Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 221 of 226
Found at i:69090221 original size:20 final size:20
Alignment explanation
Indices: 69090192--69090233 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
69090182 GGATTTTTTT
* *
69090192 TTCTTTATTTCTCCTTATTC
1 TTCTTCATTTCTACTTATTC
*
69090212 TTCTTCATTTCTATTTATTC
1 TTCTTCATTTCTACTTATTC
69090232 TT
1 TT
69090234 ATTCTTCTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.67
Consensus pattern (20 bp):
TTCTTCATTTCTACTTATTC
Found at i:69090491 original size:10 final size:10
Alignment explanation
Indices: 69090478--69090505 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
69090468 TAATTTTGTT
69090478 AAATTTAAGA
1 AAATTTAAGA
69090488 AAATTTAAGA
1 AAATTTAAGA
69090498 AAATTTAA
1 AAATTTAA
69090506 TACATTGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (10 bp):
AAATTTAAGA
Found at i:69092986 original size:23 final size:23
Alignment explanation
Indices: 69092952--69092997 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
69092942 AATGCAACAA
* * *
69092952 GAGACCAGCAGCAGTTCAGCATG
1 GAGACCAACAGCAGCTCAACATG
69092975 GAGACCAACAGCAGCTCAACATG
1 GAGACCAACAGCAGCTCAACATG
69092998 AAGATAAGCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.35, C:0.28, G:0.26, T:0.11
Consensus pattern (23 bp):
GAGACCAACAGCAGCTCAACATG
Found at i:69095580 original size:18 final size:19
Alignment explanation
Indices: 69095557--69095592 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
69095547 CCCCAAATTA
69095557 TTTTTTTCT-TTTTTTTTG
1 TTTTTTTCTCTTTTTTTTG
69095575 TTTTTTTCTCTTTTTTTT
1 TTTTTTTCTCTTTTTTTT
69095593 ATGCTTTAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.00, C:0.08, G:0.03, T:0.89
Consensus pattern (19 bp):
TTTTTTTCTCTTTTTTTTG
Found at i:69096626 original size:19 final size:19
Alignment explanation
Indices: 69096604--69096657 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
69096594 ATATCCAAAT
69096604 AAGTAATAAATAATAAAGA
1 AAGTAATAAATAATAAAGA
69096623 AAGTAATAAATAAAGTAAAGA
1 AAGTAATAAAT-AA-TAAAGA
69096644 AA--AAT-AATAATAAA
1 AAGTAATAAATAATAAA
69096658 TAATAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
16 4 0.12
17 2 0.06
18 3 0.09
19 14 0.42
20 2 0.06
21 8 0.24
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.20
Consensus pattern (19 bp):
AAGTAATAAATAATAAAGA
Found at i:69096655 original size:21 final size:20
Alignment explanation
Indices: 69096600--69096678 Score: 67
Period size: 23 Copynumber: 3.9 Consensus size: 20
69096590 ATTAATATCC
69096600 AAATAAGTAATAAATAATA-AA
1 AAATAA-TAATAAATAA-AGAA
69096621 GAAAGTAATAAATAAAGTAAAGAA
1 -AAA-TAAT-AATAAA-TAAAGAA
*
69096645 AAATAATAATAAAT-AA-TA
1 AAATAATAATAAATAAAGAA
69096663 AAATAATAA-AAATAAA
1 AAATAATAATAAATAAA
69096679 AATTGGGTTG
Statistics
Matches: 51, Mismatches: 1, Indels: 14
0.77 0.02 0.21
Matches are distributed among these distances:
17 4 0.08
18 12 0.24
19 2 0.04
20 1 0.02
21 6 0.12
22 8 0.16
23 13 0.25
24 5 0.10
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (20 bp):
AAATAATAATAAATAAAGAA
Found at i:69096667 original size:15 final size:14
Alignment explanation
Indices: 69096649--69096679 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
69096639 AAAGAAAAAT
69096649 AATAATAAATAATAA
1 AATAATAAA-AATAA
69096664 AATAATAAAAATAA
1 AATAATAAAAATAA
69096678 AA
1 AA
69096680 ATTGGGTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AATAATAAAAATAA
Found at i:69096681 original size:15 final size:17
Alignment explanation
Indices: 69096643--69096680 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
69096633 TAAAGTAAAG
69096643 AAAAATAATAATAAATA
1 AAAAATAATAATAAATA
69096660 ATAAAATAATAA-AAATA
1 A-AAAATAATAATAAATA
69096677 AAAA
1 AAAA
69096681 TTGGGTTGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 3 0.15
17 7 0.35
18 10 0.50
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAAATAATAATAAATA
Found at i:69107630 original size:18 final size:19
Alignment explanation
Indices: 69107597--69107636 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
69107587 AGGAGAGAAT
*
69107597 AAAAAAAAGGGAAAATGGA
1 AAAAAAAAGGGAAAATAGA
*
69107616 AAAAAAAAGTG-AAATAGA
1 AAAAAAAAGGGAAAATAGA
69107634 AAA
1 AAA
69107637 TTAGAATGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.72, C:0.00, G:0.20, T:0.07
Consensus pattern (19 bp):
AAAAAAAAGGGAAAATAGA
Found at i:69115874 original size:3 final size:3
Alignment explanation
Indices: 69115868--69115902 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
69115858 ATCAAAGTAA
69115868 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
69115903 ATACTTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:69125587 original size:15 final size:15
Alignment explanation
Indices: 69125565--69125600 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
69125555 ATTTTATTTT
69125565 ATTTTAT-TTTAAT-
1 ATTTTATATTTAATA
69125578 ATTTTATATTTAATA
1 ATTTTATATTTAATA
69125593 ATTTTATA
1 ATTTTATA
69125601 CATTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.33
14 6 0.29
15 8 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTTTATATTTAATA
Found at i:69125605 original size:17 final size:14
Alignment explanation
Indices: 69125564--69125600 Score: 58
Period size: 13 Copynumber: 2.6 Consensus size: 14
69125554 TATTTTATTT
69125564 TATTTTAT-TTTAA
1 TATTTTATATTTAA
69125577 TATTTTATATTTAA
1 TATTTTATATTTAA
69125591 TAATTTTATA
1 T-ATTTTATA
69125601 CATTTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 8 0.36
14 6 0.27
15 8 0.36
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTTTATATTTAA
Found at i:69125692 original size:15 final size:15
Alignment explanation
Indices: 69125672--69125700 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
69125662 AAGTAGTATT
69125672 ATATATTTAGTATAG
1 ATATATTTAGTATAG
69125687 ATATATTTAGTATA
1 ATATATTTAGTATA
69125701 TCTCATGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (15 bp):
ATATATTTAGTATAG
Found at i:69125990 original size:7 final size:7
Alignment explanation
Indices: 69125978--69126002 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
69125968 ACATCAATAA
69125978 ATAATTT
1 ATAATTT
69125985 ATAATTT
1 ATAATTT
69125992 ATAATTT
1 ATAATTT
69125999 ATAA
1 ATAA
69126003 AATATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
ATAATTT
Found at i:69129594 original size:12 final size:12
Alignment explanation
Indices: 69129577--69129603 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
69129567 GTAAGCATAT
69129577 TTTCGAACCTAG
1 TTTCGAACCTAG
69129589 TTTCGAACCTAG
1 TTTCGAACCTAG
69129601 TTT
1 TTT
69129604 TAAGATCAAG
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:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (12 bp):
TTTCGAACCTAG
Found at i:69130937 original size:16 final size:16
Alignment explanation
Indices: 69130906--69130942 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
69130896 ATATGAAGAA
69130906 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
69130922 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
69130938 TATTA
1 TATTA
69130943 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:69135485 original size:16 final size:17
Alignment explanation
Indices: 69135447--69135488 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
69135437 ACAAACTTGA
69135447 TTATTATA-ATGAAATG
1 TTATTATAGATGAAATG
* *
69135463 TTGTTATAGATGATA-G
1 TTATTATAGATGAAATG
69135479 TTATTATAGA
1 TTATTATAGA
69135489 GATGGCTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (17 bp):
TTATTATAGATGAAATG
Found at i:69136811 original size:6 final size:6
Alignment explanation
Indices: 69136796--69136853 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
69136786 GAGTAGGATC
* * * * * *
69136796 TGTATA TGTATT TGTATC TGTATC TATATC TGCATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
69136844 TGTATA TGTA
1 TGTATA TGTA
69136854 ATTGCACCTA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.28, C:0.07, G:0.16, T:0.50
Consensus pattern (6 bp):
TGTATA
Found at i:69139422 original size:29 final size:29
Alignment explanation
Indices: 69139386--69139462 Score: 136
Period size: 29 Copynumber: 2.7 Consensus size: 29
69139376 AAAAAAATGA
69139386 ATAGTTGGGTGACCATTTTTCAACTTTTC
1 ATAGTTGGGTGACCATTTTTCAACTTTTC
*
69139415 ATAGTTGGGTGACCAATTTTCAACTTTTC
1 ATAGTTGGGTGACCATTTTTCAACTTTTC
*
69139444 ATAGTTGGATGACCATTTT
1 ATAGTTGGGTGACCATTTT
69139463 GTAGTTTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (29 bp):
ATAGTTGGGTGACCATTTTTCAACTTTTC
Found at i:69140558 original size:274 final size:273
Alignment explanation
Indices: 69139923--69140548 Score: 769
Period size: 274 Copynumber: 2.3 Consensus size: 273
69139913 CCACTAAACC
** *
69139923 AAAACTTTATTTTAATATATTTTATACATTTTGGTTTTAATAT-TCACAATTCGTTATATTCATC
1 AAAACTTTATTTTAATATATTTTATACATTTTGGTTTTAATATGT-ACAATTTATTATCTTCATC
* * * * ** *
69139987 AGTTGTATATCTATACTTACTATTTATTAAGCCCTTGACTGAGTTGGTGTCACCCTCAACCGGGT
65 AATTGTATATATATACTTAATATTTATTAAGCCCCTGACTGAGTCAGTGTCACCCTCAACCGAGT
* * * *
69140052 CACCAACTTGATCAAGAAATTATAAAAATGTTCTTTCATAATTAAAAAAAGGTTATATTATTCAA
130 CACCAACTTGATCAAAAAATTACAAAAATGTCCTTTCATAATTAAAAAAAGGTTATATAATTCAA
* * *
69140117 GGGTATTTTAGTCTTTTCATTTTAACAAAAACCAATTAAAAAATATACATACGGTGAGATTTGAA
195 GGGTATTTTAGTCTTTTCATTTTAACAAAAACCAATTAAAAAATATACATAAGATGAGACTTGAA
*
69140182 CCTATGCCAATTCT
260 CCCATGCCAATTCT
* * * *
69140196 AAACCTTTATTTTAATGTATTTTTATACATTTTGGTTTTAATATGCACAATATATTATCTTCATC
1 AAAACTTTATTTTAATATA-TTTTATACATTTTGGTTTTAATATGTACAATTTATTATCTTCATC
* * *
69140261 AATTGTATATATATACTTAATATTTATTAAGCCCCTGACTGAGTCAGTTTCACTCTCAATCGAGT
65 AATTGTATATATATACTTAATATTTATTAAGCCCCTGACTGAGTCAGTGTCACCCTCAACCGAGT
* * *
69140326 CACCAACTT-AGTCAAAAAATTACGAAAATGTCCTTTCGTAATT-AGAAAA-GTTATATAATTCA
130 CACCAACTTGA-TCAAAAAATTACAAAAATGTCCTTTCATAATTAAAAAAAGGTTATATAATTCA
** *
69140388 AGGGTATTTTAGGT-TTTTCATTTT-AGGAAAACCAATTAAAAAATATACATAAGATGGGACTTG
194 AGGGTATTTTA-GTCTTTTCATTTTAACAAAAACCAATTAAAAAATATACATAAGATGAGACTTG
* *
69140451 AACCCGTGCCAATTAAATTATT
258 AACCCATGCC-----AATT-CT
* * * *
69140473 AAAACTTTATCTTAATATATTTTATACATTTTGATTTTAATATGTATAATTTATTATCTCCATCA
1 AAAACTTTATTTTAATATATTTTATACATTTTGGTTTTAATATGTACAATTTATTATCTTCATCA
* *
69140538 CTTATATATAT
66 ATTGTATATAT
69140549 TAATAATATT
Statistics
Matches: 300, Mismatches: 43, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
271 41 0.14
272 33 0.11
273 25 0.08
274 130 0.43
276 54 0.18
277 17 0.06
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.40
Consensus pattern (273 bp):
AAAACTTTATTTTAATATATTTTATACATTTTGGTTTTAATATGTACAATTTATTATCTTCATCA
ATTGTATATATATACTTAATATTTATTAAGCCCCTGACTGAGTCAGTGTCACCCTCAACCGAGTC
ACCAACTTGATCAAAAAATTACAAAAATGTCCTTTCATAATTAAAAAAAGGTTATATAATTCAAG
GGTATTTTAGTCTTTTCATTTTAACAAAAACCAATTAAAAAATATACATAAGATGAGACTTGAAC
CCATGCCAATTCT
Found at i:69155011 original size:3 final size:3
Alignment explanation
Indices: 69155005--69155042 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
69154995 TTTAATAATT
*
69155005 ATG ATG ATG ATG ACG ATG ATG ATG ATG ATG AT- ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
69155043 TTGCATATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.34, C:0.03, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:69176514 original size:6 final size:6
Alignment explanation
Indices: 69176505--69176548 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
69176495 AAAAGAGAAT
* * *
69176505 GAGACA GAGACA GAGACA GTGACA GTGACA GGAGACA GTGACA G
1 GAGACA GAGACA GAGACA GAGACA GAGACA -GAGACA GAGACA G
69176549 CTAAAGGAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
6 29 0.85
7 5 0.15
ACGTcount: A:0.41, C:0.16, G:0.36, T:0.07
Consensus pattern (6 bp):
GAGACA
Found at i:69176541 original size:19 final size:18
Alignment explanation
Indices: 69176507--69176548 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
69176497 AAGAGAATGA
69176507 GACAGAGACAGAGACAGT
1 GACAGAGACAGAGACAGT
*
69176525 GACAGTGACAGGAGACAGT
1 GACAGAGACA-GAGACAGT
69176544 GACAG
1 GACAG
69176549 CTAAAGGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.40, C:0.17, G:0.36, T:0.07
Consensus pattern (18 bp):
GACAGAGACAGAGACAGT
Found at i:69176556 original size:19 final size:19
Alignment explanation
Indices: 69176517--69176560 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
69176507 GACAGAGACA
*
69176517 GAGACAGTGACAGTGACAG
1 GAGACAGTGACAGTGAAAG
69176536 GAGACAGTGACAGCT-AAAG
1 GAGACAGTGACAG-TGAAAG
69176555 GAGACA
1 GAGACA
69176561 ATATAGGTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.41, C:0.16, G:0.34, T:0.09
Consensus pattern (19 bp):
GAGACAGTGACAGTGAAAG
Found at i:69176924 original size:3 final size:3
Alignment explanation
Indices: 69176918--69176943 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
69176908 AACTTGTCGG
69176918 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
69176944 AACTCCATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:69177234 original size:15 final size:12
Alignment explanation
Indices: 69177198--69177226 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
69177188 TTCTCTCTCC
69177198 TCCTC-TCTTCT
1 TCCTCGTCTTCT
69177209 TCCTCGTCTTCT
1 TCCTCGTCTTCT
69177221 TCCTCG
1 TCCTCG
69177227 AAGTCTTCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.00, C:0.45, G:0.07, T:0.48
Consensus pattern (12 bp):
TCCTCGTCTTCT
Found at i:69177449 original size:2 final size:2
Alignment explanation
Indices: 69177444--69177469 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
69177434 ACACACTCCC
69177444 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
69177470 TCTGTTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:69177486 original size:6 final size:6
Alignment explanation
Indices: 69177477--69177503 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
69177467 TCTTCTGTTG
69177477 TTTTTA TTTTTA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT
69177504 CCACTTTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:69178283 original size:16 final size:16
Alignment explanation
Indices: 69178260--69178292 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
69178250 TATGCTTATA
69178260 AAATTAA-TTAAAAAT
1 AAATTAATTTAAAAAT
69178275 AAATATAATTTAAAAAT
1 AAAT-TAATTTAAAAAT
69178292 A
1 A
69178293 TCATCAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 3 0.19
17 9 0.56
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATTAATTTAAAAAT
Found at i:69178964 original size:20 final size:19
Alignment explanation
Indices: 69178941--69178987 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
69178931 GGATTTTGAG
* *
69178941 GTTTTTTTTTTATTTTTTAA
1 GTTTTTTATATATTTTTT-A
*
69178961 GTTTATTATATATTTTTTA
1 GTTTTTTATATATTTTTTA
69178980 GTTTTTTA
1 GTTTTTTA
69178988 ATAAAATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.74
Consensus pattern (19 bp):
GTTTTTTATATATTTTTTA
Found at i:69182838 original size:26 final size:25
Alignment explanation
Indices: 69182798--69182865 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 25
69182788 ATAAACAAAC
* *
69182798 ATATTTTCTTCTTTTGCAAATTTTA
1 ATATTTTCTTTTTTTGCAAATGTTA
* * *
69182823 ATCATTTTGTTTTTTTCCATATGTTA
1 AT-ATTTTCTTTTTTTGCAAATGTTA
*
69182849 ATATTTTTTTATTTTTG
1 ATATTTTCTT-TTTTTG
69182866 TGCAACCAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
25 9 0.26
26 25 0.74
ACGTcount: A:0.21, C:0.09, G:0.06, T:0.65
Consensus pattern (25 bp):
ATATTTTCTTTTTTTGCAAATGTTA
Found at i:69183005 original size:20 final size:21
Alignment explanation
Indices: 69182980--69183018 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
69182970 ATCCAAAATC
*
69182980 CTGAACCTTGAA-CTTGAACT
1 CTGAACCTTAAATCTTGAACT
69183000 CTGAACCTTAAATCTTGAA
1 CTGAACCTTAAATCTTGAA
69183019 TCACAAATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (21 bp):
CTGAACCTTAAATCTTGAACT
Found at i:69186830 original size:2 final size:2
Alignment explanation
Indices: 69186823--69186866 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
69186813 TATAATCTTA
69186823 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
69186865 AT
1 AT
69186867 CGTGTTTATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:69189158 original size:2 final size:2
Alignment explanation
Indices: 69189151--69189178 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
69189141 AATATTAGTG
69189151 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
69189179 ATAATANNNN
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:69191199 original size:11 final size:11
Alignment explanation
Indices: 69191185--69191247 Score: 51
Period size: 11 Copynumber: 5.7 Consensus size: 11
69191175 TTTTTTTTAA
69191185 TTTTAAAATAT
1 TTTTAAAATAT
69191196 TTTTAAAATACT
1 TTTTAAAATA-T
* *
69191208 TTTT---TTAA
1 TTTTAAAATAT
69191216 TTTTAAAATAT
1 TTTTAAAATAT
*
69191227 TTTAAAAATACTT
1 TTTTAAAATA--T
69191240 TTTTAAAA
1 TTTTAAAA
69191248 AAAATTTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
8 4 0.10
9 2 0.05
11 21 0.52
12 5 0.12
13 8 0.20
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:69191235 original size:42 final size:39
Alignment explanation
Indices: 69191184--69191284 Score: 105
Period size: 42 Copynumber: 2.5 Consensus size: 39
69191174 TTTTTTTTTA
***
69191184 ATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTAAAAT
1 ATTTTAAAATATTTTTAAAA-A-AAATTTTAATTTTAAAAT
69191225 ATTTTAAAAATACTTTTTTAAAAAAAATTTTAATTTTAAAAT
1 ATTTT-AAAATA--TTTTTAAAAAAAATTTTAATTTTAAAAT
*
69191267 ACTTTTTAAAT-TTTTTAA
1 A-TTTTAAAATATTTTTAA
69191285 TTTTTAAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
39 7 0.13
41 5 0.10
42 26 0.50
43 5 0.10
44 9 0.17
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (39 bp):
ATTTTAAAATATTTTTAAAAAAAATTTTAATTTTAAAAT
Found at i:69191245 original size:30 final size:31
Alignment explanation
Indices: 69191176--69191243 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
69191166 ATTTTTAATT
*
69191176 TTTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTTAATTTTAAAATATTTTAAAAATAC
69191207 TTTTTTTAATTTTAAAATATTTTAAAAATAC
1 TTTTTTTAATTTTAAAATATTTTAAAAATAC
69191238 TTTTTT
1 TTTTTT
69191244 AAAAAAAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (31 bp):
TTTTTTTAATTTTAAAATATTTTAAAAATAC
Found at i:69198598 original size:2 final size:2
Alignment explanation
Indices: 69198593--69198639 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
69198583 GTTCTTTGTT
69198593 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
69198635 TA TA T
1 TA TA T
69198640 TTGTTTATGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:69200146 original size:14 final size:15
Alignment explanation
Indices: 69200127--69200155 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
69200117 ACCACCTTTA
69200127 TTTTTATT-TTATTT
1 TTTTTATTATTATTT
69200141 TTTTTATTATTATTT
1 TTTTTATTATTATTT
69200156 AAATTATCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTATTATTATTT
Found at i:69202995 original size:35 final size:35
Alignment explanation
Indices: 69202956--69203025 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
69202946 ACGATCTTCA
69202956 ATTAGTACTTTTAACAAATTTACTATGACATACTT
1 ATTAGTACTTTTAACAAATTTACTATGACATACTT
*
69202991 ATTAGTACTTTTAACAAATTTTCTATGACATACTT
1 ATTAGTACTTTTAACAAATTTACTATGACATACTT
69203026 TAACCATTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (35 bp):
ATTAGTACTTTTAACAAATTTACTATGACATACTT
Found at i:69204454 original size:31 final size:31
Alignment explanation
Indices: 69204393--69204458 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
69204383 TTATTATACC
* **
69204393 ATTTGGTACATGAGTTTGGCTTTGAGGTTCA
1 ATTTGGTACATGAATTTGGCTTCAAGGTTCA
*
69204424 ATTTGGTACATGAATTTGGCTTCAATGTTCA
1 ATTTGGTACATGAATTTGGCTTCAAGGTTCA
69204455 ATTT
1 ATTT
69204459 AATACCTAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.44
Consensus pattern (31 bp):
ATTTGGTACATGAATTTGGCTTCAAGGTTCA
Found at i:69206609 original size:15 final size:15
Alignment explanation
Indices: 69206571--69206611 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
69206561 TAAATAACTG
69206571 AATTTAATAAGT-CAA
1 AATTTAA-AAGTACAA
69206586 AATTT-AAAGTACAA
1 AATTTAAAAGTACAA
*
69206600 ATTTTAAAAGTA
1 AATTTAAAAGTA
69206612 AAGCGAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 4 0.17
14 8 0.35
15 11 0.48
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.34
Consensus pattern (15 bp):
AATTTAAAAGTACAA
Found at i:69210390 original size:117 final size:116
Alignment explanation
Indices: 69210209--69210421 Score: 311
Period size: 117 Copynumber: 1.8 Consensus size: 116
69210199 TTTCAGGACA
**
69210209 AAATTAAACCACTAACTGAAATGACTCCTGAAACCGAGAACAATTTGCTCCATGTTTTTCCATAC
1 AAATTAAACCACTAACTGAAATGACTCCTGAAACCGAGAACAATTTGCTCCACATTTTTCCATAC
*
69210274 AGTTCATGTTTCTCAAACTCAAATGCTGTATGCAGCCACATTTCTCAAATTC
66 AGTT-ATGTTTCTCAAACTCAAAAGCTGTATGCAGCCACATTTCTCAAATTC
* * ** *
69210326 AAATTGAATCACTAACTGAAATGACTCCTGAAATTGAGAACCATTTGCTCCACATTTCTT-CATA
1 AAATTAAACCACTAACTGAAATGACTCCTGAAACCGAGAACAATTTGCTCCACATTT-TTCCATA
* *
69210390 CGGTTATGTTTCTCAAACTCAAAAGTTGTATG
65 CAGTTATGTTTCTCAAACTCAAAAGCTGTATG
69210422 TAGCTAAGGA
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
116 25 0.29
117 58 0.68
118 2 0.02
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.32
Consensus pattern (116 bp):
AAATTAAACCACTAACTGAAATGACTCCTGAAACCGAGAACAATTTGCTCCACATTTTTCCATAC
AGTTATGTTTCTCAAACTCAAAAGCTGTATGCAGCCACATTTCTCAAATTC
Found at i:69224105 original size:25 final size:24
Alignment explanation
Indices: 69224064--69224114 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
69224054 CTTTTAAATA
**
69224064 TATTATAATTATTATATTTAATTT
1 TATTATAATTAAAATATTTAATTT
69224088 TATTATTAATTAAAATATTTAATTT
1 TATTA-TAATTAAAATATTTAATTT
69224113 TA
1 TA
69224115 AAAAACATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TATTATAATTAAAATATTTAATTT
Found at i:69230813 original size:68 final size:68
Alignment explanation
Indices: 69230704--69230842 Score: 260
Period size: 68 Copynumber: 2.0 Consensus size: 68
69230694 GTAAGATCAA
*
69230704 CTAGAACTAAAATGGTAAAAGTACCATAGAGGCCCTTGTACTAGAAGTTAGTTTGTATTTTCCCT
1 CTAGAACTAAAATGGTAAAAGTACCATAGAGGCCCTTGTACTAGAAGTTAGTTTGCATTTTCCCT
69230769 CAT
66 CAT
*
69230772 CTAGAACTAAAATGGTAAAAGTACCATGGAGGCCCTTGTACTAGAAGTTAGTTTGCATTTTCCCT
1 CTAGAACTAAAATGGTAAAAGTACCATAGAGGCCCTTGTACTAGAAGTTAGTTTGCATTTTCCCT
69230837 CAT
66 CAT
69230840 CTA
1 CTA
69230843 CTAAAAAATG
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (68 bp):
CTAGAACTAAAATGGTAAAAGTACCATAGAGGCCCTTGTACTAGAAGTTAGTTTGCATTTTCCCT
CAT
Found at i:69238568 original size:40 final size:39
Alignment explanation
Indices: 69238524--69238610 Score: 102
Period size: 39 Copynumber: 2.2 Consensus size: 39
69238514 TTCAAAAAAT
69238524 GCCGCTAAAGATCAAGTATTAGCGGCGTTTTTGAAAATGC
1 GCCGCTAAAGATCAA-TATTAGCGGCGTTTTTGAAAATGC
* * * * * *
69238564 GCCGCTAATGCTCTATTTTAGTGGCGTTTTTGAAAGTGC
1 GCCGCTAAAGATCAATATTAGCGGCGTTTTTGAAAATGC
*
69238603 GTCGCTAA
1 GCCGCTAA
69238611 TACTAGTATT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
39 28 0.70
40 12 0.30
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.32
Consensus pattern (39 bp):
GCCGCTAAAGATCAATATTAGCGGCGTTTTTGAAAATGC
Found at i:69238623 original size:39 final size:39
Alignment explanation
Indices: 69238538--69238623 Score: 104
Period size: 39 Copynumber: 2.2 Consensus size: 39
69238528 CTAAAGATCA
*
69238538 AGTA-TTAGCGGCGTTTTTGAAAATGCGCCGCTAATGCT
1 AGTATTTAGCGGCGTTTTTGAAAATGCGCCGCTAATACT
* * * *
69238576 -CTATTTTAGTGGCGTTTTTGAAAGTGCGTCGCTAATACT
1 AGTA-TTTAGCGGCGTTTTTGAAAATGCGCCGCTAATACT
69238615 AGTATTTAG
1 AGTATTTAG
69238624 GTAGAAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
37 2 0.05
39 35 0.90
40 2 0.05
ACGTcount: A:0.23, C:0.15, G:0.24, T:0.37
Consensus pattern (39 bp):
AGTATTTAGCGGCGTTTTTGAAAATGCGCCGCTAATACT
Found at i:69242208 original size:24 final size:24
Alignment explanation
Indices: 69242161--69242208 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
69242151 TGGAAGTGGT
* *
69242161 GGTGGACTAGGTGGAGGGTTTGGA
1 GGTGGAATAGGTGGAGGGTCTGGA
69242185 GGTGGAATAGGTGG-GGGTGCTGGA
1 GGTGGAATAGGTGGAGGGT-CTGGA
69242209 TTTGGATTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.17, C:0.04, G:0.56, T:0.23
Consensus pattern (24 bp):
GGTGGAATAGGTGGAGGGTCTGGA
Found at i:69242689 original size:22 final size:23
Alignment explanation
Indices: 69242638--69242692 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
69242628 TATGCAAGGT
69242638 CAAGTCTCAATACATAAGGTTAA
1 CAAGTCTCAATACATAAGGTTAA
*
69242661 CAAGTCTCAATACATAAGG-TAG
1 CAAGTCTCAATACATAAGGTTAA
69242683 CAAGTCTCAA
1 CAAGTCTCAA
69242693 GACTATACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 12 0.39
23 19 0.61
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.24
Consensus pattern (23 bp):
CAAGTCTCAATACATAAGGTTAA
Found at i:69244054 original size:20 final size:20
Alignment explanation
Indices: 69244031--69244068 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
69244021 ATATATTTTT
69244031 ATTTTTAAAATACATTTCCC
1 ATTTTTAAAATACATTTCCC
*
69244051 ATTTTTAAAATATATTTC
1 ATTTTTAAAATACATTTC
69244069 ATATGTGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTTTAAAATACATTTCCC
Found at i:69245002 original size:19 final size:20
Alignment explanation
Indices: 69244960--69245025 Score: 71
Period size: 19 Copynumber: 3.3 Consensus size: 20
69244950 AATATAAAAT
* *
69244960 AAAATTCAAAATAATTTTTG
1 AAAATTCAAAATAATTTATA
69244980 AAAATTCAAAAT-ATTTATA
1 AAAATTCAAAATAATTTATA
* * *
69244999 AAAATTTAAAAAAATTCTAAA
1 AAAATTCAAAATAATT-TATA
69245020 AAAATT
1 AAAATT
69245026 AAGGAATATG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
19 15 0.38
20 15 0.38
21 9 0.23
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.35
Consensus pattern (20 bp):
AAAATTCAAAATAATTTATA
Found at i:69245011 original size:10 final size:10
Alignment explanation
Indices: 69244987--69245025 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
69244977 TTGAAAATTC
*
69244987 AAAATATTTA
1 AAAAAATTTA
*
69244997 TAAAAATTTA
1 AAAAAATTTA
69245007 AAAAAATTCTA
1 AAAAAATT-TA
69245018 AAAAAATT
1 AAAAAATT
69245026 AAGGAATATG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
10 15 0.60
11 10 0.40
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAAAATTTA
Found at i:69245027 original size:20 final size:20
Alignment explanation
Indices: 69244980--69245027 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
69244970 ATAATTTTTG
* *
69244980 AAAATTCAAAATATTTATAA
1 AAAATTAAAAAAATTTATAA
*
69245000 AAATTTAAAAAAATTCTA-AA
1 AAAATTAAAAAAATT-TATAA
69245020 AAAATTAA
1 AAAATTAA
69245028 GGAATATGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAATTAAAAAAATTTATAA
Found at i:69253380 original size:24 final size:24
Alignment explanation
Indices: 69253353--69253404 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
69253343 TTAGTAAGTC
*
69253353 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
69253377 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
69253401 AAAT
1 AAAT
69253405 CTTCTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:69255348 original size:24 final size:24
Alignment explanation
Indices: 69255321--69255372 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
69255311 TTAGTAAGTC
*
69255321 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
69255345 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
69255369 AAAT
1 AAAT
69255373 CTTCTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:69255461 original size:6 final size:6
Alignment explanation
Indices: 69255450--69255478 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
69255440 CAATTCTAAC
69255450 AATATA AATATA AATATA AATAT- AATATA
1 AATATA AATATA AATATA AATATA AATATA
69255479 TTTTAACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
AATATA
Found at i:69256985 original size:15 final size:16
Alignment explanation
Indices: 69256965--69256998 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
69256955 ACACAAGGCC
*
69256965 GTGTCAC-CTGGCCGT
1 GTGTCACTCTGCCCGT
69256980 GTGTCACTCTGCCCGT
1 GTGTCACTCTGCCCGT
69256996 GTG
1 GTG
69256999 GACAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.06, C:0.32, G:0.32, T:0.29
Consensus pattern (16 bp):
GTGTCACTCTGCCCGT
Found at i:69265006 original size:43 final size:41
Alignment explanation
Indices: 69264958--69265046 Score: 142
Period size: 43 Copynumber: 2.1 Consensus size: 41
69264948 TAATCACGTC
*
69264958 AATTTTTAATTGTAAAAATAAATGAAACTTTAATAAAAAAACT
1 AATTTTTAATTGTAAAAATAAATAAAACTTTAAT--AAAAACT
*
69265001 AATTTTTAATTGTAAAAATGAATAAAACTTTAATAAAAACT
1 AATTTTTAATTGTAAAAATAAATAAAACTTTAATAAAAACT
69265042 AATTT
1 AATTT
69265047 ATTTTTTATT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
41 12 0.27
43 32 0.73
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.37
Consensus pattern (41 bp):
AATTTTTAATTGTAAAAATAAATAAAACTTTAATAAAAACT
Found at i:69272133 original size:73 final size:73
Alignment explanation
Indices: 69272014--69272160 Score: 294
Period size: 73 Copynumber: 2.0 Consensus size: 73
69272004 GAGCCTCGAG
69272014 TAAGACATTTTTGGCCCGAGCCTGACTCAACCCAGCCCGAATTCACTAAATGGCAAAAAAAAGTT
1 TAAGACATTTTTGGCCCGAGCCTGACTCAACCCAGCCCGAATTCACTAAATGGCAAAAAAAAGTT
69272079 TATTTTTT
66 TATTTTTT
69272087 TAAGACATTTTTGGCCCGAGCCTGACTCAACCCAGCCCGAATTCACTAAATGGCAAAAAAAAGTT
1 TAAGACATTTTTGGCCCGAGCCTGACTCAACCCAGCCCGAATTCACTAAATGGCAAAAAAAAGTT
69272152 TATTTTTT
66 TATTTTTT
69272160 T
1 T
69272161 GTTATTTTAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (73 bp):
TAAGACATTTTTGGCCCGAGCCTGACTCAACCCAGCCCGAATTCACTAAATGGCAAAAAAAAGTT
TATTTTTT
Found at i:69278801 original size:13 final size:13
Alignment explanation
Indices: 69278783--69278807 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
69278773 TGTTGAAATT
69278783 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
69278796 AAAAAAAAAAAA
1 AAAAAAAAAAAA
69278808 AGAAGACAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.96, C:0.00, G:0.04, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:69278802 original size:14 final size:14
Alignment explanation
Indices: 69278783--69278811 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
69278773 TGTTGAAATT
69278783 AAAAAAAAAAAAGA
1 AAAAAAAAAAAAGA
69278797 AAAAAAAAAAAAGA
1 AAAAAAAAAAAAGA
69278811 A
1 A
69278812 GACAAATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAGA
Found at i:69280044 original size:103 final size:101
Alignment explanation
Indices: 69279923--69280114 Score: 255
Period size: 103 Copynumber: 1.9 Consensus size: 101
69279913 AACTACTAAC
* ** * * *
69279923 TAATATAAATTATTATATAGAATT-TGACCTATTGAAATGTT-GTTGTTGTTT-TTTTTTATTAG
1 TAATATAAATTATTATATAAAATTAT-ACCTATCCAAAAGTTCATT-TT-TTTCTATTTTATTAG
*
69279985 TTTTGATGGAGTCTTAAATAATTTCTTTTTGTAATTAATTG
63 TTTTGATGAAGTCTTAAAT-ATTT-TTTTTGTAATTAATTG
69280026 TAATATAAATTATTATATAAAATTATACCTATCCAAAAGTTCATTTTTTTCTATTTTATTAGTTT
1 TAATATAAATTATTATATAAAATTATACCTATCCAAAAGTTCATTTTTTTCTATTTTATTAGTTT
69280091 TGATGAAGTCTTAAATATTTTTTT
66 TGATGAAGTCTTAAATATTTTTTT
69280115 AATCATTATA
Statistics
Matches: 79, Mismatches: 7, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
101 4 0.05
102 7 0.09
103 65 0.82
104 3 0.04
ACGTcount: A:0.32, C:0.06, G:0.10, T:0.53
Consensus pattern (101 bp):
TAATATAAATTATTATATAAAATTATACCTATCCAAAAGTTCATTTTTTTCTATTTTATTAGTTT
TGATGAAGTCTTAAATATTTTTTTTGTAATTAATTG
Found at i:69280787 original size:31 final size:30
Alignment explanation
Indices: 69280752--69280831 Score: 76
Period size: 29 Copynumber: 2.7 Consensus size: 30
69280742 AGATCAAAAT
*
69280752 TATACATTAATTA-TGATTTAATGTGCAATTG
1 TATACATTAAATATTGATTT--TGTGCAATTG
* *
69280783 TATACA-TAAATATTGATTTTGTGTAATTT
1 TATACATTAAATATTGATTTTGTGCAATTG
*
69280812 TATACATAAAAT-TTGTATTT
1 TATACATTAAATATTG-ATTT
69280832 GATTCAGTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
29 17 0.40
30 13 0.31
31 12 0.29
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.49
Consensus pattern (30 bp):
TATACATTAAATATTGATTTTGTGCAATTG
Found at i:69280815 original size:29 final size:30
Alignment explanation
Indices: 69280751--69280821 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
69280741 AAGATCAAAA
*
69280751 TTATACATTAATTATGATTTAATGTGCAATT
1 TTATACATAAATTATGATTT-ATGTGCAATT
* *
69280782 GTATACATAAA-TATTGATTT-TGTGTAATT
1 TTATACATAAATTA-TGATTTATGTGCAATT
69280811 TTATACATAAA
1 TTATACATAAA
69280822 ATTTGTATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 18 0.51
30 2 0.06
31 15 0.43
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (30 bp):
TTATACATAAATTATGATTTATGTGCAATT
Found at i:69290949 original size:30 final size:29
Alignment explanation
Indices: 69290894--69290950 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
69290884 ACAATGTCAC
**
69290894 ACATAAATTTTGATTTTGTGTAATTTTAT
1 ACATAAATTTTGATTTTGTCCAATTTTAT
69290923 ACATAAAATTTTGA-TTTGATCCAATTTT
1 ACAT-AAATTTTGATTTTG-TCCAATTTT
69290951 CGTAAATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.51
Consensus pattern (29 bp):
ACATAAATTTTGATTTTGTCCAATTTTAT
Found at i:69294985 original size:26 final size:28
Alignment explanation
Indices: 69294956--69295010 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
69294946 AGATGTACAC
* *
69294956 ATATTTTACAA-TTT-ATATATACATAT
1 ATATTTCACAATTTTAAAATATACATAT
69294982 ATATTTCACAATTTTAAAATATACATAT
1 ATATTTCACAATTTTAAAATATACATAT
69295010 A
1 A
69295011 CATCTCTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 10 0.40
27 3 0.12
28 12 0.48
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (28 bp):
ATATTTCACAATTTTAAAATATACATAT
Found at i:69295968 original size:15 final size:14
Alignment explanation
Indices: 69295941--69295967 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
69295931 TTTTAACCCT
69295941 TTTTTATTTTTTTC
1 TTTTTATTTTTTTC
69295955 TTTTTATTTTTTT
1 TTTTTATTTTTTT
69295968 TGTTCATTTA
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:0.07, C:0.04, G:0.00, T:0.89
Consensus pattern (14 bp):
TTTTTATTTTTTTC
Found at i:69296857 original size:20 final size:22
Alignment explanation
Indices: 69296831--69296877 Score: 71
Period size: 20 Copynumber: 2.2 Consensus size: 22
69296821 GAGTTCAGAT
69296831 TCAAAAAAAAAAAC-AAAAAAA
1 TCAAAAAAAAAAACGAAAAAAA
*
69296852 -CAAAAAAAAAATCGAAAAAAA
1 TCAAAAAAAAAAACGAAAAAAA
69296873 TCAAA
1 TCAAA
69296878 GTCAAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 12 0.52
21 7 0.30
22 4 0.17
ACGTcount: A:0.81, C:0.11, G:0.02, T:0.06
Consensus pattern (22 bp):
TCAAAAAAAAAAACGAAAAAAA
Found at i:69296921 original size:5 final size:6
Alignment explanation
Indices: 69296890--69296928 Score: 60
Period size: 6 Copynumber: 6.2 Consensus size: 6
69296880 CAAAAATAGG
69296890 AGAAAA AGAAATA AGAAAAA AGAAAA AGAAAA AGAAAA A
1 AGAAAA AGAAA-A AG-AAAA AGAAAA AGAAAA AGAAAA A
69296929 TGAGAGGTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 22 0.71
7 6 0.19
8 3 0.10
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (6 bp):
AGAAAA
Found at i:69296928 original size:7 final size:7
Alignment explanation
Indices: 69296892--69296928 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
69296882 AAAATAGGAG
69296892 AAAAAGA
1 AAAAAGA
*
69296899 AATAAGA
1 AAAAAGA
69296906 AAAAAG-
1 AAAAAGA
69296912 AAAAAG-
1 AAAAAGA
69296918 AAAAAGA
1 AAAAAGA
69296925 AAAA
1 AAAA
69296929 TGAGAGGTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 12 0.44
7 15 0.56
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.03
Consensus pattern (7 bp):
AAAAAGA
Found at i:69299514 original size:50 final size:50
Alignment explanation
Indices: 69299443--69300265 Score: 464
Period size: 50 Copynumber: 16.5 Consensus size: 50
69299433 AATTCAAAAT
* *
69299443 ATTGAAGCCACAACGGCGAATCTTACTTTCCAAGCGATGCAGCGGAACAG
1 ATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGATGCAGCGGAACAG
* * * * * * * ** *
69299493 ATTGAAGCTACGACGGTGAATCTCACTTCCCCGAC-ATTGCGGTTGAATAG
1 ATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGA-TGCAGCGGAACAG
* * *
69299543 ATTGAAGCTACAACAGCGAATCTTACTTTCCAGGCGGTGCAGCGAAACAG
1 ATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGATGCAGCGGAACAG
* *** * * * *** *
69299593 ATTGAAGCTACAACGGTGAATCTCGTTTTCCCCGAC-ATTACA-ATTAAAAG
1 ATTGAAGCTACAACGGCGAATCTTACTTT-CCAGGCGA-TGCAGCGGAACAG
* *
69299643 ATTGAAGCTACAACGGCGAATCTTA-TTTCCCAGGCGATGTAGCAGAACAG
1 ATTGAAGCTACAACGGCGAATCTTACTTT-CCAGGCGATGCAGCGGAACAG
* ** * * * **** *
69299693 ATTGAAG-TCACAACGGTGAATCTCGCTTCCCCGAC-ATTGCAATTTAAAAG
1 ATTGAAGCT-ACAACGGCGAATCTTACTTTCCAGGCGA-TGCAGCGGAACAG
* * * *
69299743 ATTGAAGCCACAACGGCGAATCTTACTTCCCAGGTGATGCGGCGGAACAG
1 ATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGATGCAGCGGAACAG
* *
69299793 ATTGAAGCCACAACGGCGAATCTTA-TTTCCCAGGTGATGCAGCGGAACAG
1 ATTGAAGCTACAACGGCGAATCTTACTTT-CCAGGCGATGCAGCGGAACAG
* ** * * * **** *
69299843 ATTGAAGTTACAACGGCGAATCTCGCTTCCCCGAC-ATTGCAATTTAAAAG
1 ATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGA-TGCAGCGGAACAG
* * * * * *
69299893 ATTGAAGCCACAACGGCGAATCTTACTTCCCAGGTGATGCGGCAGAATAG
1 ATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGATGCAGCGGAACAG
* * * * * **** *
69299943 ATTGAAGCTACGACGGCGAATCTCACTTCCCCGAC-ATTGCAATTTAAAAG
1 ATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGA-TGCAGCGGAACAG
* * * *
69299993 ATTGAAGCTACAATGACGAATCTTACTTTCCAGGCGGTGCAGTGGAACAG
1 ATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGATGCAGCGGAACAG
* * * * * **** *
69300043 ATTGAAGCTACAACGGCGAATATT-GTTTCCTCGAC-ATTACAATTAAAAAG
1 ATTGAAGCTACAACGGCGAATCTTACTTTCC-AGGCGA-TGCAGCGGAACAG
* *
69300093 ATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGGTGTAGCGGAACAG
1 ATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGATGCAGCGGAACAG
* * * * * * * *** *
69300143 ATTGAAGCTAGAACGGTGAATCTTGCTTCCCTGAC-ATTGCGGTTAAATAG
1 ATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGA-TGCAGCGGAACAG
* * * * * ** * *
69300193 ATTGAAGCTACAACAGCGAATCTTACTTCCCTGGCGGTGTAATGAAATAG
1 ATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGATGCAGCGGAACAG
* *
69300243 ATTGAAGCTACGACGGTGAATCT
1 ATTGAAGCTACAACGGCGAATCT
69300266 AATTTCTCCG
Statistics
Matches: 574, Mismatches: 176, Indels: 46
0.72 0.22 0.06
Matches are distributed among these distances:
49 22 0.04
50 534 0.93
51 18 0.03
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.24
Consensus pattern (50 bp):
ATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGATGCAGCGGAACAG
Found at i:69300078 original size:100 final size:100
Alignment explanation
Indices: 69299791--69300265 Score: 567
Period size: 100 Copynumber: 4.8 Consensus size: 100
69299781 GCGGCGGAAC
* * * *
69299791 AGATTGAAGCCACAACGGCGAATCTTA-TTTCCCAGGTGATGCAGCGGAACAGATTGAAGTTACA
1 AGATTGAAGCTACAACGGCGAATCTTACTTT-CCAGGCGGTGCAGCGGAACAGATTGAAGCTACA
69299855 ACGGCGAATCTCGCTTCCCCGACATTGCAATTTAAA
65 ACGGCGAATCTCGCTTCCCCGACATTGCAATTTAAA
* * * * * * * *
69299891 AGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGTGATGCGGCAGAATAGATTGAAGCTACGA
1 AGATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGGTGCAGCGGAACAGATTGAAGCTACAA
*
69299956 CGGCGAATCTCACTTCCCCGACATTGCAATTTAAA
66 CGGCGAATCTCGCTTCCCCGACATTGCAATTTAAA
* * *
69299991 AGATTGAAGCTACAATGACGAATCTTACTTTCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGGTGCAGCGGAACAGATTGAAGCTACAA
* * * * * *
69300056 CGGCGAATATTGTTTCCTCGACATTACAATTAAAA
66 CGGCGAATCTCGCTTCCCCGACATTGCAATTTAAA
* *
69300091 AGATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGGTGTAGCGGAACAGATTGAAGCTAGAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGGTGCAGCGGAACAGATTGAAGCTACAA
* * * **
69300156 CGGTGAATCTTGCTTCCCTGACATTGC-GGTTAAA
66 CGGCGAATCTCGCTTCCCCGACATTGCAATTTAAA
* * * * ** * * *
69300190 TAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGGCGGTGTAATGAAATAGATTGAAGCTACG
1 -AGATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGGTGCAGCGGAACAGATTGAAGCTACA
*
69300255 ACGGTGAATCT
65 ACGGCGAATCT
69300266 AATTTCTCCG
Statistics
Matches: 325, Mismatches: 48, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
99 4 0.01
100 319 0.98
101 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.24
Consensus pattern (100 bp):
AGATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGGTGCAGCGGAACAGATTGAAGCTACAA
CGGCGAATCTCGCTTCCCCGACATTGCAATTTAAA
Found at i:69300245 original size:150 final size:150
Alignment explanation
Indices: 69299438--69300271 Score: 598
Period size: 150 Copynumber: 5.6 Consensus size: 150
69299428 GCAGCAATTC
* * * ** * *
69299438 AAAATATTGAAGCCACAACGGCGAATCTTACTTTCCAAGCGATGCAGCGGAACAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAATGAAATAGATTGAAGCTA
* * * * * * * ** * * *
69299503 CGACGGTGAATCTCACTTCCCCGAC-ATTGCGGTTGAATAGATTGAAGCTACAACAGCGAATCTT
66 CAACGGCGAATCTTATTTCCCAGGCGA-TGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTC
* * * * ** **
69299567 ACTTTCCAGGCGGTGC-AGCG
130 GCTTCCCCGACATTGCAAGTT
* * * * * * *
69299587 AAACAGATTGAAGCTACAACGGTGAATCTCGT-TTTCCCCGAC-ATTACAATTAAA-AGATTGAA
1 AAA-AGATTGAAGCCACAACGGCGAATCT--TACTTCCCAGGCGA-TGCAATGAAATAGATTGAA
* * *
69299649 GCTACAACGGCGAATCTTATTTCCCAGGCGATGTAGCAGAACAGATTGAAG-TCACAACGGTGAA
62 GCTACAACGGCGAATCTTATTTCCCAGGCGATGCAGCGGAACAGATTGAAGCT-ACAACGGCGAA
*
69299713 TCTCGCTTCCCCGACATTGCAATTT
126 TCTCGCTTCCCCGACATTGCAAGTT
* *** * * *
69299738 AAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGTGATGCGGCGGAACAGATTGAAGCCA
1 AAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAATGAAATAGATTGAAGCTA
* *
69299803 CAACGGCGAATCTTATTTCCCAGGTGATGCAGCGGAACAGATTGAAGTTACAACGGCGAATCTCG
66 CAACGGCGAATCTTATTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTCG
*
69299868 CTTCCCCGACATTGCAATTT
131 CTTCCCCGACATTGCAAGTT
* *
69299888 AAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGTGATGC--GGCAGAATAGATTGAAGC
1 AAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAATG-A-AATAGATTGAAGC
* * * * * **** * * *
69299951 TACGACGGCGAATCTCACTTCCCCGAC-ATTGCAATTTAAAAGATTGAAGCTACAATGACGAATC
64 TACAACGGCGAATCTTATTTCCCAGGCGA-TGCAGCGGAACAGATTGAAGCTACAACGGCGAATC
** * * * ** *
69300015 TTACTTTCCAGGCGGTGC-AGTGG
128 TCGCTTCCCCGACATTGCAAGT-T
* * * ** * * * *
69300038 AACAGATTGAAGCTACAACGGCGAATATTGTTTCCTC-GAC-ATTACAATTAAAAAGATTGAAGC
1 AAAAGATTGAAGCCACAACGGCGAATCTTACTTCC-CAGGCGA-TGCAATGAAATAGATTGAAGC
* * * *
69300101 TACAACGGCGAATCTTACTTT-CCAGGCGGTGTAGCGGAACAGATTGAAGCTAGAACGGTGAATC
64 TACAACGGCGAATCTTA-TTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAATC
* * *
69300165 TTGCTTCCCTGACATTGC-GGTT
128 TCGCTTCCCCGACATTGCAAGTT
* * * * *
69300187 AAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGGCGGTGTAATGAAATAGATTGAAGCT
1 AAA-AGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAATGAAATAGATTGAAGCT
* * *
69300252 ACGACGGTGAATCTAATTTC
65 ACAACGGCGAATCTTATTTC
69300272 TCCGACATCG
Statistics
Matches: 531, Mismatches: 129, Indels: 49
0.75 0.18 0.07
Matches are distributed among these distances:
148 2 0.00
149 24 0.05
150 484 0.91
151 20 0.04
152 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (150 bp):
AAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAATGAAATAGATTGAAGCTA
CAACGGCGAATCTTATTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTCG
CTTCCCCGACATTGCAAGTT
Found at i:69305801 original size:3 final size:3
Alignment explanation
Indices: 69305793--69305819 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
69305783 GATATAGTTT
69305793 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
69305820 TGCCAAATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:69313791 original size:21 final size:23
Alignment explanation
Indices: 69313767--69313808 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
69313757 TATGACTAAA
69313767 AATTTAT-TATA-TTATAAAAAT
1 AATTTATGTATATTTATAAAAAT
*
69313788 AATTTATGTGTATTTATAAAA
1 AATTTATGTATATTTATAAAA
69313809 TTACGACCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 3 0.17
23 8 0.44
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (23 bp):
AATTTATGTATATTTATAAAAAT
Found at i:69315750 original size:40 final size:40
Alignment explanation
Indices: 69315706--69315788 Score: 157
Period size: 40 Copynumber: 2.1 Consensus size: 40
69315696 AATTTTTGAA
69315706 TTGAGTTTGAAAAAACATTCTGTAGTATATTTTGTATTTT
1 TTGAGTTTGAAAAAACATTCTGTAGTATATTTTGTATTTT
*
69315746 TTGAGTTTGAAAAAACATTCTGTGGTATATTTTGTATTTT
1 TTGAGTTTGAAAAAACATTCTGTAGTATATTTTGTATTTT
69315786 TTG
1 TTG
69315789 CTTAAAAATG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.28, C:0.05, G:0.17, T:0.51
Consensus pattern (40 bp):
TTGAGTTTGAAAAAACATTCTGTAGTATATTTTGTATTTT
Found at i:69323440 original size:31 final size:30
Alignment explanation
Indices: 69323398--69323455 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
69323388 TTTTGTGTCG
69323398 ATATATTGAATCAAAACTAAAGTTTCATGA
1 ATATATTGAATCAAAACTAAAGTTTCATGA
* * *
69323428 ATATATATGAATCATAATTTAAGTTTCA
1 ATATAT-TGAATCAAAACTAAAGTTTCA
69323456 CATGTATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 6 0.25
31 18 0.75
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.38
Consensus pattern (30 bp):
ATATATTGAATCAAAACTAAAGTTTCATGA
Found at i:69334755 original size:16 final size:16
Alignment explanation
Indices: 69334731--69334776 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
69334721 TTATATTTAA
*
69334731 TAATATAATAAATTAT
1 TAATTTAATAAATTAT
*
69334747 TAATTTAATTAATTA-
1 TAATTTAATAAATTAT
69334762 T--TTTAATAAATTAT
1 TAATTTAATAAATTAT
69334776 T
1 T
69334777 TAATATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 11 0.42
14 1 0.04
15 1 0.04
16 13 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATTTAATAAATTAT
Found at i:69334789 original size:29 final size:29
Alignment explanation
Indices: 69334736--69334802 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 29
69334726 TTTAATAATA
69334736 TAATAAATTATTAATTTAATTAA-TTATTT
1 TAATAAATTATTAATTTAA-TAATTTATTT
69334765 TAATAAATTATTTAATATTAA-AATTTTATTT
1 TAATAAATTA-TTAAT-TTAATAA-TTTATTT
69334796 TAA-AAAT
1 TAATAAAT
69334803 AAATTTTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
29 12 0.35
30 9 0.26
31 13 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
TAATAAATTATTAATTTAATAATTTATTT
Found at i:69334849 original size:6 final size:6
Alignment explanation
Indices: 69334838--69334867 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
69334828 ATTGTTGAAA
69334838 ATATTT ATATTT ATATTT ATATTT ATATTT
1 ATATTT ATATTT ATATTT ATATTT ATATTT
69334868 TAATAATAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
ATATTT
Found at i:69335226 original size:16 final size:16
Alignment explanation
Indices: 69335189--69335228 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
69335179 TTAATAAAAT
* *
69335189 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
69335205 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
69335221 TAAAATTA
1 TAAAATTA
69335229 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:69335228 original size:22 final size:22
Alignment explanation
Indices: 69335161--69335213 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
69335151 TTATTAAAAT
* * *
69335161 TAAAATTAAAATTATTTTTTAA
1 TAAAATTAAAACTAATTGTTAA
*
69335183 TAAAATTAAAACTAATTGTTAT
1 TAAAATTAAAACTAATTGTTAA
69335205 TAAAATTAA
1 TAAAATTAA
69335214 TTGTTAGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAAATTAAAACTAATTGTTAA
Found at i:69335280 original size:50 final size:52
Alignment explanation
Indices: 69335217--69335351 Score: 184
Period size: 59 Copynumber: 2.5 Consensus size: 52
69335207 AAATTAATTG
*
69335217 TTAGTAAAATTATCAAATTATTAATT-A-TTGTAATAAAATCTAACATTTGA
1 TTAGTAAATTTATCAAATTATTAATTAATTTGTAATAAAATCTAACATTTGA
69335267 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGA
1 TTAGTAAATTTATCAAATTATT-A----ATTAA-T-TTGTAATAAAATCTAACATTTGA
69335326 TTAGTAAATTTATCAAATTATTAATT
1 TTAGTAAATTTATCAAATTATTAATT
69335352 GTATTAATTG
Statistics
Matches: 75, Mismatches: 1, Indels: 14
0.83 0.01 0.16
Matches are distributed among these distances:
50 21 0.28
51 1 0.01
54 3 0.04
55 3 0.04
56 1 0.01
58 1 0.01
59 45 0.60
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (52 bp):
TTAGTAAATTTATCAAATTATTAATTAATTTGTAATAAAATCTAACATTTGA
Found at i:69335356 original size:9 final size:9
Alignment explanation
Indices: 69335344--69335371 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
69335334 TTTATCAAAT
69335344 TATTAATTG
1 TATTAATTG
69335353 TATTAATTG
1 TATTAATTG
69335362 TATTAATTG
1 TATTAATTG
69335371 T
1 T
69335372 TGTAGTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:69335361 original size:59 final size:59
Alignment explanation
Indices: 69335235--69335362 Score: 247
Period size: 59 Copynumber: 2.2 Consensus size: 59
69335225 ATTATCAAAT
*
69335235 TATTAATTATTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAATTG
1 TATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAATTG
69335294 TATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAATTG
1 TATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAATTG
69335353 TATTAATTGT
1 TATTAATTGT
69335363 ATTAATTGTT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
59 68 1.00
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.47
Consensus pattern (59 bp):
TATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAATTG
Found at i:69335515 original size:23 final size:24
Alignment explanation
Indices: 69335468--69335513 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
69335458 AAATAAACTT
69335468 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
69335492 AAAATAAAAAA-TATATATATTT
1 AAAATAAAAAACTAT-TATATTT
69335514 AATATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:69335888 original size:23 final size:24
Alignment explanation
Indices: 69335841--69335886 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
69335831 GAAAAATATT
69335841 AAATATATATATTTTTTATTTTTA
1 AAATATATATATTTTTTATTTTTA
69335865 AAATATA-ATAGTTTTTTATTTT
1 AAATATATATA-TTTTTTATTTT
69335887 AAGTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AAATATATATATTTTTTATTTTTA
Found at i:69335997 original size:9 final size:9
Alignment explanation
Indices: 69335983--69336010 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
69335973 TTTTGTTACA
69335983 ACAATTAAT
1 ACAATTAAT
69335992 ACAATTAAT
1 ACAATTAAT
69336001 ACAATTAAT
1 ACAATTAAT
69336010 A
1 A
69336011 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:69336032 original size:68 final size:68
Alignment explanation
Indices: 69335953--69336150 Score: 292
Period size: 59 Copynumber: 3.1 Consensus size: 68
69335943 TCAAGTTTGT
* *
69335953 TTTACTAATCAAATATTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
69336018 AAA
66 AAA
69336021 TTTACTAATCAAATGTTAGATTTTATT---AC-----A-ACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
69336077 AAA
66 AAA
69336080 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
69336143 AAT
66 AAA
69336146 TTTAC
1 TTTAC
69336151 GAACAATTAG
Statistics
Matches: 118, Mismatches: 3, Indels: 20
0.84 0.02 0.14
Matches are distributed among these distances:
59 56 0.47
60 1 0.01
62 2 0.02
65 2 0.02
66 24 0.20
67 2 0.02
68 31 0.26
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:69336184 original size:16 final size:17
Alignment explanation
Indices: 69336163--69336194 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
69336153 ACAATTAGTT
69336163 TAATTTT-ATTAAAAAA
1 TAATTTTAATTAAAAAA
69336179 TAATTTTAATTAAAAA
1 TAATTTTAATTAAAAA
69336195 CAGGCCGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTTTAATTAAAAAA
Found at i:69340897 original size:26 final size:26
Alignment explanation
Indices: 69340861--69340916 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
69340851 TTTGAATATT
69340861 AAAGTAAAACTGAGGTACCACATTCA
1 AAAGTAAAACTGAGGTACCACATTCA
69340887 AAAGTAAAACTGAGGTACCACATTCA
1 AAAGTAAAACTGAGGTACCACATTCA
69340913 AAAG
1 AAAG
69340917 CCCTATTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.48, C:0.18, G:0.16, T:0.18
Consensus pattern (26 bp):
AAAGTAAAACTGAGGTACCACATTCA
Found at i:69341573 original size:2 final size:2
Alignment explanation
Indices: 69341566--69341591 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
69341556 AATTGTGTTC
69341566 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
69341592 CATGAAACTT
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:69345909 original size:28 final size:28
Alignment explanation
Indices: 69345869--69345925 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
69345859 TTTCCTGTGC
69345869 TCTAGAAGGAATTATTTGATTATATATG
1 TCTAGAAGGAATTATTTGATTATATATG
*
69345897 TCTAGAAGGAATTATTTGATTATTTATG
1 TCTAGAAGGAATTATTTGATTATATATG
69345925 T
1 T
69345926 GCTTTATTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.46
Consensus pattern (28 bp):
TCTAGAAGGAATTATTTGATTATATATG
Found at i:69347521 original size:35 final size:35
Alignment explanation
Indices: 69347475--69347545 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
69347465 GGCATCCAAA
*
69347475 AGTGAGGATGATTTTTCTTGTACTTTTCCTAGAAG
1 AGTGAGGATGATTTTCCTTGTACTTTTCCTAGAAG
*
69347510 AGTGAGGATGATTTTCCTTTTACTTTTCCTAGAAG
1 AGTGAGGATGATTTTCCTTGTACTTTTCCTAGAAG
69347545 A
1 A
69347546 CTTTGTTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.42
Consensus pattern (35 bp):
AGTGAGGATGATTTTCCTTGTACTTTTCCTAGAAG
Found at i:69350403 original size:14 final size:15
Alignment explanation
Indices: 69350377--69350405 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
69350367 TTTAATGTTT
69350377 TATATTATAGTATGA
1 TATATTATAGTATGA
69350392 TATATT-TAGTATGA
1 TATATTATAGTATGA
69350406 GTTTTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (15 bp):
TATATTATAGTATGA
Found at i:69352972 original size:16 final size:16
Alignment explanation
Indices: 69352951--69352997 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
69352941 AATTAATGTC
69352951 TTTC-TTAAAATATTAT
1 TTTCTTTAAAA-ATTAT
*
69352967 TTTCTTTAAAAATTAG
1 TTTCTTTAAAAATTAT
* *
69352983 TATCTTTTAAAATTA
1 TTTCTTTAAAAATTA
69352998 AAACACTTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 21 0.78
17 6 0.22
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.53
Consensus pattern (16 bp):
TTTCTTTAAAAATTAT
Found at i:69358777 original size:14 final size:14
Alignment explanation
Indices: 69358750--69358788 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
69358740 GTCGTACAAA
*
69358750 TTAC-TTTTTCTTT
1 TTACTTTTTTATTT
69358763 TTACTTTTTTATTT
1 TTACTTTTTTATTT
*
69358777 TTATTTTTTTAT
1 TTACTTTTTTAT
69358789 AAAATGGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 4 0.17
14 19 0.83
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (14 bp):
TTACTTTTTTATTT
Found at i:69358903 original size:13 final size:13
Alignment explanation
Indices: 69358885--69358910 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
69358875 TTCAAGCTTT
69358885 TTTTTAATTAATA
1 TTTTTAATTAATA
69358898 TTTTTAATTAATA
1 TTTTTAATTAATA
69358911 AATATATTGA
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTAATTAATA
Found at i:69359007 original size:16 final size:16
Alignment explanation
Indices: 69358960--69359010 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 16
69358950 TTTTTAATTA
69358960 ATAAATATT-TTATTT
1 ATAAATATTATTATTT
*
69358975 ATTAAATTAAATAATTATTT
1 A-TAAA-T--ATTATTATTT
69358995 ATAAATATTATTATTT
1 ATAAATATTATTATTT
69359011 TTAGTAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
15 1 0.03
16 13 0.45
17 1 0.03
18 1 0.03
19 6 0.21
20 7 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATAAATATTATTATTT
Found at i:69359024 original size:35 final size:34
Alignment explanation
Indices: 69358960--69359031 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 34
69358950 TTTTTAATTA
*
69358960 ATAAATATTTTATTTATTAAATTAAATAATTATTT
1 ATAAATATTTTATTTATTAAATAAAATAATT-TTT
*
69358995 ATAAATATTATTATTT-TT-AGTAAATATAATTTTT
1 ATAAATATT-TTATTTATTAAATAAA-ATAATTTTT
69359029 ATA
1 ATA
69359032 TGTGTAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
34 10 0.30
35 17 0.52
36 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (34 bp):
ATAAATATTTTATTTATTAAATAAAATAATTTTT
Found at i:69360438 original size:20 final size:22
Alignment explanation
Indices: 69360413--69360471 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
69360403 ATTTAATATT
69360413 TTTGTAACTG-TAAAA-AACAG
1 TTTGTAACTGCTAAAATAACAG
* **
69360433 TTTGTAACTGTTGAAAATAATGG
1 TTTGTAACTGCT-AAAATAACAG
69360456 TTTGTAACTGCTAAAA
1 TTTGTAACTGCTAAAA
69360472 CAAATTTGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 10 0.30
21 1 0.03
22 8 0.24
23 14 0.42
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (22 bp):
TTTGTAACTGCTAAAATAACAG
Found at i:69361827 original size:39 final size:39
Alignment explanation
Indices: 69361582--69361826 Score: 260
Period size: 39 Copynumber: 6.3 Consensus size: 39
69361572 AGAAAATCTT
* * * *
69361582 ATTCAGTAGAATCAGTAGATAATGCTCGTTTGTGTAAGC
1 ATTCAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGC
* *
69361621 ATTCAGTATAATCAGTGGATAATGTTCG-TTGAACAAGC
1 ATTCAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGC
* * * *
69361659 ATTCGGTATAATCAGTGAATATTGCTCTTTTGAGCAAGC
1 ATTCAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGC
* * *
69361698 ATTCAGTATAATCAATGAATAATGCTCGTTTGAACAAGC
1 ATTCAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGC
* * * * *
69361737 ATTTAGTATGATTAATGGATATTGCTCGTTTGAGCAAGC
1 ATTCAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGC
* * * *
69361776 AATT-AATATAATTAGTGGATAATGCTCGTATGAGCAAAC
1 -ATTCAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGC
*
69361815 ATTTAGTATAAT
1 ATTCAGTATAAT
69361827 TGGTATTCCA
Statistics
Matches: 173, Mismatches: 30, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
38 33 0.19
39 137 0.79
40 3 0.02
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (39 bp):
ATTCAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGC
Found at i:69363935 original size:26 final size:26
Alignment explanation
Indices: 69363886--69363943 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
69363876 ATATACTTAC
* * *
69363886 ACTTTATTTTATTGTTTTCTATAGGA
1 ACTTTATTTTATTCTTTACAATAGGA
*
69363912 ACTTTCTTTTATTCTTTACAATAGG-
1 ACTTTATTTTATTCTTTACAATAGGA
69363937 -CTTTATT
1 ACTTTATT
69363944 AATGAAATCT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 6 0.22
26 21 0.78
ACGTcount: A:0.22, C:0.12, G:0.09, T:0.57
Consensus pattern (26 bp):
ACTTTATTTTATTCTTTACAATAGGA
Found at i:69365573 original size:19 final size:20
Alignment explanation
Indices: 69365537--69365575 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
69365527 ACCCAACAAG
* *
69365537 AAAATCAATTTTATTATTTA
1 AAAATCAATATTACTATTTA
69365557 AAAATC-ATATTACTATTTA
1 AAAATCAATATTACTATTTA
69365576 CATATTTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (20 bp):
AAAATCAATATTACTATTTA
Found at i:69373345 original size:12 final size:12
Alignment explanation
Indices: 69373328--69373358 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
69373318 GATCAATTGA
69373328 CTTGTTCTTCAT
1 CTTGTTCTTCAT
69373340 CTTGTTCTTCAT
1 CTTGTTCTTCAT
69373352 CTTGTTC
1 CTTGTTC
69373359 ATGTTCTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.26, G:0.10, T:0.58
Consensus pattern (12 bp):
CTTGTTCTTCAT
Found at i:69374192 original size:181 final size:175
Alignment explanation
Indices: 69373895--69374273 Score: 498
Period size: 181 Copynumber: 2.1 Consensus size: 175
69373885 TAGGGCTAGA
69373895 TTTAGGGTTT-GGGATTTTGGATCTCCAAGCCAAAACAAGGTCCGTCACGACCAGGTTTTTTACA
1 TTTAGGGTTTAGGG-TTTTGGATCTCCAAGCCAAAACAAGGTCCGTCACGACCAGGTTTTTTACA
69373959 TTACCGCTCTTGTTAACCACTGTGTTTTAGAGTTTAAGGTTCTGGATCTCCATGCCGGAACAAGG
65 TTACCGCTCTTGTTAACCACTGTGTTTTAGAGTTTAAGGTTCTGGATCTCCATGCCGGAACAAGG
69374024 TCACCACCGTGCTTTTCGACA-TATC-TCTGGCATTAACTACTGTAT
130 TCACCACCGTGCTTTTCGACATTATCTTC-GGCATTAACTACTGTAT
* * * * * *
69374069 TTTAGGGTTTAGGGTTTTGGATTTTCAGGCCAAAACAAGGTCCTTCACGACCAGTTTTTTTATAT
1 TTTAGGGTTTAGGGTTTTGGATCTCCAAGCCAAAACAAGGTCCGTCACGACCAGGTTTTTTACAT
* * * *
69374134 TATCTCATG-TGTTAAGTGTTAACCACTGTGTTTTAGAGTTTAGGGTTTTGGATCTCCATGCTGG
66 TA-C-C--GCT-CT---TGTTAACCACTGTGTTTTAGAGTTTAAGGTTCTGGATCTCCATGCCGG
* * * *
69374198 AACAAGGTCCCCACCGTGCTTTTTGACATTATCTTCGGCATTAACTATTGTGT
123 AACAAGGTCACCACCGTGCTTTTCGACATTATCTTCGGCATTAACTACTGTAT
*
69374251 TTTA-GGTTTAGGGTTTTGAATCT
1 TTTAGGGTTTAGGGTTTTGGATCT
69374274 AATGCTTACA
Statistics
Matches: 178, Mismatches: 16, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
174 57 0.32
175 4 0.02
176 1 0.01
177 1 0.01
178 2 0.01
181 88 0.49
182 23 0.13
183 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.37
Consensus pattern (175 bp):
TTTAGGGTTTAGGGTTTTGGATCTCCAAGCCAAAACAAGGTCCGTCACGACCAGGTTTTTTACAT
TACCGCTCTTGTTAACCACTGTGTTTTAGAGTTTAAGGTTCTGGATCTCCATGCCGGAACAAGGT
CACCACCGTGCTTTTCGACATTATCTTCGGCATTAACTACTGTAT
Found at i:69375610 original size:13 final size:13
Alignment explanation
Indices: 69375592--69375618 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
69375582 GAAGTTTTTG
69375592 TATACCCAAAAAT
1 TATACCCAAAAAT
69375605 TATACCCAAAAAT
1 TATACCCAAAAAT
69375618 T
1 T
69375619 TTAACAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (13 bp):
TATACCCAAAAAT
Found at i:69376090 original size:18 final size:18
Alignment explanation
Indices: 69376063--69376103 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
69376053 TAATCAAATG
69376063 ATAT-AAAAAAAATCTTA
1 ATATGAAAAAAAATCTTA
*
69376080 ATATGAAAAAAATTCTTA
1 ATATGAAAAAAAATCTTA
*
69376098 GTATGA
1 ATATGA
69376104 TTCAAATACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (18 bp):
ATATGAAAAAAAATCTTA
Found at i:69386819 original size:28 final size:26
Alignment explanation
Indices: 69386774--69386837 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 26
69386764 TAAGATAATT
69386774 ATATATAAAATTTTAATAAATAAAA-A
1 ATATATAAAATTTTAAT-AATAAAATA
*
69386800 ATATATAAAATTATTAAATATTAAAATA
1 ATATATAAAATT-TT-AATAATAAAATA
69386828 ATAATATAAA
1 AT-ATATAAA
69386838 TATATATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
26 12 0.36
27 8 0.24
28 6 0.18
29 7 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
ATATATAAAATTTTAATAATAAAATA
Found at i:69386838 original size:28 final size:28
Alignment explanation
Indices: 69386758--69386837 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 28
69386748 AAACATTAAA
*
69386758 AAATATTAAGATAATTATATATAAAATTTT
1 AAATATTAAAATAA-TA-ATATAAAATTTT
*
69386788 -AATAAATAAAA-AAT-ATATAAAATTATT
1 AAAT-ATTAAAATAATAATATAAAATT-TT
69386815 AAATATTAAAATAATAATATAAA
1 AAATATTAAAATAATAATATAAA
69386838 TATATATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
26 10 0.24
27 8 0.19
28 7 0.17
29 12 0.29
30 5 0.12
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (28 bp):
AAATATTAAAATAATAATATAAAATTTT
Found at i:69390419 original size:24 final size:23
Alignment explanation
Indices: 69390391--69390438 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
69390381 TTTATCTATG
69390391 ATTTTATATGTATTTTT-TTATAAA
1 ATTTT-TATGTATTTTTATTA-AAA
69390415 A-TTTTATGTATTTTTATTAAAA
1 ATTTTTATGTATTTTTATTAAAA
69390437 AT
1 AT
69390439 GAACTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
22 15 0.68
23 6 0.27
24 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (23 bp):
ATTTTTATGTATTTTTATTAAAA
Found at i:69390422 original size:22 final size:22
Alignment explanation
Indices: 69390397--69390438 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
69390387 TATGATTTTA
69390397 TATGTATTTTT-TTATAAAATTT
1 TATGTATTTTTATTA-AAAATTT
69390419 TATGTATTTTTATTAAAAAT
1 TATGTATTTTTATTAAAAAT
69390439 GAACTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (22 bp):
TATGTATTTTTATTAAAAATTT
Found at i:69390862 original size:21 final size:22
Alignment explanation
Indices: 69390838--69390885 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
69390828 GAAAATGTGC
*
69390838 AATTTAAACCCTTTA-AAAAAT
1 AATTTAAAACCTTTATAAAAAT
* **
69390859 AATTCAAAATGTTTATAAAAAT
1 AATTTAAAACCTTTATAAAAAT
69390881 AATTT
1 AATTT
69390886 TCCAAAATTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (22 bp):
AATTTAAAACCTTTATAAAAAT
Found at i:69392898 original size:2 final size:2
Alignment explanation
Indices: 69392891--69392920 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
69392881 TTATATTGTA
69392891 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
69392921 GTTACGTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:69395931 original size:19 final size:19
Alignment explanation
Indices: 69395907--69395969 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
69395897 TATTAGAAAC
*
69395907 CAAGGAACAACACATAAGA
1 CAAGGAACAACAAATAAGA
* * *
69395926 CAAGG-AC-A-TATTAGAAA
1 CAAGGAACAACAAATA-AGA
69395943 CCAAGGAACAACAAATAAGA
1 C-AAGGAACAACAAATAAGA
69395963 CAAGGAA
1 CAAGGAA
69395970 GAGAGGAGGC
Statistics
Matches: 32, Mismatches: 7, Indels: 10
0.65 0.14 0.20
Matches are distributed among these distances:
16 2 0.06
17 4 0.12
18 6 0.19
19 13 0.41
20 4 0.12
21 3 0.09
ACGTcount: A:0.57, C:0.17, G:0.17, T:0.08
Consensus pattern (19 bp):
CAAGGAACAACAAATAAGA
Found at i:69395944 original size:37 final size:37
Alignment explanation
Indices: 69395894--69395968 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
69395884 CAACACAAAC
*
69395894 ACATATTAGAAACCAAGGAACAACACATAAGACAAGG
1 ACATATTAGAAACCAAGGAACAACAAATAAGACAAGG
69395931 ACATATTAGAAACCAAGGAACAACAAATAAGACAAGG
1 ACATATTAGAAACCAAGGAACAACAAATAAGACAAGG
69395968 A
1 A
69395969 AGAGAGGAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.56, C:0.17, G:0.16, T:0.11
Consensus pattern (37 bp):
ACATATTAGAAACCAAGGAACAACAAATAAGACAAGG
Found at i:69395990 original size:2 final size:2
Alignment explanation
Indices: 69395980--69396025 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
69395970 GAGAGGAGGC
69395980 TA TA T- TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
69396020 TA TA TA
1 TA TA TA
69396026 AACCAAGGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:69397935 original size:2 final size:2
Alignment explanation
Indices: 69397928--69397960 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
69397918 TAATATTGTA
69397928 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
69397961 AAAATTTGGT
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:69401270 original size:25 final size:25
Alignment explanation
Indices: 69401215--69401272 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
69401205 TCAAGTAAAA
**
69401215 TAAAAAAATATAATAATTAAATTTT
1 TAAAAAAATATAATAATTAAATGAT
* *
69401240 TCAAAAAATATAATAATT-GATAGAT
1 TAAAAAAATATAATAATTAAAT-GAT
69401265 TAAAAAAA
1 TAAAAAAA
69401273 CATTCAAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 2 0.07
25 25 0.93
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (25 bp):
TAAAAAAATATAATAATTAAATGAT
Found at i:69401637 original size:13 final size:13
Alignment explanation
Indices: 69401619--69401643 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
69401609 TCAGCTATTG
69401619 TTTTTCCTTTTTC
1 TTTTTCCTTTTTC
69401632 TTTTTCCTTTTT
1 TTTTTCCTTTTT
69401644 TCGCTTGGCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTCCTTTTTC
Done.