Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold57
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: 4071704
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82236 characters in sequence are not A, C, G, or T
File 16 of 27
Found at i:2116913 original size:21 final size:22
Alignment explanation
Indices: 2116884--2116926 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
2116874 ATGTCAAAAG
*
2116884 TTATTAAAAT-TATATAAAATA
1 TTATCAAAATATATATAAAATA
2116905 TTATCAAAATCATATATAAAAT
1 TTATCAAAAT-ATATATAAAAT
2116927 TACTAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
23 10 0.53
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (22 bp):
TTATCAAAATATATATAAAATA
Found at i:2116928 original size:21 final size:20
Alignment explanation
Indices: 2116857--2116928 Score: 63
Period size: 21 Copynumber: 3.5 Consensus size: 20
2116847 TTTTTTATAT
* * *
2116857 TAAAAACTATCAAGATCATG
1 TAAAAATTATCAAAATCATA
* * *
2116877 TCAAAAGTTATTAAAATTATA
1 T-AAAAATTATCAAAATCATA
2116898 TAAAATATTATCAAAATCATA
1 TAAAA-ATTATCAAAATCATA
2116919 TATAAAATTA
1 TA-AAAATTA
2116929 CTAAAATTAA
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
20 5 0.12
21 32 0.80
22 3 0.08
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.33
Consensus pattern (20 bp):
TAAAAATTATCAAAATCATA
Found at i:2116934 original size:21 final size:19
Alignment explanation
Indices: 2116888--2116935 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 19
2116878 CAAAAGTTAT
*
2116888 TAAAATTATATAAAATATTA
1 TAAAATCATATAAAA-ATTA
2116908 TCAAAATCATATATAAAATTA
1 T-AAAATCATATA-AAAATTA
2116929 CTAAAAT
1 -TAAAAT
2116936 TAAACAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 19 0.79
22 4 0.17
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAATCATATAAAAATTA
Found at i:2120606 original size:3 final size:3
Alignment explanation
Indices: 2120593--2120623 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2120583 GAGGAGCAAC
*
2120593 AAG AAG CAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
2120624 CAAACCCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.03, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2121362 original size:11 final size:11
Alignment explanation
Indices: 2121346--2121370 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2121336 TCCGAATATA
2121346 TATGACACTAT
1 TATGACACTAT
2121357 TATGACACTAT
1 TATGACACTAT
2121368 TAT
1 TAT
2121371 TTTAATGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (11 bp):
TATGACACTAT
Found at i:2123643 original size:15 final size:15
Alignment explanation
Indices: 2123619--2123653 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
2123609 TATTTTTTTA
2123619 TTAT-TTAAATATAT
1 TTATATTAAATATAT
2123633 TTATATTAAATATAT
1 TTATATTAAATATAT
2123648 TTATAT
1 TTATAT
2123654 ATTTAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATATTAAATATAT
Found at i:2123647 original size:17 final size:18
Alignment explanation
Indices: 2123626--2123671 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
2123616 TTATTATTTA
2123626 AATATATTTATATTAAAT
1 AATATATTTATATTAAAT
*
2123644 -ATAT-TTATATATTTAAT
1 AATATATT-TATATTAAAT
2123661 AATTATATTTA
1 AA-TATATTTA
2123672 AAATAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
16 2 0.09
17 13 0.57
18 1 0.04
19 5 0.22
20 2 0.09
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AATATATTTATATTAAAT
Found at i:2123649 original size:25 final size:23
Alignment explanation
Indices: 2123620--2123673 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 23
2123610 ATTTTTTTAT
2123620 TATTTAAATATATTTATATTAAATA
1 TATTTAAATATATTTA-A-TAAATA
*
2123645 TATTT--ATATATTTAATAATTA
1 TATTTAAATATATTTAATAAATA
2123666 TATTTAAA
1 TATTTAAA
2123674 ATAATATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 10 0.38
22 1 0.04
23 10 0.38
25 5 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TATTTAAATATATTTAATAAATA
Found at i:2123666 original size:15 final size:16
Alignment explanation
Indices: 2123616--2123668 Score: 58
Period size: 15 Copynumber: 3.4 Consensus size: 16
2123606 AAATATTTTT
2123616 TTAT-TATTTAAATATA
1 TTATATATTT-AATATA
*
2123632 TT-TATATTAAATATA
1 TTATATATTTAATATA
2123647 TTTATATATTTAATA-A
1 -TTATATATTTAATATA
2123663 TTATAT
1 TTATAT
2123669 TTAAAATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
15 13 0.41
16 9 0.28
17 10 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTATATATTTAATATA
Found at i:2123676 original size:15 final size:15
Alignment explanation
Indices: 2123620--2123705 Score: 52
Period size: 15 Copynumber: 5.5 Consensus size: 15
2123610 ATTTTTTTAT
*
2123620 TATTTAAATATATTTA
1 TATTTAAA-ATAATTA
*
2123636 TA-TTAAATATATTTA
1 TATTTAAA-ATAATTA
*
2123651 TATATT-TAATAATTA
1 TAT-TTAAAATAATTA
2123666 TATTTAAAATAATATAA
1 TATTTAAAATAAT-T-A
*
2123683 TTTTTTAAAATAAGTT-
1 -TATTTAAAATAA-TTA
2123699 TATTTAA
1 TATTTAA
2123706 TAAATTATTA
Statistics
Matches: 58, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
14 2 0.03
15 36 0.62
16 4 0.07
17 3 0.05
18 12 0.21
19 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (15 bp):
TATTTAAAATAATTA
Found at i:2124579 original size:44 final size:44
Alignment explanation
Indices: 2124496--2124579 Score: 100
Period size: 44 Copynumber: 1.9 Consensus size: 44
2124486 TATATATTAT
** *
2124496 TTTTATAATATAATAATATTTTAAATATTATATATTTATATAAC
1 TTTTATAATATAATAATATTTTAAATAAAATATAATTATATAAC
*
2124540 TTTTATAATATATTTAAT-TTATTAAATAAAATA-AATTATA
1 TTTTATAATATA-ATAATATT-TTAAATAAAATATAATTATA
2124580 ATAAAATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
44 20 0.59
45 14 0.41
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (44 bp):
TTTTATAATATAATAATATTTTAAATAAAATATAATTATATAAC
Found at i:2124599 original size:16 final size:16
Alignment explanation
Indices: 2124558--2124601 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
2124548 TATATTTAAT
*
2124558 TTATTAAATAAAATAA
1 TTATTTAATAAAATAA
2124574 --ATTATAATAAAATAA
1 TTATT-TAATAAAATAA
2124589 TTATTTAATAAAA
1 TTATTTAATAAAA
2124602 ATAAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
14 3 0.12
15 10 0.42
16 8 0.33
17 3 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TTATTTAATAAAATAA
Found at i:2124603 original size:32 final size:31
Alignment explanation
Indices: 2124558--2124624 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 31
2124548 TATATTTAAT
*
2124558 TTATTAAATAAAATAAATTATAA-TAAAATAA
1 TTATTAAATAAAATAAAATA-AAGTAAAATAA
*
2124589 TTATTTAATAAAAATAAAATAAAGTAAAATAA
1 TTATTAAAT-AAAATAAAATAAAGTAAAATAA
2124621 TTAT
1 TTAT
2124625 AGTGTCCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
31 10 0.31
32 22 0.69
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (31 bp):
TTATTAAATAAAATAAAATAAAGTAAAATAA
Found at i:2124884 original size:10 final size:12
Alignment explanation
Indices: 2124861--2124887 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2124851 CAATATACTT
2124861 TATAAATTTATA
1 TATAAATTTATA
2124873 TATAAATTTATA
1 TATAAATTTATA
2124885 TAT
1 TAT
2124888 TTAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TATAAATTTATA
Found at i:2125422 original size:18 final size:16
Alignment explanation
Indices: 2125393--2125447 Score: 65
Period size: 18 Copynumber: 3.2 Consensus size: 16
2125383 TATGTCAAAA
*
2125393 ATAATTAAAATATAAT
1 ATAATAAAAATATAAT
*
2125409 ATAATTTAAAAATAAAAT
1 ATAA--TAAAAATATAAT
2125427 ATAATAAAAATATAAAT
1 ATAATAAAAATAT-AAT
2125444 ATAA
1 ATAA
2125448 ATATATTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
16 12 0.36
17 7 0.21
18 14 0.42
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAATAAAAATATAAT
Found at i:2125449 original size:23 final size:23
Alignment explanation
Indices: 2125400--2125472 Score: 67
Period size: 23 Copynumber: 3.0 Consensus size: 23
2125390 AAAATAATTA
* * *
2125400 AAATATAAT-ATAATTTAAAAAT
1 AAATATAATAAAAATATAAATAT
2125422 AAAATATAATAAAAATATAAATAT
1 -AAATATAATAAAAATATAAATAT
*
2125446 AAATATATTAAAATTTATATAAATAT
1 AAATATAATAAAA---ATATAAATAT
2125472 A
1 A
2125473 TCATATTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
23 21 0.50
24 10 0.24
26 11 0.26
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
AAATATAATAAAAATATAAATAT
Found at i:2125458 original size:22 final size:21
Alignment explanation
Indices: 2125418--2125473 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
2125408 TATAATTTAA
2125418 AAATA-AAATATAATAAAAATAT
1 AAATATAAATAT-ATAAAAAT-T
*
2125440 AAATATAAATATATTAAAATT
1 AAATATAAATATATAAAAATT
*
2125461 -TATATAAATATAT
1 AAATATAAATATAT
2125474 CATATTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.39
21 1 0.03
22 12 0.39
23 6 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATATAAATATATAAAAATT
Found at i:2125520 original size:21 final size:21
Alignment explanation
Indices: 2125487--2125532 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2125477 ATTTTATGTG
*
2125487 ATAA-TAATATGTAAAAATAT
1 ATAATTAAGATGTAAAAATAT
*
2125507 ATAATTAAGATGTAAATATAT
1 ATAATTAAGATGTAAAAATAT
2125528 -TAATT
1 ATAATT
2125533 GCTAGATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (21 bp):
ATAATTAAGATGTAAAAATAT
Found at i:2125656 original size:21 final size:22
Alignment explanation
Indices: 2125630--2125671 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2125620 AGTACAAATT
2125630 AAATATTATTTAATT-ATATAA
1 AAATATTATTTAATTAATATAA
* *
2125651 AAATATTTTTTATTTAATATA
1 AAATATTATTTAATTAATATA
2125672 TTATTTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AAATATTATTTAATTAATATAA
Found at i:2128394 original size:7 final size:7
Alignment explanation
Indices: 2128384--2128423 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
2128374 AATATTTAAT
2128384 AATTTTA
1 AATTTTA
2128391 AATTTTA
1 AATTTTA
2128398 AATTTTA
1 AATTTTA
2128405 AATTTT-
1 AATTTTA
2128411 -ATTTTA
1 AATTTTA
2128417 TAATTTT
1 -AATTTT
2128424 GAATAGTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.17
7 20 0.67
8 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
AATTTTA
Found at i:2129871 original size:20 final size:20
Alignment explanation
Indices: 2129845--2129897 Score: 58
Period size: 19 Copynumber: 2.7 Consensus size: 20
2129835 ATTTTTATAA
2129845 ATAAAATTAATAAAACAATAT
1 ATAAAATTAATAAAA-AATAT
2129866 -TAAAA-T-ATATAAAAATAT
1 ATAAAATTAATA-AAAAATAT
*
2129884 ATAAAATAAATAAA
1 ATAAAATTAATAAA
2129898 TATAACATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
18 8 0.30
19 9 0.33
20 7 0.26
21 3 0.11
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (20 bp):
ATAAAATTAATAAAAAATAT
Found at i:2129872 original size:8 final size:9
Alignment explanation
Indices: 2129861--2129901 Score: 50
Period size: 8 Copynumber: 4.7 Consensus size: 9
2129851 TTAATAAAAC
2129861 AATAT-TAA
1 AATATATAA
2129869 AATATATAAA
1 AATATAT-AA
2129879 AATATATAA
1 AATATATAA
*
2129888 AATAAAT-A
1 AATATATAA
2129896 AATATA
1 AATATA
2129902 ACATGATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 11 0.38
9 9 0.31
10 9 0.31
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AATATATAA
Found at i:2129902 original size:10 final size:9
Alignment explanation
Indices: 2129841--2129902 Score: 52
Period size: 9 Copynumber: 6.4 Consensus size: 9
2129831 TTTAATTTTT
2129841 ATAAATAAA
1 ATAAATAAA
*
2129850 ATTAATAAA
1 ATAAATAAA
*
2129859 ACAATATTAAA
1 ATAA-A-TAAA
*
2129870 ATATATAAAA
1 ATAAAT-AAA
*
2129880 ATATATAAA
1 ATAAATAAA
2129889 ATAAATAAA
1 ATAAATAAA
2129898 TATAA
1 -ATAA
2129903 CATGATTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
9 22 0.51
10 15 0.35
11 6 0.14
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (9 bp):
ATAAATAAA
Found at i:2130791 original size:17 final size:17
Alignment explanation
Indices: 2130771--2130803 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2130761 TTTATAATTG
2130771 GTTTAAAATGGGTTTGT
1 GTTTAAAATGGGTTTGT
*
2130788 GTTTAACATGGGTTTG
1 GTTTAAAATGGGTTTG
2130804 GATAGTTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.03, G:0.30, T:0.45
Consensus pattern (17 bp):
GTTTAAAATGGGTTTGT
Found at i:2131954 original size:21 final size:21
Alignment explanation
Indices: 2131929--2131970 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2131919 AGAGTAACAT
2131929 AGGTATAGAGGGAGTAGCAAC
1 AGGTATAGAGGGAGTAGCAAC
2131950 AGGTATAGAGGGAGTAGCAAC
1 AGGTATAGAGGGAGTAGCAAC
2131971 GGAAATAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.38, T:0.14
Consensus pattern (21 bp):
AGGTATAGAGGGAGTAGCAAC
Found at i:2138050 original size:2 final size:2
Alignment explanation
Indices: 2138045--2138084 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2138035 CACACATGTG
2138045 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2138085 TGATGATGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2138418 original size:2 final size:2
Alignment explanation
Indices: 2138411--2138436 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2138401 GAGTATGATA
2138411 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
2138437 TTCATAAGTA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2142070 original size:20 final size:20
Alignment explanation
Indices: 2142047--2142090 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2142037 TGAATCTAAA
*
2142047 TATAATTTTTTTATCATATT
1 TATAATTTTTTTATCATAAT
* *
2142067 TATATTTTTTTTATTATAAT
1 TATAATTTTTTTATCATAAT
2142087 TATA
1 TATA
2142091 GATGAATTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (20 bp):
TATAATTTTTTTATCATAAT
Found at i:2144719 original size:21 final size:22
Alignment explanation
Indices: 2144673--2144719 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
2144663 AATTTGAATC
2144673 AATTTAGTTTAATAT--AAATT
1 AATTTAGTTTAATATAAAAATT
2144693 ACAATTTA-TTTAATATAAAAATT
1 --AATTTAGTTTAATATAAAAATT
2144716 AATT
1 AATT
2144720 AAATTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
21 12 0.52
22 6 0.26
23 5 0.22
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
AATTTAGTTTAATATAAAAATT
Found at i:2144727 original size:23 final size:22
Alignment explanation
Indices: 2144701--2144784 Score: 66
Period size: 22 Copynumber: 3.7 Consensus size: 22
2144691 TTACAATTTA
2144701 TTTAATATAAAAAT-TAATTAAAT
1 TTTAATATAAAAATAT-A-TAAAT
2144724 TTTAAT-TATAAAATATATAAAT
1 TTTAATATA-AAAATATATAAAT
* *
2144746 ATTAATATAAAAA-ATTTAATATT
1 TTTAATATAAAAATATATAA-A-T
*
2144769 TTTAAATATTAAAATA
1 TTT-AATATAAAAATA
2144785 AATGTTTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
21 5 0.10
22 17 0.34
23 17 0.34
24 10 0.20
25 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TTTAATATAAAAATATATAAAT
Found at i:2144744 original size:22 final size:21
Alignment explanation
Indices: 2144701--2144784 Score: 62
Period size: 21 Copynumber: 3.7 Consensus size: 21
2144691 TTACAATTTA
2144701 TTTAATATAAAA-ATTAATTAAAT
1 TTTAATATAAAATA-T-A-TAAAT
2144724 TTTAATTATAAAATATATAAAT
1 TTTAA-TATAAAATATATAAAT
* * *
2144746 ATTAATATAAAAAATTTAATATT
1 TTTAATATAAAATATATAA-A-T
2144769 TTTAAATATTAAAATA
1 TTT-AATA-TAAAATA
2144785 AATGTTTAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
21 12 0.24
22 10 0.20
23 9 0.18
24 12 0.24
25 7 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTAATATAAAATATATAAAT
Found at i:2144961 original size:34 final size:34
Alignment explanation
Indices: 2144896--2145079 Score: 262
Period size: 34 Copynumber: 5.4 Consensus size: 34
2144886 GAGCTAATGT
* *
2144896 TTGTTGATTAAAT-GGTGATTTGGTAGTTTACCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
* *
2144929 TTGTTGACTAAATGGGAAATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
2144963 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
* * * *
2144997 TTATTGATTAAATGGGTGATTTGGTGGTTTACCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
* * *
2145031 TTGTTGACTAAATGGGAGATTTGGTAGGTTGCCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
2145065 TTGTTGATTAAATGG
1 TTGTTGATTAAATGG
2145080 TGGTTTTTAC
Statistics
Matches: 133, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 12 0.09
34 121 0.91
ACGTcount: A:0.26, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
Found at i:2145440 original size:19 final size:19
Alignment explanation
Indices: 2145384--2145446 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
2145374 TGGTTGTCGA
**
2145384 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
2145403 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
2145422 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
2145441 GTTACT
1 GGTACT
2145447 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:2149578 original size:34 final size:34
Alignment explanation
Indices: 2149512--2149696 Score: 264
Period size: 34 Copynumber: 5.5 Consensus size: 34
2149502 AAGTGGGAGA
* *
2149512 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
2149545 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
2149579 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
2149613 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
2149647 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
2149681 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2149697 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 13 0.10
34 121 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:2151488 original size:2 final size:2
Alignment explanation
Indices: 2151478--2151508 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2151468 TGTATATAGT
*
2151478 TA TA AA 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
2151509 TAATCGAACC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2156865 original size:33 final size:33
Alignment explanation
Indices: 2156811--2156916 Score: 110
Period size: 35 Copynumber: 3.1 Consensus size: 33
2156801 AAAATTTATG
*
2156811 TATTTGTAT-TATTTTTT-TATATAA-AATATTA
1 TATTTTTATATATTTTTTATATATAATAAT-TTA
2156842 TATTTTTATATATTTTTTATATATTAATAATTTA
1 TATTTTTATATATTTTTTATATA-TAATAATTTA
* *
2156876 TTTATTTTATATATTTTTTTATATATACGTATATTTA
1 TAT-TTTTATATA-TTTTTTATATATA-ATA-ATTTA
2156913 TATT
1 TATT
2156917 ATGTGTATAT
Statistics
Matches: 63, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
31 8 0.13
32 8 0.13
33 4 0.06
34 8 0.13
35 14 0.22
36 14 0.22
37 7 0.11
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (33 bp):
TATTTTTATATATTTTTTATATATAATAATTTA
Found at i:2157062 original size:24 final size:23
Alignment explanation
Indices: 2157018--2157063 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
2157008 TTTTTACACG
* *
2157018 TTAATTATTTATTTATCTATATT
1 TTAATTATTCATGTATCTATATT
*
2157041 TTAATATATTCATGTATTTATAT
1 TTAAT-TATTCATGTATCTATAT
2157064 CGTATTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (23 bp):
TTAATTATTCATGTATCTATATT
Found at i:2157550 original size:12 final size:12
Alignment explanation
Indices: 2157531--2157663 Score: 73
Period size: 12 Copynumber: 11.0 Consensus size: 12
2157521 TGTATTTAAA
2157531 ATAT-TATTTTT
1 ATATATATTTTT
2157542 ATATATATTTTT
1 ATATATATTTTT
*
2157554 ATATATTAATAATTT
1 ATATA-T-AT-TTTT
*
2157569 AT-TTTA-TTTT
1 ATATATATTTTT
*
2157579 ATGTATATTTTT
1 ATATATATTTTT
2157591 ATATATATGTGTATT
1 ATATATAT-T-T-TT
* *
2157606 A-ATATAATGTGT
1 ATATAT-ATTTTT
2157618 ATAT-TATTTTT
1 ATATATATTTTT
*
2157629 ATGT-TATATTTT
1 ATATATAT-TTTT
*
2157641 AAATAT-TTTTT
1 ATATATATTTTT
*
2157652 ATAAATATTTTT
1 ATATATATTTTT
2157664 TATGTTATTT
Statistics
Matches: 94, Mismatches: 14, Indels: 27
0.70 0.10 0.20
Matches are distributed among these distances:
10 5 0.05
11 25 0.27
12 39 0.41
13 7 0.07
14 8 0.09
15 10 0.11
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (12 bp):
ATATATATTTTT
Found at i:2157590 original size:49 final size:50
Alignment explanation
Indices: 2157534--2157659 Score: 138
Period size: 49 Copynumber: 2.6 Consensus size: 50
2157524 ATTTAAAATA
* *
2157534 TTATTTTTATATATATTTTTATATATTAATAAT-T-TATTTTA-TTTTATG
1 TTATTTTTATATATATTTTTATATAAT-ATAATGTGTATATTATTTTTATG
* *
2157582 TATATTTTTATATATATGTGTAT-TAATATAATGTGTATATTATTTTTATG
1 T-TATTTTTATATATATTTTTATATAATATAATGTGTATATTATTTTTATG
*
2157632 TTATATTTTAAATAT-TTTTTATA-AATAT
1 TTAT-TTTTATATATATTTTTATATAATAT
2157660 TTTTTATGTT
Statistics
Matches: 65, Mismatches: 7, Indels: 11
0.78 0.08 0.13
Matches are distributed among these distances:
47 5 0.08
48 5 0.08
49 38 0.58
50 17 0.26
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (50 bp):
TTATTTTTATATATATTTTTATATAATATAATGTGTATATTATTTTTATG
Found at i:2158172 original size:20 final size:20
Alignment explanation
Indices: 2158143--2158217 Score: 60
Period size: 19 Copynumber: 4.2 Consensus size: 20
2158133 TAGTTCTAGT
*
2158143 TTTATTTAAAATTTTATATA
1 TTTATATAAAATTTTATATA
2158163 TTTATAT-AAATTTTA-ATA
1 TTTATATAAAATTTTATATA
*
2158181 --TAT-TATAA--TT-TAT-
1 TTTATATAAAATTTTATATA
*
2158194 TTTATATAAAATTTGATATA
1 TTTATATAAAATTTTATATA
2158214 TTTA
1 TTTA
2158218 CCTTATGTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 18
0.66 0.06 0.28
Matches are distributed among these distances:
14 4 0.10
15 4 0.10
16 9 0.21
18 4 0.10
19 11 0.26
20 10 0.24
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (20 bp):
TTTATATAAAATTTTATATA
Found at i:2159635 original size:31 final size:31
Alignment explanation
Indices: 2159597--2159661 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
2159587 AGGCTTCATC
2159597 AAATACGCATGATAATTCTGTAAAGAGGTGT
1 AAATACGCATGATAATTCTGTAAAGAGGTGT
2159628 AAATACGCATGATAATTCTGTAAAGAGGTGT
1 AAATACGCATGATAATTCTGTAAAGAGGTGT
2159659 AAA
1 AAA
2159662 AGCAATAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.28
Consensus pattern (31 bp):
AAATACGCATGATAATTCTGTAAAGAGGTGT
Found at i:2160787 original size:2 final size:2
Alignment explanation
Indices: 2160780--2160811 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2160770 CATTGTATTA
2160780 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
2160812 GCTACAAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2163201 original size:5 final size:5
Alignment explanation
Indices: 2163186--2163239 Score: 58
Period size: 5 Copynumber: 11.2 Consensus size: 5
2163176 ATATTAATAT
* * *
2163186 TATTA TTTTA TATTA TATTT TATCA TATTA TA-TA T-TTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
*
2163234 AATTA T
1 TATTA T
2163240 TAAAATTATT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
4 6 0.15
5 33 0.85
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (5 bp):
TATTA
Found at i:2163213 original size:15 final size:13
Alignment explanation
Indices: 2163182--2163232 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
2163172 CATCATATTA
2163182 ATATTAT-TATTTT
1 ATATTATAT-TTTT
2163195 ATATTATATTTTAT
1 ATATTATATTTT-T
*
2163209 CATATTATATATTT
1 -ATATTATATTTTT
2163223 ATATTATATT
1 ATATTATATT
2163233 AAATTATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 19 0.58
14 3 0.09
15 11 0.33
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (13 bp):
ATATTATATTTTT
Found at i:2165658 original size:36 final size:36
Alignment explanation
Indices: 2165618--2165703 Score: 172
Period size: 36 Copynumber: 2.4 Consensus size: 36
2165608 TCACTCTCCG
2165618 CTGGTTCTTTCCAACGCGTTGCTTTTACTTGTAATT
1 CTGGTTCTTTCCAACGCGTTGCTTTTACTTGTAATT
2165654 CTGGTTCTTTCCAACGCGTTGCTTTTACTTGTAATT
1 CTGGTTCTTTCCAACGCGTTGCTTTTACTTGTAATT
2165690 CTGGTTCTTTCCAA
1 CTGGTTCTTTCCAA
2165704 TGTGGCGATC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.47
Consensus pattern (36 bp):
CTGGTTCTTTCCAACGCGTTGCTTTTACTTGTAATT
Found at i:2170321 original size:16 final size:15
Alignment explanation
Indices: 2170280--2170323 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
2170270 ATTATATTTT
*
2170280 TAATTTAAGTAAATA
1 TAATTTAATTAAATA
2170295 TAATTTAAATTAAATTA
1 TAATTT-AATTAAA-TA
*
2170312 TTATTTAATTAA
1 TAATTTAATTAA
2170324 TAAAATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.24
16 12 0.48
17 7 0.28
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (15 bp):
TAATTTAATTAAATA
Found at i:2170543 original size:28 final size:29
Alignment explanation
Indices: 2170511--2170645 Score: 124
Period size: 28 Copynumber: 4.7 Consensus size: 29
2170501 GTAGACAAGT
*
2170511 TAATTTTTATATTTATGTTA-TA-TTTACA
1 TAATTTTTATATTTATATTATTATTTTA-A
2170539 TAA-TTTTATATATTATTATTATTATTTTAA
1 TAATTTTTATAT-TTA-TATTATTATTTTAA
* *
2170569 -AATATTATATATTTATA-TA-AATTTTAA
1 TAAT-TTTTATATTTATATTATTATTTTAA
2170596 TATATTTTTATATTTATATTATT-TTTTAA
1 TA-ATTTTTATATTTATATTATTATTTTAA
*
2170625 TTATTTTTATA-TTATAATTAT
1 TAATTTTTATATTTAT-ATTAT
2170646 ATTATATTTA
Statistics
Matches: 90, Mismatches: 6, Indels: 22
0.76 0.05 0.19
Matches are distributed among these distances:
27 19 0.21
28 35 0.39
29 19 0.21
30 6 0.07
31 11 0.12
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (29 bp):
TAATTTTTATATTTATATTATTATTTTAA
Found at i:2170561 original size:9 final size:10
Alignment explanation
Indices: 2170544--2170650 Score: 50
Period size: 10 Copynumber: 11.1 Consensus size: 10
2170534 TTACATAATT
2170544 TTATATATTA
1 TTATATATTA
2170554 TTAT-TATTA
1 TTATATATTA
* * *
2170563 TTTTAAAATA
1 TTATATATTA
2170573 TTATATATT-
1 TTATATATTA
*
2170582 TATATAAATT-
1 T-TATATATTA
*
2170592 TTAATATATTT
1 TT-ATATATTA
2170603 TTATAT-TTA
1 TTATATATTA
2170612 -TAT-TATT-
1 TTATATATTA
*
2170619 TTTTA-ATTA
1 TTATATATTA
*
2170628 TTTTTATATTA
1 -TTATATATTA
*
2170639 TAATTATATTA
1 TTA-TATATTA
2170650 T
1 T
2170651 ATTTATCACT
Statistics
Matches: 74, Mismatches: 12, Indels: 21
0.69 0.11 0.20
Matches are distributed among these distances:
7 1 0.01
8 10 0.14
9 12 0.16
10 37 0.50
11 14 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TTATATATTA
Found at i:2170584 original size:27 final size:26
Alignment explanation
Indices: 2170518--2170620 Score: 89
Period size: 27 Copynumber: 3.7 Consensus size: 26
2170508 AGTTAATTTT
* *
2170518 TATATTTATGTTATATTTACATAATTTTA
1 TATATTTATATTAT-TTTA-A-AATATTA
2170547 TATATTATTATTATTATTTTAAAATATTA
1 TATA-T-TTA-TATTATTTTAAAATATTA
* * *
2170576 TATATTTATATAAATTTTAATATATTTT
1 TATATTTATAT-TATTTTAAAATA-TTA
2170604 TATATTTATATTATTTT
1 TATATTTATATTATTTT
2170621 TTAATTATTT
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
26 3 0.05
27 18 0.29
28 14 0.22
29 14 0.22
30 2 0.03
31 7 0.11
32 5 0.08
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (26 bp):
TATATTTATATTATTTTAAAATATTA
Found at i:2170638 original size:11 final size:11
Alignment explanation
Indices: 2170517--2170656 Score: 66
Period size: 11 Copynumber: 12.9 Consensus size: 11
2170507 AAGTTAATTT
*
2170517 TTATATTTATG
1 TTATATTTATA
*
2170528 TTATATTTACA
1 TTATATTTATA
*
2170539 TAAT-TTTATA
1 TTATATTTATA
2170549 -TAT-TATTATTA
1 TTATAT-TTA-TA
2170560 TTAT-TTTAAAATA
1 TTATATTT---ATA
2170573 TTATATATT-TA
1 TTATAT-TTATA
*
2170584 TATAAATTT-TA
1 T-TATATTTATA
*
2170595 ATATA-TT-T-
1 TTATATTTATA
2170603 TTATATTTATA
1 TTATATTTATA
*
2170614 TTAT-TTTTTAA
1 TTATATTTAT-A
*
2170625 TTATTTTTATA
1 TTATATTTATA
*
2170636 TTATAATTATA
1 TTATATTTATA
2170647 TTATATTTAT
1 TTATATTTAT
2170657 CACTGTTAAT
Statistics
Matches: 101, Mismatches: 14, Indels: 28
0.71 0.10 0.20
Matches are distributed among these distances:
8 4 0.04
9 8 0.08
10 16 0.16
11 51 0.50
12 12 0.12
13 6 0.06
14 2 0.02
15 2 0.02
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (11 bp):
TTATATTTATA
Found at i:2171121 original size:33 final size:33
Alignment explanation
Indices: 2171026--2171130 Score: 122
Period size: 32 Copynumber: 3.1 Consensus size: 33
2171016 TAGATAGAAA
2171026 ATTATATTTTAATTATATTAATATATTATATATTTAT
1 ATTA-ATTTTAA-TATATTAATATATT-TATA-TTAT
* **
2171063 ATAAATTTTAATATAAAAATA-ATTTATATTAT
1 ATTAATTTTAATATATTAATATATTTATATTAT
**
2171095 ATTAATTTTAATATATTTGTATATTTATATTAT
1 ATTAATTTTAATATATTAATATATTTATATTAT
2171128 ATT
1 ATT
2171131 TATATAATTT
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
32 20 0.34
33 18 0.31
34 3 0.05
35 8 0.14
36 7 0.12
37 3 0.05
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (33 bp):
ATTAATTTTAATATATTAATATATTTATATTAT
Found at i:2171135 original size:27 final size:27
Alignment explanation
Indices: 2171087--2171219 Score: 73
Period size: 27 Copynumber: 4.8 Consensus size: 27
2171077 AAAAATAATT
2171087 TATA-TTATATTA-ATTTTAATATATTTG
1 TATATTTATATTATA-TTT-ATATATTTG
*
2171114 TATATTTATATTATATTTATATAATTTTT
1 TATATTTATATTATATTTATAT-A-TTTG
*
2171143 TATATTTATA--ATATTATACATTATATTG
1 TATATTTATATTATATT-TATA-TAT-TTG
* * * *
2171171 TA-ATTTTTTTTATAATTT-TTTATAT-
1 TATATTTATATTAT-ATTTATATATTTG
2171196 TATATTTATATTTTATATTTATAT
1 TATATTTATA--TTATATTTATAT
2171220 TGTGTTCAAA
Statistics
Matches: 81, Mismatches: 11, Indels: 27
0.68 0.09 0.23
Matches are distributed among these distances:
25 2 0.02
26 6 0.07
27 26 0.32
28 26 0.32
29 18 0.22
30 3 0.04
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.63
Consensus pattern (27 bp):
TATATTTATATTATATTTATATATTTG
Found at i:2171147 original size:29 final size:33
Alignment explanation
Indices: 2171084--2171152 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
2171074 TATAAAAATA
*
2171084 ATTTATATTATATTAATTTTAATATATTTGTAT
1 ATTTATATTATATTAATTATAATATATTTGTAT
*
2171117 ATTTATATTATATTTA-TATAAT-T-TTT-TAT
1 ATTTATATTATATTAATTATAATATATTTGTAT
2171146 ATTTATA
1 ATTTATA
2171153 ATATTATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 10 0.29
30 3 0.09
31 1 0.03
32 5 0.15
33 15 0.44
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (33 bp):
ATTTATATTATATTAATTATAATATATTTGTAT
Found at i:2171166 original size:39 final size:37
Alignment explanation
Indices: 2171081--2171213 Score: 103
Period size: 39 Copynumber: 3.4 Consensus size: 37
2171071 TAATATAAAA
* *
2171081 ATAATT-TATATTATATTAATTTTAATATATTTGTATATT
1 ATAATTATAT-TTATA-TAATTTT-TTATATTTATATATT
2171120 -TATATTATATTTATATAATTTTTTATATTTATAATATT
1 ATA-ATTATATTTATATAATTTTTTATATTTAT-ATATT
* *
2171158 ATACATTATATTGTA-AT-TTTTTTTATAATTTTTTATATT
1 ATA-ATTATATT-TATATAATTTTTTAT-A-TTTATATATT
*
2171197 ATATTTATATTTTATAT
1 ATAATTATA-TTTATAT
2171214 TTATATTGTG
Statistics
Matches: 79, Mismatches: 6, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
37 8 0.10
38 29 0.37
39 33 0.42
40 9 0.11
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (37 bp):
ATAATTATATTTATATAATTTTTTATATTTATATATT
Found at i:2171183 original size:32 final size:34
Alignment explanation
Indices: 2171140--2171218 Score: 101
Period size: 32 Copynumber: 2.4 Consensus size: 34
2171130 TTATATAATT
2171140 TTTTATATTTATAATATTATACATTATATTGTA-A
1 TTTTATATTTATAATATTATACATTATATT-TATA
* * *
2171174 TTTT-T-TTTATAATTTTTTATATTATATTTATA
1 TTTTATATTTATAATATTATACATTATATTTATA
2171206 TTTTATATTTATA
1 TTTTATATTTATA
2171219 TTGTGTTCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
31 2 0.05
32 25 0.64
33 2 0.05
34 10 0.26
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (34 bp):
TTTTATATTTATAATATTATACATTATATTTATA
Found at i:2171233 original size:45 final size:48
Alignment explanation
Indices: 2171106--2171220 Score: 121
Period size: 45 Copynumber: 2.4 Consensus size: 48
2171096 TTAATTTTAA
2171106 TATATTTGTATATTTATATTATATTTATATAATTTTTTATATTTATAATAT
1 TATATTT-TATATTTATATTATATTTA-A-AATTTTTTATATTTATAATAT
** * * *
2171157 TATACATTATATTGTA-ATTTTTTTTATAATTTTTTATA-TTAT-AT-T
1 TATATTTTATATT-TATATTATATTTAAAATTTTTTATATTTATAATAT
2171202 TATATTTTATATTTATATT
1 TATATTTTATATTTATATT
2171221 GTGTTCAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
44 2 0.04
45 15 0.27
46 2 0.04
47 4 0.07
48 11 0.20
50 14 0.25
51 7 0.13
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (48 bp):
TATATTTTATATTTATATTATATTTAAAATTTTTTATATTTATAATAT
Found at i:2171370 original size:24 final size:21
Alignment explanation
Indices: 2171323--2171392 Score: 60
Period size: 20 Copynumber: 3.5 Consensus size: 21
2171313 AAATAAAATA
* *
2171323 TAAATAT-ATAATATATTTAT
1 TAAATATAATAAAATATATAT
2171343 T--ATAT-ATGAAAATATTATAT
1 TAAATATAAT-AAAATA-TATAT
*
2171363 TAAATATAATATAATATAT-T
1 TAAATATAATAAAATATATAT
2171383 TAAATATAAT
1 TAAATATAAT
2171393 TAATATGATT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
18 6 0.14
19 5 0.12
20 17 0.40
21 3 0.07
22 9 0.21
23 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (21 bp):
TAAATATAATAAAATATATAT
Found at i:2171562 original size:22 final size:21
Alignment explanation
Indices: 2171534--2171576 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
2171524 AAATTAAAAT
2171534 TTTATTTT-TATATTAATATTTA
1 TTTATTTTATA-ATTAA-ATTTA
2171556 TTTATTTTATAATTAAATTTA
1 TTTATTTTATAATTAAATTTA
2171577 AATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 13 0.65
23 2 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTATTTTATAATTAAATTTA
Found at i:2171565 original size:21 final size:22
Alignment explanation
Indices: 2171534--2171576 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
2171524 AAATTAAAAT
2171534 TTTATTTTTAT-ATTAATATTTA
1 TTTATTTTTATAATTAA-ATTTA
2171556 TTTA-TTTTATAATTAAATTTA
1 TTTATTTTTATAATTAAATTTA
2171577 AATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTATTTTTATAATTAAATTTA
Found at i:2171786 original size:14 final size:13
Alignment explanation
Indices: 2171754--2171817 Score: 60
Period size: 12 Copynumber: 5.0 Consensus size: 13
2171744 ATATTTATAA
*
2171754 TTATAATT-TTAA
1 TTATAATTATTAT
*
2171766 ATATAATTAATTAT
1 TTATAATT-ATTAT
2171780 TTATAATTATTA-
1 TTATAATTATTAT
*
2171792 TTATTATTATTAT
1 TTATAATTATTAT
**
2171805 GAATAATTATTAT
1 TTATAATTATTAT
2171818 GCATTGACAC
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
12 18 0.43
13 14 0.33
14 10 0.24
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (13 bp):
TTATAATTATTAT
Found at i:2172267 original size:17 final size:16
Alignment explanation
Indices: 2172245--2172276 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
2172235 TTATTCGATA
2172245 TTAATTTAATTATTTTT
1 TTAATTTAATT-TTTTT
2172262 TTAATTTAATTTTTT
1 TTAATTTAATTTTTT
2172277 AATTTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTAATTTAATTTTTTT
Found at i:2172283 original size:14 final size:13
Alignment explanation
Indices: 2172249--2172281 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2172239 TCGATATTAA
*
2172249 TTTAA-TTATTTT
1 TTTAATTTAATTT
2172261 TTTAATTTAATTT
1 TTTAATTTAATTT
2172274 TTTAATTT
1 TTTAATTT
2172282 TATAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTAATTTAATTT
Found at i:2172901 original size:16 final size:17
Alignment explanation
Indices: 2172871--2172943 Score: 60
Period size: 16 Copynumber: 4.3 Consensus size: 17
2172861 TGATTATATA
2172871 AATAT-AATTTAAAAAT
1 AATATAAATTTAAAAAT
*
2172887 AAT-TAAATTTTAAAAT
1 AATATAAATTTAAAAAT
* *
2172903 AATATAAATATATAAAT
1 AATATAAATTTAAAAAT
* * *
2172920 ATTTTAAAATTTATATAAT
1 AATAT-AAATTTA-AAAAT
2172939 AATAT
1 AATAT
2172944 TTATTAATAT
Statistics
Matches: 42, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
15 1 0.02
16 16 0.38
17 13 0.31
18 6 0.14
19 6 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AATATAAATTTAAAAAT
Found at i:2172904 original size:27 final size:27
Alignment explanation
Indices: 2172869--2173004 Score: 82
Period size: 27 Copynumber: 4.9 Consensus size: 27
2172859 TATGATTATA
* *
2172869 TAAATATAATTTAAAAATAATTAA-ATTT
1 TAAA-ATAATATAAAAAT-ATAAATATTT
*
2172897 TAAAATAATATAAATATATAAATATTT
1 TAAAATAATATAAAAATATAAATATTT
* * *
2172924 TAAAATTTATATAATAATATTTATTAATATAT
1 TAAAA-TAATATAA-AA-A--TATAAATATTT
* *
2172956 TAAAAT-TTATATAAATATAAAATATTT
1 TAAAATAATATAAAAATAT-AAATATTT
* *
2172983 T-AAATAA-ATTATAATATAAATA
1 TAAAATAATATAAAAATATAAATA
2173005 CTCAGATTAA
Statistics
Matches: 85, Mismatches: 15, Indels: 19
0.71 0.13 0.16
Matches are distributed among these distances:
25 5 0.06
26 18 0.21
27 27 0.32
28 12 0.14
29 3 0.04
30 5 0.06
31 1 0.01
32 14 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
TAAAATAATATAAAAATATAAATATTT
Found at i:2172929 original size:18 final size:19
Alignment explanation
Indices: 2172905--2172984 Score: 76
Period size: 18 Copynumber: 4.1 Consensus size: 19
2172895 TTTAAAATAA
2172905 TATAAATATATAAATATTT
1 TATAAATATATAAATATTT
*
2172924 TA-AAATTTATATAATAATATT
1 TATAAATATATA-AAT-AT-TT
*
2172945 TATTAATATATTAAA-ATTT
1 TATAAATATA-TAAATATTT
2172964 ATATAAATATA-AAATATTT
1 -TATAAATATATAAATATTT
2172983 TA
1 TA
2172985 AATAAATTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
18 13 0.26
19 11 0.22
20 13 0.26
21 4 0.08
22 7 0.14
23 2 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TATAAATATATAAATATTT
Found at i:2172954 original size:20 final size:21
Alignment explanation
Indices: 2172931--2172999 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 21
2172921 TTTTAAAATT
2172931 TATATAATAATATTTAT-TAA
1 TATATAATAATATTTATATAA
*
2172951 TATAT--TAAAATTTATATAA
1 TATATAATAATATTTATATAA
2172970 -ATATAA-AATATTT-TA-AA
1 TATATAATAATATTTATATAA
* *
2172987 TAAATTATAATAT
1 TATATAATAATAT
2173000 AAATACTCAG
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
17 2 0.05
18 19 0.47
19 14 0.35
20 5 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TATATAATAATATTTATATAA
Found at i:2172999 original size:19 final size:20
Alignment explanation
Indices: 2172906--2172996 Score: 64
Period size: 20 Copynumber: 4.5 Consensus size: 20
2172896 TTAAAATAAT
2172906 ATAAATATATAAATATTTTAAA
1 ATAAATATA-AAATATTTT-AA
**
2172928 ATTTATATAATAATA-TTT-A
1 ATAAATATAA-AATATTTTAA
* * *
2172947 TTAATATATTAAA-A-TTTAT
1 ATAA-ATATAAAATATTTTAA
2172966 ATAAATATAAAATATTTTAA
1 ATAAATATAAAATATTTTAA
2172986 ATAAATTATAA
1 ATAAA-TATAA
2172997 TATAAATACT
Statistics
Matches: 53, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
18 11 0.21
19 8 0.15
20 14 0.26
21 9 0.17
22 11 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATAAATATAAAATATTTTAA
Found at i:2173717 original size:18 final size:19
Alignment explanation
Indices: 2173674--2173717 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
2173664 TTATCATTTA
*
2173674 TAAATATAAAATTCACTTAT
1 TAAATATAAAAGTCAC-TAT
2173694 TAAATATAAAAGTCA-TAT
1 TAAATATAAAAGTCACTAT
*
2173712 TTAATA
1 TAAATA
2173718 ATAATTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 8 0.36
20 14 0.64
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (19 bp):
TAAATATAAAAGTCACTAT
Found at i:2173815 original size:10 final size:10
Alignment explanation
Indices: 2173802--2173837 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
2173792 TTTCTTAAAA
2173802 AATATTAATT
1 AATATTAATT
2173812 AATATCTAA-T
1 AATAT-TAATT
2173822 AATATTAATT
1 AATATTAATT
2173832 AATATT
1 AATATT
2173838 GTATTTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 3 0.12
10 18 0.75
11 3 0.12
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (10 bp):
AATATTAATT
Found at i:2174388 original size:30 final size:31
Alignment explanation
Indices: 2174343--2174422 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 31
2174333 TTTAAAAATA
2174343 AAAAATATTTTTTATAAATTAATATA-AAATTT
1 AAAAATA--TTTTATAAATTAATATATAAATTT
**
2174375 AAAAATATTTTAT--ATTAATATATATTTTT
1 AAAAATATTTTATAAATTAATATATAAATTT
* *
2174404 ATAAATAATTT-TAAATTAA
1 AAAAATATTTTATAAATTAA
2174423 AAATATTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
28 10 0.24
29 13 0.32
30 11 0.27
32 7 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
AAAAATATTTTATAAATTAATATATAAATTT
Found at i:2174401 original size:17 final size:16
Alignment explanation
Indices: 2174373--2174452 Score: 67
Period size: 17 Copynumber: 4.9 Consensus size: 16
2174363 AATATAAAAT
*
2174373 TTAAAAATATTTTATA
1 TTAAATATATTTTATA
2174389 TTAATATATATTTT-TA
1 TTAA-ATATATTTTATA
*
2174405 -TAAATA-ATTTTAAA
1 TTAAATATATTTTATA
*
2174419 TTAAAAATATTTTTAATTA
1 TTAAATATA-TTTT-A-TA
2174438 TTAAATAATATTTTA
1 TTAAAT-ATATTTTA
2174453 ATTTAATTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
13 5 0.10
14 4 0.08
15 8 0.16
16 7 0.14
17 12 0.24
18 2 0.04
19 10 0.20
20 3 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAATATATTTTATA
Found at i:2174428 original size:29 final size:29
Alignment explanation
Indices: 2174372--2174434 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
2174362 TAATATAAAA
* *
2174372 TTTAAAAATATTTTATATTAATATATATT
1 TTTAAAAATATTTTAAATTAATAAATATT
*
2174401 TTTATAAATAATTTTAAATTAA-AAATATT
1 TTTAAAAAT-ATTTTAAATTAATAAATATT
2174430 TTTAA
1 TTTAA
2174435 TTATTAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 18 0.62
30 11 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
TTTAAAAATATTTTAAATTAATAAATATT
Found at i:2174436 original size:16 final size:16
Alignment explanation
Indices: 2174373--2174437 Score: 57
Period size: 16 Copynumber: 4.2 Consensus size: 16
2174363 AATATAAAAT
2174373 TTAAAAATA-TTTTATA
1 TTAAAAATATTTTTA-A
*
2174389 TTAATATATATTTTT-A
1 TTAA-AAATATTTTTAA
* *
2174405 -TAAATA-ATTTTAAA
1 TTAAAAATATTTTTAA
2174419 TTAAAAATATTTTTAA
1 TTAAAAATATTTTTAA
2174435 TTA
1 TTA
2174438 TTAAATAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
13 5 0.12
14 4 0.10
15 8 0.20
16 15 0.38
17 4 0.10
18 4 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAAATATTTTTAA
Found at i:2174449 original size:20 final size:18
Alignment explanation
Indices: 2174406--2174455 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 18
2174396 ATATTTTTAT
2174406 AAATAATTTTAA--ATTAA
1 AAAT-ATTTTAATTATTAA
2174423 AAATATTTTTAATTATTAA
1 AAATA-TTTTAATTATTAA
2174442 ATAATATTTTAATT
1 A-AATATTTTAATT
2174456 TAATTTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 1 0.03
17 10 0.34
19 14 0.48
20 4 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATATTTTAATTATTAA
Found at i:2174458 original size:17 final size:17
Alignment explanation
Indices: 2174370--2174458 Score: 59
Period size: 17 Copynumber: 5.4 Consensus size: 17
2174360 ATTAATATAA
2174370 AATTTAAA-AATATTTT
1 AATTTAAATAATATTTT
2174386 -ATATT-AATATATATTTT
1 AAT-TTAAATA-ATATTTT
*
2174403 --TATAAAT-A-ATTTT
1 AATTTAAATAATATTTT
*
2174416 AAATTAAA-AATATTTTT
1 AATTTAAATAATA-TTTT
2174433 AATTATTAAATAATATTTT
1 AA-T-TTAAATAATATTTT
2174452 AATTTAA
1 AATTTAA
2174459 TTTAAATTTA
Statistics
Matches: 57, Mismatches: 4, Indels: 23
0.68 0.05 0.27
Matches are distributed among these distances:
13 5 0.09
14 1 0.02
15 10 0.18
16 8 0.14
17 17 0.30
18 1 0.02
19 11 0.19
20 4 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AATTTAAATAATATTTT
Found at i:2174858 original size:21 final size:21
Alignment explanation
Indices: 2174834--2174873 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2174824 ATTTTTATAT
2174834 AAAAAT-TTATAATTTAAAATA
1 AAAAATATTAT-ATTTAAAATA
*
2174855 AAAAATATTATTTTTAAAA
1 AAAAATATTATATTTAAAA
2174874 ATTATTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAAATATTATATTTAAAATA
Found at i:2175282 original size:28 final size:28
Alignment explanation
Indices: 2175240--2175318 Score: 94
Period size: 27 Copynumber: 2.9 Consensus size: 28
2175230 TGTTTATCGA
2175240 ATATTTAATA-A-TTTATATATACGT-ATT
1 ATATTTAATATATTTTATATATA--TAATT
*
2175267 ATATTTTATAT-TTTTATATATATAATT
1 ATATTTAATATATTTTATATATATAATT
*
2175294 ATATTTAATATATTTTATATTTATA
1 ATATTTAATATATTTTATATATATA
2175319 TAAATTTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
26 1 0.02
27 22 0.49
28 22 0.49
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (28 bp):
ATATTTAATATATTTTATATATATAATT
Found at i:2175325 original size:26 final size:28
Alignment explanation
Indices: 2175242--2175333 Score: 79
Period size: 27 Copynumber: 3.4 Consensus size: 28
2175232 TTTATCGAAT
*
2175242 ATTTAATA-A-TTTATATATACGT-ATTAT
1 ATTTAATATATTTTATATATA--TAATTAA
* *
2175269 ATTTTATAT-TTTTATATATATAATTAT
1 ATTTAATATATTTTATATATATAATTAA
*
2175296 ATTTAATATATTTTATATTTAT-A-TAA
1 ATTTAATATATTTTATATATATAATTAA
*
2175322 ATTTAAAATATT
1 ATTTAATATATT
2175334 AATAATTTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
26 14 0.25
27 21 0.38
28 21 0.38
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (28 bp):
ATTTAATATATTTTATATATATAATTAA
Found at i:2175326 original size:16 final size:16
Alignment explanation
Indices: 2175283--2175356 Score: 59
Period size: 16 Copynumber: 4.7 Consensus size: 16
2175273 TATATTTTTA
2175283 TATATATAA-TTATATT
1 TATATA-AATTTATATT
*
2175299 TA-ATATATTTTATATT
1 TATATA-AATTTATATT
*
2175315 TATATAAATTTAAAATAT
1 TATATAAATTT-ATAT-T
2175333 TA-AT-AATTTATA-T
1 TATATAAATTTATATT
2175346 TATATAAATTT
1 TATATAAATTT
2175357 TTAAATATTA
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
13 3 0.06
14 2 0.04
15 12 0.25
16 20 0.42
17 8 0.17
18 3 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATATAAATTTATATT
Found at i:2175343 original size:32 final size:32
Alignment explanation
Indices: 2175263--2175372 Score: 98
Period size: 32 Copynumber: 3.3 Consensus size: 32
2175253 TATATATACG
* * * * *
2175263 TATT-ATATTTTATATTTTTATATATATAATTA
1 TATTAATAATTTATATTTATATAAATTTAA-AA
2175295 TATTTAATATATTTTATATTTATATAAATTTAAAA
1 TA-TTAATA-A-TTTATATTTATATAAATTTAAAA
*
2175330 TATTAATAATTTATA-TTATATAAATTTTTAAA
1 TATTAATAATTTATATTTATATAAA-TTTAAAA
2175362 TATTATATAAT
1 TATTA-ATAAT
2175373 GCTAATATTT
Statistics
Matches: 66, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
31 9 0.14
32 19 0.29
33 8 0.12
34 9 0.14
35 3 0.05
36 18 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (32 bp):
TATTAATAATTTATATTTATATAAATTTAAAA
Found at i:2175352 original size:31 final size:33
Alignment explanation
Indices: 2175298--2175372 Score: 100
Period size: 32 Copynumber: 2.2 Consensus size: 33
2175288 ATAATTATAT
2175298 TTAATATATTTTATATTTATATAAA-TTTAAAATA
1 TTAATA-A-TTTATATTTATATAAATTTTAAAATA
*
2175332 TTAATAATTTATA-TTATATAAATTTTTAAATA
1 TTAATAATTTATATTTATATAAATTTTAAAATA
2175364 TTATATAAT
1 TTA-ATAAT
2175373 GCTAATATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
31 9 0.24
32 17 0.45
33 6 0.16
34 6 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
TTAATAATTTATATTTATATAAATTTTAAAATA
Found at i:2175837 original size:25 final size:26
Alignment explanation
Indices: 2175809--2175862 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
2175799 TTAAAATTAC
2175809 ATTTAGTAAT-TATTC-TTGTATTATA
1 ATTTA-TAATATATTCATTGTATTATA
*
2175834 ATTTATTATATATTCATTGTATTATA
1 ATTTATAATATATTCATTGTATTATA
2175860 ATT
1 ATT
2175863 ATATTTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 3 0.12
25 10 0.38
26 13 0.50
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.57
Consensus pattern (26 bp):
ATTTATAATATATTCATTGTATTATA
Found at i:2175859 original size:26 final size:27
Alignment explanation
Indices: 2175819--2175875 Score: 91
Period size: 26 Copynumber: 2.1 Consensus size: 27
2175809 ATTTAGTAAT
2175819 TATTCTTGTATTATAATT-TA-TTATA
1 TATTCTTGTATTATAATTATATTTATA
2175844 TATTCATTGTATTATAATTATATTTATA
1 TATTC-TTGTATTATAATTATATTTATA
2175872 TATT
1 TATT
2175876 TTTTATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
25 5 0.17
26 13 0.45
27 2 0.07
28 9 0.31
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (27 bp):
TATTCTTGTATTATAATTATATTTATA
Found at i:2175911 original size:31 final size:30
Alignment explanation
Indices: 2175853--2175911 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 30
2175843 ATATTCATTG
*
2175853 TATTATAATTATATTTATATATTTTTTATA
1 TATTATAATTATATTTATATATATTTTATA
2175883 TATTAATAATT-TATATTATATATATTTTA
1 TATT-ATAATTATAT-TTATATATATTTTA
2175912 ATTTATTCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 7 0.27
31 19 0.73
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (30 bp):
TATTATAATTATATTTATATATATTTTATA
Found at i:2181350 original size:2 final size:2
Alignment explanation
Indices: 2181343--2181381 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2181333 AATTTAATTG
2181343 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2181382 AAACTACTAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2186671 original size:2 final size:2
Alignment explanation
Indices: 2186664--2186703 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2186654 CAGAACCAAA
2186664 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
2186704 TTGTTCTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2187231 original size:75 final size:75
Alignment explanation
Indices: 2187146--2187364 Score: 420
Period size: 75 Copynumber: 2.9 Consensus size: 75
2187136 ATAATTTAAG
* *
2187146 ATAATTACAAGAACAAATAAAGATAAATCAGAGTTTAACAATCAAACATTTTAAAGCCCTTAAAA
1 ATAATTACAAGAACAAATAAAGTTTAATCAGAGTTTAACAATCAAACATTTTAAAGCCCTTAAAA
2187211 ACTAATTATA
66 ACTAATTATA
2187221 ATAATTACAAGAACAAATAAAGTTTAATCAGAGTTTAACAATCAAACATTTTAAAGCCCTTAAAA
1 ATAATTACAAGAACAAATAAAGTTTAATCAGAGTTTAACAATCAAACATTTTAAAGCCCTTAAAA
2187286 ACTAATTATA
66 ACTAATTATA
2187296 ATAATTACAAGAACAAATAAAGTTTAATCAGAGTTTAACAATCAAACATTTTAAAGCCCTTAAAA
1 ATAATTACAAGAACAAATAAAGTTTAATCAGAGTTTAACAATCAAACATTTTAAAGCCCTTAAAA
2187361 ACTA
66 ACTA
2187365 TCTTCCAGGC
Statistics
Matches: 142, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 142 1.00
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.28
Consensus pattern (75 bp):
ATAATTACAAGAACAAATAAAGTTTAATCAGAGTTTAACAATCAAACATTTTAAAGCCCTTAAAA
ACTAATTATA
Found at i:2187740 original size:18 final size:18
Alignment explanation
Indices: 2187717--2187754 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2187707 TTTTAAATAC
*
2187717 AAATATATTATATGTATT
1 AAATATATCATATGTATT
*
2187735 AAATATATCATATTTATT
1 AAATATATCATATGTATT
2187753 AA
1 AA
2187755 TTAAATGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (18 bp):
AAATATATCATATGTATT
Found at i:2190379 original size:21 final size:21
Alignment explanation
Indices: 2190350--2190480 Score: 119
Period size: 21 Copynumber: 6.4 Consensus size: 21
2190340 ATTTAGATTT
2190350 TTTTG-TAATTTTTTATATAA
1 TTTTGATAATTTTTTATATAA
* *
2190370 TTTTGATAA-TATTTATA-AT
1 TTTTGATAATTTTTTATATAA
* ** *
2190389 TTTTTATAACATTTGA-ATAA
1 TTTTGATAATTTTTTATATAA
*
2190409 TTTTGAGAATTTTTTATATAA
1 TTTTGATAATTTTTTATATAA
*
2190430 TTTTGATAATTTTTT-TAATAG
1 TTTTGATAATTTTTTAT-ATAA
* * *
2190451 TTTTAATAATTTTATATAAAA
1 TTTTGATAATTTTTTATATAA
2190472 TTTTGATAA
1 TTTTGATAA
2190481 CCTTTAAAAT
Statistics
Matches: 86, Mismatches: 19, Indels: 11
0.74 0.16 0.09
Matches are distributed among these distances:
19 10 0.12
20 28 0.33
21 47 0.55
22 1 0.01
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.57
Consensus pattern (21 bp):
TTTTGATAATTTTTTATATAA
Found at i:2190391 original size:30 final size:29
Alignment explanation
Indices: 2190316--2190442 Score: 132
Period size: 30 Copynumber: 4.3 Consensus size: 29
2190306 GAATGTTTAT
* * *
2190316 ATAATTTTAATAACTTTTTGTATAATTTAG
1 ATAATTTT-ATAATTTTTTATATAATTTTG
** *
2190346 ATTTTTTTGTAATTTTTTATATAATTTTG
1 ATAATTTTATAATTTTTTATATAATTTTG
2190375 ATAATATTTATAATTTTTTATA-ACA-TTTG
1 ATAAT-TTTATAATTTTTTATATA-ATTTTG
*
2190404 AATAATTTTGAGAATTTTTTATATAATTTTG
1 -ATAATTTT-ATAATTTTTTATATAATTTTG
2190435 ATAATTTT
1 ATAATTTT
2190443 TTTAATAGTT
Statistics
Matches: 81, Mismatches: 10, Indels: 12
0.79 0.10 0.12
Matches are distributed among these distances:
29 28 0.35
30 48 0.59
31 5 0.06
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (29 bp):
ATAATTTTATAATTTTTTATATAATTTTG
Found at i:2190397 original size:19 final size:19
Alignment explanation
Indices: 2190365--2190412 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
2190355 TAATTTTTTA
*
2190365 TATAA-TTTTGATAATATT
1 TATAATTTTTGATAACATT
*
2190383 TATAATTTTTTATAACATT
1 TATAATTTTTGATAACATT
2190402 TGAATAATTTT
1 T--ATAATTTT
2190413 GAGAATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.20
19 12 0.48
21 8 0.32
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (19 bp):
TATAATTTTTGATAACATT
Found at i:2190460 original size:30 final size:29
Alignment explanation
Indices: 2190316--2190463 Score: 122
Period size: 30 Copynumber: 5.0 Consensus size: 29
2190306 GAATGTTTAT
* * *
2190316 ATAATTTTAATAACTTTTTGTATAATTTAG
1 ATAATTTTTATAA-TTTTTATATAATTTTG
* *
2190346 AT-TTTTTTGTAATTTTTTATATAATTTTG
1 ATAATTTTTATAA-TTTTTATATAATTTTG
* *
2190375 ATAATATTTATAATTTTT-TATAACATTTG
1 ATAATTTTTATAATTTTTATATAA-TTTTG
* *
2190404 AATAATTTTGAGAATTTTTTATATAATTTTG
1 -ATAATTTTTATAA-TTTTTATATAATTTTG
*
2190435 ATAATTTTTTTAATAGTTTTA-ATAATTTT
1 ATAATTTTTATAAT--TTTTATATAATTTT
2190464 ATATAAAATT
Statistics
Matches: 94, Mismatches: 17, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
28 5 0.05
29 33 0.35
30 37 0.39
31 14 0.15
32 5 0.05
ACGTcount: A:0.34, C:0.01, G:0.06, T:0.59
Consensus pattern (29 bp):
ATAATTTTTATAATTTTTATATAATTTTG
Found at i:2190498 original size:42 final size:42
Alignment explanation
Indices: 2190416--2190500 Score: 100
Period size: 42 Copynumber: 2.0 Consensus size: 42
2190406 TAATTTTGAG
* * ** **
2190416 AATTTTTTATATAATTTTGATAATTTTTTTAATAGTTTTAAT
1 AATTTTATATAAAATTTTGATAACCTTTAAAATAGTTTTAAT
2190458 AATTTTATATAAAATTTTGATAACCTTTAAAATAAG-TTTAAT
1 AATTTTATATAAAATTTTGATAACCTTTAAAAT-AGTTTTAAT
2190500 A
1 A
2190501 TGTTTTCTAC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
42 34 0.94
43 2 0.06
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (42 bp):
AATTTTATATAAAATTTTGATAACCTTTAAAATAGTTTTAAT
Found at i:2190585 original size:21 final size:20
Alignment explanation
Indices: 2190529--2190586 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 20
2190519 GTAACTATTA
2190529 ATAAAATTGTGATAACTTTTTAT
1 ATAAAATT-TG-TAA-TTTTTAT
* * *
2190552 ATGATATTGGTAATGTTTTAT
1 ATAAAATTTGTAAT-TTTTAT
2190573 ATAAAATTTGTAAT
1 ATAAAATTTGTAAT
2190587 AATTTTGATA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
20 1 0.04
21 20 0.71
22 1 0.04
23 6 0.21
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (20 bp):
ATAAAATTTGTAATTTTTAT
Found at i:2190647 original size:13 final size:13
Alignment explanation
Indices: 2190629--2190654 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2190619 TTTTATTTAC
2190629 TTTTAATAATTTT
1 TTTTAATAATTTT
2190642 TTTTAATAATTTT
1 TTTTAATAATTTT
2190655 GTAAATAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAATAATTTT
Found at i:2190906 original size:17 final size:17
Alignment explanation
Indices: 2190884--2190917 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2190874 AATTGCAATA
2190884 AAGGAAAAGACAAGAGT
1 AAGGAAAAGACAAGAGT
*
2190901 AAGGAAAAGTCAAGAGT
1 AAGGAAAAGACAAGAGT
2190918 TCTAAGATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.29, T:0.09
Consensus pattern (17 bp):
AAGGAAAAGACAAGAGT
Found at i:2191395 original size:22 final size:21
Alignment explanation
Indices: 2191370--2191419 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
2191360 AAAATAATTT
2191370 TTATTTAAAATAAATTATAAAA
1 TTATTTAAAATAAA-TATAAAA
* *
2191392 TTATATAAAAATTAATATAAAA
1 TTAT-TTAAAATAAATATAAAA
*
2191414 ATATTT
1 TTATTT
2191420 TAATATTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 1 0.04
22 14 0.61
23 8 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTATTTAAAATAAATATAAAA
Found at i:2193499 original size:16 final size:17
Alignment explanation
Indices: 2193478--2193515 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
2193468 TTTTGAATTC
2193478 AAAAAA-AATA-ATATGA
1 AAAAAATAATATATAT-A
2193494 AAAAAATAATATATATA
1 AAAAAATAATATATATA
2193511 AAAAA
1 AAAAA
2193516 TCTCTAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 10 0.50
18 4 0.20
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (17 bp):
AAAAAATAATATATATA
Found at i:2193516 original size:16 final size:14
Alignment explanation
Indices: 2193479--2193505 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2193469 TTTGAATTCA
2193479 AAAAAAATAATATG
1 AAAAAAATAATATG
2193493 AAAAAAATAATAT
1 AAAAAAATAATAT
2193506 ATATAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (14 bp):
AAAAAAATAATATG
Found at i:2193580 original size:9 final size:9
Alignment explanation
Indices: 2193541--2193598 Score: 53
Period size: 9 Copynumber: 6.0 Consensus size: 9
2193531 TACATAACAC
*
2193541 ATATTAATT
1 ATATTTATT
*
2193550 ATATTTAAAT
1 ATATTT-ATT
2193560 ATATTATATT
1 ATATT-TATT
2193570 ATATTTATT
1 ATATTTATT
*
2193579 ATATTATTTTT
1 ATA-T-TTATT
2193590 ATATTTATT
1 ATATTTATT
2193599 TTATATATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
9 16 0.40
10 16 0.40
11 8 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
ATATTTATT
Found at i:2193597 original size:20 final size:19
Alignment explanation
Indices: 2193541--2193608 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 19
2193531 TACATAACAC
*
2193541 ATATTA-ATTATATTTAAAT
1 ATATTATATTATATTT-ATT
2193560 ATATTATATTATATTTATT
1 ATATTATATTATATTTATT
*
2193579 ATATTATTTTTATATTTATT
1 ATATTA-TATTATATTTATT
*
2193599 TTATATATAT
1 ATAT-TATAT
2193609 ATCATATTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 14 0.33
20 26 0.62
21 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATATTATATTATATTTATT
Found at i:2193658 original size:20 final size:20
Alignment explanation
Indices: 2193630--2193669 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2193620 ATTACTTTCT
*
2193630 ATCTCATAAAAAATAATCGA
1 ATCTAATAAAAAATAATCGA
* *
2193650 ATCTAATAAATACTAATCGA
1 ATCTAATAAAAAATAATCGA
2193670 TACAAACATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.15, G:0.05, T:0.28
Consensus pattern (20 bp):
ATCTAATAAAAAATAATCGA
Found at i:2193868 original size:23 final size:21
Alignment explanation
Indices: 2193832--2193877 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
2193822 AATTAATAAT
2193832 AATTATAGTTAATTTATAAGTTA
1 AATTATAGTTAATTTA-AA-TTA
2193855 AATTATA-TTAAATTTAAATTA
1 AATTATAGTT-AATTTAAATTA
2193876 AA
1 AA
2193878 AATATTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 5 0.23
22 4 0.18
23 13 0.59
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (21 bp):
AATTATAGTTAATTTAAATTA
Found at i:2195582 original size:13 final size:12
Alignment explanation
Indices: 2195556--2195588 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2195546 AATGTATTTT
2195556 AAAATTAAATAA
1 AAAATTAAATAA
*
2195568 AAAATTTAATAA
1 AAAATTAAATAA
2195580 AAAA-TAAAT
1 AAAATTAAAT
2195589 TCAAATCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 4 0.21
12 15 0.79
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
AAAATTAAATAA
Found at i:2195928 original size:26 final size:25
Alignment explanation
Indices: 2195882--2195938 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
2195872 ATTTGATTAA
*
2195882 AAATATTTTATATTAAATTAATAATT
1 AAATATTTTAAATTAAATTAA-AATT
* *
2195908 AAATATTTTAAATTTACTTAAAATT
1 AAATATTTTAAATTAAATTAAAATT
*
2195933 TAATAT
1 AAATAT
2195939 ATCATATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 9 0.33
26 18 0.67
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
AAATATTTTAAATTAAATTAAAATT
Found at i:2199286 original size:42 final size:42
Alignment explanation
Indices: 2199222--2199305 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
2199212 ATGTAGGTTT
2199222 CCCAGACTGGTGTGCCTACACGTAATTACAATACAAACTGAA
1 CCCAGACTGGTGTGCCTACACGTAATTACAATACAAACTGAA
* *
2199264 CCCAGACTGGTGTGCCTGCACGTAATTACAATACAAGCTGAA
1 CCCAGACTGGTGTGCCTACACGTAATTACAATACAAACTGAA
2199306 GCACTTCCAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (42 bp):
CCCAGACTGGTGTGCCTACACGTAATTACAATACAAACTGAA
Found at i:2200640 original size:19 final size:18
Alignment explanation
Indices: 2200616--2200686 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
2200606 ATAATTTTAG
2200616 TAATAATATGAATATAAAA
1 TAATAATAT-AATATAAAA
*
2200635 TAATAAAATAAT-TAAAA
1 TAATAATATAATATAAAA
2200652 T-ATAATATAATATCAAAA
1 TAATAATATAATAT-AAAA
* *
2200670 AAATAACATAAATATAA
1 TAATAATAT-AATATAA
2200687 TTTAATACAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
16 9 0.20
17 7 0.16
18 7 0.16
19 16 0.36
20 5 0.11
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (18 bp):
TAATAATATAATATAAAA
Found at i:2200656 original size:16 final size:17
Alignment explanation
Indices: 2200616--2200662 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
2200606 ATAATTTTAG
*
2200616 TAATAATATGAATATAAAA
1 TAATAAAAT-AAT-TAAAA
2200635 TAATAAAATAATTAAAA
1 TAATAAAATAATTAAAA
*
2200652 T-ATAATATAAT
1 TAATAAAATAAT
2200663 ATCAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 9 0.35
17 6 0.23
18 3 0.12
19 8 0.31
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
TAATAAAATAATTAAAA
Found at i:2200693 original size:35 final size:35
Alignment explanation
Indices: 2200618--2200693 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 35
2200608 AATTTTAGTA
* *
2200618 ATAATATGAATATAAAATAATAAAATAATTAAAAT
1 ATAATATGAATATAAAAAAATAAAATAAATAAAAT
* *
2200653 ATAATAT-AATATCAAAAAAATAACATAAATATAAT
1 ATAATATGAATAT-AAAAAAATAAAATAAATAAAAT
*
2200688 TTAATA
1 ATAATA
2200694 CATAAATATA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 5 0.14
35 30 0.86
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (35 bp):
ATAATATGAATATAAAAAAATAAAATAAATAAAAT
Found at i:2206177 original size:44 final size:44
Alignment explanation
Indices: 2206105--2206228 Score: 203
Period size: 44 Copynumber: 2.8 Consensus size: 44
2206095 TTGTTAGAAT
* *
2206105 TTGGATGGCTATGCCAATCCACAGAAAAATAAATAAATATGCAA
1 TTGGGTGGCTATGCCAATCCACAGAAAAATAAATAAATATACAA
*
2206149 TTGGGTGGCTATGCCAATCCACAAAAAAATAAATAAATATACAA
1 TTGGGTGGCTATGCCAATCCACAGAAAAATAAATAAATATACAA
* *
2206193 TTGGGTGGCTATACCAATCCACGGAAAAATAAATAA
1 TTGGGTGGCTATGCCAATCCACAGAAAAATAAATAA
2206229 TAAAAACACC
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 74 1.00
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (44 bp):
TTGGGTGGCTATGCCAATCCACAGAAAAATAAATAAATATACAA
Found at i:2207367 original size:66 final size:66
Alignment explanation
Indices: 2207253--2207381 Score: 170
Period size: 66 Copynumber: 2.0 Consensus size: 66
2207243 GGAAATTTAA
* *
2207253 AAGGGAAATATTCTTACAAGCCAAAAGTAAGACATCGAAAGAACTTGATATGTATTGAGTTGATT
1 AAGGGAAATATTCTTACAAGACAAAAGTAAGACATCGAAAGAACTTGATATATATTGAGTTGATT
2207318 T
66 T
* * * * * *
2207319 AAGGGAAATATTTTTACAATACAAAAGTATGACATTGAAA-AACTTTGATGTATATTGATTTGA
1 AAGGGAAATATTCTTACAAGACAAAAGTAAGACATCGAAAGAAC-TTGATATATATTGAGTTGA
2207382 ATGATTGAGC
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
65 3 0.06
66 51 0.94
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.32
Consensus pattern (66 bp):
AAGGGAAATATTCTTACAAGACAAAAGTAAGACATCGAAAGAACTTGATATATATTGAGTTGATT
T
Found at i:2208146 original size:2 final size:2
Alignment explanation
Indices: 2208139--2208163 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2208129 TTCCTACCAG
2208139 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
2208164 CGATCAATAA
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:2208202 original size:2 final size:2
Alignment explanation
Indices: 2208195--2208229 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2208185 TGTAGAAGGC
2208195 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 T
2208230 GTGTGTGTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2213280 original size:36 final size:34
Alignment explanation
Indices: 2213186--2213280 Score: 79
Period size: 36 Copynumber: 2.7 Consensus size: 34
2213176 TTAAATTTTT
*
2213186 TTATTAAATT-AA-TAAAATATTTAAATTAAATA
1 TTATTAAATTAAATTTAAATATTTAAATTAAATA
* * * *
2213218 TTATGATATTCAAATTTCACTCATTTAAA-TATAATAA
1 TTATTAAATT-AAATTTAAAT-ATTTAAATTA-AAT-A
2213255 TTATTAAATTAAATTTAAATAATTTA
1 TTATTAAATTAAATTTAAAT-ATTTA
2213281 TAAATATATA
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
32 8 0.17
34 2 0.04
35 5 0.11
36 23 0.49
37 9 0.19
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (34 bp):
TTATTAAATTAAATTTAAATATTTAAATTAAATA
Found at i:2214446 original size:3 final size:3
Alignment explanation
Indices: 2214434--2214472 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
2214424 GTGCTGATAG
2214434 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2214473 CAGTAAGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:2214825 original size:13 final size:14
Alignment explanation
Indices: 2214807--2214835 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2214797 TAATATTTAA
2214807 TAAATTCAAAT-TT
1 TAAATTCAAATATT
2214820 TAAATTCAAATATT
1 TAAATTCAAATATT
2214834 TA
1 TA
2214836 TAATCATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (14 bp):
TAAATTCAAATATT
Found at i:2217708 original size:50 final size:50
Alignment explanation
Indices: 2217603--2217712 Score: 161
Period size: 50 Copynumber: 2.2 Consensus size: 50
2217593 ATATACTTAA
*
2217603 AGTCAACAATTATGGCCACCTGCCTCTATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTATGGCCACCTGCCTCTATTGTCAAAGGTTGGTAAAGAAT
* *
2217653 TGTCAACGATTATGGCCACCT-CTCTCTATTGTCAAAGGTTGGTAAATG-AT
1 AGTCAACAATTATGGCCACCTGC-CTCTATTGTCAAAGGTTGGTAAA-GAAT
2217703 AGTCAACAAT
1 AGTCAACAAT
2217713 GACAACAACT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
49 1 0.02
50 51 0.96
51 1 0.02
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (50 bp):
AGTCAACAATTATGGCCACCTGCCTCTATTGTCAAAGGTTGGTAAAGAAT
Found at i:2221804 original size:50 final size:50
Alignment explanation
Indices: 2221745--2221953 Score: 339
Period size: 50 Copynumber: 4.2 Consensus size: 50
2221735 TATATTTAGA
2221745 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
* * * *
2221795 GTCAACAATTATGGTCACCTCCTTCTATTGTCAAAAGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
*
2221845 GTCAACAATTATGGCCACCTGCCTCTATTGTCAAAGGTTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
* *
2221895 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAATG-ATA
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAA-GAATT
2221945 GTCAACAAT
1 GTCAACAAT
2221954 GACAACAACT
Statistics
Matches: 146, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
50 145 0.99
51 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
Found at i:2224829 original size:7 final size:7
Alignment explanation
Indices: 2224817--2224850 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
2224807 AATATAAACT
2224817 AATTTAA
1 AATTTAA
2224824 AATTTAA
1 AATTTAA
2224831 AATTTAA
1 AATTTAA
*
2224838 AGTTTAA
1 AATTTAA
2224845 AATTTA
1 AATTTA
2224851 CGGATATCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (7 bp):
AATTTAA
Found at i:2225167 original size:26 final size:29
Alignment explanation
Indices: 2225118--2225170 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
2225108 TTGATTTTAA
*
2225118 AATATGATTTTTATAATTTAAATTAATTT
1 AATATAATTTTTATAATTTAAATTAATTT
2225147 AATATAATTTTT-T-ATTT-AATTAAT
1 AATATAATTTTTATAATTTAAATTAAT
2225171 AAAAAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 7 0.30
27 4 0.17
28 1 0.04
29 11 0.48
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (29 bp):
AATATAATTTTTATAATTTAAATTAATTT
Done.