics
Matches: 287, Mismatches: 37, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
199 1 0.00
200 285 0.99
201 1 0.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (199 bp):
TTTTCATGAAATACATTTGTCCTATACATATTCGAACACGGTATCTAACACTTAGACCCAAATCC
GAGCAATATAGATATCAAGCACTAGATTCATAGCAACTAGGCCAAGCAATCAACCTAGAAGGGAT
TTCACTCCTTTTCCTTAGTAATCACAACTCAACCTATAGTTAACATCAAAGATAGCTAAGACTCT
TCGA
Found at i:141787 original size:14 final size:15
Alignment explanation
Indices: 141768--141805 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
141758 TAGAAATATA
141768 TTTTT-ATTTTAAAT
1 TTTTTAATTTTAAAT
141782 TTTTTAATTTTAAAAT
1 TTTTTAATTTT-AAAT
141798 ATTTTTAA
1 -TTTTTAA
141806 AATACTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.24
15 5 0.24
16 4 0.19
17 7 0.33
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTTAATTTTAAAT
Found at i:149946 original size:138 final size:138
Alignment explanation
Indices: 149698--149948 Score: 414
Period size: 138 Copynumber: 1.8 Consensus size: 138
149688 ATCTTTGCCC
* *
149698 GTGGTTTTTTTATCCTCTTTGGAGGGGTTTTTCCCGTTAAATTTGTGTCTTCATCTTCTTAATTT
1 GTGGTTTTTTTATCCTCTTTGGAGGGGTTTTTCACGTTAAATTTGTGTCTTCATCTTCTCAATTT
*
149763 CTTCTGCTATTTTTACTTGTTCGTTGCTTAATCAGGACAATCCTAACAGTTTCACTTCATCCACT
66 ATTCTGCTATTTTTACTTGTTCGTTGCTTAATCAGGACAATCCTAACAGTTTCACTTCATCCACT
149828 CAAGTGTT
131 CAAGTGTT
* *
149836 GTGG-TTTTTTATCCTCTTTGGAGAGGTTTTTTCACGTTAAATTTGTGTGTTCATCTTCTCAATT
1 GTGGTTTTTTTATCCTCTTTGGAG-GGGTTTTTCACGTTAAATTTGTGTCTTCATCTTCTCAATT
* * *
149900 TATTCTGCTATTTTTACTTGTTTGTTGCTTAATCGGGACGATCCTAACA
65 TATTCTGCTATTTTTACTTGTTCGTTGCTTAATCAGGACAATCCTAACA
149949 AAAATGCATT
Statistics
Matches: 104, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
137 19 0.18
138 85 0.82
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.48
Consensus pattern (138 bp):
GTGGTTTTTTTATCCTCTTTGGAGGGGTTTTTCACGTTAAATTTGTGTCTTCATCTTCTCAATTT
ATTCTGCTATTTTTACTTGTTCGTTGCTTAATCAGGACAATCCTAACAGTTTCACTTCATCCACT
CAAGTGTT
Found at i:151007 original size:13 final size:13
Alignment explanation
Indices: 150989--151016 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
150979 TGGGGCTACT
150989 CATTGTGATGCTA
1 CATTGTGATGCTA
151002 CATTGTGATGCTA
1 CATTGTGATGCTA
151015 CA
1 CA
151017 ATCTATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (13 bp):
CATTGTGATGCTA
Found at i:172168 original size:14 final size:14
Alignment explanation
Indices: 172149--172178 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
172139 ATCATTAGTT
*
172149 TTACTAAGTGGTAC
1 TTACTAAGCGGTAC
172163 TTACTAAGCGGTAC
1 TTACTAAGCGGTAC
172177 TT
1 TT
172179 TTTTTTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (14 bp):
TTACTAAGCGGTAC
Found at i:176470 original size:92 final size:93
Alignment explanation
Indices: 176304--176503 Score: 366
Period size: 92 Copynumber: 2.1 Consensus size: 93
176294 AAATTTTTAT
*
176304 AATATTACTCGTATTTAAGTGTGAGTATTTGATATATATATATATATTTCAACACGAGTATATTC
1 AATATT-CTCGTATTTAAGTGTGAGTATTTGA-ATATAGATATATATTTCAACACGAGTATATTC
176369 AATCTCTTGGTAAGTTTTTTTACGTATTTG
64 AATCTCTTGGTAAGTTTTTTTACGTATTTG
176399 AATATTCTCGTATTTAAGTGTGAGTATTTG-ATATAGATATATATTTCAACACGAGTATATTCAA
1 AATATTCTCGTATTTAAGTGTGAGTATTTGAATATAGATATATATTTCAACACGAGTATATTCAA
176463 TCTCTTGGTAAGTTTTTTTACGTATTTG
66 TCTCTTGGTAAGTTTTTTTACGTATTTG
176491 AATATTCTCGTAT
1 AATATTCTCGTAT
176504 CCATGTCTAG
Statistics
Matches: 104, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
92 74 0.71
94 24 0.23
95 6 0.06
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.46
Consensus pattern (93 bp):
AATATTCTCGTATTTAAGTGTGAGTATTTGAATATAGATATATATTTCAACACGAGTATATTCAA
TCTCTTGGTAAGTTTTTTTACGTATTTG
Found at i:178465 original size:2 final size:2
Alignment explanation
Indices: 178458--178507 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
178448 GGGTTTTCTT
178458 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
178500 CA CA CA CA
1 CA CA CA CA
178508 TATATATACA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:179771 original size:8 final size:8
Alignment explanation
Indices: 179755--179788 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
179745 AGTTATGAAT
179755 TATATAAA
1 TATATAAA
*
179763 TAAATAAA
1 TATATAAA
*
179771 TATATATA
1 TATATAAA
179779 TATATAAA
1 TATATAAA
179787 TA
1 TA
179789 GAATTTAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
TATATAAA
Found at i:186479 original size:32 final size:32
Alignment explanation
Indices: 186443--186508 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
186433 TTTAAATAGA
186443 ATAATATATATTTGATAAGATAGAGATAATAT
1 ATAATATATATTTGATAAGATAGAGATAATAT
186475 ATAATATATATTTGATAAGATAGAGATAATAT
1 ATAATATATATTTGATAAGATAGAGATAATAT
186507 AT
1 AT
186509 TTTAAGATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (32 bp):
ATAATATATATTTGATAAGATAGAGATAATAT
Found at i:187762 original size:22 final size:22
Alignment explanation
Indices: 187719--187762 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
187709 AATGTTAATG
* *
187719 GTCAAATTTGACTCAAATAAAT
1 GTCAAATTTAACTCAAAAAAAT
187741 GTCAAATTTAACT-AGAAAAAAT
1 GTCAAATTTAACTCA-AAAAAAT
187763 AGGGATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (22 bp):
GTCAAATTTAACTCAAAAAAAT
Found at i:189306 original size:53 final size:51
Alignment explanation
Indices: 189248--189349 Score: 143
Period size: 53 Copynumber: 2.0 Consensus size: 51
189238 ATACTAATGG
* *
189248 TCACCCAACTATAAAAAATTACAAAATGGTCA-TTCAACTATTAATAATTTTTC
1 TCACCCAACTATAAAAAACTACAAAATGATCACTT-AACTATT--TAATTTTTC
*
189301 TCACCCAACTATAAAAAACTACAAACTGATCACTTAACTATTTAATTTT
1 TCACCCAACTATAAAAAACTACAAAATGATCACTTAACTATTTAATTTT
189350 ATCTGTTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
51 7 0.16
53 36 0.80
54 2 0.04
ACGTcount: A:0.43, C:0.21, G:0.03, T:0.33
Consensus pattern (51 bp):
TCACCCAACTATAAAAAACTACAAAATGATCACTTAACTATTTAATTTTTC
Found at i:189782 original size:15 final size:16
Alignment explanation
Indices: 189757--189786 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
189747 TTTTAAACCC
189757 AAAATATAAAAAAAAT
1 AAAATATAAAAAAAAT
189773 AAAA-ATAAAAAAAA
1 AAAATATAAAAAAAA
189787 ACCTCAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (16 bp):
AAAATATAAAAAAAAT
Found at i:191195 original size:166 final size:166
Alignment explanation
Indices: 190921--191240 Score: 523
Period size: 166 Copynumber: 1.9 Consensus size: 166
190911 AATGGACCAA
* *
190921 AGTTAATTAGAACGAGGAATAAAACCATGAAACAAAGCAAACACAATATACAAACATGACACAAG
1 AGTTAATTAGAACAAGGAATAAAACCATGAAACAAAGCAAACACAACATACAAACATGACACAAG
* * * *
190986 TTTATTTTGCTAAAATCAAATGCAACAGCCAATGTTTTCGAGATGTCTTCGATGGTTCTAACAGC
66 TTTATTTTGCTAAAACCAAATGCAACACCCAATGTTTTCGAGATGTCTTCAAGGGTTCTAACAGC
191051 AGCTATTGTGAACTTACAAAATTTCCCATAAACACT
131 AGCTATTGTGAACTTACAAAATTTCCCATAAACACT
* * *
191087 AGTTAATTAGAACAAGGAATAAGACCATGAAACAAAGCAAACACAACATGCAAACATGATACAAG
1 AGTTAATTAGAACAAGGAATAAAACCATGAAACAAAGCAAACACAACATACAAACATGACACAAG
* * * *
191152 TTTGTTTTGCTAAAACCGAGTGCAACACCCAATGTTTTCGAGATGTCTTCAAGGGTTTTAACAGC
66 TTTATTTTGCTAAAACCAAATGCAACACCCAATGTTTTCGAGATGTCTTCAAGGGTTCTAACAGC
191217 AGCTATTGTGAACTTACAAAATTT
131 AGCTATTGTGAACTTACAAAATTT
191241 ATAATTAGAA
Statistics
Matches: 141, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
166 141 1.00
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (166 bp):
AGTTAATTAGAACAAGGAATAAAACCATGAAACAAAGCAAACACAACATACAAACATGACACAAG
TTTATTTTGCTAAAACCAAATGCAACACCCAATGTTTTCGAGATGTCTTCAAGGGTTCTAACAGC
AGCTATTGTGAACTTACAAAATTTCCCATAAACACT
Found at i:204190 original size:30 final size:31
Alignment explanation
Indices: 204151--204212 Score: 74
Period size: 30 Copynumber: 2.0 Consensus size: 31
204141 GCACGTATAT
* * *
204151 ATTATATTAT-AATTTATTATAAAAATTA-AA
1 ATTAAATTATAAATATA-TATAAAAATTTAAA
204181 ATTAAATTATAAATATATATAAAAATTTAAA
1 ATTAAATTATAAATATATATAAAAATTTAAA
204212 A
1 A
204213 ATATCAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 19 0.70
31 8 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (31 bp):
ATTAAATTATAAATATATATAAAAATTTAAA
Found at i:214371 original size:191 final size:188
Alignment explanation
Indices: 213834--214443 Score: 670
Period size: 191 Copynumber: 3.2 Consensus size: 188
213824 AGCACATTGC
* * * ** *
213834 TATACC-GACATAACACTCTCTAGAAAAGAATGTTTAGAACCTAGAAACCGATGTCTTTACGAGT
1 TATACCAGACGTAACACCCTCTAGAAAAGAATGTTTAGAACC-CGAAAATGATGTCTTTGCGAGT
*** * *
213898 AGCAGTGTGAATTCATGACTTGTATGCTTTTATAATGACATGTTTTCTA-TGTCTAGAGCATCCT
65 AG-A-TGTGAATTC-TGACGCATATGCTTTTATAATGAAATGTTTTC-AGTGTCTAGAGCACCCT
* * * * *
213962 TTTGATCGAAACCATATTCATGTTCAGCTGCATATTATGAACTTGAATGAATGAAGCATGTTG
126 TTTGATTGAAGCCATATTCATGTTCTGCTGCATATTATGAACTTGAATGAATGAAACACGTTG
* * * * *
214025 CTATA-CAGACGTAAAACCTTCTAGAAAAGAATGTTTAGAA-CCGAGAAATCAAGGTAC-TAGC-
1 -TATACCAGACGTAACACCCTCTAGAAAAGAATGTTTAGAACCCGA-AAAT-GATGT-CTTTGCG
*
214086 AG-AGATGTGAA-TCTG-CGACATATGCATTTATAATGAAATGTTTTC-GATGTCTAGAGCACCC
62 AGTAGATGTGAATTCTGACG-CATATGCTTTTATAATGAAATGTTTTCAG-TGTCTAGAGCA-CC
* * *
214147 CTTTTGATTGAAGCCATATTCATGTTCTGCTGCATATTTTGAATTTGAATGAATGAAACACATTG
124 CTTTTGATTGAAGCCATATTCATGTTCTGCTGCATATTATGAACTTGAATGAATGAAACACGTTG
* ** *
214212 TATACCAG-CGTAACACCCTATATTAAGGAATGTTTAGAACCCGGAAAATGATGTCTTTGCGAGT
1 TATACCAGACGTAACACCCTCTAGAAAAGAATGTTTAGAACCC-GAAAATGATGTCTTTGCGAGT
*
214276 AGGTATGTGAATTCGTGAAGCATATGCTTTTATAATGAAATGTTTTCAGTGTCTAGAGCACCCTT
65 A-G-ATGTGAATTC-TGACGCATATGCTTTTATAATGAAATGTTTTCAGTGTCTAGAGCACCCTT
* *
214341 TTGATTGCAGTCATATTCATGTTCTGCTGCATATTATGAACTTGAATGAATGAAGA-ACGTTG
127 TTGATTGAAGCCATATTCATGTTCTGCTGCATATTATGAACTTGAATGAATGAA-ACACGTTG
* *
214403 TATGCC-GACGTAACACCGTCTAGAAAAGAATGTTTAGAACC
1 TATACCAGACGTAACACCCTCTAGAAAAGAATGTTTAGAACC
214444 TAGAAAAGAA
Statistics
Matches: 349, Mismatches: 47, Indels: 45
0.79 0.11 0.10
Matches are distributed among these distances:
185 2 0.01
186 71 0.20
187 71 0.20
188 9 0.03
189 2 0.01
190 12 0.03
191 101 0.29
192 78 0.22
193 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (188 bp):
TATACCAGACGTAACACCCTCTAGAAAAGAATGTTTAGAACCCGAAAATGATGTCTTTGCGAGTA
GATGTGAATTCTGACGCATATGCTTTTATAATGAAATGTTTTCAGTGTCTAGAGCACCCTTTTGA
TTGAAGCCATATTCATGTTCTGCTGCATATTATGAACTTGAATGAATGAAACACGTTG
Found at i:214448 original size:21 final size:21
Alignment explanation
Indices: 214422--214465 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
214412 GTAACACCGT
214422 CTAGAAAAGAATGTTTAGAAC
1 CTAGAAAAGAATGTTTAGAAC
214443 CTAGAAAAGAATGTTTAGAAC
1 CTAGAAAAGAATGTTTAGAAC
214464 CT
1 CT
214466 GGAACCCGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.25
Consensus pattern (21 bp):
CTAGAAAAGAATGTTTAGAAC
Found at i:214879 original size:193 final size:193
Alignment explanation
Indices: 214550--215092 Score: 838
Period size: 194 Copynumber: 2.8 Consensus size: 193
214540 CTAAAGCAAT
* * * *
214550 TATGAACTTGAATGAATGAAGCACATCG-TTTAACCGATGTAACACCCTCTAGAAAGGAATGTTT
1 TATGAACTTGAATGAATGAAGCACATTGCTAT-ACCGACGTAACACCCTCTAGAAAAGAATGTTT
*
214614 AGAATTCGGAAACCAATATCTTTACAAGTAGCGGTGTGAATTCGTGACTTTTATGCATTTATAAT
65 AGAATTCGGAAACCAATATCTTTACAAGTAGCGGTGTGAATTCGTGACTTTTATGCTTTTATAAT
214679 GAAATGTTTTTTATGTCTAGTGCACCCCTTTTGATTGAAGCCATATTCATGTTCTGCTGCATAC
130 GAAATGTTTTTTATGTCTAGTGCACCCCTTTTGATTGAAGCCATATTCATGTTCTGCTGCATAC
214743 TATGAACTTGAATGAATGAAGCACATTGCTATACCGACGTAACACCCTCTAGAAAAGAATGTTTA
1 TATGAACTTGAATGAATGAAGCACATTGCTATACCGACGTAACACCCTCTAGAAAAGAATGTTTA
*
214808 GAATTCGGAAACCAATATCTTTACAAGTAGCGGTGTGAATTCGTAACTTTTATGCTTTTATAATG
66 GAATTCGGAAACCAATATCTTTACAAGTAGCGGTGTGAATTCGTGACTTTTATGCTTTTATAATG
* *
214873 AAATGTTTTTTATGTATAGTGCAACCCCTTTTGATTGAAGCGATATTCATGTTCTGCTGCATAC
131 AAATGTTTTTTATGTCTAGTGC-ACCCCTTTTGATTGAAGCCATATTCATGTTCTGCTGCATAC
* * *
214937 TGTGAACTTGAATGAATGAAGCACGTTGCTATACCG-CGGTAACACCCTCTAGAAAAGAAGGTTT
1 TATGAACTTGAATGAATGAAGCACATTGCTATACCGAC-GTAACACCCTCTAGAAAAGAATGTTT
* * * ** * * * *
215001 AGAACTCGAAAACCAATGTCTTTATGAGTAGCGATATGAATCCGTGACTTATATGCTTTTATAAT
65 AGAATTCGGAAACCAATATCTTTACAAGTAGCGGTGTGAATTCGTGACTTTTATGCTTTTATAAT
* * *
215066 GAAATGTTTTTGATGGCTAGAGCACCC
130 GAAATGTTTTTTATGTCTAGTGCACCC
215093 TTTGGTAAAA
Statistics
Matches: 322, Mismatches: 25, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
193 147 0.46
194 175 0.54
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (193 bp):
TATGAACTTGAATGAATGAAGCACATTGCTATACCGACGTAACACCCTCTAGAAAAGAATGTTTA
GAATTCGGAAACCAATATCTTTACAAGTAGCGGTGTGAATTCGTGACTTTTATGCTTTTATAATG
AAATGTTTTTTATGTCTAGTGCACCCCTTTTGATTGAAGCCATATTCATGTTCTGCTGCATAC
Found at i:215920 original size:17 final size:18
Alignment explanation
Indices: 215887--215920 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
215877 TTTCAAAGCT
*
215887 TTCGTAGAAATTTTATTC
1 TTCGTAGAAAATTTATTC
215905 TTCGTA-AAAATTTATT
1 TTCGTAGAAAATTTATT
215921 TTAAATTATA
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:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (18 bp):
TTCGTAGAAAATTTATTC
Found at i:216374 original size:19 final size:20
Alignment explanation
Indices: 216350--216389 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
216340 TAGCAATTAC
*
216350 TTAATA-TATAAAAATACTT
1 TTAATATTATAAAAAAACTT
*
216369 TTAATATTTTAAAAAAACTT
1 TTAATATTATAAAAAAACTT
216389 T
1 T
216390 AAGTAACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAATATTATAAAAAAACTT
Found at i:223330 original size:30 final size:31
Alignment explanation
Indices: 223294--223363 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
223284 AATAAACCTT
**
223294 AATAGTTCAATGACTTAAAT-AAAACTTTCG
1 AATAGTTCAACAACTTAAATGAAAACTTTCG
* * *
223324 AATAGTTCAGCAACTTAGATGAAAACTTTTG
1 AATAGTTCAACAACTTAAATGAAAACTTTCG
223355 AATAGTTCA
1 AATAGTTCA
223364 GTGATCAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 16 0.47
31 18 0.53
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (31 bp):
AATAGTTCAACAACTTAAATGAAAACTTTCG
Found at i:223352 original size:31 final size:30
Alignment explanation
Indices: 223306--223364 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
223296 TAGTTCAATG
223306 ACTTAAATAAAACTTTCGAATAGTTCAGCA
1 ACTTAAATAAAACTTTCGAATAGTTCAGCA
* *
223336 ACTTAGATGAAAACTTTTGAATAGTTCAG
1 ACTTAAAT-AAAACTTTCGAATAGTTCAG
223365 TGATCAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 7 0.27
31 19 0.73
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (30 bp):
ACTTAAATAAAACTTTCGAATAGTTCAGCA
Found at i:224787 original size:79 final size:80
Alignment explanation
Indices: 224682--224845 Score: 314
Period size: 79 Copynumber: 2.1 Consensus size: 80
224672 TTAAAATATA
224682 ATTTTATTATTTATTAAATTATAATTATGTAAAACTTAAAGGGCCAAAAGTGAAATTTTACATTT
1 ATTTTATTATTTATTAAATTATAATTATGTAAAACTTAAAGGGCCAAAAGTGAAATTTTACATTT
224747 TGATAACAACCTTTT
66 TGATAACAACCTTTT
224762 ATTTTATTA-TTATTAAATTATAATTATGTAAAACTTAAAGGGCCAAAAGTGAAATTTTACATTT
1 ATTTTATTATTTATTAAATTATAATTATGTAAAACTTAAAGGGCCAAAAGTGAAATTTTACATTT
224826 TGATAACAACCTTTT
66 TGATAACAACCTTTT
224841 -TTTTA
1 ATTTTA
224846 CCTCGAGATT
Statistics
Matches: 84, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
78 5 0.06
79 70 0.83
80 9 0.11
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.43
Consensus pattern (80 bp):
ATTTTATTATTTATTAAATTATAATTATGTAAAACTTAAAGGGCCAAAAGTGAAATTTTACATTT
TGATAACAACCTTTT
Found at i:225797 original size:30 final size:29
Alignment explanation
Indices: 225763--225822 Score: 68
Period size: 30 Copynumber: 2.0 Consensus size: 29
225753 TCGATTTTAA
225763 TAAAATAAAT-TATTAAAAAATCATACAAAT
1 TAAAA-AAATATATTAAAAAATCATA-AAAT
* * *
225793 TAAAAAGATATATTAATAAATTATAAAAT
1 TAAAAAAATATATTAAAAAATCATAAAAT
225822 T
1 T
225823 TGATTCAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (29 bp):
TAAAAAAATATATTAAAAAATCATAAAAT
Found at i:226692 original size:22 final size:22
Alignment explanation
Indices: 226650--226692 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
226640 ATTAAAATTT
* *
226650 TTAAAAAATTTAAAGTTTAATA
1 TTAAAAAATATAAAGTCTAATA
226672 TTAAAAAA-ATAAAGGTCTAAT
1 TTAAAAAATATAAA-GTCTAAT
226693 TAATTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.35
Consensus pattern (22 bp):
TTAAAAAATATAAAGTCTAATA
Found at i:242102 original size:30 final size:29
Alignment explanation
Indices: 242032--242103 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
242022 AAAAATTTTC
*
242032 AAAATTTTGAAACTTTTGAAGACTCAAGT
1 AAAATTTTAAAACTTTTGAAGACTCAAGT
* * *
242061 AAAATTCTTAAAACTTTTGAGAGGCTTAATT
1 AAAATT-TTAAAACTTTTGA-AGACTCAAGT
*
242092 GAAATTTTAAAA
1 AAAATTTTAAAA
242104 AATTTCAAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 6 0.17
30 18 0.50
31 12 0.33
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.36
Consensus pattern (29 bp):
AAAATTTTAAAACTTTTGAAGACTCAAGT
Found at i:250485 original size:30 final size:29
Alignment explanation
Indices: 250415--250486 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
250405 AAAATTTTTC
*
250415 AAAATTTTTAAACTTTTGAAGACTCAAGT
1 AAAATTTTAAAACTTTTGAAGACTCAAGT
* * *
250444 AAAATTCTTAAAACTTTTGAGAGGCTTAATT
1 AAAATT-TTAAAACTTTTGA-AGACTCAAGT
*
250475 GAAATTTTAAAA
1 AAAATTTTAAAA
250487 AATTTCAAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 6 0.17
30 18 0.50
31 12 0.33
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (29 bp):
AAAATTTTAAAACTTTTGAAGACTCAAGT
Found at i:250825 original size:30 final size:29
Alignment explanation
Indices: 250755--250826 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
250745 AAAATTTTTC
*
250755 AAAATTTTTAAACTTTTGAAGACTCAAGT
1 AAAATTTTAAAACTTTTGAAGACTCAAGT
* * *
250784 AAAATTCTTAAAACTTTTGAGAGGCTTAATT
1 AAAATT-TTAAAACTTTTGA-AGACTCAAGT
*
250815 GAAATTTTAAAA
1 AAAATTTTAAAA
250827 AATTTCAAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 6 0.17
30 18 0.50
31 12 0.33
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (29 bp):
AAAATTTTAAAACTTTTGAAGACTCAAGT
Found at i:250932 original size:340 final size:340
Alignment explanation
Indices: 250312--250993 Score: 1346
Period size: 340 Copynumber: 2.0 Consensus size: 340
250302 TAAAAGATCT
250312 AATTAGAATTTTTAAAACTTTAGAGATTTAATTAGAATTTTTAAAAGTTTTAAGAGGCATAATTA
1 AATTAGAATTTTTAAAACTTTAGAGATTTAATTAGAATTTTTAAAAGTTTTAAGAGGCATAATTA
250377 AAACTTAAAAAAAATAAAAGGCATGATGAAAATTTTTCAAAATTTTTAAACTTTTGAAGACTCAA
66 AAACTTAAAAAAAATAAAAGGCATGATGAAAATTTTTCAAAATTTTTAAACTTTTGAAGACTCAA
250442 GTAAAATTCTTAAAACTTTTGAGAGGCTTAATTGAAATTTTAAAAAATTTCAAAGGATATAATGA
131 GTAAAATTCTTAAAACTTTTGAGAGGCTTAATTGAAATTTTAAAAAATTTCAAAGGATATAATGA
250507 AAAGTTTTCAAAATTTTTGAGAGGCGAAGATCCTTACAAGCTTCCACGCCTGTAACTAAATAGAC
196 AAAGTTTTCAAAATTTTTGAGAGGCGAAGATCCTTACAAGCTTCCACGCCTGTAACTAAATAGAC
250572 CGACTTGATTAACTCAGAATATTTAATATAACCAAAATTTTATGTATATTTTAATATTTATATTA
261 CGACTTGATTAACTCAGAATATTTAATATAACCAAAATTTTATGTATATTTTAATATTTATATTA
*
250637 AATATATGTAATATA
326 AATATATATAATATA
250652 AATTAGAATTTTTAAAACTTTAGAGATTTAATTAGAATTTTTAAAAGTTTTAAGAGGCATAATTA
1 AATTAGAATTTTTAAAACTTTAGAGATTTAATTAGAATTTTTAAAAGTTTTAAGAGGCATAATTA
250717 AAACTTAAAAAAAATAAAAGGCATGATGAAAATTTTTCAAAATTTTTAAACTTTTGAAGACTCAA
66 AAACTTAAAAAAAATAAAAGGCATGATGAAAATTTTTCAAAATTTTTAAACTTTTGAAGACTCAA
250782 GTAAAATTCTTAAAACTTTTGAGAGGCTTAATTGAAATTTTAAAAAATTTCAAAGGATATAATGA
131 GTAAAATTCTTAAAACTTTTGAGAGGCTTAATTGAAATTTTAAAAAATTTCAAAGGATATAATGA
*
250847 AAATTTTTCAAAATTTTTGAGAGGCGAAGATCCTTACAAGCTTCCACGCCTGTAACTAAATAGAC
196 AAAGTTTTCAAAATTTTTGAGAGGCGAAGATCCTTACAAGCTTCCACGCCTGTAACTAAATAGAC
250912 CGACTTGATTAACTCAGAATATTTAATATAACCAAAATTTTATGTATATTTTAATATTTATATTA
261 CGACTTGATTAACTCAGAATATTTAATATAACCAAAATTTTATGTATATTTTAATATTTATATTA
250977 AATATATATAATATA
326 AATATATATAATATA
250992 AA
1 AA
250994 ATAATTATAT
Statistics
Matches: 340, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
340 340 1.00
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (340 bp):
AATTAGAATTTTTAAAACTTTAGAGATTTAATTAGAATTTTTAAAAGTTTTAAGAGGCATAATTA
AAACTTAAAAAAAATAAAAGGCATGATGAAAATTTTTCAAAATTTTTAAACTTTTGAAGACTCAA
GTAAAATTCTTAAAACTTTTGAGAGGCTTAATTGAAATTTTAAAAAATTTCAAAGGATATAATGA
AAAGTTTTCAAAATTTTTGAGAGGCGAAGATCCTTACAAGCTTCCACGCCTGTAACTAAATAGAC
CGACTTGATTAACTCAGAATATTTAATATAACCAAAATTTTATGTATATTTTAATATTTATATTA
AATATATATAATATA
Found at i:254539 original size:25 final size:23
Alignment explanation
Indices: 254502--254552 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 23
254492 TTTTGAGCAA
254502 TTTAATTTTTTCTTTTATCTTAT
1 TTTAATTTTTTCTTTTATCTTAT
* *
254525 TTTAACTTTCTTTCTTTTTTCTTTT
1 TTTAA-TTT-TTTCTTTTATCTTAT
254550 TTT
1 TTT
254553 TCATTCTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 5 0.21
24 3 0.12
25 16 0.67
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTAATTTTTTCTTTTATCTTAT
Found at i:268804 original size:4 final size:4
Alignment explanation
Indices: 268795--268820 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
268785 AATATCCCAA
268795 AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AA
268821 ATGATCATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:271598 original size:29 final size:29
Alignment explanation
Indices: 271566--271628 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
271556 TTTTTTTAAA
*
271566 AATTAAA-CCTCCAAAATTTT-AGATATTTT
1 AATTAAACCCT-CAAAATTTTGA-AAATTTT
271595 AATTAAACCCTCAAAATTTTGAAAATTTT
1 AATTAAACCCTCAAAATTTTGAAAATTTT
271624 AATTA
1 AATTA
271629 GACTTCTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 27 0.87
30 4 0.13
ACGTcount: A:0.44, C:0.13, G:0.03, T:0.40
Consensus pattern (29 bp):
AATTAAACCCTCAAAATTTTGAAAATTTT
Found at i:272158 original size:4 final size:4
Alignment explanation
Indices: 272149--272175 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
272139 TTATCATCAA
272149 ATGT ATGT ATGT ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATG
272176 CATGCAACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:274333 original size:31 final size:31
Alignment explanation
Indices: 274298--274364 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
274288 TTAATATATT
*
274298 ATTTGATACATATGTTT-GGTGTTAATACTCA
1 ATTTGATACATATGTTTAGTTG-TAATACTCA
* * *
274329 ATTTGATACTTGTGTTTAGTTGTAATATTCA
1 ATTTGATACATATGTTTAGTTGTAATACTCA
274360 ATTTG
1 ATTTG
274365 GTATCCAGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 28 0.90
32 3 0.10
ACGTcount: A:0.27, C:0.07, G:0.16, T:0.49
Consensus pattern (31 bp):
ATTTGATACATATGTTTAGTTGTAATACTCA
Found at i:275536 original size:30 final size:29
Alignment explanation
Indices: 275500--275569 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 29
275490 TGAGAAATTC
*
275500 TTTTTAAAAAATTGAGTAGTC-TAATTAAAA
1 TTTTTAAAAAATTGA--AGGCTTAATTAAAA
*
275530 TTTTTAAAAACTTGAAGGCTTAATTAAAA
1 TTTTTAAAAAATTGAAGGCTTAATTAAAA
275559 TTTTCTAAAAA
1 TTTT-TAAAAA
275570 CTTCAAGGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
28 3 0.08
29 13 0.36
30 20 0.56
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.40
Consensus pattern (29 bp):
TTTTTAAAAAATTGAAGGCTTAATTAAAA
Found at i:275570 original size:30 final size:29
Alignment explanation
Indices: 275521--275577 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
275511 TTGAGTAGTC
*
275521 TAATTAAAATTTTTAAAAACTTGAAGGCT
1 TAATTAAAATTTTTAAAAACTTCAAGGCT
275550 TAATTAAAATTTTCTAAAAACTTCAAGG
1 TAATTAAAATTTT-TAAAAACTTCAAGG
275578 GAGAAATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (29 bp):
TAATTAAAATTTTTAAAAACTTCAAGGCT
Found at i:278556 original size:18 final size:18
Alignment explanation
Indices: 278535--278573 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
278525 TCATTAAAAA
*
278535 TTTCATCAAACGTCTTAT
1 TTTCATCAAACGTCCTAT
278553 TTTCATCAAACGTCCTAT
1 TTTCATCAAACGTCCTAT
278571 TTT
1 TTT
278574 ACTGTTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.23, G:0.05, T:0.46
Consensus pattern (18 bp):
TTTCATCAAACGTCCTAT
Found at i:279485 original size:222 final size:221
Alignment explanation
Indices: 279076--279698 Score: 918
Period size: 222 Copynumber: 2.8 Consensus size: 221
279066 ATATATCATA
* * *
279076 TATGGTACTTTCGTTTCTCTAACTCGTGTGAAAG-AAAAGACTTGTTTAGTCCTTAGAATCAATT
1 TATGGTACTTTCGTTTCTCTAGCTCGTGTGAAAGCAAAA-ACTCGTTTAGTCCTTAGAATCGATT
*
279140 TTATGCATCGAGGTTCTGAGAGTCAAATGCTGCTTCCATCCGTTGTCGATATGCCGGTTATTTTT
65 TTATGCATCGAGGTTCTGAGAGTCAAATGCTGCTTCCATCCGTTGTCGATATGCCTGTTATTTTT
* *
279205 GTGTGAATCTTGTTGTGCCTGATATTAGTTCTTAACAAGATGTCGTGTTTGCTCCCTCATCGTTA
130 GTGTGAATCTTGTTGTGTCTGATATTAGTTCTTAACAAGATGTCGTGTTTGATCCCTCATCGTTA
*
279270 AACCGAACCTTCGTCGTACTTATTGTG
195 AACCGAACCTTCATCGTACTTATTGTG
279297 TATGGTACTTTCGTTTCTCTAGCGTCGTGTGAAAGCAAAAACTCGTTTAGTCCTTAGAATCGATT
1 TATGGTACTTTCGTTTCTCTAGC-TCGTGTGAAAGCAAAAACTCGTTTAGTCCTTAGAATCGATT
* * *
279362 TTATGCATTGAGGTTCTGAGAGTCAAATGCTGCTTCCATCCGTTGTCCACATGCCTGTTATTTTT
65 TTATGCATCGAGGTTCTGAGAGTCAAATGCTGCTTCCATCCGTTGTCGATATGCCTGTTATTTTT
279427 GTGTGAATCTTGTTGTGTCTGATATTAGTTCTTAACAAGATGTCGTGTTTGATCCCTCATCGTTA
130 GTGTGAATCTTGTTGTGTCTGATATTAGTTCTTAACAAGATGTCGTGTTTGATCCCTCATCGTTA
279492 AACCGAACCTTCATCGTACTTATTGTG
195 AACCGAACCTTCATCGTACTTATTGTG
* *
279519 TATGGTACTTTCGTTTCTCTAGCATCATGTGAAAGCAAAGAA-TCGTTTAGT-C-T-G-TTCGAT
1 TATGGTACTTTCGTTTCTCTAGC-TCGTGTGAAAGCAAA-AACTCGTTTAGTCCTTAGAATCGAT
* * * * * *
279579 TTTATGCATCAAGGTTCTGAGGGTCAAATGTTGC-TCCTATCCGTTGTTGATATTCCGGTGTTTT
64 TTTATGCATCGAGGTTCTGAGAGTCAAATGCTGCTTCC-ATCCGTTGTCGATATGCC--TGTTAT
* * * * *
279643 TTTGTGTGTGAATATTATTATGTCCGATATTAGTTCTTAACAAGATATCGTGTTTG
126 TTT-TGTGTGAATCTTGTTGTGTCTGATATTAGTTCTTAACAAGATGTCGTGTTTG
279699 CTGTTCTGGA
Statistics
Matches: 368, Mismatches: 27, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
217 3 0.01
218 49 0.13
219 1 0.00
220 9 0.02
221 70 0.19
222 230 0.62
223 6 0.02
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (221 bp):
TATGGTACTTTCGTTTCTCTAGCTCGTGTGAAAGCAAAAACTCGTTTAGTCCTTAGAATCGATTT
TATGCATCGAGGTTCTGAGAGTCAAATGCTGCTTCCATCCGTTGTCGATATGCCTGTTATTTTTG
TGTGAATCTTGTTGTGTCTGATATTAGTTCTTAACAAGATGTCGTGTTTGATCCCTCATCGTTAA
ACCGAACCTTCATCGTACTTATTGTG
Found at i:280596 original size:12 final size:10
Alignment explanation
Indices: 280568--280614 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
280558 CCCTCATATG
280568 TATATATACA
1 TATATATACA
*
280578 TACATATACA
1 TATATATACA
280588 TGCATATATACA
1 T--ATATATACA
*
280600 TATATATATA
1 TATATATACA
280610 TATAT
1 TATAT
280615 GCATGTATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 23 0.72
12 9 0.28
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (10 bp):
TATATATACA
Found at i:282909 original size:15 final size:15
Alignment explanation
Indices: 282875--282917 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
282865 ATTTAGGCCT
282875 TAAATATTAAAATTTAAA
1 TAAAT-TTAAAA--TAAA
*
282893 TATATTTAAAATAAA
1 TAAATTTAAAATAAA
282908 TAAATTTAAA
1 TAAATTTAAA
282918 TTTTAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 13 0.57
17 6 0.26
18 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAAATTTAAAATAAA
Found at i:282931 original size:15 final size:16
Alignment explanation
Indices: 282878--282929 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
282868 TAGGCCTTAA
*
282878 ATATTAAAATTTAAAT
1 ATATTTAAATTTAAAT
*
282894 ATATTTAAA-ATAAAT
1 ATATTTAAATTTAAAT
* *
282909 AAATTTAAATTTTAAT
1 ATATTTAAATTTAAAT
282925 ATATT
1 ATATT
282930 AATCTATTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
15 13 0.45
16 16 0.55
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATATTTAAATTTAAAT
Found at i:284992 original size:31 final size:31
Alignment explanation
Indices: 284957--285016 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
284947 TAACAGTTCA
*
284957 ACTTTTTTTAAAAGGTTAAAACTCAAATTCG
1 ACTTTATTTAAAAGGTTAAAACTCAAATTCG
* **
284988 ACTTTATTTAGAAGGTTAAAGGTCAAATT
1 ACTTTATTTAAAAGGTTAAAACTCAAATT
285017 TAGCTTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (31 bp):
ACTTTATTTAAAAGGTTAAAACTCAAATTCG
Found at i:286403 original size:30 final size:31
Alignment explanation
Indices: 286320--286405 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 31
286310 TGAGATTGAT
* * * * *
286320 AAAAATTTCGAAAAAATTAGAAGAATTTAATC
1 AAAATTTTCAAAAAAATTAAAAG-GTATAATC
* *
286352 AAAATTTTTAAAAAAATTAAAAGGTATAATG
1 AAAATTTTCAAAAAAATTAAAAGGTATAATC
*
286383 AAAATTTTCAAAAATA-TAAAAGG
1 AAAATTTTCAAAAAAATTAAAAGG
286406 GGGCCAAATT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
30 7 0.16
31 19 0.42
32 19 0.42
ACGTcount: A:0.58, C:0.03, G:0.09, T:0.29
Consensus pattern (31 bp):
AAAATTTTCAAAAAAATTAAAAGGTATAATC
Found at i:288632 original size:235 final size:236
Alignment explanation
Indices: 288214--288684 Score: 926
Period size: 235 Copynumber: 2.0 Consensus size: 236
288204 TTTATATAGT
288214 GCTTTGTTTTTTTTTCTAATTTAAAAAAAAGATATTTTATTTTTATATTATAAAATATTAAATAA
1 GCTTTGTTTTTTTTTCTAATTTAAAAAAAAGATATTTTATTTTTATATTATAAAATATTAAATAA
288279 TATTTAAATTTTAAATCGGAAGGTATTCAAATAAATGGGATAAAAAATAAAAATTTCAAATATAT
66 TATTTAAATTTTAAATCGGAAGGTATTCAAATAAATGGGATAAAAAATAAAAATTTCAAATATAT
288344 AAGCGATTTGAATGGGGGCATTGTAGGGGTGTTTATTCGGTTAACCGATCCGAAATTACTATAAC
131 AAGCGATTTGAATGGGGGCATTGTAGGGGTGTTTATTCGGTTAACCGATCCGAAATTACTATAAC
288409 CGAATTAACCGACCTTTCAAAAATTTTAACCGTTAACCGAA
196 CGAATTAACCGACCTTTCAAAAATTTTAACCGTTAACCGAA
*
288450 GCTTTG-TTTTTTTTCTAATTTAAAAATAAGATATTTTATTTTTATATTATAAAATATTAAATAA
1 GCTTTGTTTTTTTTTCTAATTTAAAAAAAAGATATTTTATTTTTATATTATAAAATATTAAATAA
288514 TATTTAAATTTTAAATCGGAAGGTATTCAAATAAATGGGATAAAAAATAAAAATTTCAAATATAT
66 TATTTAAATTTTAAATCGGAAGGTATTCAAATAAATGGGATAAAAAATAAAAATTTCAAATATAT
288579 AAGCGATTTGAATGGGGGCATTGTAGGGGTGTTTATTCGGTTAACCGATCCGAAATTACTATAAC
131 AAGCGATTTGAATGGGGGCATTGTAGGGGTGTTTATTCGGTTAACCGATCCGAAATTACTATAAC
288644 CGAATTAACCGACCTTTCAAAAATTTTAACCGTTAACCGAA
196 CGAATTAACCGACCTTTCAAAAATTTTAACCGTTAACCGAA
288685 CCGATTTTTT
Statistics
Matches: 234, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
235 228 0.97
236 6 0.03
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (236 bp):
GCTTTGTTTTTTTTTCTAATTTAAAAAAAAGATATTTTATTTTTATATTATAAAATATTAAATAA
TATTTAAATTTTAAATCGGAAGGTATTCAAATAAATGGGATAAAAAATAAAAATTTCAAATATAT
AAGCGATTTGAATGGGGGCATTGTAGGGGTGTTTATTCGGTTAACCGATCCGAAATTACTATAAC
CGAATTAACCGACCTTTCAAAAATTTTAACCGTTAACCGAA
Found at i:298359 original size:25 final size:24
Alignment explanation
Indices: 298331--298383 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
298321 TCAGGTGCTT
*
298331 AATTGGTAAAAAAACCTGAGTATCA
1 AATTGG-AAAAAAACCTGAGTACCA
*
298356 AATT-GAAAAAAACTTGAGTACCA
1 AATTGGAAAAAAACCTGAGTACCA
298379 AATTG
1 AATTG
298384 AATTTGAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 20 0.80
24 1 0.04
25 4 0.16
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.25
Consensus pattern (24 bp):
AATTGGAAAAAAACCTGAGTACCA
Found at i:298365 original size:23 final size:23
Alignment explanation
Indices: 298338--298385 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
298328 CTTAATTGGT
*
298338 AAAAAAACCTGAGTATCAAATTG
1 AAAAAAACCTGAGTACCAAATTG
*
298361 AAAAAAACTTGAGTACCAAATTG
1 AAAAAAACCTGAGTACCAAATTG
298384 AA
1 AA
298386 TTTGAAGCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.54, C:0.12, G:0.12, T:0.21
Consensus pattern (23 bp):
AAAAAAACCTGAGTACCAAATTG
Found at i:298382 original size:79 final size:79
Alignment explanation
Indices: 298299--298446 Score: 174
Period size: 79 Copynumber: 1.9 Consensus size: 79
298289 TTTAGGTATT
** ** * * *
298299 AAATTGAACATTAAAGCCAATTTCAGGTGCTTAATTG-GTAAAAAAAC-CTGAGTATCAAATTGA
1 AAATTGAA-ATTAAAGCCAAACTCAAATACTTAATTGTGCAAAAAAACTC-GAGTATCAAATTAA
298362 AAAAAACTTGAGTACC
64 AAAAAACTTGAGTACC
* * *
298378 AAATTGAATTTGAAGCCAAACTCAAATACTTAATTGTGCACAAAAACTCGAGTATCAAATTAAAA
1 AAATTGAAATTAAAGCCAAACTCAAATACTTAATTGTGCAAAAAAACTCGAGTATCAAATTAAAA
298443 AAAA
66 AAAA
298447 AAACCTCAGT
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
78 21 0.37
79 35 0.61
80 1 0.02
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.26
Consensus pattern (79 bp):
AAATTGAAATTAAAGCCAAACTCAAATACTTAATTGTGCAAAAAAACTCGAGTATCAAATTAAAA
AAAACTTGAGTACC
Found at i:299112 original size:4 final size:4
Alignment explanation
Indices: 299103--299162 Score: 84
Period size: 4 Copynumber: 15.0 Consensus size: 4
299093 AATTACTTTT
* * * *
299103 CATA CATA CATA CATA CATA CATA CATA CATA CACA CATG CATG CATG
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
299151 CATA CATA CATA
1 CATA CATA CATA
299163 TATTTCTTAG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 52 1.00
ACGTcount: A:0.45, C:0.27, G:0.05, T:0.23
Consensus pattern (4 bp):
CATA
Found at i:301521 original size:209 final size:210
Alignment explanation
Indices: 301141--301559 Score: 759
Period size: 209 Copynumber: 2.0 Consensus size: 210
301131 TATATTATGC
* * *
301141 CAGTTTTTATTTTCGGGTTTCTCGAAGCATTTAGTACCTTTGTTGTAGTAGTTCTAGCGGGTATC
1 CAGTGTTTATTTTCGGGTTCCTCGAAGCATTTAGTACCTTTGTTGTAGTAGTTCTAGCAGGTATC
* *
301206 GTGTTCGAGTAAGCGCTCGGACTATTGCTTCTCTGTCCGATTTTAGGCATAATGGGGTAAGAATC
66 GTGTTCGAGTAAGCGCTCGGACTATTGCTTCTCGGTCCGATTTTAGGCATAATAGGGTAAGAATC
301271 CATACTCCGAGTTCGAGTGTGTCCGGGTAATCTTTCCTGCATTTATCGAACGATTTTGTAATAGA
131 CATACTCCGAGTTCGAGTGTGTCCGGGTAATCTTTCCTGCATTTATCGAACGATTTTGTAATAGA
301336 TGTATACCACTACTT
196 TGTATACCACTACTT
301351 CAGTGTTTATTTT-GGGTTCCTCGAAGCATTTAGTACCTTTGTTGTAGTAGTTCTAGCAGGTATC
1 CAGTGTTTATTTTCGGGTTCCTCGAAGCATTTAGTACCTTTGTTGTAGTAGTTCTAGCAGGTATC
*
301415 TTGTTCGAGTAAGCGCTCGGACTATTGCTTCTCGGTCCGATTTTAGGCATAATAGGGTAAGAATC
66 GTGTTCGAGTAAGCGCTCGGACTATTGCTTCTCGGTCCGATTTTAGGCATAATAGGGTAAGAATC
*
301480 CATACTCTGAGTTCGAGTGTGTCCGGGTAATCTTTCCTGCATTTATCGAACGATTTTGTAATAGA
131 CATACTCCGAGTTCGAGTGTGTCCGGGTAATCTTTCCTGCATTTATCGAACGATTTTGTAATAGA
*
301545 TGTATACTACTACTT
196 TGTATACCACTACTT
301560 GTATGAGATG
Statistics
Matches: 201, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
209 189 0.94
210 12 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (210 bp):
CAGTGTTTATTTTCGGGTTCCTCGAAGCATTTAGTACCTTTGTTGTAGTAGTTCTAGCAGGTATC
GTGTTCGAGTAAGCGCTCGGACTATTGCTTCTCGGTCCGATTTTAGGCATAATAGGGTAAGAATC
CATACTCCGAGTTCGAGTGTGTCCGGGTAATCTTTCCTGCATTTATCGAACGATTTTGTAATAGA
TGTATACCACTACTT
Found at i:302425 original size:14 final size:15
Alignment explanation
Indices: 302406--302436 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
302396 TTAACACTAA
302406 TAAATTTATTTT-GT
1 TAAATTTATTTTAGT
302420 TAAATTTATTTTAGT
1 TAAATTTATTTTAGT
302435 TA
1 TA
302437 CATTATTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (15 bp):
TAAATTTATTTTAGT
Found at i:305360 original size:26 final size:26
Alignment explanation
Indices: 305330--305381 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
305320 AAAGAAACTG
305330 TATAAAAGAATATCTAGAGAAATCAA
1 TATAAAAGAATATCTAGAGAAATCAA
305356 TATAAAAGAATATCTAGAGAAATCAA
1 TATAAAAGAATATCTAGAGAAATCAA
305382 GGAAACATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.58, C:0.08, G:0.12, T:0.23
Consensus pattern (26 bp):
TATAAAAGAATATCTAGAGAAATCAA
Found at i:307624 original size:48 final size:48
Alignment explanation
Indices: 307570--307668 Score: 171
Period size: 48 Copynumber: 2.1 Consensus size: 48
307560 GAGGTCACAT
* * *
307570 TAAAATTTGAGTTAACCATGGTGATATTTCTAATTCGATTAGTTCAAC
1 TAAAATTTGAGTTAACCATGGTGACATTTCTAATCCAATTAGTTCAAC
307618 TAAAATTTGAGTTAACCATGGTGACATTTCTAATCCAATTAGTTCAAC
1 TAAAATTTGAGTTAACCATGGTGACATTTCTAATCCAATTAGTTCAAC
307666 TAA
1 TAA
307669 TCTTGCCGGT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.37
Consensus pattern (48 bp):
TAAAATTTGAGTTAACCATGGTGACATTTCTAATCCAATTAGTTCAAC
Found at i:308738 original size:31 final size:31
Alignment explanation
Indices: 308703--308782 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 31
308693 AATAACCAAG
308703 TACTAATTTGGACCAAAAAGCCAAATTCAGC
1 TACTAATTTGGACCAAAAAGCCAAATTCAGC
* * * * *
308734 TACTAATTTGAACCAAGAAGCCAAGTTTAGG
1 TACTAATTTGGACCAAAAAGCCAAATTCAGC
308765 TATCTAA-TTGGACCAAAA
1 TA-CTAATTTGGACCAAAA
308783 TAAACATTAG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 37 0.90
32 4 0.10
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (31 bp):
TACTAATTTGGACCAAAAAGCCAAATTCAGC
Found at i:315210 original size:28 final size:29
Alignment explanation
Indices: 315161--315230 Score: 88
Period size: 28 Copynumber: 2.4 Consensus size: 29
315151 AATATATAAT
* *
315161 AAATATTTATTTTTTATTTTTTTAATTTTA
1 AAATAATT-TTTTTTATATTTTTAATTTTA
* *
315191 AAATACTTTTTTTTA-ATTTTTATTTTTA
1 AAATAATTTTTTTTATATTTTTAATTTTA
315219 AAATAATTTTTT
1 AAATAATTTTTT
315231 GGTGTTTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
28 22 0.61
29 7 0.19
30 7 0.19
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.67
Consensus pattern (29 bp):
AAATAATTTTTTTTATATTTTTAATTTTA
Found at i:321574 original size:16 final size:17
Alignment explanation
Indices: 321544--321579 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
321534 TAATTTTTAT
*
321544 AATTAAAAACTAATAAA
1 AATTAAAAACAAATAAA
321561 AATT-AAAACAAATAAA
1 AATTAAAAACAAATAAA
321577 AAT
1 AAT
321580 AGAGTAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (17 bp):
AATTAAAAACAAATAAA
Found at i:330921 original size:34 final size:35
Alignment explanation
Indices: 330862--330928 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
330852 CAAACACCAG
*
330862 AAAATATTTTCCAGTAAACCATTTTACAGAAAAGT
1 AAAAAATTTTCCAGTAAACCATTTTACAGAAAAGT
* * *
330897 AAAAAATTTTCCTG-AAATCATTTTACGGAAAA
1 AAAAAATTTTCCAGTAAACCATTTTACAGAAAA
330929 TATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAAAATTTTCCAGTAAACCATTTTACAGAAAAGT
Found at i:341598 original size:26 final size:27
Alignment explanation
Indices: 341545--341598 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
341535 ATAATAAATA
**
341545 TATTTTTTAATTTTAAAATACTTGTTT
1 TATTTTTTAATTTTAAAATAAATGTTT
*
341572 TATTTTTTATTTTTAAAATAAAT-TTT
1 TATTTTTTAATTTTAAAATAAATGTTT
341598 T
1 T
341599 GGTGTTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (27 bp):
TATTTTTTAATTTTAAAATAAATGTTT
Found at i:344923 original size:60 final size:61
Alignment explanation
Indices: 344838--344951 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 61
344828 AAATGCATCC
* * * * *
344838 GATATTATAATCATTTAAGTTTATTTTTACCTA-TTAATATTTAGGTATCATTTATACTTA
1 GATATTACAATCATTAAAATTTATTTTTACCGATTTAATATTTAGATATCATTTATACTTA
* *
344898 GATATTACAATTATTAAAATTTATTTTTACCGATTTAATATTTAGATATTATTT
1 GATATTACAATCATTAAAATTTATTTTTACCGATTTAATATTTAGATATCATTT
344952 TGTATTAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
60 28 0.61
61 18 0.39
ACGTcount: A:0.35, C:0.07, G:0.06, T:0.52
Consensus pattern (61 bp):
GATATTACAATCATTAAAATTTATTTTTACCGATTTAATATTTAGATATCATTTATACTTA
Found at i:345129 original size:4 final size:4
Alignment explanation
Indices: 345120--345162 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
345110 GTCTTGGCTT
345120 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
345163 AAATTAGTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:346287 original size:24 final size:25
Alignment explanation
Indices: 346246--346294 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
346236 TTATGATTAA
* *
346246 TATTTTTTTTTATAATGGGTTGAAT
1 TATTTTTTGTTATAATGGGTAGAAT
346271 TATTTTTTGTTAT-ATGGGTAGAAT
1 TATTTTTTGTTATAATGGGTAGAAT
346295 ATAATGATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.57
Consensus pattern (25 bp):
TATTTTTTGTTATAATGGGTAGAAT
Found at i:348052 original size:7 final size:8
Alignment explanation
Indices: 348038--348067 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
348028 AATATAATAA
348038 ATTTTTTT
1 ATTTTTTT
348046 ATTTTTTT
1 ATTTTTTT
348054 ATTTTTTT
1 ATTTTTTT
348062 AATTTT
1 -ATTTT
348068 AAAATACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 16 0.76
9 5 0.24
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (8 bp):
ATTTTTTT
Found at i:349645 original size:135 final size:136
Alignment explanation
Indices: 349456--349728 Score: 521
Period size: 135 Copynumber: 2.0 Consensus size: 136
349446 AATTTTTTCT
*
349456 TTTATATTCTTTTTTTTATTTTCTCATTAATTTCTCATTCTCCCTCTATTTTTTCCCTTATTCTT
1 TTTATATTCTTTTTTTTATTTTCTCATTAACTTCTCATTCTCCCTCTATTTTTTCCCTTATTCTT
349521 TTCTTTTAACGTAGTTTTTCTATATTTTTCATTTGTTAAAATTAGTCCACAAGCTTGCCTCACTC
66 TTCTTTTAACGTAGTTTTTCTATATTTTTCATTTGTTAAAATTAGTCCACAAGCTTGCCTCACTC
349586 GAAAAA
131 GAAAAA
*
349592 TTTATATTC-TTTTTTTATTTTTTCATTAACTTCTCATTCTCCCTCTATTTTTTCCCTTATTCTT
1 TTTATATTCTTTTTTTTATTTTCTCATTAACTTCTCATTCTCCCTCTATTTTTTCCCTTATTCTT
349656 TTCTTTTAACGTAGTTTTTCTATATTTTTCATTTGTTAAAATTAGTCCACAAGCTTGCCTCACTC
66 TTCTTTTAACGTAGTTTTTCTATATTTTTCATTTGTTAAAATTAGTCCACAAGCTTGCCTCACTC
349721 GAAAAA
131 GAAAAA
349727 TT
1 TT
349729 AAATTGTTCG
Statistics
Matches: 135, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
135 126 0.93
136 9 0.07
ACGTcount: A:0.21, C:0.20, G:0.05, T:0.54
Consensus pattern (136 bp):
TTTATATTCTTTTTTTTATTTTCTCATTAACTTCTCATTCTCCCTCTATTTTTTCCCTTATTCTT
TTCTTTTAACGTAGTTTTTCTATATTTTTCATTTGTTAAAATTAGTCCACAAGCTTGCCTCACTC
GAAAAA
Found at i:350353 original size:30 final size:31
Alignment explanation
Indices: 350317--350383 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
350307 ATTTTTCGAT
*
350317 AATTTT-ATTTCAC-CCTTAAATAATTTTAAA
1 AATTTTAATTTCACTCCTCAAA-AATTTTAAA
* *
350347 AATTTTAATTTGACTCCTCAAAAATTTTGAA
1 AATTTTAATTTCACTCCTCAAAAATTTTAAA
350378 AATTTT
1 AATTTT
350384 TATTAATTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 6 0.19
31 20 0.62
32 6 0.19
ACGTcount: A:0.39, C:0.12, G:0.03, T:0.46
Consensus pattern (31 bp):
AATTTTAATTTCACTCCTCAAAAATTTTAAA
Found at i:350449 original size:30 final size:29
Alignment explanation
Indices: 350330--350441 Score: 98
Period size: 31 Copynumber: 3.7 Consensus size: 29
350320 TTTATTTCAC
* *
350330 CCTTAAATAATTTTAAAAATTTTAATTTGACT
1 CCTTAAAT-ATTTTGAAAATTTTAA-TT-AAT
* * *
350362 CCTCAAAAATTTTGAAAATTTTTATTAAT
1 CCTTAAATATTTTGAAAATTTTAATTAAT
* * *
350391 TCTTAAATTTTTTAAAAATATTTAATTAAT
1 CCTTAAATATTTTGAAAAT-TTTAATTAAT
*
350421 CCTATCAATATTTTGAAAATT
1 CCT-TAAATATTTTGAAAATT
350442 CTCATTAAAT
Statistics
Matches: 63, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
29 16 0.25
30 14 0.22
31 27 0.43
32 6 0.10
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (29 bp):
CCTTAAATATTTTGAAAATTTTAATTAAT
Found at i:351846 original size:280 final size:281
Alignment explanation
Indices: 351333--351894 Score: 1117
Period size: 280 Copynumber: 2.0 Consensus size: 281
351323 AATCGTTTAT
351333 TTGAAATTGAATTGTAATTAAAAAATAATTTTTAAGATATTTTTTATATAATAAATTTTAAATTC
1 TTGAAATTGAATTGTAATTAAAAAATAATTTTTAAGATATTTTTTATATAATAAATTTTAAATTC
351398 AATAAAAAATTAGATTTATACACTTCTTTTTAATAATATAAGGACTAAATTAATTCATTTAATAG
66 AATAAAAAATTAGATTTATACACTTCTTTTTAATAATATAAGGACTAAATTAATTCATTTAATAG
351463 TACAATAATTAATTTTATCAAATCCCTATAATAAAAGTACGCGTGAAATACATTCACCTCCGTAA
131 TACAATAATTAATTTTATCAAATCCCTATAATAAAAGTACGCGTGAAATACATTCACCTCCGTAA
351528 AAATAGCTATGAGCACCTCAACCTCTGGCCATGGTTGTCCAACTCCAATGAGTTGTCATCTTCAT
196 AAATAGCTATGAGCACCTCAACCTCTGGCCATGGTTGTCCAACTCCAATGAGTTGTCATCTTCAT
351593 AATCTAAAACAATAAGTGGCC
261 AATCTAAAACAATAAGTGGCC
351614 TTGAAATTGAA-TGTAATTAAAAAATAATTTTTAAGATATTTTTTATATAATAAATTTTAAATTC
1 TTGAAATTGAATTGTAATTAAAAAATAATTTTTAAGATATTTTTTATATAATAAATTTTAAATTC
351678 AATAAAAAATTAGATTTATACACTTCTTTTTAATAATATAAGGACTAAATTAATTCATTTAATAG
66 AATAAAAAATTAGATTTATACACTTCTTTTTAATAATATAAGGACTAAATTAATTCATTTAATAG
351743 TACAATAATTAATTTTATCAAATCCCTATAATAAAAGTACGCGTGAAATACATTCACCTCCGTAA
131 TACAATAATTAATTTTATCAAATCCCTATAATAAAAGTACGCGTGAAATACATTCACCTCCGTAA
351808 AAATAGCTATGAGCACCTCAACCTCTGGCCATGGTTGTCCAACTCCAATGAGTTGTCATCTTCAT
196 AAATAGCTATGAGCACCTCAACCTCTGGCCATGGTTGTCCAACTCCAATGAGTTGTCATCTTCAT
351873 AATCTAAAACAATAAGTGGCC
261 AATCTAAAACAATAAGTGGCC
351894 T
1 T
351895 AAATTATTGT
Statistics
Matches: 281, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
280 270 0.96
281 11 0.04
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.36
Consensus pattern (281 bp):
TTGAAATTGAATTGTAATTAAAAAATAATTTTTAAGATATTTTTTATATAATAAATTTTAAATTC
AATAAAAAATTAGATTTATACACTTCTTTTTAATAATATAAGGACTAAATTAATTCATTTAATAG
TACAATAATTAATTTTATCAAATCCCTATAATAAAAGTACGCGTGAAATACATTCACCTCCGTAA
AAATAGCTATGAGCACCTCAACCTCTGGCCATGGTTGTCCAACTCCAATGAGTTGTCATCTTCAT
AATCTAAAACAATAAGTGGCC
Found at i:352500 original size:19 final size:20
Alignment explanation
Indices: 352464--352502 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
352454 AGTAAATAAA
**
352464 AAAATATTTTAAGTATATTT
1 AAAATATTTTAAAAATATTT
352484 AAAAT-TTTTAAAAATATTT
1 AAAATATTTTAAAAATATTT
352503 TTATTACTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
AAAATATTTTAAAAATATTT
Done.