Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold123
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: 1515550
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 66928 characters in sequence are not A, C, G, or T
File 1 of 5
Found at i:3918 original size:14 final size:15
Alignment explanation
Indices: 3901--3933 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
3891 TATGGTTTAT
3901 GGTTTAAGG-GTTGG
1 GGTTTAAGGTGTTGG
*
3915 GGTTTAAGGTTTTGG
1 GGTTTAAGGTGTTGG
3930 GGTT
1 GGTT
3934 ATGGGTACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.12, C:0.00, G:0.45, T:0.42
Consensus pattern (15 bp):
GGTTTAAGGTGTTGG
Found at i:3933 original size:21 final size:21
Alignment explanation
Indices: 3876--3926 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
3866 AGTTACTATC
* * **
3876 TTAAGGTTTATGGATTATGGT
1 TTAAGGTTTAAGGGTTGGGGT
*
3897 TTATGGTTTAAGGGTTGGGGT
1 TTAAGGTTTAAGGGTTGGGGT
3918 TTAAGGTTT
1 TTAAGGTTT
3927 TGGGGTTATG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (21 bp):
TTAAGGTTTAAGGGTTGGGGT
Found at i:4151 original size:14 final size:15
Alignment explanation
Indices: 4073--4169 Score: 65
Period size: 14 Copynumber: 6.5 Consensus size: 15
4063 TTAAGATTTT
4073 GGGGTTAGGGGTACTTA
1 GGGGTTAGGGGT--TTA
*
4090 AGGGTTAGGGGTTTA
1 GGGGTTAGGGGTTTA
* **
4105 TGATTTA-GGGTTTA
1 GGGGTTAGGGGTTTA
* * * *
4119 AGGGATAAGGG-ATA
1 GGGGTTAGGGGTTTA
*
4133 AGGGTTAGGGG-TTA
1 GGGGTTAGGGGTTTA
4147 GGGGTTAGGGGTTTA
1 GGGGTTAGGGGTTTA
*
4162 GGGTTTAG
1 GGGGTTAG
4170 ATTAATTAGT
Statistics
Matches: 64, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
14 33 0.52
15 20 0.31
17 11 0.17
ACGTcount: A:0.22, C:0.01, G:0.45, T:0.32
Consensus pattern (15 bp):
GGGGTTAGGGGTTTA
Found at i:4573 original size:21 final size:21
Alignment explanation
Indices: 4549--4591 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4539 AGGTTTAGGG
* *
4549 GTTAGTGGTTTGGGGTTAAGA
1 GTTAGTGATTTAGGGTTAAGA
*
4570 GTTAGTGATTTAGGGTTTAGA
1 GTTAGTGATTTAGGGTTAAGA
4591 G
1 G
4592 ATTCAGGGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.40, T:0.40
Consensus pattern (21 bp):
GTTAGTGATTTAGGGTTAAGA
Found at i:9278 original size:7 final size:7
Alignment explanation
Indices: 9266--9316 Score: 75
Period size: 7 Copynumber: 7.1 Consensus size: 7
9256 ATTGTAAAAG
9266 AGGGGTT
1 AGGGGTT
9273 AGGGGTT
1 AGGGGTT
*
9280 AGGAGTT
1 AGGGGTT
*
9287 AGAGGTT
1 AGGGGTT
9294 AGGGGTT
1 AGGGGTT
9301 AGGGGTTT
1 AGGGG-TT
9309 AGGGGTT
1 AGGGGTT
9316 A
1 A
9317 TGTTTTATGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
7 32 0.82
8 7 0.18
ACGTcount: A:0.20, C:0.00, G:0.51, T:0.29
Consensus pattern (7 bp):
AGGGGTT
Found at i:9293 original size:14 final size:14
Alignment explanation
Indices: 9270--9367 Score: 61
Period size: 14 Copynumber: 6.9 Consensus size: 14
9260 TAAAAGAGGG
9270 GTTAGGGGTTAGGA
1 GTTAGGGGTTAGGA
* *
9284 GTTAGAGGTTAGGG
1 GTTAGGGGTTAGGA
*
9298 GTTAGGGGTTTAGGG
1 GTTAGGGG-TTAGGA
* ** *
9313 GTTATGTTTTATGA
1 GTTAGGGGTTAGGA
* * *
9327 TTTAAGGTTTAGGA
1 GTTAGGGGTTAGGA
* *
9341 GATAGGGGTTAGGG
1 GTTAGGGGTTAGGA
*
9355 GTTTAGGGTTTAG
1 G-TTAGGGGTTAG
9368 ATTAACATTA
Statistics
Matches: 63, Mismatches: 19, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
14 43 0.68
15 20 0.32
ACGTcount: A:0.20, C:0.00, G:0.43, T:0.37
Consensus pattern (14 bp):
GTTAGGGGTTAGGA
Found at i:10482 original size:16 final size:15
Alignment explanation
Indices: 10450--10479 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10440 GCTTTTGTTT
10450 TTTTATTCTTTTAAA
1 TTTTATTCTTTTAAA
*
10465 TTTTATTGTTTTAAA
1 TTTTATTCTTTTAAA
10480 ATTGCAGGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTTATTCTTTTAAA
Found at i:10652 original size:86 final size:85
Alignment explanation
Indices: 10505--10837 Score: 389
Period size: 86 Copynumber: 3.9 Consensus size: 85
10495 TCCTTCTACT
* * * * ** *
10505 TTATAAAAGTTGAAAATTTGGTCTGGTTGTTGGTGAATGCATGAGCTTGAACTGTTGATTTTTTC
1 TTATAAAAATTGAAAATTTAGTCT-GTTGTTGGTAAATGCATGAACTTGAACCATTGATTTTTGC
*
10570 TAATTTGTTGCACATAAGTTG
65 TAATTTGTTGCATATAAGTTG
*
10591 TTATAAAAATTGAAAATTTAGTCTAGTTGTTGGTAAATGCATGAACTTGAACCATTTATTTTTGC
1 TTATAAAAATTGAAAATTTAGTCT-GTTGTTGGTAAATGCATGAACTTGAACCATTGATTTTTGC
10656 TAATTTGTTGCATATAAGTTG
65 TAATTTGTTGCATATAAGTTG
* * * *
10677 TTATAAATATTGAAAAATTAGTCTGATTTTTGGTAAATACATGAACTTGAACCATTGATTTTTGC
1 TTATAAAAATTGAAAATTTAGTCTG-TTGTTGGTAAATGCATGAACTTGAACCATTGATTTTTGC
* *
10742 TAATTTGTTGCATATAAATCG
65 TAATTTGTTGCATATAAGTTG
* * * ** ** * *
10763 TTATAGAAATTGAAGATTTAGTCCTATTGCGGGTAAATATATGAACTATGAA-TAGTTGATTTGT
1 TTATAAAAATTGAAAATTTAGT-CTGTTGTTGGTAAATGCATGAACT-TGAACCA-TTGATTTTT
10827 GCTAATTTGTT
63 GCTAATTTGTT
10838 TCACATAAAC
Statistics
Matches: 215, Mismatches: 28, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
85 1 0.00
86 189 0.88
87 25 0.12
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.42
Consensus pattern (85 bp):
TTATAAAAATTGAAAATTTAGTCTGTTGTTGGTAAATGCATGAACTTGAACCATTGATTTTTGCT
AATTTGTTGCATATAAGTTG
Found at i:10902 original size:40 final size:38
Alignment explanation
Indices: 10811--10934 Score: 122
Period size: 40 Copynumber: 3.1 Consensus size: 38
10801 ATATGAACTA
* * * * *
10811 TGAATAGTTGATTTGTGCTAATTTGTTTCACATAAACTAT
1 TGAA-AGTTGATTTTTGATAATTTCTTACATATAAA-TAT
* *
10851 TGTAAGATTGATTTTTGATAATTTCTTGCATATAAATTAT
1 TGAAAG-TTGATTTTTGATAATTTCTTACATATAAA-TAT
*
10891 TGAAATGTTGATTTTTGATAATTCCTTACATATTAAATAT
1 TGAAA-GTTGATTTTTGATAATTTCTTACATA-TAAATAT
10931 TGAA
1 TGAA
10935 GTTTTGATAT
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
39 2 0.03
40 64 0.90
41 5 0.07
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (38 bp):
TGAAAGTTGATTTTTGATAATTTCTTACATATAAATAT
Found at i:12327 original size:15 final size:15
Alignment explanation
Indices: 12307--12338 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
12297 TCTTTGTATC
12307 ATATCAAATTTATGG
1 ATATCAAATTTATGG
12322 ATATCAAATTTATGG
1 ATATCAAATTTATGG
12337 AT
1 AT
12339 TTAGTTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (15 bp):
ATATCAAATTTATGG
Found at i:14235 original size:43 final size:43
Alignment explanation
Indices: 14190--14458 Score: 260
Period size: 43 Copynumber: 6.3 Consensus size: 43
14180 ACAGTACTTT
* *
14190 TAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGATCATGTTCTT
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTCTA
* * * *
14233 TAGCGGTGTTTG-GTGGTAAAGCGTCGCTAAAGGTCATGTTCTA
1 TAGCGGCGTTTGTG-GGAAAAGCGCCGCTAAAGATCATGTTCTA
* ** **
14276 CAGTAGAATTTGTGGGAAAAGCGCCGCTAAA-AGTCATGTTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGA-TCATGTTCTA
* * * *
14319 TAACGGCGTTTGTGGGAAAAGCGTCGCTAAA-AGTCGTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGA-TCATGTTCTA
* * *
14362 TAGAGGCGTTTGTGGGAAAAGCGCCACTAAA-AGTCATGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGA-TCATGTTCTA
* * * *
14405 TAGTGGCATTTGTGGGAAAAGCACCGCTATAAG-TCATGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTA-AAGATCATGTTCTA
14448 TAGCGGCGTTT
1 TAGCGGCGTTT
14459 ATTTTTAAAA
Statistics
Matches: 189, Mismatches: 32, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
42 1 0.01
43 185 0.98
44 3 0.02
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTCTA
Found at i:14399 original size:129 final size:129
Alignment explanation
Indices: 14193--14458 Score: 329
Period size: 129 Copynumber: 2.1 Consensus size: 129
14183 GTACTTTTAG
* * * * * * *
14193 CGGCGTTTGTGGGTAAAGCGCCGCTAAAGATCATGTTCTTTAGCGGTGTTTGGTGGTAAAGCGTC
1 CGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGATCTATAGAGGCGTTTGGTGGAAAAGCGCC
* * * * *
14258 GCTAAAGGTCATGTTCTACAGTAGAATTTGTGGGAAAAGCGCCGCTAAAAGTCATGTTCTATAA
66 ACTAAAAGTCATGATCTACAGTAGAATTTGTGGGAAAAGCACCGCTAAAAGTCATGATCTATAA
* *
14322 CGGCGTTTGTGGGAAAAGCGTCGCTAAA-AGTCGTGATCTATAGAGGCGTTT-GTGGGAAAAGCG
1 CGGCGTTTGTGGGAAAAGCGCCGCTAAAGA-TCATGATCTATAGAGGCGTTTGGT-GGAAAAGCG
* * * *
14385 CCACTAAAAGTCATGATCTATAGTGGCATTTGTGGGAAAAGCACCGCTATAAGTCATGATCTATA
64 CCACTAAAAGTCATGATCTACAGTAGAATTTGTGGGAAAAGCACCGCTAAAAGTCATGATCTATA
*
14450 G
129 A
14451 CGGCGTTT
1 CGGCGTTT
14459 ATTTTTAAAA
Statistics
Matches: 116, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
128 3 0.03
129 113 0.97
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.28
Consensus pattern (129 bp):
CGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGATCTATAGAGGCGTTTGGTGGAAAAGCGCC
ACTAAAAGTCATGATCTACAGTAGAATTTGTGGGAAAAGCACCGCTAAAAGTCATGATCTATAA
Found at i:19643 original size:26 final size:26
Alignment explanation
Indices: 19614--19672 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
19604 CCTCAATAGT
** *
19614 ATTTTGATGATTTTA-CCCTTGATAAA
1 ATTTTGACAATTTTACCCCTAG-TAAA
*
19640 ATTTTGACAATTTTGCCCCTAGTAAA
1 ATTTTGACAATTTTACCCCTAGTAAA
19666 ATTTTGA
1 ATTTTGA
19673 AAAAATATGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 23 0.82
27 5 0.18
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.44
Consensus pattern (26 bp):
ATTTTGACAATTTTACCCCTAGTAAA
Found at i:21640 original size:26 final size:26
Alignment explanation
Indices: 21611--21672 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
21601 TAATACTTGA
21611 AATAGTCCTTACAGACTCATACATGG
1 AATAGTCCTTACAGACTCATACATGG
*
21637 AATAGTCCTTACGGACTCATACATGG
1 AATAGTCCTTACAGACTCATACATGG
21663 AATAGTCCTT
1 AATAGTCCTT
21673 GTGGAGTCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (26 bp):
AATAGTCCTTACAGACTCATACATGG
Found at i:24248 original size:20 final size:20
Alignment explanation
Indices: 24223--24262 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
24213 ACATCAATGC
24223 CCCTTTGGTAATTAGATATG
1 CCCTTTGGTAATTAGATATG
24243 CCCTTTGGTAATTAGATATG
1 CCCTTTGGTAATTAGATATG
24263 GTACTTCAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (20 bp):
CCCTTTGGTAATTAGATATG
Found at i:28754 original size:24 final size:24
Alignment explanation
Indices: 28722--28768 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
28712 TTATAAATAA
28722 CATTCAACAAAGGGAGGTAATTAG
1 CATTCAACAAAGGGAGGTAATTAG
*
28746 CATTCAACAAAGGGAGGTTATTA
1 CATTCAACAAAGGGAGGTAATTA
28769 CTTATTAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.23
Consensus pattern (24 bp):
CATTCAACAAAGGGAGGTAATTAG
Found at i:29049 original size:19 final size:19
Alignment explanation
Indices: 29025--29078 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
29015 AATCTTCAAG
*
29025 GATATGCAATCTTAGTTAT
1 GATATGCAATCTTAGATAT
29044 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29063 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
29079 AGATATGACT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:29104 original size:22 final size:22
Alignment explanation
Indices: 29025--29101 Score: 76
Period size: 19 Copynumber: 3.7 Consensus size: 22
29015 AATCTTCAAG
*
29025 GATATGCAATCTT---AGTTAT
1 GATATGCAATCTTAGAAGATAT
29044 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
29063 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
29085 GACTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
29102 GATTTTATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 31 0.61
22 8 0.16
23 12 0.24
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:29114 original size:21 final size:23
Alignment explanation
Indices: 29057--29101 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
29047 ATGCAATCTT
* *
29057 AGATATGA-TATGCAATCTTAGA
1 AGATATGACTTTGTAATCTTAGA
29079 AGATATGACTTTGTAATCTTAGA
1 AGATATGACTTTGTAATCTTAGA
29102 GATTTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.36
Consensus pattern (23 bp):
AGATATGACTTTGTAATCTTAGA
Found at i:30483 original size:153 final size:154
Alignment explanation
Indices: 30205--30512 Score: 609
Period size: 153 Copynumber: 2.0 Consensus size: 154
30195 CATTGGGTGT
30205 GACATTTTCTCTCTCCGAAATGAGAGTCTTAATGGGTAACTTGTTTTATATAAGTTTTTACAAAG
1 GACATTTTCTCTCTCCGAAATGAGAGTCTTAATGGGTAACTTGTTTTATATAAGTTTTTACAAAG
30270 GATCGTATTTTAAATCTCTTTAAAATTTTCGATTCTCGATATTAAGACACTAATTAATCAACTAG
66 GATCGTATTTTAAATCTCTTTAAAATTTTCGATTCTCGATATTAAGACACTAATTAATCAACTAG
30335 GTACCAATTTTT-GGCATTACGAG
131 GTACCAATTTTTGGGCATTACGAG
30358 GACATTTTCTCTCTCCGAAATGAGAGTCTTAATGGGTAACTTGTTTTATATAAGTTTTTACAAAG
1 GACATTTTCTCTCTCCGAAATGAGAGTCTTAATGGGTAACTTGTTTTATATAAGTTTTTACAAAG
30423 GATCGTATTTTAAATCTCTTTAAAATTTTCGATTCTCGATATTAAGACACTAATTAATCAACTAG
66 GATCGTATTTTAAATCTCTTTAAAATTTTCGATTCTCGATATTAAGACACTAATTAATCAACTAG
30488 GTACCAATTTTTGGGCATTACGAG
131 GTACCAATTTTTGGGCATTACGAG
30512 G
1 G
30513 GTGCTAATCC
Statistics
Matches: 154, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
153 142 0.92
154 12 0.08
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (154 bp):
GACATTTTCTCTCTCCGAAATGAGAGTCTTAATGGGTAACTTGTTTTATATAAGTTTTTACAAAG
GATCGTATTTTAAATCTCTTTAAAATTTTCGATTCTCGATATTAAGACACTAATTAATCAACTAG
GTACCAATTTTTGGGCATTACGAG
Found at i:31694 original size:17 final size:17
Alignment explanation
Indices: 31658--31693 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
31648 CAACCTTTAA
31658 TTTCCATTAAATAATTT
1 TTTCCATTAAATAATTT
*
31675 TTTCCTTTAAAT-ATTT
1 TTTCCATTAAATAATTT
31691 TTT
1 TTT
31694 TTTAAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTCCATTAAATAATTT
Found at i:32424 original size:29 final size:30
Alignment explanation
Indices: 32380--32443 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
32370 ATTTCAGGTC
*
32380 ATTTTCGTATATAATT-TTTCCCTTGGGTT
1 ATTTTCGTATATAATTAATTCCCTTGGGTT
**
32409 ATTTTCGTA-ATCAATTAATTCTTTTGGGTT
1 ATTTTCGTATAT-AATTAATTCCCTTGGGTT
32439 ATTTT
1 ATTTT
32444 TGAAAAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 2 0.07
29 13 0.43
30 15 0.50
ACGTcount: A:0.20, C:0.11, G:0.12, T:0.56
Consensus pattern (30 bp):
ATTTTCGTATATAATTAATTCCCTTGGGTT
Found at i:33808 original size:21 final size:21
Alignment explanation
Indices: 33784--33824 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
33774 TACATATAAA
33784 TTATAACTTATAATTATTTTG
1 TTATAACTTATAATTATTTTG
* *
33805 TTATAATTTTTAATTATTTT
1 TTATAACTTATAATTATTTT
33825 CTAAAGTCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (21 bp):
TTATAACTTATAATTATTTTG
Found at i:34759 original size:50 final size:50
Alignment explanation
Indices: 34691--34930 Score: 264
Period size: 50 Copynumber: 4.7 Consensus size: 50
34681 TTTTCTGTAC
* * * **
34691 TGCCAATGCCATATCCCAGATATGGTCTTACATGCGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
* * *** * *
34741 TGCCCATGCCATGTCCCAGACATGGTTTTATGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
* ** * *
34791 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTTGTCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
*
34841 TGCCAATGCCATGTCCCAAACATGGTCTTACATGAGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCAT-A--TC--GG
34896 ATGCCAATGCCATGTCCCAGACATGGTCTTACATG
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATG
34931 GGATCTCTTT
Statistics
Matches: 156, Mismatches: 28, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
50 120 0.77
53 2 0.01
55 1 0.01
56 33 0.21
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
Found at i:34903 original size:56 final size:50
Alignment explanation
Indices: 34652--34939 Score: 247
Period size: 50 Copynumber: 5.7 Consensus size: 50
34642 TGTCAAAGCT
* * * * * *
34652 ATGTCCCAGACATAGTCTTACATGGGA--TGTTTTCTGTACTGCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGAGACCTCTTGTCT-CAGTGCCAATGCC
* * * ** ** * * *
34701 ATATCCCAGATATGGTCTTACATGCGAGTTCTCATATCGGTGCCCATGCC
1 ATGTCCCAGACATGGTCTTACATGAGACCTCTTGTCTCAGTGCCAATGCC
* *** * ** * *
34751 ATGTCCCAGACATGGTTTTATGGGGGACCTCTCATCTCGGTGCCAACGCC
1 ATGTCCCAGACATGGTCTTACATGAGACCTCTTGTCTCAGTGCCAATGCC
34801 ATGTCCCAGACATGGTCTTACATGAGACCTCTTGTCTCAGTGCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGAGACCTCTTGTCTCAGTGCCAATGCC
*
34851 ATGTCCCAAACATGGTCTTACATGAGACCTCTCATGATCTCAAGGATGCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGAGACCTCT--TG-TCTC-A-G-TGCCAATGCC
* *
34907 ATGTCCCAGACATGGTCTTACATGGGATCTCTT
1 ATGTCCCAGACATGGTCTTACATGAGACCTCTT
34940 TACCCAAATG
Statistics
Matches: 194, Mismatches: 37, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
49 23 0.12
50 119 0.61
51 4 0.02
52 2 0.01
53 4 0.02
54 2 0.01
55 1 0.01
56 39 0.20
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.29
Consensus pattern (50 bp):
ATGTCCCAGACATGGTCTTACATGAGACCTCTTGTCTCAGTGCCAATGCC
Found at i:42789 original size:21 final size:21
Alignment explanation
Indices: 42763--42803 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
42753 GACATATAAA
42763 TTATAACTCATAATTATTTTT
1 TTATAACTCATAATTATTTTT
* **
42784 TTATAATTTTTAATTATTTT
1 TTATAACTCATAATTATTTT
42804 CTAAAGTCAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (21 bp):
TTATAACTCATAATTATTTTT
Found at i:43268 original size:50 final size:50
Alignment explanation
Indices: 43205--43384 Score: 162
Period size: 50 Copynumber: 3.4 Consensus size: 50
43195 TCACATATCT
* ** * * *
43205 CAGATATGGTCTTACATGGGAGTTCTCATATCAGTGCCCATGCCATGTCT
1 CAGACATGGTCTTACATGGGACCTCTCATATCAGTGCCAACGCCATGTCC
* * * *
43255 TAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAACGCCATGTCC
1 CAGACATGGTCTTACATGGGACCTCTCATATCAGTGCCAACGCCATGTCC
* * *
43305 CAGACATGGTCTTACATGGGGCCTCTCATAATCTCAATAATGATGCCAATGTCATGTCC
1 CAGACATGGTCTTACATGGGACCTCTCAT-A--TC----A-G-TGCCAACGCCATGTCC
43364 CAGACATGGTCTTACATGGGA
1 CAGACATGGTCTTACATGGGA
43385 TCTCATTCCC
Statistics
Matches: 103, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
50 66 0.64
53 2 0.02
58 1 0.01
59 34 0.33
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (50 bp):
CAGACATGGTCTTACATGGGACCTCTCATATCAGTGCCAACGCCATGTCC
Found at i:45283 original size:28 final size:27
Alignment explanation
Indices: 45248--45337 Score: 64
Period size: 26 Copynumber: 3.4 Consensus size: 27
45238 CATATTTGTA
*
45248 ATATTAT-TAGTATTTATTTTTAAATT
1 ATATTATATTGTATTTATTTTTAAATT
* * *
45274 ATATTATATTTTAACTTATCTTT-AATT
1 ATATTATATTGT-ATTTATTTTTAAATT
*
45301 -TATTATATTG--TTAATTTTTTAAATTT
1 ATATTATATTGTATTTA-TTTTTAAA-TT
45327 ATAATTATATT
1 AT-ATTATATT
45338 AGTAATCTCA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
23 2 0.04
24 4 0.08
25 2 0.04
26 18 0.37
27 7 0.14
28 16 0.33
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (27 bp):
ATATTATATTGTATTTATTTTTAAATT
Found at i:46116 original size:20 final size:21
Alignment explanation
Indices: 46079--46117 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
46069 TCATGAAGTT
* *
46079 AAGAAAATAACTCTTAATTTA
1 AAGAAAATAACACATAATTTA
46100 AAGAAAATAA-ACATAATT
1 AAGAAAATAACACATAATT
46118 ATCTAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.28
Consensus pattern (21 bp):
AAGAAAATAACACATAATTTA
Found at i:46322 original size:29 final size:29
Alignment explanation
Indices: 46263--46329 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
46253 TTAAATTAAG
* * *
46263 ATTTATTTTTTTAATTTCACGTATGATTT
1 ATTTATTTTATTAATTTCACATATGAATT
*
46292 ATTTATTTTATTATTTTTCACATAT-AATT
1 ATTTATTTTATTA-ATTTCACATATGAATT
46321 ATCTTATTT
1 AT-TTATTT
46330 AGTTACTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 17 0.53
30 15 0.47
ACGTcount: A:0.27, C:0.07, G:0.03, T:0.63
Consensus pattern (29 bp):
ATTTATTTTATTAATTTCACATATGAATT
Found at i:49214 original size:78 final size:78
Alignment explanation
Indices: 49085--49243 Score: 309
Period size: 78 Copynumber: 2.0 Consensus size: 78
49075 TTAGCTGTCA
49085 CTTGCCATGCATGACTTTGCATGTTTCTTGTCCCTATTTGATTGTCTATATAATACGTGGATCTT
1 CTTGCCATGCATGACTTTGCATGTTTCTTGTCCCTATTTGATTGTCTATATAATACGTGGATCTT
49150 TTAATATTCAAAC
66 TTAATATTCAAAC
*
49163 CTTGCCATGCATGACTTTGCATGTTTCTTGTCCCTATTTTATTGTCTATATAATACGTGGATCTT
1 CTTGCCATGCATGACTTTGCATGTTTCTTGTCCCTATTTGATTGTCTATATAATACGTGGATCTT
49228 TTAATATTCAAAC
66 TTAATATTCAAAC
49241 CTT
1 CTT
49244 TGGAGTATTT
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (78 bp):
CTTGCCATGCATGACTTTGCATGTTTCTTGTCCCTATTTGATTGTCTATATAATACGTGGATCTT
TTAATATTCAAAC
Found at i:55814 original size:21 final size:20
Alignment explanation
Indices: 55775--55816 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
55765 ATTCTAAACT
**
55775 TTTATAAAAATGCATAAAAA
1 TTTATAAAAATAAATAAAAA
55795 TTTATAAAATATAAATAAAAA
1 TTTATAAAA-ATAAATAAAAA
55816 T
1 T
55817 AAAAATGGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
TTTATAAAAATAAATAAAAA
Found at i:66218 original size:26 final size:26
Alignment explanation
Indices: 66189--66246 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
66179 AATTTTCTAC
66189 CTGCAGGTTTTTGTCATTGATATTAG
1 CTGCAGGTTTTTGTCATTGATATTAG
*
66215 CTGCAGGTTTTTGTCATTGGTATTAG
1 CTGCAGGTTTTTGTCATTGATATTAG
66241 CTGCAG
1 CTGCAG
66247 TATTTAACGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.17, C:0.14, G:0.26, T:0.43
Consensus pattern (26 bp):
CTGCAGGTTTTTGTCATTGATATTAG
Found at i:66351 original size:12 final size:12
Alignment explanation
Indices: 66331--66360 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
66321 TTTCTTTTCC
*
66331 TTTGTTCGTTCT
1 TTTGCTCGTTCT
66343 TTTGCTCGTTCT
1 TTTGCTCGTTCT
66355 TTTGCT
1 TTTGCT
66361 TAAAATGCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.20, G:0.17, T:0.63
Consensus pattern (12 bp):
TTTGCTCGTTCT
Found at i:66529 original size:25 final size:25
Alignment explanation
Indices: 66498--66546 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
66488 AGTTGCATTT
*
66498 TCAAGAGGTGTTTTATAGTTGCAAA
1 TCAAGAGGTATTTTATAGTTGCAAA
66523 TCAAGAGGTATTTTATAGTTGCAA
1 TCAAGAGGTATTTTATAGTTGCAA
66547 TTCCAGTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (25 bp):
TCAAGAGGTATTTTATAGTTGCAAA
Found at i:66717 original size:18 final size:19
Alignment explanation
Indices: 66694--66734 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
66684 TATTGGGCTT
66694 TATAGGATAA-TTTATTGG
1 TATAGGATAATTTTATTGG
66712 TATAGGATAATTTTTATTGG
1 TATAGGATAA-TTTTATTGG
66732 TAT
1 TAT
66735 TTTTATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 10 0.48
20 11 0.52
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.49
Consensus pattern (19 bp):
TATAGGATAATTTTATTGG
Found at i:70930 original size:39 final size:41
Alignment explanation
Indices: 70885--70990 Score: 135
Period size: 44 Copynumber: 2.5 Consensus size: 41
70875 TTTCCTTATG
* *
70885 CTATTACACCTCTATTCCATTCAACCAAACACAAGAA-TAC
1 CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
70925 C-ATTACGCCTCTATTCCATTACATTCAACCAAACAAAAGAATTAC
1 CTATTACGCCTCTATT-C----CATTCAACCAAACAAAAGAATTAC
70970 CTATTACGCCTCTATTCCATT
1 CTATTACGCCTCTATTCCATT
70991 ACGCTTCTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
39 13 0.23
40 2 0.04
41 4 0.07
44 19 0.33
45 5 0.09
46 14 0.25
ACGTcount: A:0.36, C:0.31, G:0.04, T:0.29
Consensus pattern (41 bp):
CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
Found at i:70965 original size:44 final size:46
Alignment explanation
Indices: 70902--70992 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
70892 ACCTCTATTC
*
70902 CATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
70946 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
70992 C
1 C
70993 GCTTCTATTC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 19 0.43
45 4 0.09
46 21 0.48
ACGTcount: A:0.38, C:0.31, G:0.04, T:0.26
Consensus pattern (46 bp):
CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
Found at i:70993 original size:16 final size:16
Alignment explanation
Indices: 70972--71008 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
70962 AGAATTACCT
70972 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
70988 ATTACGCTTCTATTCC
1 ATTACGCCTCTATTCC
71004 ATTAC
1 ATTAC
71009 AGCGAACCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.22, C:0.32, G:0.05, T:0.41
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:71731 original size:15 final size:15
Alignment explanation
Indices: 71713--71744 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
71703 GGCTAGGGGT
71713 ATTGGGCTTAGGCTA
1 ATTGGGCTTAGGCTA
*
71728 ATTGGGTTTAGGCTA
1 ATTGGGCTTAGGCTA
71743 AT
1 AT
71745 AGGGTTTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.09, G:0.31, T:0.38
Consensus pattern (15 bp):
ATTGGGCTTAGGCTA
Found at i:71749 original size:15 final size:15
Alignment explanation
Indices: 71720--71753 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
71710 GGTATTGGGC
*
71720 TTAGGCTAATTGGGT
1 TTAGGCTAATAGGGT
71735 TTAGGCTAATAGGGT
1 TTAGGCTAATAGGGT
71750 TTAG
1 TTAG
71754 TTTACTGGGC
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:0.24, C:0.06, G:0.32, T:0.38
Consensus pattern (15 bp):
TTAGGCTAATAGGGT
Found at i:71825 original size:15 final size:15
Alignment explanation
Indices: 71796--71834 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
71786 AAACTGGACA
71796 TTGTTTA-TT-TTTT
1 TTGTTTATTTATTTT
*
71809 TTGTTTTTTTATTTT
1 TTGTTTATTTATTTT
71824 TTGTTTATTTA
1 TTGTTTATTTA
71835 ATCTGTATGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 6 0.27
14 2 0.09
15 14 0.64
ACGTcount: A:0.10, C:0.00, G:0.08, T:0.82
Consensus pattern (15 bp):
TTGTTTATTTATTTT
Found at i:74305 original size:20 final size:20
Alignment explanation
Indices: 74280--74324 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
74270 CCATGAATTG
*
74280 TTTTATTGATAATATTATAA
1 TTTTATTGATAAAATTATAA
* *
74300 TTTTATTTATAAAATTATTA
1 TTTTATTGATAAAATTATAA
74320 TTTTA
1 TTTTA
74325 ATAAATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTTATTGATAAAATTATAA
Found at i:74445 original size:18 final size:17
Alignment explanation
Indices: 74407--74447 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
74397 AAAAAAATGT
**
74407 TTTTAAATATTTTTATT
1 TTTTAAATATTTTTAAC
74424 TTTTAAATATTTTTTAAC
1 TTTTAAATA-TTTTTAAC
74442 TTTTAA
1 TTTTAA
74448 TCTTTAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTAAATATTTTTAAC
Found at i:76610 original size:3 final size:3
Alignment explanation
Indices: 76593--76633 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
76583 TCGCCTTTGC
*
76593 CTT C-T CTT CCTT CTT CTT CTC CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT -CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
76634 CTTTGTCCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (3 bp):
CTT
Found at i:78000 original size:23 final size:23
Alignment explanation
Indices: 77951--78000 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
77941 AAAATTAAGT
*
77951 AAAACATTAAAGCATTCCAATAT
1 AAAACATTAAAGCATTCCAATAC
* *
77974 AAAACATT-AAGACATTTCAATCC
1 AAAACATTAAAG-CATTCCAATAC
77997 AAAA
1 AAAA
78001 GTAACCATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.54, C:0.18, G:0.04, T:0.24
Consensus pattern (23 bp):
AAAACATTAAAGCATTCCAATAC
Found at i:84157 original size:16 final size:17
Alignment explanation
Indices: 84135--84173 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
84125 GGGAGGGAAG
84135 GGAAAAAG-AAGAGAAAA
1 GGAAAAAGAAAG-GAAAA
84152 -GAAAAAGAAAGGAAAA
1 GGAAAAAGAAAGGAAAA
84168 GGAAAA
1 GGAAAA
84174 TATATAGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (17 bp):
GGAAAAAGAAAGGAAAA
Found at i:87172 original size:20 final size:20
Alignment explanation
Indices: 87127--87172 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
87117 GGTGATATTT
87127 TCTTTATAATATTAACAACA
1 TCTTTATAATATTAACAACA
* *
87147 TATTTATACTATTAATCAA-A
1 TCTTTATAATATTAA-CAACA
87167 TCTTTA
1 TCTTTA
87173 ATTGAGTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (20 bp):
TCTTTATAATATTAACAACA
Found at i:89944 original size:22 final size:23
Alignment explanation
Indices: 89918--89963 Score: 85
Period size: 22 Copynumber: 2.0 Consensus size: 23
89908 AGTTTTAAAA
89918 AATTAAAAAGTTT-TAAATATAT
1 AATTAAAAAGTTTATAAATATAT
89940 AATTAAAAAGTTTATAAATATAT
1 AATTAAAAAGTTTATAAATATAT
89963 A
1 A
89964 TAATCTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (23 bp):
AATTAAAAAGTTTATAAATATAT
Found at i:93461 original size:91 final size:92
Alignment explanation
Indices: 93288--93461 Score: 233
Period size: 91 Copynumber: 1.9 Consensus size: 92
93278 ACAGAGGAAG
* * * *
93288 TAGTCGACAGTTCATTTGCTCGACCAGTGGTTTATCCACAATATATTAGCAACTTTTATCTACAC
1 TAGTCGACAGTTCATCTACTCGACCAGTGGTTTATCAACAACATATTAGCAACTTTTATCTACAC
*
93353 AAATGAATGGTTCATCCACCAAGATTC
66 AAACGAATGGTTCATCCACCAAGATTC
* * * **
93380 TAGTCGGCAG-TCATCTACTCGACTAGTGGTTTATCAACAACGTATTAGCAGTTTTTATCTACAC
1 TAGTCGACAGTTCATCTACTCGACCAGTGGTTTATCAACAACATATTAGCAACTTTTATCTACAC
* *
93444 AGACGGATGGTTCATCCA
66 AAACGAATGGTTCATCCA
93462 TCAATATATT
Statistics
Matches: 70, Mismatches: 12, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
91 61 0.87
92 9 0.13
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (92 bp):
TAGTCGACAGTTCATCTACTCGACCAGTGGTTTATCAACAACATATTAGCAACTTTTATCTACAC
AAACGAATGGTTCATCCACCAAGATTC
Found at i:95905 original size:71 final size:71
Alignment explanation
Indices: 95746--95912 Score: 181
Period size: 71 Copynumber: 2.4 Consensus size: 71
95736 GCGTACAGCA
* * * * *
95746 CATTTATTGTTGGTTATGCCGACCAGTACTGGGCACACATATTTATCGATTTTATCGACTAGTGC
1 CATTTATTGTTGATTATACCGACCAGTACTGGGCACACATATTTATCGATTCTACCGACCAGTGC
* **
95811 AGGGTG
66 AAGACG
** * * * * *
95817 CATTTATTGTCAATTATACCGACCAGTGCTGTGCACACATATTTTTTGGTTCTACCGACCAGTGC
1 CATTTATTGTTGATTATACCGACCAGTACTGGGCACACATATTTATCGATTCTACCGACCAGTGC
95882 AAGACG
66 AAGACG
* *
95888 CATTTATTATTGTTTATACCGACCA
1 CATTTATTGTTGATTATACCGACCA
95913 ATGTTAGGAA
Statistics
Matches: 77, Mismatches: 19, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
71 77 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (71 bp):
CATTTATTGTTGATTATACCGACCAGTACTGGGCACACATATTTATCGATTCTACCGACCAGTGC
AAGACG
Found at i:100292 original size:29 final size:29
Alignment explanation
Indices: 100260--100326 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
100250 CACAGTCTGT
*
100260 CACACGGTCATGTGTCACACACGA-CCTAC
1 CACACGGCCATGTGTCACACAC-ATCCTAC
* *
100289 CACACGGCCGTGTGTTACACACATCCTAC
1 CACACGGCCATGTGTCACACACATCCTAC
*
100318 CACAAGGCC
1 CACACGGCC
100327 TGGCACACGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 1 0.03
29 32 0.97
ACGTcount: A:0.27, C:0.39, G:0.18, T:0.16
Consensus pattern (29 bp):
CACACGGCCATGTGTCACACACATCCTAC
Found at i:124342 original size:14 final size:14
Alignment explanation
Indices: 124323--124352 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
124313 ATTATTCTTC
124323 ATTTGTCAAATCAG
1 ATTTGTCAAATCAG
124337 ATTTGTCAAATCAG
1 ATTTGTCAAATCAG
124351 AT
1 AT
124353 GATGTGGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (14 bp):
ATTTGTCAAATCAG
Found at i:125469 original size:18 final size:18
Alignment explanation
Indices: 125435--125469 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
125425 CTCAAAACAA
**
125435 TAAAAATAAATTTTAAAT
1 TAAAAATAAATAGTAAAT
125453 TAAAAATAAATAGTAAA
1 TAAAAATAAATAGTAAA
125470 AACATTTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (18 bp):
TAAAAATAAATAGTAAAT
Found at i:135902 original size:46 final size:47
Alignment explanation
Indices: 135786--135916 Score: 124
Period size: 46 Copynumber: 2.9 Consensus size: 47
135776 TAATATTACG
* * * ***
135786 TATTCTTTAGTTCGCAACATATGCA-AGAGTTGGGAACCTAAATTTG
1 TATTCTCTAGTCCGCAACATATGCAGAGAGATGGGAACCTAAATCCA
* * * *
135832 TATTCTCAAATCCGCAAAAAATGCAGAG-GATGGGAACCTAAATCCA
1 TATTCTCTAGTCCGCAACATATGCAGAGAGATGGGAACCTAAATCCA
* * *
135878 TATTCTCTAGTCCACAACATATGCAG-GAGCTAGGAACCT
1 TATTCTCTAGTCCGCAACATATGCAGAGAGATGGGAACCT
135917 GGGCAAAAAC
Statistics
Matches: 66, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
45 1 0.02
46 63 0.95
47 2 0.03
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (47 bp):
TATTCTCTAGTCCGCAACATATGCAGAGAGATGGGAACCTAAATCCA
Found at i:144789 original size:25 final size:25
Alignment explanation
Indices: 144752--144799 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
144742 TAAGTAGGCC
144752 CATATTCACAACTCATGTGAGCATT
1 CATATTCACAACTCATGTGAGCATT
* *
144777 CATATTCATAACTCGTGTGAGCA
1 CATATTCACAACTCATGTGAGCA
144800 ATTCTATCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (25 bp):
CATATTCACAACTCATGTGAGCATT
Found at i:147134 original size:22 final size:23
Alignment explanation
Indices: 147095--147153 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 23
147085 TGAATTTTGG
* *
147095 AAAAATTAATTTTGATCAAATGA
1 AAAAATTAATATTAATCAAATGA
*
147118 AAAAATTAA-ATTAATCAAATTA
1 AAAAATTAATATTAATCAAATGA
147140 ATTAAAATTAATAT
1 A--AAAATTAATAT
147154 GATATTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 11 0.37
23 9 0.30
24 8 0.27
25 2 0.07
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (23 bp):
AAAAATTAATATTAATCAAATGA
Found at i:148433 original size:22 final size:22
Alignment explanation
Indices: 148395--148447 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 22
148385 TTTTAAATTC
*
148395 TAAAAAAATATTAAATA-TT-A
1 TAAAAAAATATAAAATACTTGA
148415 TAAAAAAATATCAATAATACTTGA
1 TAAAAAAATAT-AA-AATACTTGA
*
148439 GAAAAAAAT
1 TAAAAAAAT
148448 TCTTCAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 11 0.41
21 1 0.04
22 4 0.15
23 2 0.07
24 9 0.33
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (22 bp):
TAAAAAAATATAAAATACTTGA
Found at i:148799 original size:90 final size:91
Alignment explanation
Indices: 148661--148889 Score: 288
Period size: 90 Copynumber: 2.5 Consensus size: 91
148651 TTAATGGTGC
* * * *
148661 AAAAA-ACCCTCAAACTTTTTCAAAAAAAGCAATTCAGCCTCTGTTTTTTTTTTGCACTCAATTG
1 AAAAAGACCCTCAAACCTTTTCAAAAAAAGCAATTAAGCCCCTGCTTTTTTTTTGCACTCAATTG
* *
148725 -GATACTTGAACTTTCAAAATGCAT-C
66 AG-TACTTGAACCTTCAAAATGCATAA
* * * *
148750 AAAAAGGCTCTCAAACCTTTTCAAAAAAAGCAATTAAGCCCCTACTTTTTTTTTGCATTCAATTG
1 AAAAAGACCCTCAAACCTTTTCAAAAAAAGCAATTAAGCCCCTGCTTTTTTTTTGCACTCAATTG
148815 AGTACTTGAACCTTCAAAATGCATAAA
66 AGTACTTGAACCTTCAAAATGCAT-AA
* *
148842 AAAAATACCCTCAAA-CTTATT-AAAAAAAGTAATTAAGCCCCTGCTTTT
1 AAAAAGACCCTCAAACCTT-TTCAAAAAAAGCAATTAAGCCCCTGCTTTT
148890 ATTAAAAATT
Statistics
Matches: 120, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
89 5 0.04
90 72 0.60
91 29 0.24
92 14 0.12
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (91 bp):
AAAAAGACCCTCAAACCTTTTCAAAAAAAGCAATTAAGCCCCTGCTTTTTTTTTGCACTCAATTG
AGTACTTGAACCTTCAAAATGCATAA
Found at i:149011 original size:17 final size:19
Alignment explanation
Indices: 148989--149025 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
148979 AAATTTATTA
148989 AAAATT-AGAAAAA-ATAT
1 AAAATTCAGAAAAATATAT
*
149006 AAAATTCATAAAAATATAT
1 AAAATTCAGAAAAATATAT
149025 A
1 A
149026 TAAAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 6 0.35
19 5 0.29
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.27
Consensus pattern (19 bp):
AAAATTCAGAAAAATATAT
Found at i:149018 original size:38 final size:37
Alignment explanation
Indices: 148938--149059 Score: 95
Period size: 38 Copynumber: 3.2 Consensus size: 37
148928 AATAAAAGCT
* * *
148938 ATAAAAA-TTATTAAAATTTAATAAAAAAATTCAAATT-
1 ATAAAAATTTATTAAAAATTAA-AAAAATA-TAAAATTC
*
148975 TTAAAAATTTATTAAAAATTAGAAAAAATATAAAATTC
1 ATAAAAATTTATTAAAAATTA-AAAAAATATAAAATTC
* ** *
149013 ATAAAAATATATATAAAAAATTATAAAATTTTATAAAAATC
1 ATAAAAAT-T-TATTAAAAATTA-AAAA-AATATAAAATTC
149054 ATAAAA
1 ATAAAA
149060 TATAATNNNN
Statistics
Matches: 69, Mismatches: 10, Indels: 8
0.79 0.11 0.09
Matches are distributed among these distances:
37 12 0.17
38 25 0.36
39 2 0.03
40 15 0.22
41 15 0.22
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (37 bp):
ATAAAAATTTATTAAAAATTAAAAAAATATAAAATTC
Found at i:149030 original size:12 final size:11
Alignment explanation
Indices: 148976--149052 Score: 53
Period size: 10 Copynumber: 7.6 Consensus size: 11
148966 ATTCAAATTT
148976 TAAAAAT-TTA
1 TAAAAATATTA
*
148986 TTAAAA-ATTA
1 TAAAAATATTA
*
148996 GAAAAA-A-TA
1 TAAAAATATTA
*
149005 T-AAAAT-TCA
1 TAAAAATATTA
149014 TAAAAATATATA
1 TAAAAATAT-TA
149026 TAAAAA-ATTA
1 TAAAAATATTA
*
149036 T-AAAATTTTA
1 TAAAAATATTA
149046 TAAAAAT
1 TAAAAAT
149053 CATAAAATAT
Statistics
Matches: 52, Mismatches: 7, Indels: 15
0.70 0.09 0.20
Matches are distributed among these distances:
8 4 0.08
9 8 0.15
10 25 0.48
11 8 0.15
12 7 0.13
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (11 bp):
TAAAAATATTA
Found at i:149052 original size:19 final size:19
Alignment explanation
Indices: 148937--149060 Score: 61
Period size: 19 Copynumber: 6.9 Consensus size: 19
148927 CAATAAAAGC
148937 TATAAAAATTATTAAAATTT
1 TATAAAAATTA-TAAAATTT
* * *
148957 AATAAAAA-AATTCAAATTT
1 TATAAAAATTA-TAAAATTT
* *
148976 TA-AAAATTTATTAAAA-AT
1 TATAAAAATTA-TAAAATTT
* *
148994 TAGAAAAAATATAAAA-TT
1 TATAAAAATTATAAAATTT
* *
149012 CATAAAAA-TAT---A-TA
1 TATAAAAATTATAAAATTT
149026 TA-AAAAATTATAAAATTT
1 TATAAAAATTATAAAATTT
*
149044 TATAAAAATCATAAAAT
1 TATAAAAATTATAAAAT
149061 ATAATNNNNN
Statistics
Matches: 79, Mismatches: 17, Indels: 17
0.70 0.15 0.15
Matches are distributed among these distances:
13 5 0.06
14 6 0.08
17 4 0.05
18 22 0.28
19 35 0.44
20 7 0.09
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (19 bp):
TATAAAAATTATAAAATTT
Found at i:149437 original size:91 final size:89
Alignment explanation
Indices: 149284--149449 Score: 260
Period size: 91 Copynumber: 1.8 Consensus size: 89
149274 NNNNNNNNAG
* * * *
149284 GGGGCTTAATTGCTTTTTTGAAAAAATTTGAGGGTTTTTTTATGCATTTTGAAAGTTTAAGTGGC
1 GGGGCTTAATTGCTTTTTTGAAAAAATTTAAGGGTTTTTTAATGCATTTTGAAAGTTCAAGTGCC
149349 CAATTGAGTGGGGGGAAAAAAGCA
66 CAATTGAGTGGGGGGAAAAAAGCA
* *
149373 GGGGCTTAATTGCTTTTTTTGAAGAAGTTTAAGGGTCTTTTTAATGCATTTTGAAAGTTCAAGTG
1 GGGGCTTAATTGC-TTTTTTGAAAAAATTTAAGGGT-TTTTTAATGCATTTTGAAAGTTCAAGTG
149438 CCCAATTGAGTG
64 CCCAATTGAGTG
149450 CAAAAAAAGA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
89 13 0.19
90 19 0.28
91 37 0.54
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.38
Consensus pattern (89 bp):
GGGGCTTAATTGCTTTTTTGAAAAAATTTAAGGGTTTTTTAATGCATTTTGAAAGTTCAAGTGCC
CAATTGAGTGGGGGGAAAAAAGCA
Found at i:152132 original size:20 final size:21
Alignment explanation
Indices: 152098--152136 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
152088 ACTTGAATTA
152098 AAAAAATCCATATTAAAAACC
1 AAAAAATCCATATTAAAAACC
*
152119 AAAAAATCGA-ATTAAAAA
1 AAAAAATCCATATTAAAAA
152137 TTTTCAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.67, C:0.13, G:0.03, T:0.18
Consensus pattern (21 bp):
AAAAAATCCATATTAAAAACC
Found at i:163138 original size:6 final size:6
Alignment explanation
Indices: 163127--163151 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
163117 ATCAAAGTTC
163127 ATTGTT ATTGTT ATTGTT ATTGTT A
1 ATTGTT ATTGTT ATTGTT ATTGTT A
163152 ACCAAAGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.16, T:0.64
Consensus pattern (6 bp):
ATTGTT
Found at i:163905 original size:44 final size:45
Alignment explanation
Indices: 163850--163942 Score: 170
Period size: 44 Copynumber: 2.1 Consensus size: 45
163840 TAAATTATTA
163850 TTATTTAATTACCCATTATTCAAGTAAAACTCTTGCATTA-TTTC
1 TTATTTAATTACCCATTATTCAAGTAAAACTCTTGCATTATTTTC
*
163894 TTATTTAATTACCCCTTATTCAAGTAAAACTCTTGCATTATTTTC
1 TTATTTAATTACCCATTATTCAAGTAAAACTCTTGCATTATTTTC
163939 TTAT
1 TTAT
163943 AAATAGTATC
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 39 0.83
45 8 0.17
ACGTcount: A:0.30, C:0.18, G:0.04, T:0.47
Consensus pattern (45 bp):
TTATTTAATTACCCATTATTCAAGTAAAACTCTTGCATTATTTTC
Found at i:168554 original size:6 final size:6
Alignment explanation
Indices: 168543--168577 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
168533 GTTGTATTTA
168543 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
168578 AGGACATGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:171534 original size:23 final size:22
Alignment explanation
Indices: 171502--171563 Score: 88
Period size: 22 Copynumber: 2.7 Consensus size: 22
171492 CCCGGCCCGT
*
171502 TTTTTAATTAAAATTAAAATTATA
1 TTTTT-ATTAAAATTAAAACTA-A
171526 TTTTTATTAAAATTAAAACTAA
1 TTTTTATTAAAATTAAAACTAA
*
171548 TTGTTATTAAAATTAA
1 TTTTTATTAAAATTAA
171564 TTGTTATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 16 0.44
23 15 0.42
24 5 0.14
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTTATTAAAATTAAAACTAA
Found at i:171558 original size:16 final size:16
Alignment explanation
Indices: 171537--171593 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
171527 TTTTATTAAA
*
171537 ATTAAAACTAATTGTT
1 ATTAAAATTAATTGTT
171553 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
* *
171569 ATCAAAATTAATTATT
1 ATTAAAATTAATTGTT
171585 ATTAAAATT
1 ATTAAAATT
171594 GTATCAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (16 bp):
ATTAAAATTAATTGTT
Found at i:186244 original size:19 final size:19
Alignment explanation
Indices: 186212--186258 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
186202 ATGTTGAATG
186212 TGGAAAGA--AATATGTTT
1 TGGAAAGACTAATATGTTT
186229 TGGAAAGACTAATATGTTT
1 TGGAAAGACTAATATGTTT
186248 TGGAAAGACTA
1 TGGAAAGACTA
186259 CCTACTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 8 0.29
19 20 0.71
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.32
Consensus pattern (19 bp):
TGGAAAGACTAATATGTTT
Found at i:198327 original size:12 final size:13
Alignment explanation
Indices: 198306--198334 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
198296 TGAGATAATG
198306 TTTTAGTTTTTAT
1 TTTTAGTTTTTAT
198319 TTTTA-TTTTTAT
1 TTTTAGTTTTTAT
198331 TTTT
1 TTTT
198335 TCTCTCATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (13 bp):
TTTTAGTTTTTAT
Found at i:199063 original size:18 final size:17
Alignment explanation
Indices: 199036--199069 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
199026 AGCCAGGCCA
199036 TGTGGGCCACACGGGCG
1 TGTGGGCCACACGGGCG
199053 TGTGAGGCCACACGGGC
1 TGTG-GGCCACACGGGC
199070 AAGCCATACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.15, C:0.29, G:0.44, T:0.12
Consensus pattern (17 bp):
TGTGGGCCACACGGGCG
Found at i:218782 original size:22 final size:21
Alignment explanation
Indices: 218756--218798 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
218746 ATGACCTTAA
218756 AATTT-ATCTGTTCGAACGTGTT
1 AATTTCAT-TGTTC-AACGTGTT
*
218778 AATTTCATTGTTCAATGTGTT
1 AATTTCATTGTTCAACGTGTT
218799 GTTATTTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 7 0.37
22 10 0.53
23 2 0.11
ACGTcount: A:0.23, C:0.12, G:0.16, T:0.49
Consensus pattern (21 bp):
AATTTCATTGTTCAACGTGTT
Found at i:219843 original size:34 final size:34
Alignment explanation
Indices: 219800--219864 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
219790 AATGCTTTAG
219800 ATGTGAATCGATATACATATACTTAGAATAGAGA
1 ATGTGAATCGATATACATATACTTAGAATAGAGA
* * * *
219834 ATGTGAATCGGTATATATATAGTTGGAATAG
1 ATGTGAATCGATATACATATACTTAGAATAG
219865 GTTAATAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.32
Consensus pattern (34 bp):
ATGTGAATCGATATACATATACTTAGAATAGAGA
Found at i:223419 original size:37 final size:37
Alignment explanation
Indices: 223369--223470 Score: 161
Period size: 37 Copynumber: 2.8 Consensus size: 37
223359 TGCTGTGGTG
*
223369 TGTTATCTGTTGGATTAGCTCTTATGAGCATTTAGCA
1 TGTTATCGGTTGGATTAGCTCTTATGAGCATTTAGCA
* *
223406 TGTTATCGGTTGGATTATCTCTTATGAGCATTTGGCA
1 TGTTATCGGTTGGATTAGCTCTTATGAGCATTTAGCA
223443 TGTTATCAGG-TGGATTAGCTCTTATGAG
1 TGTTATC-GGTTGGATTAGCTCTTATGAG
223471 AAATTGACGT
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
37 58 0.97
38 2 0.03
ACGTcount: A:0.21, C:0.13, G:0.25, T:0.42
Consensus pattern (37 bp):
TGTTATCGGTTGGATTAGCTCTTATGAGCATTTAGCA
Found at i:224546 original size:54 final size:54
Alignment explanation
Indices: 224502--224646 Score: 229
Period size: 54 Copynumber: 2.7 Consensus size: 54
224492 GGCTTGACTT
*
224502 AGTGAGTTACACGGGCAGGGACATAGGCTGGGACATGACAGTGTGGCCCAAATG
1 AGTGAGTTACACGGGCAGGGACATAGGCTGGGACATGACAGTGTGGCCCAAATC
* *
224556 AGTGAGTTACACGGGCAGGGACATAGGCTGGGACTTGACCGTGTGGCCCAAATC
1 AGTGAGTTACACGGGCAGGGACATAGGCTGGGACATGACAGTGTGGCCCAAATC
* *
224610 AGTGAGTTACATGGGCAGGGACA-CGAGCTGGGACATG
1 AGTGAGTTACACGGGCAGGGACATAG-GCTGGGACATG
224647 GTCGTGTGTC
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
53 1 0.01
54 83 0.99
ACGTcount: A:0.26, C:0.19, G:0.37, T:0.17
Consensus pattern (54 bp):
AGTGAGTTACACGGGCAGGGACATAGGCTGGGACATGACAGTGTGGCCCAAATC
Found at i:226133 original size:152 final size:152
Alignment explanation
Indices: 225902--226208 Score: 515
Period size: 152 Copynumber: 2.0 Consensus size: 152
225892 ACATATCACC
* * *
225902 TTATTACTTGATTCGACTTGTATACTTGTACAAATCACGTACCATTTCACACGTGAAAAGTTTTT
1 TTATTACTTGATTCGACGTGTATACTTGCACAAATCACATACCATTTCACACGTGAAAAGTTTTT
* *
225967 GGCATCGTTACCGGGGATCAACAATTTGGTGTAATTTGGTTTTGTTATTTTACTTAATTCCATTA
66 GGCACCGTTACCGGGGATCAACAATTTGGTGTAATTTGGTTTGGTTATTTTACTTAATTCCATTA
226032 GTTTTATTTAACTTAGTTTAAT
131 GTTTTATTTAACTTAGTTTAAT
* * *
226054 TTATTACTTGATTCGACGTGTATACTTGCACAAATCACATATCATTTCACATGTGACAAGTTTTT
1 TTATTACTTGATTCGACGTGTATACTTGCACAAATCACATACCATTTCACACGTGAAAAGTTTTT
* * *
226119 GGCACCGTTGCCGGGGATCAGCAATTTGGTGTAATTTGGTTTGGTTATTTTACTTAATTTCATTA
66 GGCACCGTTACCGGGGATCAACAATTTGGTGTAATTTGGTTTGGTTATTTTACTTAATTCCATTA
226184 GTTTTATTTAACTTAGTTTAAT
131 GTTTTATTTAACTTAGTTTAAT
226206 TTA
1 TTA
226209 ATTTCTACAG
Statistics
Matches: 144, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
152 144 1.00
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.44
Consensus pattern (152 bp):
TTATTACTTGATTCGACGTGTATACTTGCACAAATCACATACCATTTCACACGTGAAAAGTTTTT
GGCACCGTTACCGGGGATCAACAATTTGGTGTAATTTGGTTTGGTTATTTTACTTAATTCCATTA
GTTTTATTTAACTTAGTTTAAT
Found at i:226201 original size:15 final size:15
Alignment explanation
Indices: 226172--226209 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
226162 GTTATTTTAC
*
226172 TTAATTTCA-TTAGT
1 TTAATTTAACTTAGT
*
226186 TTTATTTAACTTAGT
1 TTAATTTAACTTAGT
226201 TTAATTTAA
1 TTAATTTAA
226210 TTTCTACAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (15 bp):
TTAATTTAACTTAGT
Found at i:237112 original size:20 final size:20
Alignment explanation
Indices: 237060--237140 Score: 65
Period size: 20 Copynumber: 4.0 Consensus size: 20
237050 ATAGTGCAAT
* *
237060 CAGAGGCACTAGAGTGTAAA
1 CAGAGGCACCAAAGTGTAAA
* * *
237080 TAGAGACAACAAAGTGTGAAA
1 CAGAGGCACCAAAGTGT-AAA
* *
237101 -AGAGGCACCAAAATGCAAA
1 CAGAGGCACCAAAGTGTAAA
* *
237120 CAGAGGCACCGAAGTGCAAA
1 CAGAGGCACCAAAGTGTAAA
237140 C
1 C
237141 TCATACAAGC
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
19 3 0.06
20 42 0.88
21 3 0.06
ACGTcount: A:0.46, C:0.19, G:0.26, T:0.10
Consensus pattern (20 bp):
CAGAGGCACCAAAGTGTAAA
Found at i:241695 original size:20 final size:20
Alignment explanation
Indices: 241643--241723 Score: 65
Period size: 20 Copynumber: 4.0 Consensus size: 20
241633 ATAGTGCAAT
* *
241643 CAGAGGCACTAGAGTGTAAA
1 CAGAGGCACCAAAGTGTAAA
* * *
241663 TAGAGACAACAAAGTGTGAAA
1 CAGAGGCACCAAAGTGT-AAA
* *
241684 -AGAGGCACCAAAATGCAAA
1 CAGAGGCACCAAAGTGTAAA
* *
241703 CAGAGGCACCGAAGTGCAAA
1 CAGAGGCACCAAAGTGTAAA
241723 C
1 C
241724 TCATACAAGC
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
19 3 0.06
20 42 0.88
21 3 0.06
ACGTcount: A:0.46, C:0.19, G:0.26, T:0.10
Consensus pattern (20 bp):
CAGAGGCACCAAAGTGTAAA
Found at i:249890 original size:86 final size:86
Alignment explanation
Indices: 249777--249950 Score: 330
Period size: 86 Copynumber: 2.0 Consensus size: 86
249767 TTAACAAAAA
249777 ATATATATATATATATATAAATAAATATGACTCTTTCAATATATTTGTAAAATCTAAGAGATTTA
1 ATATATATATATATATATAAATAAATATGACTCTTTCAATATATTTGTAAAATCTAAGAGATTTA
249842 CTAATAATATATAAAATAATT
66 CTAATAATATATAAAATAATT
*
249863 ATATATATATATATATATAAATAAATATGACTCTTTCAATCTATTTGTAAAATCTAAGAGATTTA
1 ATATATATATATATATATAAATAAATATGACTCTTTCAATATATTTGTAAAATCTAAGAGATTTA
*
249928 CTAATAATATATCAAATAATT
66 CTAATAATATATAAAATAATT
249949 AT
1 AT
249951 GTTTAAAAAT
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
86 86 1.00
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (86 bp):
ATATATATATATATATATAAATAAATATGACTCTTTCAATATATTTGTAAAATCTAAGAGATTTA
CTAATAATATATAAAATAATT
Found at i:252986 original size:42 final size:42
Alignment explanation
Indices: 252939--253022 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
252929 ATACAACATA
* * *
252939 CAGTAACAATCTGGGCCTGATCCCTAAGCAGTAACAGTCTGG
1 CAGTAACAATATAGGCCTGAGCCCTAAGCAGTAACAGTCTGG
* *
252981 CAGTAACAGTATAGGCCTGAGCCCTAAGCAGTAATAGTCTGG
1 CAGTAACAATATAGGCCTGAGCCCTAAGCAGTAACAGTCTGG
253023 GCCTGAGCCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.30, C:0.24, G:0.25, T:0.21
Consensus pattern (42 bp):
CAGTAACAATATAGGCCTGAGCCCTAAGCAGTAACAGTCTGG
Found at i:253025 original size:28 final size:28
Alignment explanation
Indices: 252980--253105 Score: 112
Period size: 28 Copynumber: 4.5 Consensus size: 28
252970 TAACAGTCTG
252980 GCAGTAACAGTATAGGCCTGAGCCCTAA
1 GCAGTAACAGTATAGGCCTGAGCCCTAA
* * * *
253008 GCAGTAATAGTCTGGGCCTGAGCCATAA
1 GCAGTAACAGTATAGGCCTGAGCCCTAA
* * * *
253036 GCAGTAATAGTTTAGGCCTTAGCCCAAA
1 GCAGTAACAGTATAGGCCTGAGCCCTAA
* * *
253064 GTAGTAACAGTGT-GGCCTTAGCCC-AA
1 GCAGTAACAGTATAGGCCTGAGCCCTAA
* *
253090 TACAGAAACAGTATAG
1 -GCAGTAACAGTATAG
253106 TACAGTAATG
Statistics
Matches: 80, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
26 2 0.03
27 20 0.25
28 58 0.73
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (28 bp):
GCAGTAACAGTATAGGCCTGAGCCCTAA
Found at i:253099 original size:27 final size:27
Alignment explanation
Indices: 253050--253101 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
253040 TAATAGTTTA
* *
253050 GGCCTTAGCCCAAAGTAGTAACAGTGT
1 GGCCTTAGCCCAAAGCAGAAACAGTGT
253077 GGCCTTAGCCCAATA-CAGAAACAGT
1 GGCCTTAGCCCAA-AGCAGAAACAGT
253102 ATAGTACAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.19
Consensus pattern (27 bp):
GGCCTTAGCCCAAAGCAGAAACAGTGT
Found at i:253480 original size:27 final size:27
Alignment explanation
Indices: 253450--253689 Score: 257
Period size: 27 Copynumber: 8.9 Consensus size: 27
253440 ACCCTATAGT
** * *
253450 GGTATTTTGGTCATTTTATCCTTCGGG
1 GGTATTTCAGTCATTTTACCCTTCGAG
* * * *
253477 GGTATTTTAGTTATTTTACCGTTCGGG
1 GGTATTTCAGTCATTTTACCCTTCGAG
* *
253504 GGTATTTC-GATCATTGTACCTTTCGAG
1 GGTATTTCAG-TCATTTTACCCTTCGAG
* *
253531 GGTATTTCAGTAATTTTACCCTTCGGG
1 GGTATTTCAGTCATTTTACCCTTCGAG
*
253558 GGTATTTCAGTCATTTTACCCTTTGAG
1 GGTATTTCAGTCATTTTACCCTTCGAG
* * *
253585 GTTATTTCAATTATTTTACCCTTCGAG
1 GGTATTTCAGTCATTTTACCCTTCGAG
* *
253612 GGTATTTTAGTCATTTTACACTTCGAG
1 GGTATTTCAGTCATTTTACCCTTCGAG
* * **
253639 GGCATTTCGGTCATTTTACCCTTTAAG
1 GGTATTTCAGTCATTTTACCCTTCGAG
*
253666 GGCATTTCAGTCATTTTACCCTTC
1 GGTATTTCAGTCATTTTACCCTTC
253690 AAAGGCATTT
Statistics
Matches: 178, Mismatches: 33, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
26 1 0.01
27 176 0.99
28 1 0.01
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.44
Consensus pattern (27 bp):
GGTATTTCAGTCATTTTACCCTTCGAG
Found at i:260182 original size:28 final size:28
Alignment explanation
Indices: 260142--260243 Score: 150
Period size: 28 Copynumber: 3.6 Consensus size: 28
260132 ATGTGACATA
* * *
260142 CAGTAACAATCTGGGCTTGATCCCTAAG
1 CAGTAACAGTCTGGGCCTGAACCCTAAG
* *
260170 TAGTAATAGTCTGGGCCTGAACCCTAAG
1 CAGTAACAGTCTGGGCCTGAACCCTAAG
260198 CAGTAACAGTCTGGGCCTGAACCCTAAG
1 CAGTAACAGTCTGGGCCTGAACCCTAAG
*
260226 CAGTAACAGTCTAGGCCT
1 CAGTAACAGTCTGGGCCT
260244 TAGGCTAAAG
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 66 1.00
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.23
Consensus pattern (28 bp):
CAGTAACAGTCTGGGCCTGAACCCTAAG
Found at i:260673 original size:27 final size:27
Alignment explanation
Indices: 260643--260828 Score: 171
Period size: 27 Copynumber: 6.9 Consensus size: 27
260633 GGTATAACAA
260643 TCATTTTACCTTATAG-GGGTATTTTGG
1 TCATTTTACCTT-TAGAGGGTATTTTGG
* * * *
260670 TCATTCTATTCTTCAG-GGGTATTTTGA
1 TCATTTTA-CCTTTAGAGGGTATTTTGG
* *
260697 TCATTTTACCTTTCGAGGGAATTTTGG
1 TCATTTTACCTTTAGAGGGTATTTTGG
* * * *
260724 TCATTTTACCATTCGGGGGTATTTTAG
1 TCATTTTACCTTTAGAGGGTATTTTGG
* **
260751 TCATTTGACCCTTT-GAGGGTATTTCAG
1 TCATTTTA-CCTTTAGAGGGTATTTTGG
*
260778 TCATTTTACCTTTCGAGGGTATTTTGG
1 TCATTTTACCTTTAGAGGGTATTTTGG
* * *
260805 TCATTTTACCCTTCGAGGGCATTT
1 TCATTTTACCTTTAGAGGGTATTT
260829 CGATTAGTTT
Statistics
Matches: 132, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
26 9 0.07
27 116 0.88
28 7 0.05
ACGTcount: A:0.18, C:0.16, G:0.21, T:0.45
Consensus pattern (27 bp):
TCATTTTACCTTTAGAGGGTATTTTGG
Found at i:260829 original size:54 final size:54
Alignment explanation
Indices: 260686--260829 Score: 189
Period size: 54 Copynumber: 2.7 Consensus size: 54
260676 TATTCTTCAG
* * ** *
260686 GGGTATTTTGATCATTTTACCTTTCGAGGGAATTTTGGTCATTTTACCATTCGG
1 GGGTATTTTGGTCATTTTACCCTTCGAGGGAATTTCAGTCATTTTACCATTCGA
* * * * *
260740 GGGTATTTTAGTCATTTGACCCTTTGAGGGTATTTCAGTCATTTTACCTTTCGA
1 GGGTATTTTGGTCATTTTACCCTTCGAGGGAATTTCAGTCATTTTACCATTCGA
*
260794 GGGTATTTTGGTCATTTTACCCTTCGAGGGCATTTC
1 GGGTATTTTGGTCATTTTACCCTTCGAGGGAATTTC
260830 GATTAGTTTA
Statistics
Matches: 76, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 76 1.00
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.44
Consensus pattern (54 bp):
GGGTATTTTGGTCATTTTACCCTTCGAGGGAATTTCAGTCATTTTACCATTCGA
Found at i:270181 original size:29 final size:29
Alignment explanation
Indices: 270123--270181 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
270113 CTAGGTTTTC
*
270123 TTTAGTTTTTCTCTGTTCTTTACTTGGGTT
1 TTTAGTTTTTCTC-GTTCTTTACTTAGGTT
270153 TTTA-TTTTTCTC-TTCTTCTACCTTAGGTT
1 TTTAGTTTTTCTCGTTCTT-TA-CTTAGGTT
270182 AGAGTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
27 5 0.19
28 2 0.08
29 15 0.58
30 4 0.15
ACGTcount: A:0.08, C:0.17, G:0.12, T:0.63
Consensus pattern (29 bp):
TTTAGTTTTTCTCGTTCTTTACTTAGGTT
Found at i:272155 original size:263 final size:263
Alignment explanation
Indices: 271688--272213 Score: 1007
Period size: 263 Copynumber: 2.0 Consensus size: 263
271678 TAAAATACTA
*
271688 TCAAGATAAATATTAAATTAAATTTAATATTAAATTTATTAAAATAATATTATCTTTCAAAAATT
1 TCAAGATAAATATTAAATTAAATTTAATATTAAATTTATTAAAATAATATTATCTTTCAAAAAGT
*
271753 TAATTTGAAATCAATTTACCTCGTAATATCCCACTAAGAGAATAGTTTTTTAACTCCATCAAATA
66 TAATTTGAAATCAATTTACCTCGTAATATCCCACTAAGAGAATAGTTTTTTAACTCCATCAAAGA
271818 ATTGTCGCCATCGACCATCTGTCAGATCGTCATCATCGCAGTCATCGTGCTCGGAGGTTCAATCA
131 ATTGTCGCCATCGACCATCTGTCAGATCGTCATCATCGCAGTCATCGTGCTCGGAGGTTCAATCA
271883 CTGGTACGACTCCTTCGGAACCCCGAATCGTCATCATTTTGCCCAAATGGTCCTGGGCTACTCGC
196 CTGGTACGACTCCTTCGGAACCCCGAATCGTCATCATTTTGCCCAAATGGTCCTGGGCTACTCGC
271948 TGC
261 TGC
271951 TCAAGATAAATATTAAATTAAATTTAATATTAAATTTATTAAAATAATATTATCTTTCAAAAAGT
1 TCAAGATAAATATTAAATTAAATTTAATATTAAATTTATTAAAATAATATTATCTTTCAAAAAGT
* *
272016 TAATTTGAAATCAATTTACCTCGTAATATCCCACTAAGAGAATGGTTTTTTAACTCCATGAAAGA
66 TAATTTGAAATCAATTTACCTCGTAATATCCCACTAAGAGAATAGTTTTTTAACTCCATCAAAGA
272081 ATTGTCGCCATCGACCATCTGTCAGATCGTCATCATCGCAGTCATCGTGCTCGGAGGTTCAATCA
131 ATTGTCGCCATCGACCATCTGTCAGATCGTCATCATCGCAGTCATCGTGCTCGGAGGTTCAATCA
*
272146 CTGGTACGACTCCTTCGGAACCCCGAATCGTCATCATTTTGCCCAAATGGTCTTGGGCTACTCGC
196 CTGGTACGACTCCTTCGGAACCCCGAATCGTCATCATTTTGCCCAAATGGTCCTGGGCTACTCGC
272211 TGC
261 TGC
272214 CCTTATAAGG
Statistics
Matches: 258, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
263 258 1.00
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (263 bp):
TCAAGATAAATATTAAATTAAATTTAATATTAAATTTATTAAAATAATATTATCTTTCAAAAAGT
TAATTTGAAATCAATTTACCTCGTAATATCCCACTAAGAGAATAGTTTTTTAACTCCATCAAAGA
ATTGTCGCCATCGACCATCTGTCAGATCGTCATCATCGCAGTCATCGTGCTCGGAGGTTCAATCA
CTGGTACGACTCCTTCGGAACCCCGAATCGTCATCATTTTGCCCAAATGGTCCTGGGCTACTCGC
TGC
Found at i:277663 original size:10 final size:10
Alignment explanation
Indices: 277650--277690 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
277640 AAAATTAGCC
277650 TAATTAACTA
1 TAATTAACTA
277660 TAATTAACTA
1 TAATTAACTA
*
277670 -AACTTAATTA
1 TAA-TTAACTA
277680 TAATTAA-TA
1 TAATTAACTA
277689 TA
1 TA
277691 GTTGGTAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
9 6 0.21
10 20 0.71
11 2 0.07
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (10 bp):
TAATTAACTA
Found at i:282814 original size:5 final size:5
Alignment explanation
Indices: 282804--282835 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
282794 AATTCAGCCC
282804 ATTCA ATTCA ATTCA ATTCA ATTCA ATTCA AT
1 ATTCA ATTCA ATTCA ATTCA ATTCA ATTCA AT
282836 ACAAAAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (5 bp):
ATTCA
Found at i:298441 original size:41 final size:41
Alignment explanation
Indices: 298383--298494 Score: 109
Period size: 42 Copynumber: 2.7 Consensus size: 41
298373 ATCCATTACT
*
298383 CGGTGGATTCAGCACTTAGCAACCA-TGTTAAATTCAGTGATA
1 CGGTGAATT-AGCACTTAGCAACCACT-TTAAATTCAGTGATA
* * *
298425 CGGTGAATTAGCACTTAACAACCACCTTTATATTTAGTGATA
1 CGGTGAATTAGCACTTAGCAACCA-CTTTAAATTCAGTGATA
* ** * *
298467 CGGGGAATCGGCACATAGCAACCCCTTT
1 CGGTGAATTAGCACTTAGCAACCACTTT
298495 CACAATCAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
41 18 0.31
42 39 0.67
43 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (41 bp):
CGGTGAATTAGCACTTAGCAACCACTTTAAATTCAGTGATA
Found at i:298580 original size:26 final size:26
Alignment explanation
Indices: 298551--298603 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
298541 AATCAATAAT
298551 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACTTAGCAACCCC
* *
298577 TCGGGGAATCTGCACTTAGCGACCCC
1 TCGGGGAATCAGCACTTAGCAACCCC
298603 T
1 T
298604 TTTTATCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.23, C:0.34, G:0.25, T:0.19
Consensus pattern (26 bp):
TCGGGGAATCAGCACTTAGCAACCCC
Found at i:316788 original size:40 final size:40
Alignment explanation
Indices: 316706--316788 Score: 103
Period size: 40 Copynumber: 2.1 Consensus size: 40
316696 CTCTTCCCAC
* *
316706 ATGGCCAAAAGGTTATAAATATAGTTTAAGAAATAGGGCA
1 ATGGCCAAAAGGTTATAAATATAGTTTAAGAAACAAGGCA
* * * * *
316746 ATGGCCATAGGGTTATAAATGTAGTTTAAGATACAAGTCA
1 ATGGCCAAAAGGTTATAAATATAGTTTAAGAAACAAGGCA
316786 ATG
1 ATG
316789 AGATGGAGAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.41, C:0.08, G:0.23, T:0.28
Consensus pattern (40 bp):
ATGGCCAAAAGGTTATAAATATAGTTTAAGAAACAAGGCA
Found at i:317192 original size:16 final size:16
Alignment explanation
Indices: 317168--317221 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
317158 TTTGGTTCGC
* *
317168 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
317184 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
317200 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
317216 TGTAAT
1 TGTAAT
317222 AGCAAATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.31
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:317266 original size:45 final size:44
Alignment explanation
Indices: 317200--317297 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 44
317190 GGAATAGAGG
* *
317200 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATAGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
317245 TGTAATAGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATAGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
*
317289 TGAAATAGA
1 TGTAATAGA
317298 GGTATAATAG
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 24 0.52
45 22 0.48
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATAGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:317476 original size:18 final size:17
Alignment explanation
Indices: 317455--317489 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
317445 TTATTATTAA
*
317455 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
317473 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
317490 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:323170 original size:14 final size:14
Alignment explanation
Indices: 323147--323181 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
323137 TAAAACTTTT
323147 CTTT-AAAACATAA
1 CTTTAAAAACATAA
323160 CTTTAAAAACATAA
1 CTTTAAAAACATAA
*
323174 CTTGAAAA
1 CTTTAAAA
323182 CTTATCTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.54, C:0.14, G:0.03, T:0.29
Consensus pattern (14 bp):
CTTTAAAAACATAA
Found at i:335238 original size:81 final size:81
Alignment explanation
Indices: 335103--335260 Score: 280
Period size: 81 Copynumber: 2.0 Consensus size: 81
335093 AACATATCAA
* * * *
335103 CTATCGGCTCAGTCATCTTTAGAGCATAAGCCTCCACTTATATCAAAGCACATAAGTTACGTACG
1 CTATCGCCTCAATCATCTTTAGAGAATAAGCCTCCACTTATATCAAAGCACATAAGTTACATACG
335168 CATGGTCAGTGACTAG
66 CATGGTCAGTGACTAG
335184 CTATCGCCTCAATCATCTTTAGAGAATAAGCCTCCACTTATATCAAAGCACATAAGTTACATACG
1 CTATCGCCTCAATCATCTTTAGAGAATAAGCCTCCACTTATATCAAAGCACATAAGTTACATACG
335249 CATGGTCAGTGA
66 CATGGTCAGTGA
335261 TTAACTCAAG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 73 1.00
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (81 bp):
CTATCGCCTCAATCATCTTTAGAGAATAAGCCTCCACTTATATCAAAGCACATAAGTTACATACG
CATGGTCAGTGACTAG
Found at i:336749 original size:17 final size:17
Alignment explanation
Indices: 336727--336764 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
336717 TAGATTTGGG
336727 TTAAGAAAATTA-TTTAA
1 TTAAG-AAATTAGTTTAA
*
336744 TTAAGAAATTAGTTTAT
1 TTAAGAAATTAGTTTAA
336761 TTAA
1 TTAA
336765 ATTAATTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (17 bp):
TTAAGAAATTAGTTTAA
Found at i:344054 original size:29 final size:29
Alignment explanation
Indices: 344008--344068 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
343998 TACTGGTTGT
*
344008 ACCTATTCATTGCAACCAATTTCGATTGC
1 ACCTATTCATTGCAACCAATTTCAATTGC
*
344037 ACCTATTCATTGCGACCAATTTCAATTGC
1 ACCTATTCATTGCAACCAATTTCAATTGC
344066 ACC
1 ACC
344069 AGTCGATGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.33
Consensus pattern (29 bp):
ACCTATTCATTGCAACCAATTTCAATTGC
Found at i:344069 original size:15 final size:15
Alignment explanation
Indices: 344013--344066 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
344003 GTTGTACCTA
344013 TTCATTGCAACCAAT
1 TTCATTGCAACCAAT
*
344028 TTCGATTGC-ACCTA-
1 TTC-ATTGCAACCAAT
*
344042 TTCATTGCGACCAAT
1 TTCATTGCAACCAAT
344057 TTCAATTGCA
1 TTC-ATTGCA
344067 CCAGTCGATG
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
13 5 0.16
14 7 0.22
15 10 0.31
16 10 0.31
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (15 bp):
TTCATTGCAACCAAT
Found at i:344222 original size:3 final size:3
Alignment explanation
Indices: 344214--344243 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
344204 GTAGAAAATT
344214 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
344244 AAGTAAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:344586 original size:16 final size:17
Alignment explanation
Indices: 344554--344592 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
344544 AATCTAATTC
*
344554 ATTTGATATATTTAAAT
1 ATTTTATATATTTAAAT
344571 ATTTTATATA-TTAAAT
1 ATTTTATATATTTAAAT
344587 ATTTTA
1 ATTTTA
344593 CAAAAATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
ATTTTATATATTTAAAT
Found at i:345627 original size:2 final size:2
Alignment explanation
Indices: 345620--345657 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
345610 TCAAGTAATC
345620 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
345658 TTAAACTCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:345887 original size:17 final size:17
Alignment explanation
Indices: 345852--345890 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
345842 TTCAATTGTT
**
345852 TTAAATATTTTAATTAA
1 TTAAATATTTTAAAAAA
*
345869 TTAAATTTTTTAAAAAA
1 TTAAATATTTTAAAAAA
345886 TTAAA
1 TTAAA
345891 GATTACTTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTAAATATTTTAAAAAA
Found at i:351759 original size:50 final size:50
Alignment explanation
Indices: 351686--351988 Score: 275
Period size: 50 Copynumber: 6.1 Consensus size: 50
351676 AATTTATTTA
* ** *
351686 ACTGCAATGTCGGGGAAGAAAGATTTTCCGTTGTGGCTTCAATCTGTTCC
1 ACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCC
** * * * ** * * **
351736 ACTGCACCGCCTGAGAAGTAAGATTCGCTATTTTAGCTTCAATCTTTTTA
1 ACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCC
* *
351786 ACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCC
1 ACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCC
* ** * * * * **
351836 ACTGC-ATCGTCTGAAAAGTAAGATTCGCTGCTGTAGCTTTAATCTTTTTA
1 ACTGCAAT-GTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCC
* * * *
351886 ACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTCAATCTATTCC
1 ACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCC
* * ** *
351936 ACTGCAATGTCAGGGAAATAAGATTAACCGTCGTAGCTTCAATCTGTTCC
1 ACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCC
351986 ACT
1 ACT
351989 ACTGCTTAGG
Statistics
Matches: 197, Mismatches: 54, Indels: 4
0.77 0.21 0.02
Matches are distributed among these distances:
49 2 0.01
50 193 0.98
51 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.32
Consensus pattern (50 bp):
ACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCC
Found at i:351855 original size:100 final size:100
Alignment explanation
Indices: 351682--351941 Score: 394
Period size: 100 Copynumber: 2.6 Consensus size: 100
351672 GTCCAATTTA
* **
351682 TTTAACTGCAATGTCGGGGAAGAAAGATTTTCCGTTGTGGCTTCAATCTGTTCCACTGCACCGCC
1 TTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTCAATCTGTTCCACTGCACCGCC
* * *
351747 TGAGAAGTAAGATTCGCTATTTTAGCTTCAATCTT
66 TGAAAAGTAAGATTCGCTACTGTAGCTTCAATCTT
* * * * *
351782 TTTAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTGCATCGTC
1 TTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTCAATCTGTTCCACTGCACCGCC
* *
351847 TGAAAAGTAAGATTCGCTGCTGTAGCTTTAATCTT
66 TGAAAAGTAAGATTCGCTACTGTAGCTTCAATCTT
*
351882 TTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTCAATCTATTCCACTGCA
1 TTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTCAATCTGTTCCACTGCA
351942 ATGTCAGGGA
Statistics
Matches: 144, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
100 144 1.00
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (100 bp):
TTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTCAATCTGTTCCACTGCACCGCC
TGAAAAGTAAGATTCGCTACTGTAGCTTCAATCTT
Found at i:351972 original size:100 final size:99
Alignment explanation
Indices: 351682--351980 Score: 350
Period size: 100 Copynumber: 3.0 Consensus size: 99
351672 GTCCAATTTA
* ** ** *
351682 TTTAACTGCAATGTCGGGGAAGAAAGATTTTCCGTTGTGGCTTCAATCTGTTCCACTGCACCGCC
1 TTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTCAATCTGTTCCACTGCAATGTC
* * * **
351747 TGAGAAGTAAGATTCGCTATTTTAGCTTCAATCTT
66 -GGGAAATAAGATTCGCTGTCGTAGCTTCAATCTT
* * *
351782 TTTAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTGC-ATCGT
1 TTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTCAATCTGTTCCACTGCAAT-GT
* * *
351846 CTGAAAAGTAAGATTCGCTG-CTGTAGCTTTAATCTT
65 CGGGAAA-TAAGATTCGCTGTC-GTAGCTTCAATCTT
*
351882 TTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTCAATCTATTCCACTGCAATGTC
1 TTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTCAATCTGTTCCACTGCAATGTC
** *
351947 AGGGAAATAAGATTAACCGTCGTAGCTTCAATCT
66 -GGGAAATAAGATTCGCTGTCGTAGCTTCAATCT
351981 GTTCCACTAC
Statistics
Matches: 167, Mismatches: 26, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
99 2 0.01
100 158 0.95
101 7 0.04
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.32
Consensus pattern (99 bp):
TTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTCAATCTGTTCCACTGCAATGTC
GGGAAATAAGATTCGCTGTCGTAGCTTCAATCTT
Found at i:352138 original size:44 final size:44
Alignment explanation
Indices: 352040--352141 Score: 161
Period size: 44 Copynumber: 2.3 Consensus size: 44
352030 ACTACTGCTA
*
352040 AGGGAGATAAGGCTTACAATCTTCAACCTATTCCTACTGCTAACC
1 AGGGAGAT-AGGATTACAATCTTCAACCTATTCCTACTGCTAACC
*
352085 AGGGAGATAGGATTCACAATCTTCAACCTATTCC-ACTGCTGACC
1 AGGGAGATAGGATT-ACAATCTTCAACCTATTCCTACTGCTAACC
352129 AGGGAGATAGGAT
1 AGGGAGATAGGAT
352142 CAGTGGCTTA
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
44 27 0.50
45 27 0.50
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.25
Consensus pattern (44 bp):
AGGGAGATAGGATTACAATCTTCAACCTATTCCTACTGCTAACC
Found at i:354292 original size:6 final size:6
Alignment explanation
Indices: 354283--354359 Score: 120
Period size: 6 Copynumber: 12.7 Consensus size: 6
354273 TGGCCTCTCC
*
354283 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCC
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
354331 TTTTCT TTTT-T CTTTTCTT TTTTCT TTTT
1 TTTTCT TTTTCT -TTTTC-T TTTTCT TTTT
354360 ATCATTGTCA
Statistics
Matches: 66, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
5 1 0.02
6 59 0.89
7 5 0.08
8 1 0.02
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:354435 original size:21 final size:21
Alignment explanation
Indices: 354395--354434 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
354385 ACTTTGATCA
354395 TTTTTTAATTTTGACTTTTTC
1 TTTTTTAATTTTGACTTTTTC
*
354416 TTTTTT-ATTTTGATTTTTT
1 TTTTTTAATTTTGACTTTTT
354435 TATTGAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.12, C:0.05, G:0.05, T:0.78
Consensus pattern (21 bp):
TTTTTTAATTTTGACTTTTTC
Found at i:355574 original size:24 final size:24
Alignment explanation
Indices: 355516--355576 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
355506 GAAGAAAATC
* *
355516 CAAAATAATGAAAGAATAATTATT
1 CAAAAAAATGAAAGAATAATTACT
* *
355540 CGAAAAGAATGAAAGAAT-ATTGGCT
1 C-AAAAAAATGAAAGAATAATT-ACT
355565 CAAAAAAATGAA
1 CAAAAAAATGAA
355577 TGCAAAGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
24 14 0.45
25 17 0.55
ACGTcount: A:0.57, C:0.07, G:0.15, T:0.21
Consensus pattern (24 bp):
CAAAAAAATGAAAGAATAATTACT
Found at i:356448 original size:9 final size:9
Alignment explanation
Indices: 356434--356468 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
356424 TCTGCCTGCA
356434 TTATTCCCC
1 TTATTCCCC
356443 TTATTCCCC
1 TTATTCCCC
*
356452 TTATTCCTC
1 TTATTCCCC
*
356461 TTCTTCCC
1 TTATTCCC
356469 TAGGACCCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.09, C:0.43, G:0.00, T:0.49
Consensus pattern (9 bp):
TTATTCCCC
Found at i:357036 original size:27 final size:27
Alignment explanation
Indices: 356976--357038 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
356966 AGACTAATAA
356976 GCGGCACCAAAGGTGCCATTCCCATAG
1 GCGGCACCAAAGGTGCCATTCCCATAG
* * * *
357003 GCAGCACCGATGGTGCCATTCCCATGG
1 GCGGCACCAAAGGTGCCATTCCCATAG
*
357030 GTGGCACCA
1 GCGGCACCA
357039 CTCATGTTAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.22, C:0.33, G:0.29, T:0.16
Consensus pattern (27 bp):
GCGGCACCAAAGGTGCCATTCCCATAG
Found at i:357395 original size:40 final size:36
Alignment explanation
Indices: 357335--357420 Score: 93
Period size: 40 Copynumber: 2.3 Consensus size: 36
357325 AAACTAGTAT
* * *
357335 TATTATTATGGTTAGTTATTATTTTTAGTA-AAACCC
1 TATTATTATTGTTAGTTATTATTTTGAGTATAAA-AC
357371 TAATTATTATTGTTAGTTACTATTATTTTGAGTATAAAAC
1 T-ATTATTATTGTTAG-T--TATTATTTTGAGTATAAAAC
357411 TATTATTATT
1 TATTATTATT
357421 TTTATTGTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
36 1 0.02
37 13 0.31
38 1 0.02
39 9 0.21
40 15 0.36
41 3 0.07
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.52
Consensus pattern (36 bp):
TATTATTATTGTTAGTTATTATTTTGAGTATAAAAC
Found at i:362913 original size:158 final size:155
Alignment explanation
Indices: 362513--362966 Score: 473
Period size: 158 Copynumber: 2.9 Consensus size: 155
362503 GCATGTTGAA
* *
362513 AAAAAAGTTAGTAAAACACTCTTACTTCGGACATTTCTTCGTATTTTTTTCTCAGCATTTTATTA
1 AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTTCTCAGCATTTTATTA
* * * * *
362578 TTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTAAGTGCATTATGTTTG-AA
66 CTTTAAAAAATATCATATTTTCTAATTTTATAATTTTATATTATTTCAGTGCATTTTGTTTGAAA
* *
362642 -ATTTATTAATTTAGTGTGTTTTTT
131 TATTTATTAATTTAGTCTGATTTTT
* * * * * * * * *
362666 AAATTAATTTAGTGTCAAAAAACCCTTA-TTCCTGCC-CTTCGCTCGTATTATTTTC-CCGAATT
1 AAA-AAATTTA--GT-AAAACACTCTTACTT-CGGCCATTTC-TTCGTATTTTTTTCTCAGCATT
* * *
362728 TTATTACTTTCAATAAAAAAT-ATTATTTTCGT-ATTTTATTATTTTATATTATTTCAGTACATT
60 TTATTACTTT-AA-AAAATATCA-TATTTTC-TAATTTTATAATTTTATATTATTTCAGTGCATT
*
362791 TTGTTTGAAATATTTGTATTAA-TTATTTCTGAATTTTT
121 TTGTTTGAAATA-TT-TATTAATTTA-GTCTG-ATTTTT
*
362829 AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTTCTCTGCATTTTATTA
1 AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTTCTCAGCATTTTATTA
362894 CTTTAAAAAATATCATATTTTCTAATTTTATAATTTTACT-TTATTTCAGTGC-TTTATGTTTG-
66 CTTTAAAAAATATCATATTTTCTAATTTTATAATTTTA-TATTATTTCAGTGCATTT-TGTTTGA
362956 AA-ATTTATTAA
129 AATATTTATTAA
362967 ATATGCCATT
Statistics
Matches: 244, Mismatches: 34, Indels: 45
0.76 0.11 0.14
Matches are distributed among these distances:
153 3 0.01
154 11 0.05
155 2 0.01
156 22 0.09
157 34 0.14
158 88 0.36
159 33 0.14
160 23 0.09
161 5 0.02
162 15 0.06
163 8 0.03
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (155 bp):
AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTTCTCAGCATTTTATTA
CTTTAAAAAATATCATATTTTCTAATTTTATAATTTTATATTATTTCAGTGCATTTTGTTTGAAA
TATTTATTAATTTAGTCTGATTTTT
Found at i:363385 original size:10 final size:10
Alignment explanation
Indices: 363357--363494 Score: 71
Period size: 10 Copynumber: 14.0 Consensus size: 10
363347 TTCTTCTTTT
363357 TTTTCTCTTCTC
1 TTTTCT-TTC-C
*
363369 TTTTCCTTTTC
1 TTTT-CTTTCC
* *
363380 -TTTCCTTCT
1 TTTTCTTTCC
*
363389 TTTTCTTTCT
1 TTTTCTTTCC
*
363399 TTTTGCTTATTC
1 TTTT-CTT-TCC
363411 -TT-CTTTCC
1 TTTTCTTTCC
363419 TTTTCTTTCC
1 TTTTCTTTCC
363429 TTCTT-TTT-C
1 TT-TTCTTTCC
363438 -TTTCTTTCC
1 TTTTCTTTCC
*
363447 -TCTCATTTCC
1 TTTTC-TTTCC
*
363457 TTTTCTTTCT
1 TTTTCTTTCC
363467 TTTTCTTT-C
1 TTTTCTTTCC
363476 -TTTCTTT-C
1 TTTTCTTTCC
363484 TTCTTCTTTCC
1 TT-TTCTTTCC
363495 CTCTCCTTCT
Statistics
Matches: 100, Mismatches: 12, Indels: 29
0.71 0.09 0.21
Matches are distributed among these distances:
7 2 0.02
8 14 0.14
9 14 0.14
10 49 0.49
11 12 0.12
12 7 0.07
13 2 0.02
ACGTcount: A:0.01, C:0.28, G:0.01, T:0.70
Consensus pattern (10 bp):
TTTTCTTTCC
Done.