Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 79 of 103
Found at i:29552003 original size:12 final size:11
Alignment explanation
Indices: 29551962--29552013 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
29551952 TTATGGAGAC
29551962 AAAATTA-TAA
1 AAAATTATTAA
*
29551972 AAAATTTTTAA
1 AAAATTATTAA
29551983 AAAA-TA--AA
1 AAAATTATTAA
*
29551991 AATA-TATTAA
1 AAAATTATTAA
29552001 AAAATTATTAA
1 AAAATTATTAA
29552012 AA
1 AA
29552014 TTTTATGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
8 7 0.21
10 12 0.35
11 15 0.44
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AAAATTATTAA
Found at i:29554870 original size:17 final size:16
Alignment explanation
Indices: 29554848--29554882 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
29554838 TCATTTTTTA
29554848 TTATTTAATTATTATTT
1 TTATTTAATT-TTATTT
*
29554865 TTATTTTATTTTATTT
1 TTATTTAATTTTATTT
29554881 TT
1 TT
29554883 TATTATCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTATTTAATTTTATTT
Found at i:29554876 original size:32 final size:32
Alignment explanation
Indices: 29554821--29554907 Score: 92
Period size: 32 Copynumber: 2.7 Consensus size: 32
29554811 ATGCTAATGC
*
29554821 AATTATCTATTTTT-TTGTCATTTTTTATTATTT
1 AATTATCTATTTTTATT-TTATTTTTTATT-TTT
29554854 AATTAT-TATTTTTATTTTA--TTTTATTTTT
1 AATTATCTATTTTTATTTTATTTTTTATTTTT
*
29554883 TATTATCATATTTTCTATTTTATTT
1 AATTATC-TATTTT-TATTTTATTT
29554908 CTAATTANNN
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
29 8 0.17
30 7 0.15
31 6 0.13
32 16 0.35
33 8 0.17
34 1 0.02
ACGTcount: A:0.23, C:0.05, G:0.01, T:0.71
Consensus pattern (32 bp):
AATTATCTATTTTTATTTTATTTTTTATTTTT
Found at i:29556000 original size:16 final size:16
Alignment explanation
Indices: 29555966--29556004 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
29555956 TGTCATGGTA
** *
29555966 ATTTTTATATATTTTT
1 ATTTTTATATACATGT
29555982 ATTTTTATATACATGT
1 ATTTTTATATACATGT
29555998 ATTTTTA
1 ATTTTTA
29556005 ATGGTTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (16 bp):
ATTTTTATATACATGT
Found at i:29569796 original size:89 final size:89
Alignment explanation
Indices: 29569645--29569823 Score: 340
Period size: 89 Copynumber: 2.0 Consensus size: 89
29569635 CTTAATTAAT
*
29569645 TACATCCACTTGATCTCTAAAATTTCATGAAGTTTTAACACCCTAGAATGGCATTCTAAGAACTA
1 TACATCCACTTAATCTCTAAAATTTCATGAAGTTTTAACACCCTAGAATGGCATTCTAAGAACTA
29569710 CATGTATATTAATCTCCAAGACTA
66 CATGTATATTAATCTCCAAGACTA
29569734 TACATCCACTTAATCTCTAAAATTTCATGAAGTTTTAACACCCTAGAATGGCATTCTAAGAACTA
1 TACATCCACTTAATCTCTAAAATTTCATGAAGTTTTAACACCCTAGAATGGCATTCTAAGAACTA
*
29569799 CATGTATATTAATCTTCAAGACTA
66 CATGTATATTAATCTCCAAGACTA
29569823 T
1 T
29569824 CTCCCACCTT
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 88 1.00
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (89 bp):
TACATCCACTTAATCTCTAAAATTTCATGAAGTTTTAACACCCTAGAATGGCATTCTAAGAACTA
CATGTATATTAATCTCCAAGACTA
Found at i:29575375 original size:2 final size:2
Alignment explanation
Indices: 29575370--29575398 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29575360 ATATATATAT
29575370 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
29575399 CAAAACGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29575444 original size:2 final size:2
Alignment explanation
Indices: 29575439--29575466 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29575429 ATATATATAT
29575439 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
29575467 CAAAAACGAA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29584581 original size:39 final size:39
Alignment explanation
Indices: 29584527--29584603 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
29584517 CTTCACCGTA
* *
29584527 CAATGCATATTTTTGGTTGTTTTCTGGTTTGCTGGAATT
1 CAATGCATATTTTTGGTTGTTTTCTAGTTCGCTGGAATT
*
29584566 CAATGCATGTTTTTGGTTGTTTTCTAGTTCGCTGGAAT
1 CAATGCATATTTTTGGTTGTTTTCTAGTTCGCTGGAAT
29584604 GAGCCTTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.16, C:0.12, G:0.23, T:0.49
Consensus pattern (39 bp):
CAATGCATATTTTTGGTTGTTTTCTAGTTCGCTGGAATT
Found at i:29585094 original size:20 final size:21
Alignment explanation
Indices: 29585055--29585095 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
29585045 TGCTGCTATA
29585055 AGTTTCCAGCACCATCCTTTTC
1 AGTTTCCAG-ACCATCCTTTTC
*
29585077 AGTTTCCAG-CCATTCTTTT
1 AGTTTCCAGACCATCCTTTT
29585096 GTAATCAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
22 9 0.50
ACGTcount: A:0.17, C:0.32, G:0.10, T:0.41
Consensus pattern (21 bp):
AGTTTCCAGACCATCCTTTTC
Found at i:29599254 original size:2 final size:2
Alignment explanation
Indices: 29599247--29599278 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
29599237 CAGTGCAGAC
29599247 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
29599279 TTGGAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:29603142 original size:21 final size:21
Alignment explanation
Indices: 29603118--29603180 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
29603108 TTACCAGTGA
* *
29603118 TTCTCCCAGGTTTAACATTGG
1 TTCTCCCAGGTTTAACACTAG
*
29603139 TTCTCCCAGGTTTAATACTAG
1 TTCTCCCAGGTTTAACACTAG
*
29603160 TTCTCCCAGGTTTAATACTAG
1 TTCTCCCAGGTTTAACACTAG
29603181 CTTCAAGAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (21 bp):
TTCTCCCAGGTTTAACACTAG
Found at i:29608353 original size:3 final size:3
Alignment explanation
Indices: 29608345--29608372 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
29608335 TGAAAGTAAT
29608345 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
29608373 GATTCGACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:29614503 original size:24 final size:23
Alignment explanation
Indices: 29614465--29614536 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 23
29614455 TAGAAAGAAC
29614465 AAACAAA-AAACCAAAACAAGACAA
1 AAACAAACAAA-CAAAACAA-ACAA
**
29614489 AAACAAACAAACAAAGGAAACAA
1 AAACAAACAAACAAAACAAACAA
29614512 AAGA-AAACCAAACAAAACAAACAA
1 AA-ACAAA-CAAACAAAACAAACAA
29614536 A
1 A
29614537 CACTGGGTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
23 9 0.22
24 29 0.71
25 3 0.07
ACGTcount: A:0.75, C:0.19, G:0.06, T:0.00
Consensus pattern (23 bp):
AAACAAACAAACAAAACAAACAA
Found at i:29614537 original size:28 final size:28
Alignment explanation
Indices: 29614462--29614538 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 28
29614452 TACTAGAAAG
* *
29614462 AACAAACAAAA-AACCAAAACAAGACAAA
1 AACAAACAAAACAAAC-AAACAAAACAAA
* *
29614490 AACAAAC-AAACAAAGGAAACAAAAGAAA
1 AACAAACAAAACAAA-CAAACAAAACAAA
*
29614518 ACCAAACAAAACAAACAAACA
1 AACAAACAAAACAAACAAACA
29614539 CTGGGTTAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
27 3 0.08
28 30 0.75
29 7 0.17
ACGTcount: A:0.74, C:0.21, G:0.05, T:0.00
Consensus pattern (28 bp):
AACAAACAAAACAAACAAACAAAACAAA
Found at i:29617939 original size:75 final size:75
Alignment explanation
Indices: 29617801--29617941 Score: 180
Period size: 75 Copynumber: 1.9 Consensus size: 75
29617791 TATTCATATG
* * * * * *
29617801 TCAATTATATCATGTGAACATAATATTATTGTGATAAGTTAAGTTGGTACATGAACAGATAAAAT
1 TCAATTATATCATATGAACAGAATATTATTGTGATAAATTAAGTTGGCACATAAAAAGATAAAAT
29617866 TAACCATGTC
66 TAACCATGTC
29617876 TCAATTATATCATATGAACAGAATATTATCT-TGATAAATTAA-TATGGCACATAAATAAG-TAA
1 TCAATTATATCATATGAACAGAATATTAT-TGTGATAAATTAAGT-TGGCACATAAA-AAGATAA
29617938 AATT
63 AATT
29617942 CAAAAAATTT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
74 1 0.02
75 53 0.93
76 3 0.05
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (75 bp):
TCAATTATATCATATGAACAGAATATTATTGTGATAAATTAAGTTGGCACATAAAAAGATAAAAT
TAACCATGTC
Found at i:29620953 original size:39 final size:39
Alignment explanation
Indices: 29620899--29620974 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
29620889 AACTAGGAAA
*
29620899 CTTTAACAGATAAGGAAGGAACGTTATCCTATGTACCTT
1 CTTTAACAGATAAGGAAGGAACGTTATCCTATATACCTT
* *
29620938 CTTTAACATATAAGGAAGGAACTTTATCCTATATACC
1 CTTTAACAGATAAGGAAGGAACGTTATCCTATATACC
29620975 GGCACTGGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (39 bp):
CTTTAACAGATAAGGAAGGAACGTTATCCTATATACCTT
Found at i:29622357 original size:2 final size:2
Alignment explanation
Indices: 29622350--29622376 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29622340 TCTTATTTAA
29622350 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
29622377 AAGGCTCGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:29625335 original size:19 final size:18
Alignment explanation
Indices: 29625294--29625337 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
29625284 TAATATTTTC
29625294 ATAAAATAATAAAAAAGA
1 ATAAAATAATAAAAAAGA
*
29625312 ATAAAATGATAAATGAAA-A
1 ATAAAATAATAAA--AAAGA
29625331 ATAAAAT
1 ATAAAAT
29625338 TATTTTGTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 12 0.52
19 8 0.35
20 3 0.13
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (18 bp):
ATAAAATAATAAAAAAGA
Found at i:29641824 original size:2 final size:2
Alignment explanation
Indices: 29641807--29641900 Score: 126
Period size: 2 Copynumber: 49.0 Consensus size: 2
29641797 AATAAAATGA
*
29641807 AG AG AG GG A- AG A- AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
29641847 AG AG AG AG AG AG AG AG -G A- AG A- AT AG NAG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG -AG AG AG AG AG AG AG
29641887 AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG
29641901 GAAGTAAGAT
Statistics
Matches: 83, Mismatches: 3, Indels: 12
0.85 0.03 0.12
Matches are distributed among these distances:
1 5 0.06
2 76 0.92
3 2 0.02
ACGTcount: A:0.50, C:0.00, G:0.48, T:0.01
Consensus pattern (2 bp):
AG
Found at i:29645482 original size:38 final size:38
Alignment explanation
Indices: 29645431--29645507 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
29645421 GTTAAAAGAT
* *
29645431 AGAATGATTTCTACTGATATTAGGCTTCTTATAGATGA
1 AGAATCATTTCTACTGATATTAGGCATCTTATAGATGA
29645469 AGAATCATTTCTACTGATATTAGGCATCTTATAGATGA
1 AGAATCATTTCTACTGATATTAGGCATCTTATAGATGA
29645507 A
1 A
29645508 CAAGTTGACT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.38
Consensus pattern (38 bp):
AGAATCATTTCTACTGATATTAGGCATCTTATAGATGA
Found at i:29662641 original size:28 final size:30
Alignment explanation
Indices: 29662596--29662663 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
29662586 GAAAAATTTT
*
29662596 AAATAAA-TATTTATTTTTTATTAT-AAT-
1 AAATAAATTTTTTATTTTTTATTATAAATC
*
29662623 AAATTAAATTTTTTA-TTTTTATTTTAAATC
1 AAA-TAAATTTTTTATTTTTTATTATAAATC
29662653 AAATAAATTTT
1 AAATAAATTTT
29662664 ATATAAAAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 3 0.09
28 13 0.37
29 16 0.46
30 3 0.09
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (30 bp):
AAATAAATTTTTTATTTTTTATTATAAATC
Found at i:29671309 original size:14 final size:14
Alignment explanation
Indices: 29671273--29671376 Score: 51
Period size: 14 Copynumber: 7.6 Consensus size: 14
29671263 TTCTAATTTT
*
29671273 TAATAAAAAATTAA
1 TAATAAAATATTAA
*
29671287 TATTTTAAAATATTAA
1 TA--ATAAAATATTAA
*
29671303 TAATAAATTA-T-A
1 TAATAAAATATTAA
29671315 -AATAAAATATTAA
1 TAATAAAATATTAA
* *
29671328 TAGTTTAAATATTAA
1 TA-ATAAAATATTAA
*
29671343 -AAT-TAA-ATT-A
1 TAATAAAATATTAA
*
29671353 TAAACAAAATATTAA
1 T-AATAAAATATTAA
*
29671368 TAATTAAAT
1 TAATAAAAT
29671377 TATCAATTAT
Statistics
Matches: 66, Mismatches: 13, Indels: 22
0.65 0.13 0.22
Matches are distributed among these distances:
10 1 0.02
11 11 0.17
12 6 0.09
13 5 0.08
14 19 0.29
15 12 0.18
16 12 0.18
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (14 bp):
TAATAAAATATTAA
Found at i:29671350 original size:40 final size:41
Alignment explanation
Indices: 29671274--29671369 Score: 142
Period size: 40 Copynumber: 2.4 Consensus size: 41
29671264 TCTAATTTTT
* *
29671274 AATAAAAAATTAATATTTTAAAATATTAATAATAAATTATA
1 AATAAAATATTAATAGTTTAAAATATTAATAATAAATTATA
29671315 AATAAAATATTAATAGTTT-AAATATTAA-AATTAAATTATA
1 AATAAAATATTAATAGTTTAAAATATTAATAA-TAAATTATA
*
29671355 AACAAAATATTAATA
1 AATAAAATATTAATA
29671370 ATTAAATTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
39 2 0.04
40 32 0.63
41 17 0.33
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (41 bp):
AATAAAATATTAATAGTTTAAAATATTAATAATAAATTATA
Found at i:29671402 original size:23 final size:22
Alignment explanation
Indices: 29671362--29671410 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
29671352 ATAAACAAAA
* *
29671362 TATTAATAATTAAATTATCAAT
1 TATTAATAAATAAATTATAAAT
29671384 TATTAATAAAATAAATTATAAAT
1 TATTAAT-AAATAAATTATAAAT
29671407 TATT
1 TATT
29671411 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TATTAATAAATAAATTATAAAT
Found at i:29672239 original size:15 final size:15
Alignment explanation
Indices: 29672219--29672292 Score: 59
Period size: 15 Copynumber: 5.2 Consensus size: 15
29672209 TTAAGTTAAA
*
29672219 TAAAATACTAATATT
1 TAAATTACTAATATT
* *
29672234 TAAAATATTAATGA-T
1 TAAATTACTAAT-ATT
29672249 TAAATTA-TAA-A--
1 TAAATTACTAATATT
29672260 TAAATTACTAATATT
1 TAAATTACTAATATT
* *
29672275 TAAATTATTAATTTT
1 TAAATTACTAATATT
29672290 TAA
1 TAA
29672293 TATATTAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
11 7 0.14
12 4 0.08
13 1 0.02
14 3 0.06
15 34 0.68
16 1 0.02
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (15 bp):
TAAATTACTAATATT
Found at i:29672933 original size:15 final size:15
Alignment explanation
Indices: 29672913--29672952 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
29672903 AATAAATTCA
*
29672913 TGTTGATGTGACACT
1 TGTTGATGTGACAAT
* *
29672928 TGTTGATATGATAAT
1 TGTTGATGTGACAAT
29672943 TGTTGATGTG
1 TGTTGATGTG
29672953 GCTATTAATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.23, C:0.05, G:0.28, T:0.45
Consensus pattern (15 bp):
TGTTGATGTGACAAT
Found at i:29673422 original size:16 final size:16
Alignment explanation
Indices: 29673401--29673431 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29673391 CCACCCAAGA
*
29673401 CCCTAACTGGCTAACT
1 CCCTAACCGGCTAACT
29673417 CCCTAACCGGCTAAC
1 CCCTAACCGGCTAAC
29673432 CCAGTAACCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.42, G:0.13, T:0.19
Consensus pattern (16 bp):
CCCTAACCGGCTAACT
Found at i:29673597 original size:88 final size:88
Alignment explanation
Indices: 29673439--29673628 Score: 290
Period size: 88 Copynumber: 2.2 Consensus size: 88
29673429 AACCCAGTAA
** *
29673439 CCCCAAATCCACAAATCCCCAAATCCCCCACCGCCCGACTGCCCGAGCCATCTGTTATGCACCGT
1 CCCCAAATCGGCAAATCCCCAAATACCCCACCGCCCGACTGCCCGAGCCATCTGTTATGCACCGT
*
29673504 CGCTCGACTTTTGGACAAAAATT
66 AGCTCGACTTTTGGACAAAAATT
* * * * * *
29673527 CCCTAAATCGGCAAATCCCCAAATACCCCGCCGCCTGACTGCTCGAGCCATCTGTTCTGCACTGT
1 CCCCAAATCGGCAAATCCCCAAATACCCCACCGCCCGACTGCCCGAGCCATCTGTTATGCACCGT
29673592 AGCTCGACTTTTGGACAAAAATT
66 AGCTCGACTTTTGGACAAAAATT
29673615 CCCCAAATCGGCAA
1 CCCCAAATCGGCAA
29673629 TCAGCAATCG
Statistics
Matches: 91, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 91 1.00
ACGTcount: A:0.26, C:0.38, G:0.15, T:0.21
Consensus pattern (88 bp):
CCCCAAATCGGCAAATCCCCAAATACCCCACCGCCCGACTGCCCGAGCCATCTGTTATGCACCGT
AGCTCGACTTTTGGACAAAAATT
Found at i:29675494 original size:14 final size:14
Alignment explanation
Indices: 29675458--29675561 Score: 51
Period size: 14 Copynumber: 7.6 Consensus size: 14
29675448 TTCTAATTTT
*
29675458 TAATAAAAAATTAA
1 TAATAAAATATTAA
*
29675472 TATTTTAAAATATTAA
1 TA--ATAAAATATTAA
*
29675488 TAATAAATTA-T-A
1 TAATAAAATATTAA
29675500 -AATAAAATATTAA
1 TAATAAAATATTAA
* *
29675513 TAGTTTAAATATTAA
1 TA-ATAAAATATTAA
*
29675528 -AAT-TAA-ATT-A
1 TAATAAAATATTAA
*
29675538 TAAACAAAATATTAA
1 T-AATAAAATATTAA
*
29675553 TAATTAAAT
1 TAATAAAAT
29675562 TATCAATTAT
Statistics
Matches: 66, Mismatches: 13, Indels: 22
0.65 0.13 0.22
Matches are distributed among these distances:
10 1 0.02
11 11 0.17
12 6 0.09
13 5 0.08
14 19 0.29
15 12 0.18
16 12 0.18
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (14 bp):
TAATAAAATATTAA
Found at i:29675535 original size:40 final size:41
Alignment explanation
Indices: 29675459--29675554 Score: 142
Period size: 40 Copynumber: 2.4 Consensus size: 41
29675449 TCTAATTTTT
* *
29675459 AATAAAAAATTAATATTTTAAAATATTAATAATAAATTATA
1 AATAAAATATTAATAGTTTAAAATATTAATAATAAATTATA
29675500 AATAAAATATTAATAGTTT-AAATATTAA-AATTAAATTATA
1 AATAAAATATTAATAGTTTAAAATATTAATAA-TAAATTATA
*
29675540 AACAAAATATTAATA
1 AATAAAATATTAATA
29675555 ATTAAATTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
39 2 0.04
40 32 0.63
41 17 0.33
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (41 bp):
AATAAAATATTAATAGTTTAAAATATTAATAATAAATTATA
Found at i:29675587 original size:23 final size:22
Alignment explanation
Indices: 29675547--29675595 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
29675537 ATAAACAAAA
* *
29675547 TATTAATAATTAAATTATCAAT
1 TATTAATAAATAAATTATAAAT
29675569 TATTAATAAAATAAATTATAAAT
1 TATTAAT-AAATAAATTATAAAT
29675592 TATT
1 TATT
29675596 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TATTAATAAATAAATTATAAAT
Found at i:29680541 original size:19 final size:19
Alignment explanation
Indices: 29680481--29680541 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
29680471 CTATGTTGTA
* *
29680481 TAAAAAAATTGATATAATAT
1 TAAAAAAATTTAAATAA-AT
*
29680501 CTAAAAAAATATTAAAT-TAT
1 -TAAAAAAAT-TTAAATAAAT
29680521 TAAAAAAATTTAAATAAAT
1 TAAAAAAATTTAAATAAAT
29680540 TA
1 TA
29680542 TTATTGTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 6 0.18
19 13 0.38
20 2 0.06
21 9 0.26
22 4 0.12
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (19 bp):
TAAAAAAATTTAAATAAAT
Found at i:29689641 original size:2 final size:2
Alignment explanation
Indices: 29689634--29689658 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29689624 ATTGTTTTAA
29689634 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
29689659 AACTATCTCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29707128 original size:167 final size:166
Alignment explanation
Indices: 29706844--29707182 Score: 543
Period size: 167 Copynumber: 2.0 Consensus size: 166
29706834 TAGGTACATT
* ** **
29706844 AACTAGTCCTGCTTACTTGTTTGCTGTGTACTATGGTTTATGGATACTATTGATGATTGTTTCTC
1 AACTAGTCCTGCTTACTTGTTTACCATGTACTATGGTTTATGGATACTATTGATGATAATTTCTC
* * * *
29706909 TAGGCCTCTTGGATATTACTGTTTCCACCCTTTTTCTCTCTTTTCTCTCTGAGTTGCCTCTAGTA
66 TAGGCCTCTTGGATATGACTGTTTCCACCCTTTTTCCCCCTTTTCCCTCTGAGTTGCCTCTAGTA
*
29706974 GCCTCCTTTTCTCTCTACCCCTTCATCACATGTTACA
131 GCCT-CTTTTCTCTCTACACCTTCATCACATGTTACA
*
29707011 AACTAGTCCTGTTTACTTGTTTACCATGTACTATGGTTTATGGATACTATTGATGATAATTTCTC
1 AACTAGTCCTGCTTACTTGTTTACCATGTACTATGGTTTATGGATACTATTGATGATAATTTCTC
* * *
29707076 TAGGCCTCTTGGATATGACTGTTTCCTCTCTTTTTCCCCCTTTTCCCTCTGAGTTGCCTCTAGTC
66 TAGGCCTCTTGGATATGACTGTTTCCACCCTTTTTCCCCCTTTTCCCTCTGAGTTGCCTCTAGTA
29707141 GCCTCTTTTCTCTCTACACCTTCATCACATGTTACA
131 GCCTCTTTTCTCTCTACACCTTCATCACATGTTACA
29707177 AACTAG
1 AACTAG
29707183 GTGTGTAAAA
Statistics
Matches: 158, Mismatches: 14, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
166 37 0.23
167 121 0.77
ACGTcount: A:0.17, C:0.26, G:0.14, T:0.43
Consensus pattern (166 bp):
AACTAGTCCTGCTTACTTGTTTACCATGTACTATGGTTTATGGATACTATTGATGATAATTTCTC
TAGGCCTCTTGGATATGACTGTTTCCACCCTTTTTCCCCCTTTTCCCTCTGAGTTGCCTCTAGTA
GCCTCTTTTCTCTCTACACCTTCATCACATGTTACA
Found at i:29709633 original size:53 final size:54
Alignment explanation
Indices: 29709561--29709667 Score: 162
Period size: 53 Copynumber: 2.0 Consensus size: 54
29709551 CTTCTGATCA
29709561 TCTAGTTAAAATAGAACCACATAAACTAAG-TTAAAGCAAATAGTGGTGTAGTC
1 TCTAGTTAAAATAGAACCACATAAACTAAGTTTAAAGCAAATAGTGGTGTAGTC
* * * * *
29709614 TCTAGTTATAATTGTACCACATAAACTATGTTTAAAGTAAATAGTGGTGTAGTC
1 TCTAGTTAAAATAGAACCACATAAACTAAGTTTAAAGCAAATAGTGGTGTAGTC
29709668 AAACTTTCAG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
53 26 0.54
54 22 0.46
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (54 bp):
TCTAGTTAAAATAGAACCACATAAACTAAGTTTAAAGCAAATAGTGGTGTAGTC
Found at i:29712907 original size:15 final size:15
Alignment explanation
Indices: 29712876--29712941 Score: 72
Period size: 15 Copynumber: 4.8 Consensus size: 15
29712866 GTCTCATGAA
29712876 AATTTATT-ATT--T
1 AATTTATTAATTAAT
*
29712888 AATTTATAAATTAAT
1 AATTTATTAATTAAT
29712903 AATTTATTAATT--T
1 AATTTATTAATTAAT
*
29712916 -ATATATTAATTAAT
1 AATTTATTAATTAAT
29712930 AATTTATTAATT
1 AATTTATTAATT
29712942 TGTCAAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
12 17 0.39
13 4 0.09
14 1 0.02
15 22 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
AATTTATTAATTAAT
Found at i:29712925 original size:35 final size:35
Alignment explanation
Indices: 29712876--29712942 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
29712866 GTCTCATGAA
*
29712876 AATTTATTATTTAATTTATAAATTAATAATTTATT
1 AATTTATTATTTAATTAATAAATTAATAATTTATT
* *
29712911 AATTTA-TATATTAATTAATAATTTATTAATTT
1 AATTTATTAT-TTAATTAATAAATTAATAATTT
29712943 GTCAAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 3 0.11
35 25 0.89
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (35 bp):
AATTTATTATTTAATTAATAAATTAATAATTTATT
Found at i:29712926 original size:27 final size:28
Alignment explanation
Indices: 29712876--29712942 Score: 102
Period size: 27 Copynumber: 2.5 Consensus size: 28
29712866 GTCTCATGAA
*
29712876 AATTTATT-ATTTAATTTATAAATTAAT
1 AATTTATTAATTTAATATATAAATTAAT
*
29712903 AATTTATTAATTT-ATATATTAATTAAT
1 AATTTATTAATTTAATATATAAATTAAT
29712930 AATTTATTAATTT
1 AATTTATTAATTT
29712943 GTCAAAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 33 0.89
28 4 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
AATTTATTAATTTAATATATAAATTAAT
Found at i:29712954 original size:27 final size:27
Alignment explanation
Indices: 29712896--29712961 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
29712886 TTAATTTATA
* *
29712896 AATTAATAATTTATTAATTTATATATT
1 AATTAATAATTTATTAATTTATAAAAT
*
29712923 AATTAATAATTTATTAATTTGTCAAAAT
1 AATTAATAATTTATTAATTTAT-AAAAT
*
29712951 -ATTATTAATTT
1 AATTAATAATTT
29712962 TTTTCAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 31 0.91
28 3 0.09
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (27 bp):
AATTAATAATTTATTAATTTATAAAAT
Found at i:29713475 original size:17 final size:18
Alignment explanation
Indices: 29713453--29713487 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
29713443 TTTAGGACCG
29713453 ATCAAAAATATT-ATTTA
1 ATCAAAAATATTAATTTA
*
29713470 ATCAAAATTATTAATTTA
1 ATCAAAAATATTAATTTA
29713488 TTGAGTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (18 bp):
ATCAAAAATATTAATTTA
Found at i:29719208 original size:19 final size:20
Alignment explanation
Indices: 29719184--29719223 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
29719174 AATTCGAGGA
29719184 TTAC-TTAATCGGTTAAAAT
1 TTACTTTAATCGGTTAAAAT
*
29719203 TTACTTTAATTGGTTAAAAT
1 TTACTTTAATCGGTTAAAAT
29719223 T
1 T
29719224 GAAGAAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.47
Consensus pattern (20 bp):
TTACTTTAATCGGTTAAAAT
Found at i:29723378 original size:21 final size:21
Alignment explanation
Indices: 29723354--29723400 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
29723344 TTTTATGTGC
*
29723354 TTAAAAT-AGGGTTTTAATTGG
1 TTAAAATCAGGG-TTTAATTGA
*
29723375 TTAAAATCATGGTTTAATTGA
1 TTAAAATCAGGGTTTAATTGA
29723396 TTAAA
1 TTAAA
29723401 GTGGTCTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.38, C:0.02, G:0.17, T:0.43
Consensus pattern (21 bp):
TTAAAATCAGGGTTTAATTGA
Found at i:29724596 original size:47 final size:47
Alignment explanation
Indices: 29724542--29724635 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
29724532 AAACAAATTA
29724542 GATTCATGATTAATGAAAATAGCCATTTGATTTCTTATAATCATGTT
1 GATTCATGATTAATGAAAATAGCCATTTGATTTCTTATAATCATGTT
29724589 GATTCATGATTAATGAAAATAGCCATTTGATTTCTTATAATCATGTT
1 GATTCATGATTAATGAAAATAGCCATTTGATTTCTTATAATCATGTT
29724636 TTTGCTTACT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.43
Consensus pattern (47 bp):
GATTCATGATTAATGAAAATAGCCATTTGATTTCTTATAATCATGTT
Found at i:29724861 original size:30 final size:30
Alignment explanation
Indices: 29724819--29724909 Score: 128
Period size: 30 Copynumber: 3.0 Consensus size: 30
29724809 TGTGAATACA
*
29724819 TAATGACTGCTTGATGAAAATTGAGAATGCT
1 TAATGA-TGCTTGATGAAAATTGAGAATGAT
29724850 TAATGATGCTTGATGAAAATTGAGAATGAT
1 TAATGATGCTTGATGAAAATTGAGAATGAT
* ** *
29724880 GAATGACACTTGATGATAATTGAGAATGAT
1 TAATGATGCTTGATGAAAATTGAGAATGAT
29724910 ACTTGATGAC
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
30 49 0.89
31 6 0.11
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.32
Consensus pattern (30 bp):
TAATGATGCTTGATGAAAATTGAGAATGAT
Found at i:29726458 original size:32 final size:32
Alignment explanation
Indices: 29726398--29726461 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
29726388 GATGTCTAAT
* * * *
29726398 TATATTATTTAAGTGTGCAGGAGTAAGCTTAA
1 TATATTATTTAAGTATACAGAAGAAAGCTTAA
*
29726430 TATATTATTTGAGTATACAGAAGAAAGCTTAA
1 TATATTATTTAAGTATACAGAAGAAAGCTTAA
29726462 ATTCCTTAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.36
Consensus pattern (32 bp):
TATATTATTTAAGTATACAGAAGAAAGCTTAA
Found at i:29730414 original size:2 final size:2
Alignment explanation
Indices: 29730407--29730431 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29730397 ATACAAACTG
29730407 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
29730432 TGTGCATGAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29741433 original size:2 final size:2
Alignment explanation
Indices: 29741421--29741536 Score: 153
Period size: 2 Copynumber: 57.5 Consensus size: 2
29741411 ATACAAACTG
*
29741421 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
29741462 TA TA TA TA TT TNG TA TA CA AA CTG TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA T-A TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
29741506 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29741537 TTTATAATAC
Statistics
Matches: 101, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.01
2 99 0.98
3 1 0.01
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:29743277 original size:30 final size:30
Alignment explanation
Indices: 29743241--29743298 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
29743231 CTGAGTGGGC
*
29743241 AATGTTTGCCGTAGG-TTGCAATTTGTTTGT
1 AATGTTTGCCGTAGGCTT-CAATTGGTTTGT
*
29743271 AATGTTTGTCGTAGGCTTCAATTGGTTT
1 AATGTTTGCCGTAGGCTTCAATTGGTTT
29743299 TCTTCCGTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.17, C:0.10, G:0.26, T:0.47
Consensus pattern (30 bp):
AATGTTTGCCGTAGGCTTCAATTGGTTTGT
Found at i:29748886 original size:115 final size:116
Alignment explanation
Indices: 29748670--29748904 Score: 445
Period size: 115 Copynumber: 2.0 Consensus size: 116
29748660 AACTGATTAC
29748670 ATAATATCATGAATTTTTTAAAATATTTATAATTAAAAGAATAACTTCCATTCTTAATAAAAAAA
1 ATAATATCATGAATTTTTTAAAATATTTATAATTAAAAGAATAACTTCCATTCTTAATAAAAAAA
*
29748735 AAAAGGGATTCTTCCACCCCTAAAAAGGGAACCATGTTTTCAATACTTTCA
66 AAAAGGGATTCTTCCACCCCTAAAAAGGGAACCATGTTTCCAATACTTTCA
29748786 ATAATATCATGAATTTTTTAAAATATTTATAATTAAAAGAATAACTTCCATTCTT-ATAAAAAAA
1 ATAATATCATGAATTTTTTAAAATATTTATAATTAAAAGAATAACTTCCATTCTTAATAAAAAAA
*
29748850 AAGAGGGATTCTTCCACCCCTAAAAAGGGAACCATGTTTCCAATACTTTCA
66 AAAAGGGATTCTTCCACCCCTAAAAAGGGAACCATGTTTCCAATACTTTCA
29748901 ATAA
1 ATAA
29748905 CGTTAGATAG
Statistics
Matches: 117, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
115 62 0.53
116 55 0.47
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (116 bp):
ATAATATCATGAATTTTTTAAAATATTTATAATTAAAAGAATAACTTCCATTCTTAATAAAAAAA
AAAAGGGATTCTTCCACCCCTAAAAAGGGAACCATGTTTCCAATACTTTCA
Found at i:29750064 original size:3 final size:3
Alignment explanation
Indices: 29750056--29750090 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
29750046 TTCAAACTCT
* *
29750056 TTA TTA TTA TTA TTA CTA TTA TTA TTG TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
29750091 GTTTATTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:29750572 original size:30 final size:30
Alignment explanation
Indices: 29750538--29750608 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
29750528 AATAATTCAT
29750538 TATAAAGATTTATTTCA-TTCAAAATAAAAA
1 TATAAAGATTTATTT-AGTTCAAAATAAAAA
* *
29750568 TAT-AAGAACTTATTTAGTTTAAAATAAAAA
1 TATAAAG-ATTTATTTAGTTCAAAATAAAAA
* *
29750598 TAAAAAAATTT
1 TATAAAGATTT
29750609 GATTGAATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
29 4 0.12
30 27 0.82
31 2 0.06
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (30 bp):
TATAAAGATTTATTTAGTTCAAAATAAAAA
Found at i:29761983 original size:42 final size:42
Alignment explanation
Indices: 29761922--29762007 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
29761912 CTTGTGAAAG
*
29761922 ATTTCTGAGTGAATGTTATTAGAACACTTGGTTCATATATTT
1 ATTTCTGAGTGAATATTATTAGAACACTTGGTTCATATATTT
*
29761964 ATTTCTGAGTGAATATTATTATAACACTTGGTTCATATATTT
1 ATTTCTGAGTGAATATTATTAGAACACTTGGTTCATATATTT
29762006 AT
1 AT
29762008 ATATATAGGC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.47
Consensus pattern (42 bp):
ATTTCTGAGTGAATATTATTAGAACACTTGGTTCATATATTT
Found at i:29762669 original size:2 final size:2
Alignment explanation
Indices: 29762664--29762700 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
29762654 TTTACTTGAC
29762664 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29762701 AGTGTGTGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29765576 original size:18 final size:17
Alignment explanation
Indices: 29765535--29765587 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
29765525 AGAGTCATGT
* *
29765535 CTTAATCTAAATAGACA
1 CTTAATTTAAATAGTCA
29765552 CTTAATTTAAATAGTCA
1 CTTAATTTAAATAGTCA
* *
29765569 CTTTAATTTGAATAATCA
1 C-TTAATTTAAATAGTCA
29765587 C
1 C
29765588 ATATGAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 16 0.52
18 15 0.48
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.38
Consensus pattern (17 bp):
CTTAATTTAAATAGTCA
Found at i:29774854 original size:23 final size:22
Alignment explanation
Indices: 29774822--29774864 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
29774812 ATACCAAGTC
*
29774822 AGATAGACGTTGGAGCAAAACCA
1 AGATAAACGTT-GAGCAAAACCA
*
29774845 AGATAAACGTTGAGGAAAAC
1 AGATAAACGTTGAGCAAAAC
29774865 TAGGAGAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.47, C:0.14, G:0.26, T:0.14
Consensus pattern (22 bp):
AGATAAACGTTGAGCAAAACCA
Found at i:29778796 original size:19 final size:20
Alignment explanation
Indices: 29778769--29778814 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
29778759 ATGAGACAAG
*
29778769 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
29778788 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
29778807 ATAATATT
1 ATAATATT
29778815 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:29779261 original size:20 final size:20
Alignment explanation
Indices: 29779216--29779253 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
29779206 TTTTGGCCTC
29779216 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
29779236 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTGGAGTA
29779254 AGATTTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:29782790 original size:18 final size:18
Alignment explanation
Indices: 29782769--29782823 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
29782759 GGCAGCAGGG
29782769 ACAGAGGCAGCATTAGGA
1 ACAGAGGCAGCATTAGGA
* *
29782787 ACAGTGGCAG---TAGGG
1 ACAGAGGCAGCATTAGGA
* *
29782802 ACAAAGGCAACATTAGGA
1 ACAGAGGCAGCATTAGGA
29782820 ACAG
1 ACAG
29782824 TGGTAGCAGC
Statistics
Matches: 27, Mismatches: 7, Indels: 6
0.68 0.17 0.15
Matches are distributed among these distances:
15 11 0.41
18 16 0.59
ACGTcount: A:0.40, C:0.16, G:0.33, T:0.11
Consensus pattern (18 bp):
ACAGAGGCAGCATTAGGA
Found at i:29782802 original size:33 final size:33
Alignment explanation
Indices: 29782757--29782832 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
29782747 GTTGACAACG
* *
29782757 GTGGCAGCAGGGACAGAGGCAGCATTAGGAACA
1 GTGGCAGCAGGGACAAAGGCAACATTAGGAACA
*
29782790 GTGGCAGTAGGGACAAAGGCAACATTAGGAACA
1 GTGGCAGCAGGGACAAAGGCAACATTAGGAACA
*
29782823 GTGGTAGCAG
1 GTGGCAGCAG
29782833 CATTATCAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.34, C:0.16, G:0.38, T:0.12
Consensus pattern (33 bp):
GTGGCAGCAGGGACAAAGGCAACATTAGGAACA
Found at i:29783329 original size:23 final size:22
Alignment explanation
Indices: 29783297--29783339 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
29783287 ATACCAAGTC
*
29783297 AGATAGACGTTGGAGCAAAACCA
1 AGATAAACGTT-GAGCAAAACCA
*
29783320 AGATAAACGTTGAGGAAAAC
1 AGATAAACGTTGAGCAAAAC
29783340 TAGGAGAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.47, C:0.14, G:0.26, T:0.14
Consensus pattern (22 bp):
AGATAAACGTTGAGCAAAACCA
Found at i:29786445 original size:8 final size:8
Alignment explanation
Indices: 29786434--29786460 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
29786424 TCTACTTTTC
29786434 AAAAAACA
1 AAAAAACA
29786442 AAAAAACA
1 AAAAAACA
29786450 AAAAAACA
1 AAAAAACA
29786458 AAA
1 AAA
29786461 TTTTCAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAACA
Found at i:29789829 original size:2 final size:2
Alignment explanation
Indices: 29789822--29789848 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29789812 TTCAGAGACA
29789822 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
29789849 NAAAATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29789856 original size:57 final size:56
Alignment explanation
Indices: 29789789--29789905 Score: 189
Period size: 57 Copynumber: 2.1 Consensus size: 56
29789779 TATGTAACTA
*
29789789 ATAAATAATATAAGAACAAAGATTTCAGAGACAATATATATATATATATATATATAT
1 ATAAA-AATATAAGAAAAAAGATTTCAGAGACAATATATATATATATATATATATAT
* *
29789846 ATANAAAATATAAGAAAAAATATTTGAGAGACAATATATATATATATATATATATAT
1 ATA-AAAATATAAGAAAAAAGATTTCAGAGACAATATATATATATATATATATATAT
29789903 ATA
1 ATA
29789906 TATATATATA
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
57 54 0.96
58 2 0.04
ACGTcount: A:0.56, C:0.03, G:0.07, T:0.33
Consensus pattern (56 bp):
ATAAAAATATAAGAAAAAAGATTTCAGAGACAATATATATATATATATATATATAT
Found at i:29789884 original size:2 final size:2
Alignment explanation
Indices: 29789879--29789930 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
29789869 TTGAGAGACA
29789879 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
29789921 AT GT AT AT AT
1 AT AT AT AT AT
29789931 TCTAGTAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29790379 original size:27 final size:27
Alignment explanation
Indices: 29790329--29790387 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
29790319 AACATAATTG
* *
29790329 ATAAATTTCATAAATAAAATATAT-AA
1 ATAAATGTCATAAATAAAAAATATCAA
29790355 CATAAATGT-ATAAATATAAAAATATCAA
1 -ATAAATGTCATAAATA-AAAAATATCAA
29790383 ATAAA
1 ATAAA
29790388 GATACAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 7 0.25
27 19 0.68
28 2 0.07
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.31
Consensus pattern (27 bp):
ATAAATGTCATAAATAAAAAATATCAA
Found at i:29796572 original size:22 final size:22
Alignment explanation
Indices: 29796544--29796592 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
29796534 ACTTTGTAAT
*
29796544 GGCAATGATGGTTGCGATGTTA
1 GGCAATGATGGTTGCGATATTA
29796566 GGCAATGATGGTTGCGATATTA
1 GGCAATGATGGTTGCGATATTA
*
29796588 TGCAA
1 GGCAA
29796593 AACTTTGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.27, C:0.10, G:0.33, T:0.31
Consensus pattern (22 bp):
GGCAATGATGGTTGCGATATTA
Found at i:29806274 original size:28 final size:28
Alignment explanation
Indices: 29806207--29806289 Score: 114
Period size: 28 Copynumber: 3.0 Consensus size: 28
29806197 TTCGTATAAT
* *
29806207 AAAAGCACAGTGGTTTAACAGAATT-TC
1 AAAAGCACAGTAGTTTAGCAGAATTATC
**
29806234 AAAAGCATGGTAGTTTAGCAGAATTATC
1 AAAAGCACAGTAGTTTAGCAGAATTATC
*
29806262 AAGAGCACAGTAGTTTAGCAGAATTATC
1 AAAAGCACAGTAGTTTAGCAGAATTATC
29806290 TCCAGACCAA
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 21 0.44
28 27 0.56
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (28 bp):
AAAAGCACAGTAGTTTAGCAGAATTATC
Found at i:29822234 original size:14 final size:15
Alignment explanation
Indices: 29822205--29822238 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
29822195 AAACTAAATA
*
29822205 TAAAACTATAATTTG
1 TAAAACTATAAATTG
29822220 TAAAA-TATAAATTG
1 TAAAACTATAAATTG
29822234 TAAAA
1 TAAAA
29822239 AATGATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (15 bp):
TAAAACTATAAATTG
Found at i:29825437 original size:12 final size:13
Alignment explanation
Indices: 29825408--29825437 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
29825398 ATTTAGAAGA
29825408 AAAAATAAAAGGG
1 AAAAATAAAAGGG
*
29825421 AAAAATAAGAGGG
1 AAAAATAAAAGGG
29825434 AAAA
1 AAAA
29825438 GAGTATACCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (13 bp):
AAAAATAAAAGGG
Found at i:29833028 original size:41 final size:40
Alignment explanation
Indices: 29832973--29833064 Score: 130
Period size: 41 Copynumber: 2.3 Consensus size: 40
29832963 TAAAATCAGC
*
29832973 ATAAAATCAAAGTAAATCAAGATGCTGAGTCAAATAAAAT
1 ATAAAATCAGAGTAAATCAAGATGCTGAGTCAAATAAAAT
* * *
29833013 ATCAAAATCAGAGTAAATTAAGATGTTGAGTCTAATAAAAT
1 AT-AAAATCAGAGTAAATCAAGATGCTGAGTCAAATAAAAT
*
29833054 ATAAAGTCAGA
1 ATAAAATCAGA
29833065 TCACAAAATA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 10 0.22
41 36 0.78
ACGTcount: A:0.52, C:0.09, G:0.14, T:0.25
Consensus pattern (40 bp):
ATAAAATCAGAGTAAATCAAGATGCTGAGTCAAATAAAAT
Found at i:29833271 original size:314 final size:307
Alignment explanation
Indices: 29832709--29833331 Score: 838
Period size: 314 Copynumber: 2.0 Consensus size: 307
29832699 AAATCAGCAT
* * *
29832709 AAAATCAAAGTAAATCAAGATGGTAAGTCAAATAAAATATCAAGTCAGATAACAGAATATTTTAG
1 AAAATCAAAGTAAATCAAGATGGTAAGTCAAATAAAATATAAAGTCAGATAACAAAATATTCTAG
* * * * *
29832774 ATGTTTAAGAAATATCAGGCAATAAACTAAGAAAATATTTTGGATGTTTAAGATTAAGTTAGATT
66 ATGTTAAAAAAATATCAGGCAAAAAACTAAGAAAATATTTTGGATGTTTAAGACTAAGTTAGATA
* * * *
29832839 AAAAATAGAGAAAGAGTATGTAGAGAATGTTTCAGAGAAGATGAGAGGGTTATGTGTTTTTAAGT
131 AAAAATAGAGAAAGAGTATGCAGAGAAAGCTTCAGAGAAGATGAAAGGGTTATGTGTTTTTAAGT
* * * *
29832904 GAGGTAGGTAGGTTGTACTTATAGGCAAAGCAGAAAGTTAACGTCATAGAAAATCAGTATAAAAT
196 GAGGTAGGCAAGCTGTACTTATAGGCAAAGCAAAAAGTTAACGTCATAGAAAATCAGTATAAAAT
* *
29832969 CAGCATAAAA-TCAAAGTAAATCAAGATGCTGAGTCAAATAAAATATC
261 CAACATAAAAGT-AAAGAAAATCAAGATGCTGAGTCAAATAAAATATC
* * * * * * *
29833016 AAAATCAGAGTAAATTAAGATGTTGAGTCTAATAAAATATAAAGTCAGATCACAAAATATTCTGG
1 AAAATCAAAGTAAATCAAGATGGTAAGTCAAATAAAATATAAAGTCAGATAACAAAATATTCTAG
29833081 ATGTTAAAAAAATATCAGGCAACAGGCAACAGACTCAAG-AAATA-TTTGGATGTTTAAGACTAA
66 ATGTTAAAAAAATATCAGGC-A-A---AA-A-ACT-AAGAAAATATTTTGGATGTTTAAGACTAA
29833144 GTTAGATAAAAAATAGAGAAAGAGTATGCAGAGAAAGCTTCAGAGAAGATGAAAGGGTTGATGTG
123 GTTAGATAAAAAATAGAGAAAGAGTATGCAGAGAAAGCTTCAGAGAAGATGAAAGGGTT-ATGTG
* * * **
29833209 TTTTTTAGTGAGGTAGGCAAGCTGTATTTATAGGCAAAGTAAAAAGTTAACGTTGTAGAAAATCA
187 TTTTTAAGTGAGGTAGGCAAGCTGTACTTATAGGCAAAGCAAAAAGTTAACGTCATAGAAAATCA
* * *
29833274 GTATAAAATCAACATAAAAGTAGAGAAAATCAAGATGCTGAGTCAAGTAAAGTATC
252 GTATAAAATCAACATAAAAGTAAAGAAAATCAAGATGCTGAGTCAAATAAAATATC
29833330 AA
1 AA
29833332 GTTAGATAAC
Statistics
Matches: 273, Mismatches: 33, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
307 73 0.27
308 1 0.00
309 1 0.00
312 1 0.00
313 73 0.27
314 120 0.44
315 4 0.01
ACGTcount: A:0.45, C:0.08, G:0.20, T:0.26
Consensus pattern (307 bp):
AAAATCAAAGTAAATCAAGATGGTAAGTCAAATAAAATATAAAGTCAGATAACAAAATATTCTAG
ATGTTAAAAAAATATCAGGCAAAAAACTAAGAAAATATTTTGGATGTTTAAGACTAAGTTAGATA
AAAAATAGAGAAAGAGTATGCAGAGAAAGCTTCAGAGAAGATGAAAGGGTTATGTGTTTTTAAGT
GAGGTAGGCAAGCTGTACTTATAGGCAAAGCAAAAAGTTAACGTCATAGAAAATCAGTATAAAAT
CAACATAAAAGTAAAGAAAATCAAGATGCTGAGTCAAATAAAATATC
Found at i:29833548 original size:267 final size:265
Alignment explanation
Indices: 29833016--29833950 Score: 1081
Period size: 266 Copynumber: 3.5 Consensus size: 265
29833006 ATAAAATATC
* * * * * * *
29833016 AAAATCAGAGTAAATTAAGATGTTGAGTCTAATAAAATATAAAGTCAGATCACAAAATATTCTGG
1 AAAATCAGAGAAAATCAAGATGCTGAGT-AAATAAAATATCAAGTTAGATAACAAAATATTCTGG
* * * **
29833081 ATGTTAAAAAAATATCAGGCAACAGGCAACAGACTCAAGAAATA-TTTGGATGTTTAAGACTAAG
65 ATGTTTAAGAAATAT-------CAGGCAACAGACTCAGGAAATATTTTGGACATTTAAGACTAAG
* *
29833145 TTAGATAAAAAATAGAGAAAGAGTATGCAGAGAAAGCTTCAGAGAAGATGAAAGGGTT-GATGTG
123 TCAGATAAAAAATAGAGAAAGAGTATGCAGAGAAAGCTTCAGAGAAGATGAGAGGGTTAG-TGTG
* * * * * *
29833209 TTTTTTAGTGAGGTAGGCAAGCTGTATTTATAGGCAAAGTAAAAAGTTAACGTTGTAGAAAATCA
187 TTTTTGAGTGAGATAGGCAGGCTGTATTTATAGACAAAG-AAGAAGTTAACGTTATAGAAAATCA
29833274 GTATAAAATCAACAT
251 GTATAAAATCAACAT
* *
29833289 AAAAGT-AGAGAAAATCAAGATGCTGAGTCAAGTAAAGTATCAAGTTAGATAACAAAATATTCTG
1 AAAA-TCAGAGAAAATCAAGATGCTGAGT-AAATAAAATATCAAGTTAGATAACAAAATATTCTG
* * * * *
29833353 AATGTTTAAGAAATATCAGGCAACAGACTTAGGAATTATTTTGAACATTTAAGAGTAAGTCAGAT
64 GATGTTTAAGAAATATCAGGCAACAGACTCAGGAAATATTTTGGACATTTAAGACTAAGTCAGAT
* *
29833418 AAAAAATCA-AGAAAGAGTATGTAGAGAAAGCTTCAGAGAAGATGAGAGCGTTAGTGTGTTTTTG
129 AAAAAAT-AGAGAAAGAGTATGCAGAGAAAGCTTCAGAGAAGATGAGAGGGTTAGTGTGTTTTTG
* * * * * * *
29833482 AGTGAGTTAGGCAGGTTGTATTTATAAACAAAGCAAGAAGTTAACATTATAGAGAATTAATATAA
193 AGTGAGATAGGCAGGCTGTATTTATAGACAAAG-AAGAAGTTAACGTTATAGAAAATCAGTATAA
* *
29833547 AATTAGCAT
257 AATCAACAT
* * * * * *
29833556 AAAATCAAAGTAAGTCAAGATGCTGAATAAAAAAAAAATCAAGTTAGATAACAAAATATTCTGGA
1 AAAATCAGAGAAAATCAAGATGCTGAGTAAATAAAATATCAAGTTAGATAACAAAATATTCTGGA
* * * * *
29833621 TGTTTAAGAAATATCAAGCAACAAACTCAAGAAATATTTTGGACGTTTAAGACTAAGTTAGATAA
66 TGTTTAAGAAATATCAGGCAACAGACTCAGGAAATATTTTGGACATTTAAGACTAAGTCAGATAA
*
29833686 AAAATAGAGAAAGAGTATGCAAAGAAAGCTTCAGAGAAGATGAGAGGGTTAGTGTGTTTTTGAGT
131 AAAATAGAGAAAGAGTATGCAGAGAAAGCTTCAGAGAAGATGAGAGGGTTAGTGTGTTTTTGAGT
* * ** * ** * *
29833751 GAAATAGACAGGCAATATTTATAGTCAAAGTGGAAAGTTAATGTTAAAGAAAATCAGTATAAAAT
196 GAGATAGGCAGGCTGTATTTATAGACAAAGAAG-AAGTTAACGTTATAGAAAATCAGTATAAAAT
*
29833816 CAACCT
260 CAACAT
* * * *
29833822 AAAATCAGACAAAATCAAGATGCTAAGTTAAATAAAATATCAAGTTAGATAACAGAATATTTTGG
1 AAAATCAGAGAAAATCAAGATGCTGAG-TAAATAAAATATCAAGTTAGATAACAAAATATTCTGG
* * *
29833887 ATGTTTAAGAAATATTAGGCAATAGACTCAGGAAATATTTTGGACA--TAAGACTAAGTCAAATA
65 ATGTTTAAGAAATATCAGGCAACAGACTCAGGAAATATTTTGGACATTTAAGACTAAGTCAGATA
29833950 A
130 A
29833951 GAACTTTTTT
Statistics
Matches: 558, Mismatches: 96, Indels: 24
0.82 0.14 0.04
Matches are distributed among these distances:
265 18 0.03
266 239 0.43
267 232 0.42
268 2 0.00
273 66 0.12
274 1 0.00
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.26
Consensus pattern (265 bp):
AAAATCAGAGAAAATCAAGATGCTGAGTAAATAAAATATCAAGTTAGATAACAAAATATTCTGGA
TGTTTAAGAAATATCAGGCAACAGACTCAGGAAATATTTTGGACATTTAAGACTAAGTCAGATAA
AAAATAGAGAAAGAGTATGCAGAGAAAGCTTCAGAGAAGATGAGAGGGTTAGTGTGTTTTTGAGT
GAGATAGGCAGGCTGTATTTATAGACAAAGAAGAAGTTAACGTTATAGAAAATCAGTATAAAATC
AACAT
Found at i:29834189 original size:35 final size:35
Alignment explanation
Indices: 29834150--29834219 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
29834140 CAGATTCAGA
29834150 AAATATTTTGGACT-TTTAAGACT-AAGTCAGATAAG
1 AAATATTTTGGA-TGTTTAAGACTAAAG-CAGATAAG
*
29834185 AAATATTTTGGATGTTTAAGATTAAAGCAGATAAG
1 AAATATTTTGGATGTTTAAGACTAAAGCAGATAAG
29834220 GTTAAAGACT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 1 0.03
35 28 0.88
36 3 0.09
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.34
Consensus pattern (35 bp):
AAATATTTTGGATGTTTAAGACTAAAGCAGATAAG
Found at i:29835085 original size:20 final size:17
Alignment explanation
Indices: 29835023--29835074 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 17
29835013 TTTGTAAAGC
29835023 TTTTTTTAAAAAAATTA
1 TTTTTTTAAAAAAATTA
**
29835040 TTTTTAAAAAAAAAAAATTA
1 TTTTT---TTAAAAAAATTA
29835060 TTTTTTTAAAAAAAT
1 TTTTTTTAAAAAAAT
29835075 GCTTATTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
17 13 0.46
20 15 0.54
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTTTTTAAAAAAATTA
Found at i:29835347 original size:18 final size:18
Alignment explanation
Indices: 29835301--29835349 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
29835291 TTTGTAAAGC
29835301 TTTTTTTAAAAAAATTAT
1 TTTTTTTAAAAAAATTAT
**
29835319 TTTTTAAAAAAAAATTAT
1 TTTTTTTAAAAAAATTAT
29835337 TTTTTTTAAAAAA
1 TTTTTTTAAAAAA
29835350 CTGCTTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTTTTAAAAAAATTAT
Found at i:29835446 original size:278 final size:277
Alignment explanation
Indices: 29834947--29835505 Score: 1050
Period size: 278 Copynumber: 2.0 Consensus size: 277
29834937 AAACGAAAAG
29834947 AAAAGTTCTCCTAAAAAAGATGCATGTTTTTAAAAAAAGATGAGAGAAAGCTCCTATCTGAAACT
1 AAAAGTTCTCCTAAAAAAGATGCATGTTTTTAAAAAAAGATGAGAGAAAGCTCCTATCTGAAACT
29835012 TTTTGTAAAGCTTTTTTTAAAAAAATTATTTTTAAAAAAAAAAAATTATTTTTTTAAAAAAATGC
66 TTTTGTAAAGCTTTTTTTAAAAAAATTATTTTT-AAAAAAAAAAATTATTTTTTTAAAAAAATGC
29835077 TTATTTTTTAAGAGCTTTTCTAAATTCTTATTTGGCTTGGCTTTTGCTTTTAAGAGATAGATAAA
130 TTATTTTTTAAGAGCTTTTCTAAATTCTTATTTGGCTTGGCTTTTGCTTTTAAGAGATAGATAAA
29835142 CTGAAAAAAAAGTCAAGCTAAACAAGCACTTAAAAGCTATTATAAAACTCTTATGAAAAATAATA
195 CTGAAAAAAAAGTCAAGCTAAACAAGCACTTAAAAGCTATTATAAAACTCTTATGAAAAATAATA
29835207 GTTTTT-AAATTAAGTTA
260 GTTTTTAAAATTAAGTTA
29835224 AANAAGTTCTCCTAAAAAAGATGCATGTTTTTAAAAAAAGATGAGAGAAAGCTCCTATCTGAAAC
1 AA-AAGTTCTCCTAAAAAAGATGCATGTTTTTAAAAAAAGATGAGAGAAAGCTCCTATCTGAAAC
* *
29835289 TTTTTGTAAAGCTTTTTTTAAAAAAATTATTTTT-TAAAAAAAAATTATTTTTTTTAAAAAACTG
65 TTTTTGTAAAGCTTTTTTTAAAAAAATTATTTTTAAAAAAAAAAATTA-TTTTTTTAAAAAAATG
29835353 CTTATTTTTTTAAGAGCTTTTCTAAATTCTTATTTGGCTTGGCTTTTGCTTTTAAGAGATAGATA
129 CTTA-TTTTTTAAGAGCTTTTCTAAATTCTTATTTGGCTTGGCTTTTGCTTTTAAGAGATAGATA
29835418 AACTGAAAAAAAAGTCAAGCTAAACAAGCACTTAAAAGCTATTATAAAACTCTTATGAAAAATAA
193 AACTGAAAAAAAAGTCAAGCTAAACAAGCACTTAAAAGCTATTATAAAACTCTTATGAAAAATAA
29835483 TAGTTTTTAAAATTAAGTTA
258 TAGTTTTTAAAATTAAGTTA
29835503 AAA
1 AAA
29835506 CTATTTGGTA
Statistics
Matches: 276, Mismatches: 2, Indels: 7
0.97 0.01 0.02
Matches are distributed among these distances:
276 12 0.04
277 21 0.08
278 230 0.83
279 13 0.05
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.37
Consensus pattern (277 bp):
AAAAGTTCTCCTAAAAAAGATGCATGTTTTTAAAAAAAGATGAGAGAAAGCTCCTATCTGAAACT
TTTTGTAAAGCTTTTTTTAAAAAAATTATTTTTAAAAAAAAAAATTATTTTTTTAAAAAAATGCT
TATTTTTTAAGAGCTTTTCTAAATTCTTATTTGGCTTGGCTTTTGCTTTTAAGAGATAGATAAAC
TGAAAAAAAAGTCAAGCTAAACAAGCACTTAAAAGCTATTATAAAACTCTTATGAAAAATAATAG
TTTTTAAAATTAAGTTA
Found at i:29839960 original size:30 final size:29
Alignment explanation
Indices: 29839926--29839982 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 29
29839916 CTCTAAAAGG
*
29839926 ATGATTTGTAGAAAGGGGGAAAAGGAGAGA
1 ATGATTTGTAAAAAGGGGG-AAAGGAGAGA
29839956 ATGATTTGTAAAAAGGGGGAAAGGAGA
1 ATGATTTGTAAAAAGGGGGAAAGGAGA
29839983 AGGTGATCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.44, C:0.00, G:0.39, T:0.18
Consensus pattern (29 bp):
ATGATTTGTAAAAAGGGGGAAAGGAGAGA
Found at i:29839989 original size:29 final size:30
Alignment explanation
Indices: 29839922--29839989 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
29839912 AAAACTCTAA
*
29839922 AAGGATGATTTGTAGAAAGGGGGAAAAGGAG
1 AAGG-TGATTTGTAAAAAGGGGGAAAAGGAG
*
29839953 -AGAATGATTTGTAAAAAGGGGG-AAAGGAG
1 AAG-GTGATTTGTAAAAAGGGGGAAAAGGAG
29839982 AAGGTGAT
1 AAGGTGAT
29839990 CAATAGGGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
29 11 0.34
30 21 0.66
ACGTcount: A:0.43, C:0.00, G:0.40, T:0.18
Consensus pattern (30 bp):
AAGGTGATTTGTAAAAAGGGGGAAAAGGAG
Found at i:29840878 original size:38 final size:38
Alignment explanation
Indices: 29840836--29840912 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
29840826 ATAAAAATGG
29840836 ATAAAAGTATATCCATTACTTCCTTAATTAAATTGCTT
1 ATAAAAGTATATCCATTACTTCCTTAATTAAATTGCTT
29840874 ATAAAAGTATATCCATTACTTCCTTAATTAAATTGCTT
1 ATAAAAGTATATCCATTACTTCCTTAATTAAATTGCTT
29840912 A
1 A
29840913 CTCTTTGGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.42
Consensus pattern (38 bp):
ATAAAAGTATATCCATTACTTCCTTAATTAAATTGCTT
Found at i:29849411 original size:35 final size:36
Alignment explanation
Indices: 29849343--29849429 Score: 108
Period size: 35 Copynumber: 2.5 Consensus size: 36
29849333 TGAGGTGATT
*
29849343 AACTTTGCTTTACTTA-TCTTTCAAAAAAAAAAAA-
1 AACTTTGCTTTACATATTCTTTCAAAAAAAAAAAAG
* *
29849377 AACCTTTGCTTTACATATTC-TTCATAAAAGAAAAAG
1 AA-CTTTGCTTTACATATTCTTTCAAAAAAAAAAAAG
*
29849413 AACTTTGCTTTCCATAT
1 AACTTTGCTTTACATAT
29849430 AGCTTGAGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
34 2 0.04
35 40 0.87
36 4 0.09
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.37
Consensus pattern (36 bp):
AACTTTGCTTTACATATTCTTTCAAAAAAAAAAAAG
Found at i:29857280 original size:40 final size:39
Alignment explanation
Indices: 29857224--29857309 Score: 127
Period size: 39 Copynumber: 2.2 Consensus size: 39
29857214 CAACTGAAAC
* *
29857224 GGTTGGGTCGGGTCATATTGGAGGGGGGTTTTGGGCCGTG
1 GGTTGGGTCGGGTCATATGGGA-GGGGGTTTTGGGCCATG
*
29857264 GGTTGGGTCGGTTCATATGGGAGGGGGTTTTGGGCCATG
1 GGTTGGGTCGGGTCATATGGGAGGGGGTTTTGGGCCATG
*
29857303 GGATGGG
1 GGTTGGG
29857310 AAAGGAAAGG
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 22 0.52
40 20 0.48
ACGTcount: A:0.09, C:0.09, G:0.52, T:0.29
Consensus pattern (39 bp):
GGTTGGGTCGGGTCATATGGGAGGGGGTTTTGGGCCATG
Found at i:29857894 original size:16 final size:16
Alignment explanation
Indices: 29857875--29857908 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29857865 TTGATATGAT
* *
29857875 TTAAATTTGAGATATC
1 TTAAATTCGAGAAATC
29857891 TTAAATTCGAGAAATC
1 TTAAATTCGAGAAATC
29857907 TT
1 TT
29857909 TATTAATCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (16 bp):
TTAAATTCGAGAAATC
Found at i:29860748 original size:6 final size:6
Alignment explanation
Indices: 29860739--29860771 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
29860729 GAGAGAGAGG
29860739 ATGGCA ATGGCA ATGGCA ATGGCA ATTGGCA AT
1 ATGGCA ATGGCA ATGGCA ATGGCA A-TGGCA AT
29860772 ATATATTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.33, C:0.15, G:0.30, T:0.21
Consensus pattern (6 bp):
ATGGCA
Found at i:29864904 original size:6 final size:6
Alignment explanation
Indices: 29864893--29864921 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
29864883 GCAATGCCAA
29864893 CCTAAC CCTAAC CCTAAC CCTAAC CCTAA
1 CCTAAC CCTAAC CCTAAC CCTAAC CCTAA
29864922 GATGAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.48, G:0.00, T:0.17
Consensus pattern (6 bp):
CCTAAC
Found at i:29880244 original size:2 final size:2
Alignment explanation
Indices: 29880237--29880273 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
29880227 ATATGGCCCG
29880237 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29880274 GCAGAGGAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29881877 original size:45 final size:45
Alignment explanation
Indices: 29881762--29882049 Score: 211
Period size: 45 Copynumber: 6.2 Consensus size: 45
29881752 TACGTTATGA
* * * *
29881762 TGTTACACTTCATGTACAAAAATATGTTACATGCCATAGTTAGAT
1 TGTTACACGTCATGTACAAAAACATGTAACATGCCATGGTTAGAT
* ******
29881807 TGTTATACGTCATGTTTTTGTACATGTAACATGCCATGGTTAGAT
1 TGTTACACGTCATGTACAAAAACATGTAACATGCCATGGTTAGAT
* * * *
29881852 TGTTACATGTCATGTAGAAAAACATGTGACATGTCATGGTTAGAT
1 TGTTACACGTCATGTACAAAAACATGTAACATGCCATGGTTAGAT
* * * * *
29881897 TGTTACACGCCATATATAAAAACATATAACACGCCATGGTTAAGTTATGGTTAGGT
1 TGTTACACGTCATGTACAAAAACATGTAACATGCCAT-G----GTTA--G--A--T
*
29881953 TGTTACACGTCATGTACAAAAACATGTGACACAT--TATGGTTAGAT
1 TGTTACACGTCATGTACAAAAACATGT-A-ACATGCCATGGTTAGAT
* * * * *
29881998 TGTTACACGTCATATACAAAAACATATGACATGTCATGGTTAGGT
1 TGTTACACGTCATGTACAAAAACATGTAACATGCCATGGTTAGAT
29882043 TGTTACA
1 TGTTACA
29882050 TGCCATATTG
Statistics
Matches: 188, Mismatches: 40, Indels: 30
0.73 0.16 0.12
Matches are distributed among these distances:
43 4 0.02
45 140 0.74
46 1 0.01
47 1 0.01
49 1 0.01
50 4 0.02
51 4 0.02
52 1 0.01
54 1 0.01
55 1 0.01
56 26 0.14
57 1 0.01
58 3 0.02
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (45 bp):
TGTTACACGTCATGTACAAAAACATGTAACATGCCATGGTTAGAT
Found at i:29882019 original size:101 final size:101
Alignment explanation
Indices: 29881842--29882039 Score: 297
Period size: 101 Copynumber: 2.0 Consensus size: 101
29881832 GTAACATGCC
* * **
29881842 ATGGTTAGATTGTTACATGTCATGTAGAAAAACATGTGACATGTCATGGTTAGATTGTTACACGC
1 ATGGTTAGATTGTTACACGTCATGTACAAAAACATGTGACACATCATGGTTAGATTGTTACACGC
*
29881907 CATATATAAAAACATATAACACGCCATGGTTAAGTT
66 CATATACAAAAACATATAACACGCCATGGTTAAGTT
* * *
29881943 ATGGTTAGGTTGTTACACGTCATGTACAAAAACATGTGACACATTATGGTTAGATTGTTACACGT
1 ATGGTTAGATTGTTACACGTCATGTACAAAAACATGTGACACATCATGGTTAGATTGTTACACGC
* * *
29882008 CATATACAAAAACATATGACATGTCATGGTTA
66 CATATACAAAAACATATAACACGCCATGGTTA
29882040 GGTTGTTACA
Statistics
Matches: 86, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
101 86 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (101 bp):
ATGGTTAGATTGTTACACGTCATGTACAAAAACATGTGACACATCATGGTTAGATTGTTACACGC
CATATACAAAAACATATAACACGCCATGGTTAAGTT
Found at i:29882102 original size:29 final size:28
Alignment explanation
Indices: 29882065--29882139 Score: 89
Period size: 29 Copynumber: 2.7 Consensus size: 28
29882055 TATTGAAAAT
* * * *
29882065 AAAAATATTGTTGTTGCACGTTATGTTG
1 AAAAATATTATTGTTACACGTTATATTC
29882093 AAAAAGTATTATTGTTACACGTTATATTC
1 AAAAA-TATTATTGTTACACGTTATATTC
*
29882122 AAAAACATT-TTGTTACAC
1 AAAAATATTATTGTTACAC
29882140 TTTAATGCCT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 9 0.22
28 8 0.20
29 24 0.59
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (28 bp):
AAAAATATTATTGTTACACGTTATATTC
Found at i:29883074 original size:2 final size:2
Alignment explanation
Indices: 29883067--29883093 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29883057 AGTGAAAGGC
29883067 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
29883094 CTCTTTTCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29885691 original size:84 final size:84
Alignment explanation
Indices: 29885517--29885699 Score: 244
Period size: 84 Copynumber: 2.2 Consensus size: 84
29885507 GTGGAAACTG
* * *
29885517 AACTTGATAATGATGTTCAACTTGAACAAACTGATAATGTTACTCGTGGTGAGGTGTTAGATGAT
1 AACTTGGTAATGATGTTCAACTTGAACAAACTGATAATGATACTCGTGGTGAGGTGTTAGATAAT
* * *
29885582 TCAACTGATAAGGGGCATC
66 GCAACTGATAAGGAGCACC
* *
29885601 AGCTTGGTAATGATGTTCAACTTGAACAAACTGATAATGATATTCGTGGTGAGGTGTTAGATAAT
1 AACTTGGTAATGATGTTCAACTTGAACAAACTGATAATGATACTCGTGGTGAGGTGTTAGATAAT
* *
29885666 GCAACT-A-AATTTGAGTACC
66 GCAACTGATAA--GGAGCACC
29885685 AACTTGGTAATGATG
1 AACTTGGTAATGATG
29885700 GAACAATGGC
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
82 2 0.02
83 1 0.01
84 83 0.97
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (84 bp):
AACTTGGTAATGATGTTCAACTTGAACAAACTGATAATGATACTCGTGGTGAGGTGTTAGATAAT
GCAACTGATAAGGAGCACC
Found at i:29892519 original size:13 final size:15
Alignment explanation
Indices: 29892489--29892520 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
29892479 TGTCATGTCC
29892489 TTTATTTATTATATT
1 TTTATTTATTATATT
29892504 TTTATTT-TTA-ATT
1 TTTATTTATTATATT
29892517 TTTA
1 TTTA
29892521 CACAATAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 3 0.18
15 7 0.41
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTATTTATTATATT
Found at i:29901261 original size:14 final size:14
Alignment explanation
Indices: 29901242--29901271 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29901232 ATTATTAATT
29901242 TATTGATTAAATAA
1 TATTGATTAAATAA
*
29901256 TATTGATTAATTAA
1 TATTGATTAAATAA
29901270 TA
1 TA
29901272 AATTTTCATG
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:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (14 bp):
TATTGATTAAATAA
Found at i:29903999 original size:2 final size:2
Alignment explanation
Indices: 29903992--29904030 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
29903982 TTCACTGTTT
29903992 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29904031 TATTTTATAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29911758 original size:2 final size:2
Alignment explanation
Indices: 29911733--29911775 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
29911723 ATACAATTAC
* * *
29911733 CT CT CG CT CT TT CT C- CT GT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
29911774 CT
1 CT
29911776 AATTTTAACT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.00, C:0.47, G:0.05, T:0.49
Consensus pattern (2 bp):
CT
Found at i:29913028 original size:16 final size:17
Alignment explanation
Indices: 29912987--29913030 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 17
29912977 AATTATACAA
*
29912987 ATTATCTAATTAGAGTT
1 ATTATCTAATTACAGTT
29913004 ATTA--T-ATTACA-TT
1 ATTATCTAATTACAGTT
29913017 ATTATCTAATTACA
1 ATTATCTAATTACA
29913031 CTATAATACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
13 6 0.26
14 5 0.22
15 2 0.09
16 6 0.26
17 4 0.17
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.48
Consensus pattern (17 bp):
ATTATCTAATTACAGTT
Found at i:29917540 original size:33 final size:33
Alignment explanation
Indices: 29917497--29917561 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
29917487 AACAACATGT
* * *
29917497 CAGCAGAGAATGCTAACACCGGTGCGCTGGCTG
1 CAGCAAAGAATGCTAACACCGATGCACTGGCTG
*
29917530 CAGCAAAGAATGCTAACCCCGATGCACTGGCT
1 CAGCAAAGAATGCTAACACCGATGCACTGGCT
29917562 CAAACAGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.28, C:0.29, G:0.28, T:0.15
Consensus pattern (33 bp):
CAGCAAAGAATGCTAACACCGATGCACTGGCTG
Found at i:29920051 original size:2 final size:2
Alignment explanation
Indices: 29920034--29920080 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
29920024 ACATATGAGT
*
29920034 TA TA T- TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29920075 TA TA TA
1 TA TA TA
29920081 AGCATTTAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:29920098 original size:18 final size:19
Alignment explanation
Indices: 29920064--29920113 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
29920054 ATATATATAT
*
29920064 ATATATATATATATATAAGC
1 ATAT-TATATTTATATAAGC
29920084 AT-TTA-ATTTANTATAAGC
1 ATATTATATTTA-TATAAGC
29920102 ATATTATATTTA
1 ATATTATATTTA
29920114 CGGATGGCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 4 0.15
18 11 0.42
19 4 0.15
20 7 0.27
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.46
Consensus pattern (19 bp):
ATATTATATTTATATAAGC
Found at i:29923954 original size:84 final size:78
Alignment explanation
Indices: 29923797--29923955 Score: 196
Period size: 78 Copynumber: 2.0 Consensus size: 78
29923787 CAAATTTATT
* *
29923797 TCGATATTGATATTATTAACTCTTTCATCCATAAAAAAATTATTTTGATTTAAATTTACCTTGAT
1 TCGATATTGATATTATTAACTCTTTCATCCAAAAAAAAATTATTTTGATTGAAATTTACCTTGAT
29923862 TTTGATATTTACA
66 TTTGATATTTACA
29923875 TCGATATTGATATTATTAACTCTTTCA-CACGTAAAAAAAAAAAATTCAGTTTT-ATTGAAATTT
1 TCGATATTGATATTATTAACTCTTTCATC-C-----AAAAAAAAATT-A-TTTTGATTGAAATTT
* *
29923938 ACTTTGATTTTTATATTT
58 ACCTTGATTTTGATATTT
29923956 CATAAATGTT
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
77 1 0.01
78 28 0.41
83 10 0.14
84 26 0.38
85 4 0.06
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.47
Consensus pattern (78 bp):
TCGATATTGATATTATTAACTCTTTCATCCAAAAAAAAATTATTTTGATTGAAATTTACCTTGAT
TTTGATATTTACA
Found at i:29924293 original size:47 final size:47
Alignment explanation
Indices: 29924208--29924298 Score: 128
Period size: 47 Copynumber: 1.9 Consensus size: 47
29924198 ACAGGCTATC
* *
29924208 TTTTCCTTTATAACGAAAGGTTACATTGCTGTAGACGTTTGGAAACG
1 TTTTCCTTTATAACGAAAGGTTACATTGCAGTAAACGTTTGGAAACG
* * * *
29924255 TTTTCCTTTTTAGCGAAAGGTTGCGTTGCAGTAAACGTTTGGAA
1 TTTTCCTTTATAACGAAAGGTTACATTGCAGTAAACGTTTGGAA
29924299 CCGATCACCC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 38 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.37
Consensus pattern (47 bp):
TTTTCCTTTATAACGAAAGGTTACATTGCAGTAAACGTTTGGAAACG
Found at i:29949149 original size:34 final size:34
Alignment explanation
Indices: 29949099--29949167 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
29949089 AAACACATGC
*
29949099 ACGATTTGCCTCATGAATGGTCAAAATTTCTACA
1 ACGATTTGCCTCATGAATGCTCAAAATTTCTACA
* * *
29949133 ACGATTTTCCTTATGAATTCTCAAAATTTCTACA
1 ACGATTTGCCTCATGAATGCTCAAAATTTCTACA
29949167 A
1 A
29949168 AGTTAGAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.36
Consensus pattern (34 bp):
ACGATTTGCCTCATGAATGCTCAAAATTTCTACA
Found at i:29950219 original size:29 final size:29
Alignment explanation
Indices: 29950158--29950338 Score: 165
Period size: 29 Copynumber: 6.3 Consensus size: 29
29950148 TAATAGAGAC
*
29950158 AAACATGTTTAT-TTGTCTAGATTAAGACA-
1 AAACATGTTT-TCTTGTCTAAATTAAGA-AG
*
29950187 AAACATATTTTTCTTGTCTAAATTAA-AAG
1 AAACAT-GTTTTCTTGTCTAAATTAAGAAG
* * *
29950216 AAACATGTTTTCTTGTCTAACTTTAGACG
1 AAACATGTTTTCTTGTCTAAATTAAGAAG
* **
29950245 AAACATATTTTCTTGTCTAAATTAAGACC
1 AAACATGTTTTCTTGTCTAAATTAAGAAG
*
29950274 AAACATGTTTTCTTATCTAAATTAAGACA-
1 AAACATGTTTTCTTGTCTAAATTAAGA-AG
* * * * *
29950303 AAAGATGTTTTTTTCTTTAAATTAAG-AC
1 AAACATGTTTTCTTGTCTAAATTAAGAAG
29950331 AAACATGT
1 AAACATGT
29950339 AAAAGCTATC
Statistics
Matches: 128, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
27 1 0.01
28 24 0.19
29 88 0.69
30 15 0.12
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.40
Consensus pattern (29 bp):
AAACATGTTTTCTTGTCTAAATTAAGAAG
Found at i:29950223 original size:58 final size:57
Alignment explanation
Indices: 29950156--29950338 Score: 210
Period size: 58 Copynumber: 3.2 Consensus size: 57
29950146 CTTAATAGAG
29950156 ACAAACATGTTTAT-TTGTCTAGATTAAGACAAAACATATTTTTCTTGTCTAAATTAAA
1 ACAAACATGTTT-TCTTGTCTA-ATTAAGACAAAACATATTTTTCTTGTCTAAATTAAA
* * *
29950214 AGAAACATGTTTTCTTGTCTAACTTTAGACGAAACATA-TTTTCTTGTCTAAATTAAGA
1 ACAAACATGTTTTCTTGTCTAA-TTAAGACAAAACATATTTTTCTTGTCTAAATTAA-A
* * * * * * *
29950272 CCAAACATGTTTTCTTATCTAAATTAAGACAAAAGATGTTTTT-TTCTTTAAATTAAG
1 ACAAACATGTTTTCTTGTCT-AATTAAGACAAAACATATTTTTCTTGTCTAAATTAAA
29950329 ACAAACATGT
1 ACAAACATGT
29950339 AAAAGCTATC
Statistics
Matches: 106, Mismatches: 14, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
57 29 0.27
58 71 0.67
59 6 0.06
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (57 bp):
ACAAACATGTTTTCTTGTCTAATTAAGACAAAACATATTTTTCTTGTCTAAATTAAA
Found at i:29951376 original size:11 final size:11
Alignment explanation
Indices: 29951360--29951403 Score: 70
Period size: 12 Copynumber: 3.8 Consensus size: 11
29951350 TTTCTCCCTC
29951360 TTTTTTTCTTT
1 TTTTTTTCTTT
29951371 TTTTTTTCTTT
1 TTTTTTTCTTT
29951382 TTCTTTTTCTTT
1 TT-TTTTTCTTT
29951394 CTTTTTTTCT
1 -TTTTTTTCT
29951404 CTCCCAACCG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 13 0.42
12 16 0.52
13 2 0.06
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:29951443 original size:17 final size:17
Alignment explanation
Indices: 29951421--29951486 Score: 82
Period size: 17 Copynumber: 3.9 Consensus size: 17
29951411 CCGTTCCCCC
29951421 TTTCTTCTCTCTTTCTT
1 TTTCTTCTCTCTTTCTT
*
29951438 TTTCTTTTCTCTTTCTT
1 TTTCTTCTCTCTTTCTT
29951455 CTTTCTT-TCTCTTTCTT
1 -TTTCTTCTCTCTTTCTT
* *
29951472 TCT-TTCTTTCTTTCT
1 TTTCTTCTCTCTTTCT
29951487 CTTCTAGCCG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
15 2 0.05
16 10 0.23
17 26 0.59
18 6 0.14
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTCTTCTCTCTTTCTT
Found at i:29951454 original size:4 final size:4
Alignment explanation
Indices: 29951420--29951491 Score: 68
Period size: 4 Copynumber: 19.5 Consensus size: 4
29951410 ACCGTTCCCC
* *
29951420 CTTT C-TT CTCT CTTT C-TT -TTT CTTT -TCT CTTT C-TT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
29951463 C--T CTTT CTTT CTTT CTTT CTTT CTCTT CT
1 CTTT CTTT CTTT CTTT CTTT CTTT CT-TT CT
29951492 AGCCGCTCCT
Statistics
Matches: 56, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
2 2 0.04
3 12 0.21
4 38 0.68
5 4 0.07
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (4 bp):
CTTT
Found at i:29951516 original size:83 final size:83
Alignment explanation
Indices: 29951361--29951566 Score: 269
Period size: 83 Copynumber: 2.5 Consensus size: 83
29951351 TTCTCCCTCT
* * * * *
29951361 TTTTTTCTTTTTTTTTTCTTTTTC-TT-TTTCTTTCTTTTTTTCTCTCCCAACCGTTCCCCCTTT
1 TTTTTTCTTTATTCTTTCTTTCTCTTTCTTTCTTTCTTTCTTTCTCTCCCAACCGCTCCCCCTTT
*
29951424 CTTCTCTCTTTCTTTTTC
66 ATTCTCTCTTTCTTTTTC
* * * * *
29951442 TTTTCTCTTTCTTCTTTCTTTCTCTTTCTTTCTTTCTTTCTTTCTCTTCTAGCCGCTCCTCCC-T
1 TTTTTTCTTTATTCTTTCTTTCTCTTTCTTTCTTTCTTTCTTTCTCTCCCAACCGCTCC-CCCTT
29951506 TATTCTCTCTTTCTTTTTC
65 TATTCTCTCTTTCTTTTTC
29951525 TTTTTTCTTTATTCTTTCTTTCTCTTTC-TTC-TTCTTTCTTTC
1 TTTTTTCTTTATTCTTTCTTTCTCTTTCTTTCTTTCTTTCTTTC
29951567 CCCGGCTGGC
Statistics
Matches: 110, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
81 31 0.28
82 5 0.05
83 71 0.65
84 3 0.03
ACGTcount: A:0.02, C:0.29, G:0.01, T:0.67
Consensus pattern (83 bp):
TTTTTTCTTTATTCTTTCTTTCTCTTTCTTTCTTTCTTTCTTTCTCTCCCAACCGCTCCCCCTTT
ATTCTCTCTTTCTTTTTC
Found at i:29951531 original size:7 final size:7
Alignment explanation
Indices: 29951515--29951565 Score: 50
Period size: 7 Copynumber: 7.0 Consensus size: 7
29951505 TTATTCTCTC
29951515 TTTC-TT
1 TTTCTTT
29951521 TTTCTTT
1 TTTCTTT
29951528 TTTCTTT
1 TTTCTTT
*
29951535 ATTCTTT
1 TTTCTTT
29951542 CTTTCTCTT
1 -TTTCT-TT
*
29951551 TCTTCTTC
1 T-TTCTTT
29951559 TTTCTTT
1 TTTCTTT
29951566 CCCCGGCTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
6 4 0.11
7 20 0.54
8 7 0.19
9 6 0.16
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTCTTT
Found at i:29951542 original size:24 final size:24
Alignment explanation
Indices: 29951508--29951566 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
29951498 TCCTCCCTTA
* * *
29951508 TTCTCTCTTTCTTTTTCTTTTTTC
1 TTCTTTCTTTCTTTCTCTTTCTTC
29951532 TT-TATTCTTTCTTTCTCTTTCTTC
1 TTCT-TTCTTTCTTTCTCTTTCTTC
29951556 TTCTTTCTTTC
1 TTCTTTCTTTC
29951567 CCCGGCTGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 1 0.03
24 28 0.93
25 1 0.03
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (24 bp):
TTCTTTCTTTCTTTCTCTTTCTTC
Found at i:29951552 original size:10 final size:11
Alignment explanation
Indices: 29951521--29951566 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
29951511 TCTCTTTCTT
*
29951521 TTTCTTTTTTC
1 TTTCTTCTTTC
*
29951532 TTTATTCTTTC
1 TTTCTTCTTTC
29951543 TTTC-TCTTTC
1 TTTCTTCTTTC
29951553 -TTCTTCTTTC
1 TTTCTTCTTTC
29951563 TTTC
1 TTTC
29951567 CCCGGCTGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 3 0.10
10 12 0.40
11 15 0.50
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTCTTCTTTC
Found at i:29951559 original size:20 final size:21
Alignment explanation
Indices: 29951536--29951631 Score: 74
Period size: 20 Copynumber: 4.7 Consensus size: 21
29951526 TTTTTCTTTA
*
29951536 TTCTTTCTTTCTCTTTCTTC-
1 TTCTTTCTTTCTCCTTCTTCT
* ** *
29951556 TTCTTTCTTTCCCCGGCTGGC-
1 TTCTTTCTTTCTCCTTCT-TCT
** *
29951577 TTC-TTCTTTCTTTTTCCTCT
1 TTCTTTCTTTCTCCTTCTTCT
29951597 TTCTTTCTTTCTCCTTC-TCT
1 TTCTTTCTTTCTCCTTCTTCT
29951617 TTCTTTCCTTTCTCC
1 TTCTTT-CTTTCTCC
29951632 CTGCTGGCGT
Statistics
Matches: 58, Mismatches: 14, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
19 1 0.02
20 34 0.59
21 23 0.40
ACGTcount: A:0.00, C:0.34, G:0.04, T:0.61
Consensus pattern (21 bp):
TTCTTTCTTTCTCCTTCTTCT
Found at i:29951581 original size:61 final size:63
Alignment explanation
Indices: 29951516--29951639 Score: 166
Period size: 61 Copynumber: 2.0 Consensus size: 63
29951506 TATTCTCTCT
* * *
29951516 TTCTT-TTTCTTTTTTCTTTATTCTTTCTTTCTCTTTCT-TCTTCTTT-CTTTC-CCCGGCTGGC
1 TTCTTCTTTCTTTTTCCTCT-TTCTTTCTTTCTCCTTCTCT-TTCTTTCCTTTCTCCCGGCTGGC
*
29951577 TTCTTCTTTCTTTTTCCTCTTTCTTTCTTTCTCCTTCTCTTTCTTTCCTTTCTCCCTGCTGGC
1 TTCTTCTTTCTTTTTCCTCTTTCTTTCTTTCTCCTTCTCTTTCTTTCCTTTCTCCCGGCTGGC
29951640 GTCGCACTCT
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
61 28 0.51
62 18 0.33
63 9 0.16
ACGTcount: A:0.01, C:0.31, G:0.06, T:0.62
Consensus pattern (63 bp):
TTCTTCTTTCTTTTTCCTCTTTCTTTCTTTCTCCTTCTCTTTCTTTCCTTTCTCCCGGCTGGC
Found at i:29951600 original size:17 final size:16
Alignment explanation
Indices: 29951580--29951623 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
29951570 GGCTGGCTTC
*
29951580 TTCTTTCTTTTTCCTCT
1 TTCTTTCTTTCTCCT-T
29951597 TTCTTTCTTTCTCCTT
1 TTCTTTCTTTCTCCTT
*
29951613 CTCTTTCTTTC
1 TTCTTTCTTTC
29951624 CTTTCTCCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 11 0.44
17 14 0.56
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (16 bp):
TTCTTTCTTTCTCCTT
Found at i:29951604 original size:24 final size:23
Alignment explanation
Indices: 29951508--29951629 Score: 71
Period size: 24 Copynumber: 5.5 Consensus size: 23
29951498 TCCTCCCTTA
29951508 TTCTCTCTTTCTTTTT-CT-TTT-
1 TTCT-TCTTTCTTTTTCCTCTTTC
*
29951529 TTCTT-TATTCTTTCTTTCTCTTTC
1 TTCTTCT-TTCTTT-TTCCTCTTTC
** * **
29951553 TTCTTCTTTCTTTCCCCGGCTGGC
1 TTCTTCTTTCTTTTTCC-TCTTTC
29951577 TTCTTCTTTCTTTTTCCTCTTTC
1 TTCTTCTTTCTTTTTCCTCTTTC
**
29951600 -T-TTCTTTCTCCTT-CTCTTTC
1 TTCTTCTTTCTTTTTCCTCTTTC
*
29951620 TT-TCCTTTCT
1 TTCTTCTTTCT
29951630 CCCTGCTGGC
Statistics
Matches: 79, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
19 1 0.01
20 14 0.18
21 24 0.30
22 3 0.04
23 7 0.09
24 29 0.37
25 1 0.01
ACGTcount: A:0.01, C:0.30, G:0.03, T:0.66
Consensus pattern (23 bp):
TTCTTCTTTCTTTTTCCTCTTTC
Found at i:29952905 original size:2 final size:2
Alignment explanation
Indices: 29952892--29952930 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
29952882 TATTGATGTT
* *
29952892 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29952931 TTGTGCAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:29957563 original size:2 final size:2
Alignment explanation
Indices: 29957556--29957581 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29957546 TTAAAATATA
29957556 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
29957582 TGTAACATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:29958224 original size:29 final size:29
Alignment explanation
Indices: 29958183--29958372 Score: 142
Period size: 28 Copynumber: 6.7 Consensus size: 29
29958173 TAGTGGCTTA
* **
29958183 AAAAG-TATGCATCCACTTCTAGTGAAGT
1 AAAAGTTATTCATCCACTTCTAGTGGGGT
* * *
29958211 AAAAGTTATCCATCAACATT-TGGTGGGGT
1 AAAAGTTATTCATCCAC-TTCTAGTGGGGT
* *
29958240 -AAAGTTATTCATCCATTTCTAATGGGGT
1 AAAAGTTATTCATCCACTTCTAGTGGGGT
** *
29958268 -AAAGTTATTTGTCCACTTCTGGTGGGGT
1 AAAAGTTATTCATCCACTTCTAGTGGGGT
* * *
29958296 AAAAAG-TATGCGTTCACTTCTAGTGGGGT
1 -AAAAGTTATTCATCCACTTCTAGTGGGGT
* * **
29958325 AAAAGTTATCCATCCAAC-TCTGGTAAGGT
1 AAAAGTTATTCATCC-ACTTCTAGTGGGGT
29958354 -AAAGTTATTCATCCACTTC
1 AAAAGTTATTCATCCACTTC
29958373 CGGTAGGTAA
Statistics
Matches: 128, Mismatches: 26, Indels: 16
0.75 0.15 0.09
Matches are distributed among these distances:
27 4 0.03
28 68 0.53
29 48 0.38
30 8 0.06
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (29 bp):
AAAAGTTATTCATCCACTTCTAGTGGGGT
Found at i:29958377 original size:28 final size:27
Alignment explanation
Indices: 29958326--29958385 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
29958316 TAGTGGGGTA
*
29958326 AAAGTTATCCATCCAACTCTGGTAAGGT
1 AAAGTTATCCATCCAACTCCGGT-AGGT
*
29958354 AAAGTTATTCATCC-ACTTCCGGTAGGT
1 AAAGTTATCCATCCAAC-TCCGGTAGGT
29958381 AAAGT
1 AAAGT
29958386 GTGATTTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 11 0.38
28 18 0.62
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (27 bp):
AAAGTTATCCATCCAACTCCGGTAGGT
Found at i:29958515 original size:131 final size:130
Alignment explanation
Indices: 29958351--29958619 Score: 335
Period size: 131 Copynumber: 2.1 Consensus size: 130
29958341 ACTCTGGTAA
* *
29958351 GGTAAAGTTATTCATCCACTTCCGGTAGGTAAAGTGTGATTTCTTCAATGTCTATAACCATAATT
1 GGTAAAGTTATTCATCCACTTCCGGTAGGTAAAGTGTGATCTCTTCAATGTCCATAACCATAATT
* * * * *
29958416 ATTAAACGATGTCGCATTTACTATAAAGAATGGACAGATTTATGATCATTCATCCACTTCTAGTG
66 AGTAAACGATGTCGCATTTACCATAAAGAATAGACAGATTCATAATCATTCATCCACTTCTAGT-
29958481 G
130 G
* * * * *
29958482 GGTAAAGTTATTCATTCACTT-C-TTACGAGTAAAGTGTGATCTCTTCCATGTCCATTACTATAA
1 GGTAAAGTTATTCATCCACTTCCGGTA-G-GTAAAGTGTGATCTCTTCAATGTCCATAACCATAA
* ** * * *
29958545 TTAGTAAATGATGTCGCATTTACCATAGGGAATAGACTGATTCATAATTATTCATCCACTTCTGG
64 TTAGTAAACGATGTCGCATTTACCATAAAGAATAGACAGATTCATAATCATTCATCCACTTCTAG
29958610 TG
129 TG
29958612 GGTAAAGT
1 GGTAAAGT
29958620 ATGATCTTTT
Statistics
Matches: 118, Mismatches: 18, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
129 2 0.02
130 11 0.09
131 105 0.89
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (130 bp):
GGTAAAGTTATTCATCCACTTCCGGTAGGTAAAGTGTGATCTCTTCAATGTCCATAACCATAATT
AGTAAACGATGTCGCATTTACCATAAAGAATAGACAGATTCATAATCATTCATCCACTTCTAGTG
Found at i:29959209 original size:11 final size:12
Alignment explanation
Indices: 29959184--29959215 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
29959174 GGATGGATTA
29959184 AATCTTAATTCT
1 AATCTTAATTCT
29959196 AATCTTAA-TCT
1 AATCTTAATTCT
29959207 AATC-TAATT
1 AATCTTAATT
29959216 TACATTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 3 0.16
11 8 0.42
12 8 0.42
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.47
Consensus pattern (12 bp):
AATCTTAATTCT
Done.