Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold103
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: 2633873
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 16636 characters in sequence are not A, C, G, or T
File 21 of 21
Found at i:2544967 original size:15 final size:15
Alignment explanation
Indices: 2544927--2544972 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
2544917 ATTTTTTATA
2544927 TTATATTTTA-ATTT
1 TTATATTTTATATTT
* *
2544941 TT-TATATCATATTT
1 TTATATTTTATATTT
*
2544955 TTATATTTTATATAT
1 TTATATTTTATATTT
2544970 TTA
1 TTA
2544973 AAGTATTATA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
13 5 0.20
14 8 0.32
15 12 0.48
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATATTTTATATTT
Found at i:2556282 original size:18 final size:20
Alignment explanation
Indices: 2556239--2556282 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 20
2556229 TAATTTTATG
2556239 ATAAT-TTTAAATATGAAAT
1 ATAATATTTAAATATGAAAT
*
2556258 A-ATTATTT-AATAT-AAAT
1 ATAATATTTAAATATGAAAT
2556275 ATAATATT
1 ATAATATT
2556283 ATGAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
17 5 0.24
18 12 0.57
19 4 0.19
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
ATAATATTTAAATATGAAAT
Found at i:2556311 original size:16 final size:15
Alignment explanation
Indices: 2556287--2556334 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
2556277 AATATTATGA
*
2556287 AAAAAATAATTAAAAT
1 AAAAAATAAAT-AAAT
*
2556303 AAAATATAAATAAAT
1 AAAAAATAAATAAAT
*
2556318 AAATAATAATATAAAT
1 AAAAAATAA-ATAAAT
2556334 A
1 A
2556335 TGTTAAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 11 0.41
16 16 0.59
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAAAATAAATAAAT
Found at i:2556315 original size:20 final size:21
Alignment explanation
Indices: 2556290--2556368 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 21
2556280 ATTATGAAAA
2556290 AAATAATTAAAATAA-AATAT
1 AAATAATTAAAATAATAATAT
*
2556310 AAATAAAT-AAATAATAATAT
1 AAATAATTAAAATAATAATAT
*
2556330 AAATATGTTAAAATTTATATAATAT
1 AAATA-ATTAAAA--TA-ATAATAT
2556355 AAATTAATTAAAAT
1 AAA-TAATTAAAAT
2556369 TTATATAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
19 6 0.12
20 17 0.35
21 1 0.02
22 3 0.06
23 1 0.02
24 2 0.04
25 16 0.33
26 2 0.04
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (21 bp):
AAATAATTAAAATAATAATAT
Found at i:2556365 original size:25 final size:25
Alignment explanation
Indices: 2556323--2556393 Score: 90
Period size: 25 Copynumber: 2.8 Consensus size: 25
2556313 TAAATAAATA
*
2556323 ATAATATAAATATGTTAAAATTTAT
1 ATAATATAAATATATTAAAATTTAT
2556348 ATAATATAAAT-TAATTAAAATTTAT
1 ATAATATAAATAT-ATTAAAATTTAT
*
2556373 ATAAATATATAATATTTTAAA
1 AT-AATATA-AATATATTAAA
2556394 TATAATTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
24 1 0.03
25 24 0.60
26 6 0.15
27 8 0.20
28 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (25 bp):
ATAATATAAATATATTAAAATTTAT
Found at i:2556398 original size:14 final size:14
Alignment explanation
Indices: 2556379--2556430 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
2556369 TTATATAAAT
*
2556379 ATATAATATTTTAA
1 ATATAATATTATAA
2556393 ATATAATTATTATAA
1 ATATAA-TATTATAA
* ***
2556408 ATAAAATAAGGTAA
1 ATATAATATTATAA
2556422 ATATAATAT
1 ATATAATAT
2556431 AATGCAAGTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
14 18 0.60
15 12 0.40
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (14 bp):
ATATAATATTATAA
Found at i:2556408 original size:15 final size:16
Alignment explanation
Indices: 2556372--2556410 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
2556362 TTAAAATTTA
2556372 TATAAATATATAATAT
1 TATAAATATATAATAT
* *
2556388 TTTAAATATA-ATTAT
1 TATAAATATATAATAT
2556403 TATAAATA
1 TATAAATA
2556411 AAATAAGGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TATAAATATATAATAT
Found at i:2556695 original size:105 final size:105
Alignment explanation
Indices: 2556527--2556740 Score: 378
Period size: 105 Copynumber: 2.0 Consensus size: 105
2556517 GCAAGGTGAA
*
2556527 TAAG-TTCACTGTTTCAGGACATGCACCGGAACATTATAAAATTCTAAAACAACGCGAGTAAAAC
1 TAAGTTTCACTGTTTCAGGACATGCACCGGAACATTATAAAATTCTAAAACAAAGCGAGTAAAAC
2556591 AGCGTTTGGCCCTTCTCAGACATCGAAAGGTTAGTCAAAGT
66 AGCGTTTGG-CCTTCTCAGACATCGAAAGGTTAGTCAAAGT
*
2556632 TAAGTTTCATTGTTTCAGGACATGCACCGGAACATTAT-AAATTCTAAAACAAAGCGAGTAAAAC
1 TAAGTTTCACTGTTTCAGGACATGCACCGGAACATTATAAAATTCTAAAACAAAGCGAGTAAAAC
2556696 AGCGTTTGGCCTTCTCAGACATCGAAAGGTTAGTCAAAGT
66 AGCGTTTGGCCTTCTCAGACATCGAAAGGTTAGTCAAAGT
*
2556736 GAAGT
1 TAAGT
2556741 CTTTTTGTCC
Statistics
Matches: 105, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
104 35 0.33
105 38 0.36
106 32 0.30
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.26
Consensus pattern (105 bp):
TAAGTTTCACTGTTTCAGGACATGCACCGGAACATTATAAAATTCTAAAACAAAGCGAGTAAAAC
AGCGTTTGGCCTTCTCAGACATCGAAAGGTTAGTCAAAGT
Found at i:2562193 original size:3 final size:3
Alignment explanation
Indices: 2562185--2562232 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
2562175 CTTAATTAGA
2562185 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2562233 AGAATCGAGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2563131 original size:3 final size:3
Alignment explanation
Indices: 2563123--2563154 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2563113 CTTTTCTGTT
2563123 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2563155 TAAATTGACG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2564592 original size:24 final size:25
Alignment explanation
Indices: 2564565--2564614 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
2564555 TTATCTGGAG
2564565 CAAAAAAAAAGAC-AAAGTTTTTTT
1 CAAAAAAAAAGACAAAAGTTTTTTT
2564589 CAAAAAAAAAGACAGAAAGTTTTTTT
1 CAAAAAAAAAGACA-AAAGTTTTTTT
2564615 TTTTTTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 13 0.54
26 11 0.46
ACGTcount: A:0.54, C:0.08, G:0.10, T:0.28
Consensus pattern (25 bp):
CAAAAAAAAAGACAAAAGTTTTTTT
Found at i:2567284 original size:17 final size:17
Alignment explanation
Indices: 2567249--2567343 Score: 79
Period size: 17 Copynumber: 5.5 Consensus size: 17
2567239 AATAATTTTA
*
2567249 AATATAAATATAATTATAT
1 AATATAAATA-AA-AATAT
2567268 AATATAAATAAAAATAT
1 AATATAAATAAAAATAT
2567285 AATATAAA-AAATAAT-T
1 AATATAAATAAA-AATAT
* * *
2567301 AAAATAAA-ATAATATAA
1 AATATAAATA-AAAATAT
* *
2567318 AATATAATTAAAAATAA
1 AATATAAATAAAAATAT
2567335 AATATAAAT
1 AATATAAAT
2567344 TCATAATATA
Statistics
Matches: 64, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
16 14 0.22
17 37 0.58
18 3 0.05
19 10 0.16
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AATATAAATAAAAATAT
Found at i:2567312 original size:26 final size:27
Alignment explanation
Indices: 2567266--2567338 Score: 96
Period size: 26 Copynumber: 2.7 Consensus size: 27
2567256 ATATAATTAT
2567266 ATAATATAAATAA-AAATATAATATAAAAA
1 ATAAT-TAAA-AATAAA-ATAATATAAAAA
*
2567295 ATAATT-AAAATAAAATAATATAAAAT
1 ATAATTAAAAATAAAATAATATAAAAA
2567321 ATAATTAAAAATAAAATA
1 ATAATTAAAAATAAAATA
2567339 TAAATTCATA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
26 19 0.46
27 16 0.39
28 1 0.02
29 5 0.12
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (27 bp):
ATAATTAAAAATAAAATAATATAAAAA
Found at i:2567334 original size:10 final size:11
Alignment explanation
Indices: 2567249--2567334 Score: 50
Period size: 12 Copynumber: 7.2 Consensus size: 11
2567239 AATAATTTTA
*
2567249 AATATAAATAT
1 AATATAAAAAT
*
2567260 AATTATATAATAT
1 AA-TATA-AAAAT
2567273 AA-ATAAAAATAT
1 AATAT-AAAA-AT
2567285 AATATAAAAAAT
1 AATAT-AAAAAT
*
2567297 AATTAAAATAAAAT
1 AA-T-ATA-AAAAT
2567311 AATATAAAATAT
1 AATATAAAA-AT
2567323 AAT-TAAAAAT
1 AATATAAAAAT
2567333 AA
1 AA
2567335 AATATAAATT
Statistics
Matches: 63, Mismatches: 3, Indels: 19
0.74 0.04 0.22
Matches are distributed among these distances:
10 4 0.06
11 14 0.22
12 20 0.32
13 17 0.27
14 8 0.13
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AATATAAAAAT
Found at i:2567500 original size:17 final size:17
Alignment explanation
Indices: 2567447--2567500 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
2567437 AATATTAATT
*
2567447 TAAATATAATTATAATA
1 TAAATATAATTATATTA
*
2567464 TAAA-AGT-ATTA-ATTTT
1 TAAATA-TAATTATA-TTA
2567480 TAAATATAATTATATTA
1 TAAATATAATTATATTA
2567497 TAAA
1 TAAA
2567501 CATGGCGACA
Statistics
Matches: 29, Mismatches: 3, Indels: 10
0.69 0.07 0.24
Matches are distributed among these distances:
15 1 0.03
16 11 0.38
17 16 0.55
18 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAATATAATTATATTA
Found at i:2567843 original size:6 final size:6
Alignment explanation
Indices: 2567832--2567860 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2567822 ACTCCAACGT
2567832 CTGAGA CTGAGA CTGAGA CTGAGA CTGAG
1 CTGAGA CTGAGA CTGAGA CTGAGA CTGAG
2567861 GCTCAGCATT
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:0.31, C:0.17, G:0.34, T:0.17
Consensus pattern (6 bp):
CTGAGA
Found at i:2570129 original size:19 final size:19
Alignment explanation
Indices: 2570087--2570131 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
2570077 TTTTAATACT
2570087 AATTAAAAATAAAAATATA
1 AATTAAAAATAAAAATATA
*
2570106 TATTAAAAATAAAAA-ATTA
1 AATTAAAAATAAAAATA-TA
2570125 AATTAAA
1 AATTAAA
2570132 TTCACTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 1 0.04
19 22 0.96
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AATTAAAAATAAAAATATA
Found at i:2570576 original size:29 final size:29
Alignment explanation
Indices: 2570534--2570591 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
2570524 TTGACAGGTA
2570534 ATTGAAATTCGAAATAGTAGTTAGAGTTG
1 ATTGAAATTCGAAATAGTAGTTAGAGTTG
* *
2570563 ATTGAAATTTGAAATAGTGGTTAGAGTTG
1 ATTGAAATTCGAAATAGTAGTTAGAGTTG
2570592 GAAGAGATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (29 bp):
ATTGAAATTCGAAATAGTAGTTAGAGTTG
Found at i:2572134 original size:10 final size:11
Alignment explanation
Indices: 2572106--2572151 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
2572096 CCATTGCTAG
*
2572106 TAATTAAAATA
1 TAATAAAAATA
2572117 TAATAAAAATA
1 TAATAAAAATA
2572128 T--TAAAAATA
1 TAATAAAAATA
*
2572137 TAATATAAATA
1 TAATAAAAATA
2572148 -AATA
1 TAATA
2572152 TATCAAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
9 9 0.29
10 4 0.13
11 18 0.58
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAATAAAAATA
Found at i:2572211 original size:27 final size:26
Alignment explanation
Indices: 2572150--2572202 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
2572140 TATAAATAAA
*
2572150 TATATCAAAATTTATTATTTTTAAATG
1 TATAT-AAATTTTATTATTTTTAAATG
2572177 TAATATAAATTTTATTATTTTTAAAT
1 T-ATATAAATTTTATTATTTTTAAAT
2572203 AGGTTATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (26 bp):
TATATAAATTTTATTATTTTTAAATG
Found at i:2573360 original size:2 final size:2
Alignment explanation
Indices: 2573353--2573379 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2573343 TCTACTTATC
2573353 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
2573380 CCTTTCTTCA
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:2588558 original size:16 final size:19
Alignment explanation
Indices: 2588529--2588565 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
2588519 TTTTATAATA
2588529 TAGAGTAAATAT-AATTTT
1 TAGAGTAAATATAAATTTT
2588547 TAGAG-AAA-ATAAATTTT
1 TAGAGTAAATATAAATTTT
2588564 TA
1 TA
2588566 ATTCATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 2 0.11
17 11 0.61
18 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.41
Consensus pattern (19 bp):
TAGAGTAAATATAAATTTT
Found at i:2588563 original size:17 final size:18
Alignment explanation
Indices: 2588529--2588565 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2588519 TTTTATAATA
*
2588529 TAGAGTAAATATAATTTT
1 TAGAGAAAATATAATTTT
2588547 TAGAGAAAATA-AATTTT
1 TAGAGAAAATATAATTTT
2588564 TA
1 TA
2588566 ATTCATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.41
Consensus pattern (18 bp):
TAGAGAAAATATAATTTT
Found at i:2589935 original size:5 final size:5
Alignment explanation
Indices: 2589925--2589960 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
2589915 CAAAGTGGAT
* *
2589925 GGGAA GGGAA GGGAA GGGAA GGGAT GGGAT GGGAA G
1 GGGAA GGGAA GGGAA GGGAA GGGAA GGGAA GGGAA G
2589961 TCCAGATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.33, C:0.00, G:0.61, T:0.06
Consensus pattern (5 bp):
GGGAA
Found at i:2593040 original size:15 final size:17
Alignment explanation
Indices: 2593017--2593060 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
2593007 ATTTTTCTTT
*
2593017 TATTTTTTATT-TAAAA
1 TATTTTTAATTATAAAA
2593033 TATTTTTAATTATAAAA
1 TATTTTTAATTATAAAA
*
2593050 TTATCTTTAAT
1 -TATTTTTAAT
2593061 CACTATCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 10 0.42
17 5 0.21
18 9 0.38
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTTTTAATTATAAAA
Found at i:2593247 original size:15 final size:15
Alignment explanation
Indices: 2593227--2593256 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2593217 AATTTTTGTG
2593227 TCAAAAAATATTTTA
1 TCAAAAAATATTTTA
2593242 TCAAAAAATATTTTA
1 TCAAAAAATATTTTA
2593257 AACTTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (15 bp):
TCAAAAAATATTTTA
Found at i:2593499 original size:23 final size:23
Alignment explanation
Indices: 2593471--2593517 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2593461 ATAGAACCTA
*
2593471 ATTTTTTATATATTTTTTATTTTT
1 ATTTTTTAT-CATTTTTTATTTTT
* *
2593495 ATTTTTTCTCTTTTTTTATTTTT
1 ATTTTTTATCATTTTTTATTTTT
2593518 TCATTTAACC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.81
Consensus pattern (23 bp):
ATTTTTTATCATTTTTTATTTTT
Found at i:2594438 original size:13 final size:13
Alignment explanation
Indices: 2594422--2594464 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
2594412 TTTAATTTAA
*
2594422 TAATATAATATTT
1 TAATATAAAATTT
2594435 TAATATAAAATTAT
1 TAATATAAAATT-T
2594449 ATAAT-TAAAATTT
1 -TAATATAAAATTT
2594462 TAA
1 TAA
2594465 ATTTCATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 3 0.11
13 12 0.44
14 8 0.30
15 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TAATATAAAATTT
Found at i:2595988 original size:2 final size:2
Alignment explanation
Indices: 2595981--2596007 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2595971 GCAAGCAAGA
2595981 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
2596008 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2596012 original size:2 final size:2
Alignment explanation
Indices: 2596007--2596039 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2595997 ACACACACAC
2596007 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2596040 AGAAAAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2596174 original size:2 final size:2
Alignment explanation
Indices: 2596169--2596212 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
2596159 TATATGCATG
* **
2596169 TA TA TA TA TA TA TA TA TA T- TA TA TG TA CG 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
2596210 TA T
1 TA T
2596213 GTCTTATTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2596363 original size:2 final size:2
Alignment explanation
Indices: 2596322--2596350 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2596312 TCTTGCACAA
2596322 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 A
2596351 AATCCATTAT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2597603 original size:28 final size:28
Alignment explanation
Indices: 2597562--2597618 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
2597552 AGAAAAGCAG
*
2597562 ATACCTTACGACAGCAGTATACTTCAGT
1 ATACCTTACGACAGCAATATACTTCAGT
* * * *
2597590 ATACTTTATGACAGTAATATAGTTCAGT
1 ATACCTTACGACAGCAATATACTTCAGT
2597618 A
1 A
2597619 CTGGATTTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (28 bp):
ATACCTTACGACAGCAATATACTTCAGT
Found at i:2600037 original size:16 final size:18
Alignment explanation
Indices: 2600016--2600048 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
2600006 TTAATACTGT
2600016 TCTTTT-TTTT-AAGTAC
1 TCTTTTATTTTGAAGTAC
2600032 TCTTTTATTTTGAAGTA
1 TCTTTTATTTTGAAGTA
2600049 TCAGAATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.61
Consensus pattern (18 bp):
TCTTTTATTTTGAAGTAC
Found at i:2605469 original size:17 final size:17
Alignment explanation
Indices: 2605435--2605478 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
2605425 GTATTTTTTT
** *
2605435 AAATATTTTTCAATATA
1 AAATATTTTAAAAAATA
2605452 AAATATTTTAAAAAATA
1 AAATATTTTAAAAAATA
*
2605469 AATTATTTTA
1 AAATATTTTA
2605479 TTCTTAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATATTTTAAAAAATA
Found at i:2605755 original size:15 final size:14
Alignment explanation
Indices: 2605709--2605755 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
2605699 GATTTACGGG
2605709 TTTTAT-ATTTTTA
1 TTTTATAATTTTTA
2605722 TATTTATAATATTTT-
1 T-TTTATAAT-TTTTA
2605737 TTTTGATAATTTTTA
1 TTTT-ATAATTTTTA
2605752 TTTT
1 TTTT
2605756 TTTATATTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 1 0.03
14 12 0.41
15 12 0.41
16 4 0.14
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTTATAATTTTTA
Found at i:2605806 original size:17 final size:18
Alignment explanation
Indices: 2605775--2605808 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2605765 ATTATGTAAA
2605775 TATAAAAATTATTAAATG
1 TATAAAAATTATTAAATG
2605793 TATAAAAATT-TTAAAT
1 TATAAAAATTATTAAAT
2605809 AAAATATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
TATAAAAATTATTAAATG
Found at i:2609633 original size:2 final size:2
Alignment explanation
Indices: 2609626--2609658 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2609616 TAATTATCCA
2609626 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2609659 AACAGCTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2610144 original size:151 final size:147
Alignment explanation
Indices: 2609870--2610168 Score: 553
Period size: 151 Copynumber: 2.0 Consensus size: 147
2609860 GAAGTACTCT
*
2609870 TATTTCCATATCTCCGAATCTACCTTCTATAAATGTACTCTGATCCATAACATTTGTCTGGTATT
1 TATTTCCATATCTCCGAATCGACCTTCTATAAATGTACTCTGATCCATAACATTTGTCTGGTATT
2609935 TTCTAACCATGTATTCATTCGATTATTTGACCCCATTTTCAAATCCACAATATATATATATATAT
66 TTCTAACCATGTATTCATTCGATTATTTGACCCCATTTTCAAATCCAC---A-ATATATATATAT
2610000 GTATATATATTATTGTCCCCG
127 GTATATATATTATTGTCCCCG
2610021 TATTTCCATATCTCCGAATCGACCTTCTATAAATGTACTCTGATCCATAACATTTGTCTGGTATT
1 TATTTCCATATCTCCGAATCGACCTTCTATAAATGTACTCTGATCCATAACATTTGTCTGGTATT
2610086 TTCTAACCATGTATTCATTCGATTATTTGACCCCATTTTCAAATCCACAATATATATATATGTAT
66 TTCTAACCATGTATTCATTCGATTATTTGACCCCATTTTCAAATCCACAATATATATATATGTAT
2610151 ATATATTATTGTCCCCG
131 ATATATTATTGTCCCCG
2610168 T
1 T
2610169 TGCTATGCTC
Statistics
Matches: 147, Mismatches: 1, Indels: 4
0.97 0.01 0.03
Matches are distributed among these distances:
147 34 0.23
148 1 0.01
151 112 0.76
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.41
Consensus pattern (147 bp):
TATTTCCATATCTCCGAATCGACCTTCTATAAATGTACTCTGATCCATAACATTTGTCTGGTATT
TTCTAACCATGTATTCATTCGATTATTTGACCCCATTTTCAAATCCACAATATATATATATGTAT
ATATATTATTGTCCCCG
Found at i:2611886 original size:2 final size:2
Alignment explanation
Indices: 2611881--2611909 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2611871 TAATGATTAA
2611881 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 A
2611910 ATTAGAAAAA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2612245 original size:31 final size:28
Alignment explanation
Indices: 2612207--2612275 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 28
2612197 ATTTAAAAAA
*
2612207 TTTAATAAATAGTAATATATTAATTATTATT
1 TTTAATAAATAATAATAT-TTAATTA--ATT
*
2612238 TTTAATAAAAAATAATATTTAATTAATT
1 TTTAATAAATAATAATATTTAATTAATT
*
2612266 TTTAAAAAAT
1 TTTAATAAAT
2612276 TTATATTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 11 0.32
30 7 0.21
31 16 0.47
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (28 bp):
TTTAATAAATAATAATATTTAATTAATT
Found at i:2612278 original size:68 final size:70
Alignment explanation
Indices: 2612189--2612319 Score: 171
Period size: 71 Copynumber: 1.9 Consensus size: 70
2612179 TTTTTATAAA
* * * *
2612189 TTAATTAAATTTAAAAAATTTA-A-TAA-ATAGTAATATATTAATTATTATTTT-TAATAAAAAA
1 TTAATTAAATTTAAAAAATTTATATTAATAAAATAAAATATTAATTATT-TTTTAAAATAAAAAA
2612250 TAATAT
65 TAATAT
*
2612256 TTAATTAATTTTTAAAAAATTTATATTAATAAAATAAAATATTAATTATTTTTTAAAATAAAAA
1 TTAATTAA-ATTTAAAAAATTTATATTAATAAAATAAAATATTAATTATTTTTTAAAATAAAAA
2612320 TTAAATTAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
67 8 0.15
68 13 0.24
69 1 0.02
70 7 0.13
71 25 0.46
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (70 bp):
TTAATTAAATTTAAAAAATTTATATTAATAAAATAAAATATTAATTATTTTTTAAAATAAAAAAT
AATAT
Found at i:2612284 original size:25 final size:28
Alignment explanation
Indices: 2612222--2612285 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 28
2612212 TAAATAGTAA
2612222 TATATTAATTATTATTTTTAATAAAAAAT
1 TATATTAATTA-TATTTTTAATAAAAAAT
* *
2612251 AATATTTAATTA-ATTTTT-A-AAAAATT
1 TATA-TTAATTATATTTTTAATAAAAAAT
2612277 TATATTAAT
1 TATATTAAT
2612286 AAAATAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
25 5 0.16
26 9 0.29
27 1 0.03
28 6 0.19
29 3 0.10
30 7 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
TATATTAATTATATTTTTAATAAAAAAT
Found at i:2612499 original size:34 final size:34
Alignment explanation
Indices: 2612429--2612500 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
2612419 TAATTTTATG
* * *
2612429 TTTTTATAAAAATAAAAAGTATTTTTTATTATAA
1 TTTTTATAAAAATAAAAAATATATTTAATTATAA
2612463 TTTTTA-ATAAAATAAAAAATGATATTTAATTA-AA
1 TTTTTATA-AAAATAAAAAAT-ATATTTAATTATAA
2612497 TTTT
1 TTTT
2612501 AAAAAACTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 1 0.03
34 23 0.70
35 9 0.27
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (34 bp):
TTTTTATAAAAATAAAAAATATATTTAATTATAA
Found at i:2612560 original size:108 final size:109
Alignment explanation
Indices: 2612336--2612548 Score: 265
Period size: 108 Copynumber: 2.0 Consensus size: 109
2612326 TAAAAAGGGT
* *
2612336 TTATTATTATTATTATTATTATTTAATAAAATTAAAAATAATATTTAATTAAATTTAAAAAATTC
1 TTATT-TTATTATTATAATTATTTAATAAAATAAAAAATAATATTTAATTAAATTTAAAAAATTC
* * ** *
2612401 ATTAACAAATTAAAATATTAATTTTATGTTTTTATAAAAATAAAAA
65 ATTAACAAATTAAAATA-TAATTTAAAGTAATTAAAAAAATAAAAA
* *
2612447 GTATTTT-TTATTATAATT-TTTAATAAAATAAAAAATGATATTTAATTAAATTTTAAAAAACTT
1 TTATTTTATTATTATAATTATTTAATAAAATAAAAAATAATATTTAATTAAA-TTTAAAAAA-TT
2612510 ACATTAACAAATTAAAA-A-AATTTAAAG-AATTAAAAAAAT
64 -CATTAACAAATTAAAATATAATTTAAAGTAATTAAAAAAAT
2612549 TTATCATTAT
Statistics
Matches: 90, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
107 9 0.10
108 37 0.41
109 19 0.21
110 5 0.06
111 20 0.22
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (109 bp):
TTATTTTATTATTATAATTATTTAATAAAATAAAAAATAATATTTAATTAAATTTAAAAAATTCA
TTAACAAATTAAAATATAATTTAAAGTAATTAAAAAAATAAAAA
Found at i:2612815 original size:20 final size:21
Alignment explanation
Indices: 2612784--2612822 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2612774 AAAATAATAA
2612784 TAAATCTTTTTTATATTTATT
1 TAAATCTTTTTTATATTTATT
*
2612805 TAAAT-TTTTTTATTTTTA
1 TAAATCTTTTTTATATTTA
2612823 AAAATAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (21 bp):
TAAATCTTTTTTATATTTATT
Found at i:2612897 original size:26 final size:26
Alignment explanation
Indices: 2612848--2612897 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
2612838 TTAATTTGTT
*
2612848 AATATAATTTTTTTAAAAGTTAATTA
1 AATATAATTTTTTTAAAAGATAATTA
*
2612874 AATATTATTTTTATTAAAA-ATAAT
1 AATATAATTTTT-TTAAAAGATAAT
2612898 AATTAATACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
AATATAATTTTTTTAAAAGATAATTA
Found at i:2612918 original size:124 final size:116
Alignment explanation
Indices: 2612704--2612934 Score: 277
Period size: 124 Copynumber: 1.9 Consensus size: 116
2612694 TATCAAACAT
* *
2612704 AATAATTAAATTTTAATTTGTTAATGTAATTTTTTAAACGTAATTAAATATTATTTTCAATTTTA
1 AATAATTAAATTTTAATTTGTTAATATAATTTTTTAAAAGTAATTAAATATTA--TT--ATTTTA
* *
2612769 TTAAAAAAATAATAATAAATCTTTTTTATATTTATTTAAATTTTTTTATTTTTAAA
62 TTAAAAAAATAATAATAAATATTTTTTAAATTT-TTTAAATTTTTTTATTTTTAAA
*
2612825 AATAATTAATTTTTTAATTTGTTAATATAATTTTTTTAAAAGTTAATTAAATATTA-T-TTTTAT
1 AATAATTAA-ATTTTAATTTGTTAATATAA-TTTTTTAAAAG-TAATTAAATATTATTATTTTAT
2612888 TAAAAATAATAATTAATACATTATTATTTTTTAAATTTTTTAAATTT
63 TAAAAA-AATAA-TAATA-A--A-TATTTTTTAAATTTTTTAAATTT
2612935 AATTAATTTA
Statistics
Matches: 96, Mismatches: 5, Indels: 16
0.82 0.04 0.14
Matches are distributed among these distances:
118 12 0.12
119 5 0.05
120 5 0.05
121 11 0.11
122 18 0.19
123 20 0.21
124 25 0.26
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (116 bp):
AATAATTAAATTTTAATTTGTTAATATAATTTTTTAAAAGTAATTAAATATTATTATTTTATTAA
AAAAATAATAATAAATATTTTTTAAATTTTTTAAATTTTTTTATTTTTAAA
Found at i:2613587 original size:89 final size:88
Alignment explanation
Indices: 2613433--2613606 Score: 285
Period size: 89 Copynumber: 2.0 Consensus size: 88
2613423 AATCGGATTC
* * *
2613433 TTTTTTATGGAAAAAAGAAAAGTTGATTGATTATAAATGTCAGACTGTAAAGATTAGACTTATGC
1 TTTTTTATGAAAAAAAGAAAAGTTAATTGATTATAAATGTCAGACTGTAAAGATTAGACTAATGC
2613498 ATGAATTATATCTGAGAATCAAT
66 ATGAATTATATCTGAGAATCAAT
* *
2613521 TTTTTTATAGAAAAAAAGAAAAGTTAATTGATTGTAAATGTCAGACTGTAAGGATTAGACTAATG
1 TTTTTTAT-GAAAAAAAGAAAAGTTAATTGATTATAAATGTCAGACTGTAAAGATTAGACTAATG
*
2613586 CATGAATTATATTTGAGAATC
65 CATGAATTATATCTGAGAATC
2613607 GATTGTAAAT
Statistics
Matches: 79, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
88 8 0.10
89 71 0.90
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.35
Consensus pattern (88 bp):
TTTTTTATGAAAAAAAGAAAAGTTAATTGATTATAAATGTCAGACTGTAAAGATTAGACTAATGC
ATGAATTATATCTGAGAATCAAT
Found at i:2613638 original size:57 final size:58
Alignment explanation
Indices: 2613550--2613668 Score: 204
Period size: 57 Copynumber: 2.1 Consensus size: 58
2613540 AAAGTTAATT
* * *
2613550 GATTGTAAATGTCAGACTGTAAGGATTAGACTAATGCATGAATTATATTTGAGAATC-
1 GATTGTAAATGTCAGACTGCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCA
2613607 GATTGTAAATGTCAGACTGCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCA
1 GATTGTAAATGTCAGACTGCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCA
2613665 GATT
1 GATT
2613669 TTTTTTATAG
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
57 54 0.93
58 4 0.07
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (58 bp):
GATTGTAAATGTCAGACTGCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCA
Found at i:2613748 original size:234 final size:235
Alignment explanation
Indices: 2613413--2613837 Score: 590
Period size: 234 Copynumber: 1.8 Consensus size: 235
2613403 TAAATGTGAC
* * * * *
2613413 TATATCTTAAAATCGGATTCTTTTTTATGGAAAAAAGAAAAGTTGATTGATTATAAATGTCAGAC
1 TATATCTGAAAATCAGATTCTTTTTTATAGAAAAAAGAAAAGTTGACTGATTATAAATGTCAAAC
* *
2613478 TGTAAAGATTAGACTTATGCATGAATTATATCTGAGAA-TCAATTTTTTTATAG-AAAAAAAGAA
66 TATAAAGATTAGACTAATGCATGAATTATATCTGAGAATTCAATTTTTTTATAGAAAAAAAAG-A
* * * ** *
2613541 AAGTTAATTGATTGTAAATGTCAGACTGTAAGGATTAGACTAATGCATGAATTATATTTGAGAAT
130 AAG---ACTGATTGTAAATATCAAACTACAAGGATTAAACTAATGCATGAATTATATTTGAGAAT
2613606 CGATTGTAAATGTCAGACTGCAAAGATTAGACTAATGCATGAAT
192 CGATTGTAAATGTCAGACTGCAAAGATTAGACTAATGCATGAAT
* * * *
2613650 TATATCTGAGAATCAGATT-TTTTTTATAG-AAAAA-AAATGTTGACTGATTGTAAGTGTCAAAC
1 TATATCTGAAAATCAGATTCTTTTTTATAGAAAAAAGAAAAGTTGACTGATTATAAATGTCAAAC
* **
2613712 TATAAGGATTAGACTAATGCATGAATTATATCTGAGAATTGGATTTTTTTATAGAAAAAAAAGAA
66 TATAAAGATTAGACTAATGCATGAATTATATCTGAGAATTCAATTTTTTTATAGAAAAAAAAGAA
*
2613777 AGACTGATTGTGAATATCAAACTACAAGGATTAAACTAATGCATGAATTATATTTGAGAAT
131 AGACTGATTGTAAATATCAAACTACAAGGATTAAACTAATGCATGAATTATATTTGAGAAT
2613838 TAGATTCTTT
Statistics
Matches: 165, Mismatches: 21, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
232 52 0.32
234 58 0.35
235 22 0.13
236 17 0.10
237 16 0.10
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.34
Consensus pattern (235 bp):
TATATCTGAAAATCAGATTCTTTTTTATAGAAAAAAGAAAAGTTGACTGATTATAAATGTCAAAC
TATAAAGATTAGACTAATGCATGAATTATATCTGAGAATTCAATTTTTTTATAGAAAAAAAAGAA
AGACTGATTGTAAATATCAAACTACAAGGATTAAACTAATGCATGAATTATATTTGAGAATCGAT
TGTAAATGTCAGACTGCAAAGATTAGACTAATGCATGAAT
Found at i:2613757 original size:88 final size:88
Alignment explanation
Indices: 2613607--2614128 Score: 633
Period size: 88 Copynumber: 5.9 Consensus size: 88
2613597 TTTGAGAATC
* * *
2613607 GATTGTAAATGTCAGACTGCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTTTT
1 GATTGTAAATGTCAAACTACAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTTTT
* *
2613672 TTTATAGAAAAAAAATG-TTGACT
66 TTTATAGAAAAAAAA-GACTGATT
* * **
2613695 GATTGTAAGTGTCAAACTATAAGGATTAGACTAATGCATGAATTATATCTGAGAATTGGA-TTTT
1 GATTGTAAATGTCAAACTACAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTTTT
** *
2613759 TTTATAGAAAAAAAAGAAAGACT
66 TTTATAGAAAAAAAAGACTGATT
* * * * *
2613782 GATTGTGAATATCAAACTACAAGGATTAAACTAATGCATGAATTATATTTGAGAATTAGATTCTT
1 GATTGTAAATGTCAAACTACAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGA-T-TT
2613847 TTTTTATAGAAAAAAAGAAAGACTGATT
64 TTTTTATAG--AAAAA-AAAGACTGATT
* * * *
2613875 GATTATAAATGTCAAACTAGAAGGATTAGACTAATGCATGAATTATATTTGAGAATCGGATTCTT
1 GATTGTAAATGTCAAACTACAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATT-TT
*
2613940 TTTTATA-AAAAAAAAGACTAATT
65 TTTTATAGAAAAAAAAGACTGATT
* * *
2613963 GATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGA-ATTT
1 GATTGTAAATGTCAAACTACAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTTTT
2614027 TTTATAG-AAAAAAAGACTGATT
66 TTTATAGAAAAAAAAGACTGATT
* * * * * *
2614049 GATTGTAAAT-ACTAGACTGCAAAGATTAGACTAATACATGAATTATATCTGAGAATTAGATTCT
1 GATTGTAAATGTC-AAACTACAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATT-T
*
2614113 TTTTTATAGGAAAAAA
64 TTTTTATAGAAAAAAA
2614129 GAAAGACTAC
Statistics
Matches: 381, Mismatches: 40, Indels: 25
0.85 0.09 0.06
Matches are distributed among these distances:
85 1 0.00
86 78 0.20
87 76 0.20
88 127 0.33
89 11 0.03
90 11 0.03
91 1 0.00
92 15 0.04
93 61 0.16
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.33
Consensus pattern (88 bp):
GATTGTAAATGTCAAACTACAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTTTT
TTTATAGAAAAAAAAGACTGATT
Found at i:2614175 original size:70 final size:70
Alignment explanation
Indices: 2614062--2614453 Score: 601
Period size: 70 Copynumber: 5.6 Consensus size: 70
2614052 TGTAAATACT
* *
2614062 AGACTGCAAAGATTAGACTAATACATGAATTATATCTGAGAATTAGATTCTTTTTTATAGGAAAA
1 AGACTGCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAGGAAAA
2614127 AAGAA
66 AAGAA
* * * * *
2614132 AGACTACAAGGATTAGACTAACGCATGAATTATATCTGAGAATTAGATTGTTTTTTATAGGAAAA
1 AGACTGCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAGGAAAA
2614197 AAGAA
66 AAGAA
* *
2614202 AGGCTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAGGAAAA
1 AGACTGCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAGGAAAA
2614267 AAGAA
66 AAGAA
* *
2614272 AGATTGCAAAGATTAGATTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAGGAAAA
1 AGACTGCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAGGAAAA
2614337 AAGAA
66 AAGAA
* *
2614342 AAACTGCAAAGATTAGATTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAGG-AAA
1 AGACTGCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAGGAAAA
2614406 AA-AA
66 AAGAA
* * **
2614410 AGATTGCAATGATTAGACTAATATATGAATTAT-TCATGAGAATC
1 AGACTGCAAAGATTAGACTAATGCATGAATTATATC-TGAGAATC
2614454 GAATTTTTTT
Statistics
Matches: 299, Mismatches: 22, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
67 2 0.01
68 37 0.12
69 5 0.02
70 255 0.85
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.32
Consensus pattern (70 bp):
AGACTGCAAAGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAGGAAAA
AAGAA
Found at i:2616268 original size:7 final size:7
Alignment explanation
Indices: 2616256--2616281 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2616246 TTATAGTAAA
2616256 GGTTTAG
1 GGTTTAG
2616263 GGTTTAG
1 GGTTTAG
2616270 GGTTTAG
1 GGTTTAG
2616277 GGTTT
1 GGTTT
2616282 TTTCCATCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.42, T:0.46
Consensus pattern (7 bp):
GGTTTAG
Found at i:2620281 original size:16 final size:17
Alignment explanation
Indices: 2620260--2620296 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
2620250 ATTATTATGT
2620260 TTTTAAAAAT-AAAAAA
1 TTTTAAAAATAAAAAAA
*
2620276 TTTT-AAATTAAAAAAA
1 TTTTAAAAATAAAAAAA
2620292 TTTTA
1 TTTTA
2620297 TTATAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTTAAAAATAAAAAAA
Found at i:2620311 original size:124 final size:124
Alignment explanation
Indices: 2619942--2620311 Score: 470
Period size: 124 Copynumber: 3.0 Consensus size: 124
2619932 TTATTATTTT
* *
2619942 AAATAAAAAATAATATTTAATTAACTTTAAAAAATTTATATTAACAAATTAAAATATTAATTA-T
1 AAATAAAAAATAATATTTAATTAAGTTT-AAAAATTTACATTAACAAATTAAAATATTAATTATT
** * *
2620006 -T-TTTTT-AAAATAAAAAATTTAAATAAAATTAAAAAAGGTTTATTATTATTATTTTTTTAATA
65 ATGTTTTTAAAAATAAAAAATTT---T-AAATTAAAAAAATTTTATTA-TAATAATTTTTTAATA
* *
2620068 AAATTAAAAATAATATTTAATTAAGTTTAGAAAA-TTACATTAACAAAGTAAAAT-TTAATTATT
1 AAATAAAAAATAATATTTAATTAAGTTTA-AAAATTTACATTAACAAATTAAAATATTAATTATT
* * *
2620131 ATGTTTTTATAAAA-ATAAATATTTTAAAATAAAAAAAGGTTTT-TTATTATAA-TTTTTAATA
65 ATGTTTTTA-AAAATA-AAAAATTTTAAATTAAAAAAA--TTTTATTATAATAATTTTTTAATA
*
2620192 AAATAAAAAATAATATTGAATTAAGTTTAAAAATTTACATTAACAAATTAAAATATTAATTATTA
1 AAATAAAAAATAATATTTAATTAAGTTTAAAAATTTACATTAACAAATTAAAATATTAATTATTA
2620257 TGTTTTTAAAAATAAAAAATTTTAAATTAAAAAAATTTTATTATAATAATTTTTT
66 TGTTTTTAAAAATAAAAAATTTTAAATTAAAAAAATTTTATTATAATAATTTTTT
2620312 TTATTATTTT
Statistics
Matches: 213, Mismatches: 17, Indels: 30
0.82 0.07 0.12
Matches are distributed among these distances:
122 4 0.02
123 12 0.06
124 90 0.42
125 52 0.24
126 35 0.16
127 8 0.04
128 1 0.00
129 11 0.05
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (124 bp):
AAATAAAAAATAATATTTAATTAAGTTTAAAAATTTACATTAACAAATTAAAATATTAATTATTA
TGTTTTTAAAAATAAAAAATTTTAAATTAAAAAAATTTTATTATAATAATTTTTTAATA
Found at i:2620894 original size:12 final size:12
Alignment explanation
Indices: 2620877--2620907 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
2620867 TTATTCGAAA
2620877 AAAAAATATTTT
1 AAAAAATATTTT
2620889 AAAAAATATTTT
1 AAAAAATATTTT
2620901 ATAAAAA
1 A-AAAAA
2620908 ACTTATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.72
13 5 0.28
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
AAAAAATATTTT
Found at i:2624015 original size:2 final size:2
Alignment explanation
Indices: 2624008--2624047 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2623998 TATCTTGTGA
2624008 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
2624048 CCTGTGAAGA
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
Done.