Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold414
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: 2018024
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 13
Found at i:1119059 original size:21 final size:21
Alignment explanation
Indices: 1119015--1119056 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1119005 AGCTGCCTTC
* *
1119015 GCTCAATTTTAGCTTTTTTAA
1 GCTCAATATTAGCTTTTCTAA
1119036 GCTCAATATTAGCTCTTTCTA
1 GCTCAATATTAGCT-TTTCTA
1119057 GCTTCTTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.24, C:0.19, G:0.10, T:0.48
Consensus pattern (21 bp):
GCTCAATATTAGCTTTTCTAA
Found at i:1119183 original size:2 final size:2
Alignment explanation
Indices: 1119176--1119205 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1119166 TAAGTTCTTT
1119176 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1119206 GGGGGGGGAA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1123763 original size:3 final size:3
Alignment explanation
Indices: 1123755--1123798 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
1123745 TTGCTGTAGC
* * * *
1123755 TGT TGT TGT TGT TGT TGT TGT TGT CGT CGT AGT AGT TGT TGT TG
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TG
1123799 ATATGGTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.05, C:0.05, G:0.34, T:0.57
Consensus pattern (3 bp):
TGT
Found at i:1124024 original size:3 final size:3
Alignment explanation
Indices: 1124016--1124053 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
1124006 TTATTACGGT
*
1124016 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TGC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1124054 GAGGAGGAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.32, G:0.03, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:1124913 original size:2 final size:2
Alignment explanation
Indices: 1124908--1124941 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1124898 AGAAAGAAAT
1124908 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1124942 ACACGACAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1125818 original size:18 final size:17
Alignment explanation
Indices: 1125777--1125821 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1125767 AAAATATTAA
*
1125777 ATTTAAAAAATAAATCT
1 ATTTAAAAAATAAATCC
**
1125794 AAGTAAAAAATAAGATCC
1 ATTTAAAAAATAA-ATCC
1125812 ATTTAAAAAA
1 ATTTAAAAAA
1125822 CAGTTTAAAC
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.62, C:0.07, G:0.04, T:0.27
Consensus pattern (17 bp):
ATTTAAAAAATAAATCC
Found at i:1126378 original size:12 final size:12
Alignment explanation
Indices: 1126361--1126401 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
1126351 TTTAAAATTT
**
1126361 TAATAATTTTTG
1 TAATAATTTTAA
1126373 TAATAATTTTAA
1 TAATAATTTTAA
*
1126385 TAATAATTTTAT
1 TAATAATTTTAA
1126397 TAATA
1 TAATA
1126402 TTTGATATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (12 bp):
TAATAATTTTAA
Found at i:1126382 original size:21 final size:19
Alignment explanation
Indices: 1126347--1126388 Score: 66
Period size: 21 Copynumber: 2.1 Consensus size: 19
1126337 TATAATTTTT
1126347 ATTTTTTAAAATTTTAATA
1 ATTTTTTAAAATTTTAATA
1126366 ATTTTTGTAATAATTTTAATA
1 ATTTTT-TAA-AATTTTAATA
1126387 AT
1 AT
1126389 AATTTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 6 0.29
20 3 0.14
21 12 0.57
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
ATTTTTTAAAATTTTAATA
Found at i:1126400 original size:21 final size:21
Alignment explanation
Indices: 1126356--1126496 Score: 66
Period size: 21 Copynumber: 6.8 Consensus size: 21
1126346 TATTTTTTAA
*
1126356 AATTTTAATAATTTTTGTAAT
1 AATTTTAATAATATTTGTAAT
*
1126377 AATTTTAATAATAATTT-TATT
1 AATTTTAATAAT-ATTTGTAAT
* *
1126398 AATATTTGATATACTATTTATAAT
1 AAT-TTT-A-ATAATATTTGTAAT
*
1126422 -ATTTGTAAT-A-ATTT-TAAA
1 AATTT-TAATAATATTTGTAAT
*
1126440 AACTTTTAATACAGA-TT-T-AT
1 AA-TTTTAATA-ATATTTGTAAT
* * *
1126460 AACCTTTACTAATATTTGTTAT
1 AA-TTTTAATAATATTTGTAAT
1126482 AATTTTAATAA-ATTT
1 AATTTTAATAATATTT
1126497 TTATATGATT
Statistics
Matches: 94, Mismatches: 12, Indels: 29
0.70 0.09 0.21
Matches are distributed among these distances:
18 3 0.03
19 11 0.12
20 19 0.20
21 32 0.34
22 14 0.15
23 8 0.09
24 7 0.07
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (21 bp):
AATTTTAATAATATTTGTAAT
Found at i:1126432 original size:12 final size:11
Alignment explanation
Indices: 1126357--1126433 Score: 54
Period size: 12 Copynumber: 7.0 Consensus size: 11
1126347 ATTTTTTAAA
1126357 ATTTTAATAAT
1 ATTTTAATAAT
*
1126368 -TTTT-GTAAT
1 ATTTTAATAAT
1126377 AATTTTAATAAT
1 -ATTTTAATAAT
*
1126389 AATTTTATTAAT
1 -ATTTTAATAAT
* *
1126401 ATTTGATATACT
1 ATTTTA-ATAAT
1126413 A-TTT-ATAAT
1 ATTTTAATAAT
1126422 ATTTGTAATAAT
1 ATTT-TAATAAT
1126434 TTTAAAAACT
Statistics
Matches: 51, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
9 9 0.18
10 6 0.12
11 12 0.24
12 24 0.47
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (11 bp):
ATTTTAATAAT
Found at i:1126495 original size:10 final size:10
Alignment explanation
Indices: 1126482--1126600 Score: 52
Period size: 10 Copynumber: 11.7 Consensus size: 10
1126472 TATTTGTTAT
1126482 AATTTTAATA
1 AATTTTAATA
*
1126492 AATTTTTATA
1 AATTTTAATA
* *
1126502 TGATTTTAGT-
1 -AATTTTAATA
**
1126512 CCTTT-AATA
1 AATTTTAATA
1126521 TAATTTTAATA
1 -AATTTTAATA
1126532 AATCTTGTAAT-
1 AAT-TT-TAATA
*
1126543 -A-TTTGATA
1 AATTTTAATA
1126551 TAATTTTAATA
1 -AATTTTAATA
1126562 ACA-TTTAATA
1 A-ATTTTAATA
*
1126572 TAATTTTATTA
1 -AATTTTAATA
*
1126583 ACTTTTAATA
1 AATTTTAATA
1126593 TAATTTTA
1 -AATTTTA
1126601 TTTGAACTTT
Statistics
Matches: 80, Mismatches: 15, Indels: 27
0.66 0.12 0.22
Matches are distributed among these distances:
7 3 0.04
8 4 0.05
9 3 0.04
10 34 0.43
11 32 0.40
12 4 0.05
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.53
Consensus pattern (10 bp):
AATTTTAATA
Found at i:1126567 original size:21 final size:21
Alignment explanation
Indices: 1126543--1126791 Score: 93
Period size: 21 Copynumber: 11.8 Consensus size: 21
1126533 ATCTTGTAAT
1126543 ATTTGATATAATTTTAATAAC
1 ATTTGATATAATTTTAATAAC
* *
1126564 ATTTAATATAATTTTATTAAC
1 ATTTGATATAATTTTAATAAC
* * *
1126585 TTTTAATATAATTTTATTTGAAC
1 ATTTGATATAATTTTA-AT-AAC
* * **
1126608 -TTTGATATGATATTGTTAAC
1 ATTTGATATAATTTTAATAAC
** *
1126628 -TTTTTTATAACTTTTAATCTA-
1 ATTTGATATAA-TTTTAAT-AAC
*
1126649 ATTTTA-ATAATCATTTATATAA-
1 ATTTGATATAAT--TTTA-ATAAC
* * **
1126671 TTTTGATA-ATGTTTTGGTAAC
1 ATTTGATATA-ATTTTAATAAC
*
1126692 -TCTTAATATAATTTGT-ATAAC
1 AT-TTGATATAATTT-TAATAAC
* * * *
1126713 ATTTTATATAAATTTGATAAA
1 ATTTGATATAATTTTAATAAC
*
1126734 ATTTGACATAATTTTAATAAC
1 ATTTGATATAATTTTAATAAC
* * *
1126755 -TTTAAAGATAATTTTAGTAAC
1 ATTT-GATATAATTTTAATAAC
*
1126776 CTTTGATATAATTTTA
1 ATTTGATATAATTTTA
1126792 TATTAATTAT
Statistics
Matches: 173, Mismatches: 37, Indels: 36
0.70 0.15 0.15
Matches are distributed among these distances:
20 19 0.11
21 113 0.65
22 34 0.20
23 7 0.04
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.51
Consensus pattern (21 bp):
ATTTGATATAATTTTAATAAC
Found at i:1126596 original size:42 final size:41
Alignment explanation
Indices: 1126548--1126792 Score: 126
Period size: 42 Copynumber: 5.8 Consensus size: 41
1126538 GTAATATTTG
*
1126548 ATATAATTTTAATAACATTTAATATAATTTTATTAACTTTT
1 ATATAATTTTAATAACATTTGATATAATTTTATTAACTTTT
* * * *
1126589 AATATAATTTTATTTGAAC-TTTGATATGATATTGTTAACTTTT
1 -ATATAATTTTA-AT-AACATTTGATATAATTTTATTAACTTTT
* * *
1126632 TTATAACTTTTAATCTA-ATTTTA-ATAATCATTTATATAA-TTTT
1 ATATAA-TTTTAAT-AACATTTGATATAAT--TTTAT-TAACTTTT
* ** *
1126675 GATA-ATGTTTTGGTAAC-TCTTAATATAATTTGTA-TAACATTTT
1 -ATATA-ATTTTAATAACAT-TTGATATAATTT-TATTAAC-TTTT
* * * * * *
1126718 ATATAAATTTGATAAAATTTGACATAATTTTAATAACTTTAA
1 ATATAATTTTAATAACATTTGATATAATTTTATTAACTTT-T
* * *
1126760 AGATAATTTTAGTAACCTTTGATATAATTTTAT
1 ATATAATTTTAATAACATTTGATATAATTTTAT
1126793 ATTAATTATA
Statistics
Matches: 150, Mismatches: 34, Indels: 38
0.68 0.15 0.17
Matches are distributed among these distances:
41 12 0.08
42 75 0.50
43 50 0.33
44 13 0.09
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.51
Consensus pattern (41 bp):
ATATAATTTTAATAACATTTGATATAATTTTATTAACTTTT
Found at i:1130613 original size:20 final size:19
Alignment explanation
Indices: 1130573--1130625 Score: 76
Period size: 20 Copynumber: 2.9 Consensus size: 19
1130563 TTTTACCCAG
1130573 ATGTATCGATACA---TTA
1 ATGTATCGATACATTCTTA
1130589 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTT-A
1130609 ATGTATCGATACATTCT
1 ATGTATCGATACATTCT
1130626 GTCTTTTTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.39
19 2 0.06
20 18 0.55
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (19 bp):
ATGTATCGATACATTCTTA
Found at i:1134686 original size:13 final size:13
Alignment explanation
Indices: 1134668--1134693 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1134658 CAATTTTTTG
1134668 TGTATCGATACAT
1 TGTATCGATACAT
1134681 TGTATCGATACAT
1 TGTATCGATACAT
1134694 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1134758 original size:21 final size:21
Alignment explanation
Indices: 1134732--1134807 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1134722 CTGCCAAGAA
*
1134732 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1134753 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1134773 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1134794 ATGTATCGATACAT
1 ATGTATCGATACAT
1134808 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1134778 original size:20 final size:20
Alignment explanation
Indices: 1134753--1134825 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1134743 CATCTTTTTT
1134753 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1134773 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1134794 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1134814 ATGTATCGATAC
1 ATGTATCGATAC
1134826 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1134789 original size:41 final size:41
Alignment explanation
Indices: 1134732--1134825 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1134722 CTGCCAAGAA
*
1134732 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1134773 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1134814 ATGTATCGATAC
1 ATGTATCGATAC
1134826 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1135455 original size:21 final size:21
Alignment explanation
Indices: 1135429--1135502 Score: 87
Period size: 21 Copynumber: 3.4 Consensus size: 21
1135419 TCTCTCCTTT
1135429 ATCTCCCCCGTTTATTAATAA
1 ATCTCCCCCGTTTATTAATAA
* * *
1135450 ATCTCCCCC-TTAATCAAGTATTT
1 ATCTCCCCCGTTTATTAA-TA--A
1135473 ATCTCCCCCGTTTATTAATAA
1 ATCTCCCCCGTTTATTAATAA
1135494 ATCTCCCCC
1 ATCTCCCCC
1135503 TTAATCAAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
20 6 0.14
21 20 0.47
23 11 0.26
24 6 0.14
ACGTcount: A:0.26, C:0.34, G:0.04, T:0.36
Consensus pattern (21 bp):
ATCTCCCCCGTTTATTAATAA
Found at i:1135477 original size:44 final size:44
Alignment explanation
Indices: 1135426--1135513 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
1135416 CATTCTCTCC
1135426 TTTATCTCCCCCGTTTATTAATAAATCTCCCCCTTAATCAAGTA
1 TTTATCTCCCCCGTTTATTAATAAATCTCCCCCTTAATCAAGTA
1135470 TTTATCTCCCCCGTTTATTAATAAATCTCCCCCTTAATCAAGTA
1 TTTATCTCCCCCGTTTATTAATAAATCTCCCCCTTAATCAAGTA
1135514 ATTCATATCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.27, C:0.30, G:0.05, T:0.39
Consensus pattern (44 bp):
TTTATCTCCCCCGTTTATTAATAAATCTCCCCCTTAATCAAGTA
Found at i:1135479 original size:23 final size:21
Alignment explanation
Indices: 1135429--1135514 Score: 77
Period size: 21 Copynumber: 4.0 Consensus size: 21
1135419 TCTCTCCTTT
* *
1135429 ATCTCCCCCGTTTATTAA-TAA
1 ATCTCCCCC-TTAATCAAGTAA
*
1135450 ATCTCCCCCTTAATCAAGTATTT
1 ATCTCCCCCTTAATCAAGTA--A
* *
1135473 ATCTCCCCCGTTTATTAA-TAA
1 ATCTCCCCC-TTAATCAAGTAA
1135494 ATCTCCCCCTTAATCAAGTAA
1 ATCTCCCCCTTAATCAAGTAA
1135515 TTCATATCAA
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
20 12 0.23
21 23 0.44
23 11 0.21
24 6 0.12
ACGTcount: A:0.29, C:0.30, G:0.05, T:0.36
Consensus pattern (21 bp):
ATCTCCCCCTTAATCAAGTAA
Found at i:1135531 original size:44 final size:44
Alignment explanation
Indices: 1135439--1135532 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 44
1135429 ATCTCCCCCG
* * ****
1135439 TTTATTAATAAATCTCCCCCTTAATCAAGTATTTATCTCCCCCG
1 TTTATTAATAAATCTCCCCCTTAATCAAGTATTCATATCCAAAA
1135483 TTTATTAATAAATCTCCCCCTTAATCAAGTAATTCATAT-CAAAA
1 TTTATTAATAAATCTCCCCCTTAATCAAGT-ATTCATATCCAAAA
1135527 TTTATT
1 TTTATT
1135533 TGCACTTTTC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 37 0.86
45 6 0.14
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.40
Consensus pattern (44 bp):
TTTATTAATAAATCTCCCCCTTAATCAAGTATTCATATCCAAAA
Found at i:1137339 original size:13 final size:13
Alignment explanation
Indices: 1137321--1137359 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1137311 ATAATCACCC
*
1137321 TGTATCGATACAG
1 TGTATCGATACAA
1137334 TGTATCGATACAA
1 TGTATCGATACAA
1137347 TGTATCGATACAA
1 TGTATCGATACAA
1137360 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1137370 original size:20 final size:20
Alignment explanation
Indices: 1137345--1137423 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
1137335 GTATCGATAC
1137345 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
1137365 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
1137390 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
1137410 CATGTATCGATACA
1 AATGTATCGATACA
1137424 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:1139467 original size:15 final size:15
Alignment explanation
Indices: 1139431--1139468 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1139421 TACATCAATT
* *
1139431 TCATTTGGAGCTTCT
1 TCATTTTGAGCTTCC
1139446 TCATTTTGAGCTTCC
1 TCATTTTGAGCTTCC
1139461 TCATTTTG
1 TCATTTTG
1139469 GACATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.13, C:0.21, G:0.16, T:0.50
Consensus pattern (15 bp):
TCATTTTGAGCTTCC
Found at i:1143550 original size:13 final size:13
Alignment explanation
Indices: 1143532--1143557 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1143522 CAATTTTTTG
1143532 TGTATCGATACAT
1 TGTATCGATACAT
1143545 TGTATCGATACAT
1 TGTATCGATACAT
1143558 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1143622 original size:21 final size:21
Alignment explanation
Indices: 1143596--1143671 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1143586 CTGCCAAGAA
*
1143596 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1143617 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1143637 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1143658 ATGTATCGATACAT
1 ATGTATCGATACAT
1143672 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1143642 original size:20 final size:20
Alignment explanation
Indices: 1143617--1143689 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1143607 CATCTTTTTT
1143617 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1143637 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1143658 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1143678 ATGTATCGATAC
1 ATGTATCGATAC
1143690 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1143653 original size:41 final size:41
Alignment explanation
Indices: 1143596--1143689 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1143586 CTGCCAAGAA
*
1143596 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1143637 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1143678 ATGTATCGATAC
1 ATGTATCGATAC
1143690 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1150056 original size:19 final size:18
Alignment explanation
Indices: 1150032--1150145 Score: 113
Period size: 19 Copynumber: 6.7 Consensus size: 18
1150022 AGCGATACAT
*
1150032 TGTATCGATACAATACTTA
1 TGTATCGATAC-ACACTTA
1150051 TGTATCGATACACCACTTA
1 TGTATCGATACA-CACTTA
1150070 TGTATCGAT--ACA--T-
1 TGTATCGATACACACTTA
1150083 TGTATCGATACACCACTTA
1 TGTATCGATACA-CACTTA
1150102 TGTATCGAT--ACA-TTA
1 TGTATCGATACACACTTA
1150117 --TATCGATACAACACTTA
1 TGTATCGATAC-ACACTTA
1150134 TGTATCGATACA
1 TGTATCGATACA
1150146 TTATATCGAT
Statistics
Matches: 81, Mismatches: 1, Indels: 27
0.74 0.01 0.25
Matches are distributed among these distances:
13 16 0.20
14 1 0.01
15 4 0.05
16 9 0.11
17 5 0.06
18 3 0.04
19 43 0.53
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (18 bp):
TGTATCGATACACACTTA
Found at i:1150087 original size:32 final size:32
Alignment explanation
Indices: 1150053--1150165 Score: 199
Period size: 32 Copynumber: 3.5 Consensus size: 32
1150043 AATACTTATG
* *
1150053 TATCGATACACCACTTATGTATCGATACATTG
1 TATCGATACAACACTTATGTATCGATACATTA
*
1150085 TATCGATACACCACTTATGTATCGATACATTA
1 TATCGATACAACACTTATGTATCGATACATTA
1150117 TATCGATACAACACTTATGTATCGATACATTA
1 TATCGATACAACACTTATGTATCGATACATTA
1150149 TATCGATACAACACTTA
1 TATCGATACAACACTTA
1150166 CTGTTTGTAT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 79 1.00
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.34
Consensus pattern (32 bp):
TATCGATACAACACTTATGTATCGATACATTA
Found at i:1150088 original size:13 final size:13
Alignment explanation
Indices: 1150070--1150158 Score: 52
Period size: 13 Copynumber: 5.9 Consensus size: 13
1150060 ACACCACTTA
1150070 TGTATCGATACAT
1 TGTATCGATACAT
1150083 TGTATCGATACACCACTT
1 TGTATCGAT--A-CA--T
1150101 ATGTATCGATACAT
1 -TGTATCGATACAT
*
1150115 TATATCGATACAACACTT
1 TGTATCGAT---ACA--T
1150133 ATGTATCGATACAT
1 -TGTATCGATACAT
*
1150147 TATATCGATACA
1 TGTATCGATACA
1150159 ACACTTACTG
Statistics
Matches: 61, Mismatches: 3, Indels: 24
0.69 0.03 0.27
Matches are distributed among these distances:
13 28 0.46
14 2 0.03
15 1 0.02
16 10 0.16
17 1 0.02
18 2 0.03
19 17 0.28
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1158306 original size:8 final size:8
Alignment explanation
Indices: 1158293--1158322 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1158283 CTTCGTACTA
1158293 AAAAAAAT
1 AAAAAAAT
1158301 AAAAAAAT
1 AAAAAAAT
*
1158309 AAAAAAAC
1 AAAAAAAT
1158317 AAAAAA
1 AAAAAA
1158323 GAAAGGCCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.90, C:0.03, G:0.00, T:0.07
Consensus pattern (8 bp):
AAAAAAAT
Found at i:1159577 original size:28 final size:28
Alignment explanation
Indices: 1159537--1159811 Score: 310
Period size: 28 Copynumber: 9.9 Consensus size: 28
1159527 AACGTTCATT
*
1159537 TCTTGAAAGCCCACAAGTCAGTGGCATC
1 TCTTCAAAGCCCACAAGTCAGTGGCATC
* *
1159565 TCTTCAAAGCCCA-TAGATTAGTGGCATC
1 TCTTCAAAGCCCACAAG-TCAGTGGCATC
1159593 -CTTTCAAAGCCCACAAGTCAGTGGCATC
1 TC-TTCAAAGCCCACAAGTCAGTGGCATC
* *
1159621 TCTTGAAAGCCCACAGGT-AGTGGCATC
1 TCTTCAAAGCCCACAAGTCAGTGGCATC
*
1159648 -CTTTCAAAGCGCACAAGTCAGTGGCATC
1 TC-TTCAAAGCCCACAAGTCAGTGGCATC
* *
1159676 TCTTGAAAGCCCACAGGTCAGTGGCATC
1 TCTTCAAAGCCCACAAGTCAGTGGCATC
*
1159704 -CTTTCAAAGCCCACAAGTCAATGGCATC
1 TC-TTCAAAGCCCACAAGTCAGTGGCATC
*
1159732 TCTTAAAAGCCCACAAGTCAGTGGCATC
1 TCTTCAAAGCCCACAAGTCAGTGGCATC
* * * *
1159760 TTTTCAAAGTCCACAAGTTAGTAGCA-C
1 TCTTCAAAGCCCACAAGTCAGTGGCATC
* **
1159787 CCTTTTTAAGCCCACAAGTCAGTGG
1 TC-TTCAAAGCCCACAAGTCAGTGG
1159812 TAACCCTTTT
Statistics
Matches: 207, Mismatches: 30, Indels: 20
0.81 0.12 0.08
Matches are distributed among these distances:
26 1 0.00
27 27 0.13
28 174 0.84
29 5 0.02
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.24
Consensus pattern (28 bp):
TCTTCAAAGCCCACAAGTCAGTGGCATC
Found at i:1159741 original size:111 final size:111
Alignment explanation
Indices: 1159542--1159777 Score: 366
Period size: 111 Copynumber: 2.1 Consensus size: 111
1159532 TCATTTCTTG
* *
1159542 AAAGCCCACAAGTCAGTGGCATCTCTTCAAAGCCCATAGATTAGTGGCATCCTTTCAAAGCCCAC
1 AAAG-CCACAAGTCAGTGGCATCTCTTCAAAGCCCACAGATCAGTGGCATCCTTTCAAAGCCCAC
* * *
1159607 AAGTCAGTGGCATCTCTTGAAAGCCCACAGGT-AGTGGCATCCTTTC
65 AAGTCAATGGCATCTCTTAAAAGCCCACAAGTCAGTGGCATCCTTTC
* *
1159653 AAAGCGCACAAGTCAGTGGCATCTCTTGAAAGCCCACAGGTCAGTGGCATCCTTTCAAAGCCCAC
1 AAAGC-CACAAGTCAGTGGCATCTCTTCAAAGCCCACAGATCAGTGGCATCCTTTCAAAGCCCAC
*
1159718 AAGTCAATGGCATCTCTTAAAAGCCCACAAGTCAGTGGCATCTTTTC
65 AAGTCAATGGCATCTCTTAAAAGCCCACAAGTCAGTGGCATCCTTTC
1159765 AAAGTCCACAAGT
1 AAAG-CCACAAGT
1159778 TAGTAGCACC
Statistics
Matches: 114, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
110 1 0.01
111 88 0.77
112 24 0.21
113 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.22
Consensus pattern (111 bp):
AAAGCCACAAGTCAGTGGCATCTCTTCAAAGCCCACAGATCAGTGGCATCCTTTCAAAGCCCACA
AGTCAATGGCATCTCTTAAAAGCCCACAAGTCAGTGGCATCCTTTC
Found at i:1159798 original size:56 final size:56
Alignment explanation
Indices: 1159542--1159811 Score: 366
Period size: 56 Copynumber: 4.8 Consensus size: 56
1159532 TCATTTCTTG
* * *
1159542 AAAGCCCACAAGTCAGTGGCATCTCTTCAAAGCCCA-TAGATTAGTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCTCTTGAAAGCCCACAAG-TCAGTGGCATCCTTTC
*
1159598 AAAGCCCACAAGTCAGTGGCATCTCTTGAAAGCCCACAGGT-AGTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCTCTTGAAAGCCCACAAGTCAGTGGCATCCTTTC
* *
1159653 AAAGCGCACAAGTCAGTGGCATCTCTTGAAAGCCCACAGGTCAGTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCTCTTGAAAGCCCACAAGTCAGTGGCATCCTTTC
* * *
1159709 AAAGCCCACAAGTCAATGGCATCTCTTAAAAGCCCACAAGTCAGTGGCATCTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTCTTGAAAGCCCACAAGTCAGTGGCATCCTTTC
* * * * **
1159765 AAAGTCCACAAGTTAGTAGCA-CCCTTTTTAAGCCCACAAGTCAGTGG
1 AAAGCCCACAAGTCAGTGGCATCTC-TTGAAAGCCCACAAGTCAGTGG
1159812 TAACCCTTTT
Statistics
Matches: 195, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
55 56 0.29
56 138 0.71
57 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (56 bp):
AAAGCCCACAAGTCAGTGGCATCTCTTGAAAGCCCACAAGTCAGTGGCATCCTTTC
Found at i:1160056 original size:44 final size:44
Alignment explanation
Indices: 1160008--1160091 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 44
1159998 GTCTAATATC
*
1160008 GTTGGCCTTAAATCAGCACATTGACACTCTTCTTAACTTTTGTT
1 GTTGGCCTTAAATCAGCACATTGACACCCTTCTTAACTTTTGTT
* *
1160052 GTTGGCCTTAAATCAGCACATTGGCACCCTTCTTATCTTT
1 GTTGGCCTTAAATCAGCACATTGACACCCTTCTTAACTTT
1160092 AAGTCCAAGC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.21, C:0.25, G:0.14, T:0.39
Consensus pattern (44 bp):
GTTGGCCTTAAATCAGCACATTGACACCCTTCTTAACTTTTGTT
Found at i:1160104 original size:44 final size:44
Alignment explanation
Indices: 1160012--1160115 Score: 111
Period size: 44 Copynumber: 2.4 Consensus size: 44
1160002 AATATCGTTG
* * ****
1160012 GCCTTAAATCAGCACATTGACACTCTTCTTAACTTTTGTTGTTG
1 GCCTTAAATCAGCACATTGACACCCTTCTTAACTTTAGTTCCAA
* *
1160056 GCCTTAAATCAGCACATTGGCACCCTTCTTATCTTTAAG-TCCAA
1 GCCTTAAATCAGCACATTGACACCCTTCTTAACTTT-AGTTCCAA
*
1160100 GCCTTAAATCTGCACA
1 GCCTTAAATCAGCACA
1160116 CTAGCACATC
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
44 49 0.98
45 1 0.02
ACGTcount: A:0.26, C:0.27, G:0.12, T:0.35
Consensus pattern (44 bp):
GCCTTAAATCAGCACATTGACACCCTTCTTAACTTTAGTTCCAA
Found at i:1174234 original size:56 final size:56
Alignment explanation
Indices: 1174148--1174533 Score: 529
Period size: 56 Copynumber: 6.9 Consensus size: 56
1174138 CCAGAACATT
* * * * *
1174148 CATCTCTTGAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAGTAG
1 CATCTCTTCAAAGCCCACAGGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGG
* * *
1174204 CATCTCTTCAAAGCCCATAGGCCAGTGGCATTCTTTCAAAGCCCACAAGTTAGTGG
1 CATCTCTTCAAAGCCCACAGGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGG
* *
1174260 CATCTCTTCAAAGCCCACAGGCCAGTGGCATCCTTTTAAAGCCCACAAGTTAGTGG
1 CATCTCTTCAAAGCCCACAGGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGG
* ** * * * *
1174316 CATCTCTTCAAAACTGACATGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAATGG
1 CATCTCTTCAAAGCCCACAGGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGG
* *
1174372 CATCTCTTCAAAGCCCACAGGTCAATGACATCCTTTCAAAGCCCACAAGTTAGTGG
1 CATCTCTTCAAAGCCCACAGGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGG
* * * * *
1174428 CATCTCTTCAAAGCTCATAGGTCTGTGGCATCCTTTCAAAGTCCACAAGTTAGGGG
1 CATCTCTTCAAAGCCCACAGGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGG
* * *
1174484 CATCTTTTCAAAGCCCATAGGTCAGTGGCATCCTTTCAAAGTCCACAAGT
1 CATCTCTTCAAAGCCCACAGGTCAGTGGCATCCTTTCAAAGCCCACAAGT
1174534 CAGTCACAAG
Statistics
Matches: 291, Mismatches: 39, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 291 1.00
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.25
Consensus pattern (56 bp):
CATCTCTTCAAAGCCCACAGGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGG
Found at i:1174535 original size:28 final size:28
Alignment explanation
Indices: 1174157--1174537 Score: 394
Period size: 28 Copynumber: 13.6 Consensus size: 28
1174147 TCATCTCTTG
*
1174157 AAAGCCCACAAGTTAGTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
*
1174185 AAAGCCCACAAGTCAGTAGCAT-CTCTTC
1 AAAGCCCACAAGTCAGTGGCATCCT-TTC
* * * *
1174213 AAAGCCCATAGGCCAGTGGCATTCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
*
1174241 AAAGCCCACAAGTTAGTGGCAT-CTCTTC
1 AAAGCCCACAAGTCAGTGGCATCCT-TTC
* * *
1174269 AAAGCCCACAGGCCAGTGGCATCCTTTT
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
*
1174297 AAAGCCCACAAGTTAGTGGCAT-CTCTTC
1 AAAGCCCACAAGTCAGTGGCATCCT-TTC
* ** * *
1174325 AAAACTGACATGTTAGTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
*
1174353 AAAGCCCACAAGTCAATGGCAT-CTCTTC
1 AAAGCCCACAAGTCAGTGGCATCCT-TTC
* * *
1174381 AAAGCCCACAGGTCAATGACATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
*
1174409 AAAGCCCACAAGTTAGTGGCAT-CTCTTC
1 AAAGCCCACAAGTCAGTGGCATCCT-TTC
* * * *
1174437 AAAGCTCATAGGTCTGTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
* * * *
1174465 AAAGTCCACAAGTTAGGGGCATCTTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
* *
1174493 AAAGCCCATAGGTCAGTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
*
1174521 AAAGTCCACAAGTCAGT
1 AAAGCCCACAAGTCAGT
1174538 CACAAGTCGA
Statistics
Matches: 287, Mismatches: 56, Indels: 20
0.79 0.15 0.06
Matches are distributed among these distances:
27 10 0.03
28 267 0.93
29 10 0.03
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCATCCTTTC
Found at i:1174843 original size:44 final size:43
Alignment explanation
Indices: 1174750--1174848 Score: 128
Period size: 44 Copynumber: 2.3 Consensus size: 43
1174740 CCAATATCGC
* * *
1174750 TGGCCTTAAATTAGTACATTGGCACTCTTCTCATCTTTTGTAGT
1 TGGCCTTAAATTAGCACATTGGCACCCTTCTCATCTTTAGTA-T
*
1174794 TGGCCTTAAATTAGCACATTGGCACCCTTCTTATCTTTAAGT-T
1 TGGCCTTAAATTAGCACATTGGCACCCTTCTCATCTTT-AGTAT
1174837 TAGGCCTTAAAT
1 T-GGCCTTAAAT
1174849 CTACACACTA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
43 2 0.04
44 45 0.92
45 2 0.04
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.40
Consensus pattern (43 bp):
TGGCCTTAAATTAGCACATTGGCACCCTTCTCATCTTTAGTAT
Found at i:1190349 original size:28 final size:27
Alignment explanation
Indices: 1190308--1190698 Score: 478
Period size: 28 Copynumber: 14.0 Consensus size: 27
1190298 CTAGAACATT
*
1190308 CATCTCTTGAAAGCCCACAAGTCAGTGG
1 CATCT-TTCAAAGCCCACAAGTCAGTGG
* *
1190336 CATCCTTTTAAAGCCCATAAGTCAGTGG
1 CAT-CTTTCAAAGCCCACAAGTCAGTGG
*
1190364 CATCTCTTCAAAGCCCACAGGTCAGTGG
1 CATCT-TTCAAAGCCCACAAGTCAGTGG
1190392 CATCCTTTCAAAGCCCACAAGTCAGTGG
1 CAT-CTTTCAAAGCCCACAAGTCAGTGG
* *
1190420 CATCTCTTCAAAGCCCACAGGTCAGTGC
1 CATCT-TTCAAAGCCCACAAGTCAGTGG
* *
1190448 CATCTCTTCAAAGCCCACAGGTCAGTGC
1 CATCT-TTCAAAGCCCACAAGTCAGTGG
* *
1190476 CATCTCTTCAAAGCCCACAGGTCAATGG
1 CATCT-TTCAAAGCCCACAAGTCAGTGG
1190504 CATCCTTTCAAAGCCCACAAGTCAGTGG
1 CAT-CTTTCAAAGCCCACAAGTCAGTGG
*
1190532 CATCTCTTCAAAGCCCACAGGTCAGTGG
1 CATCT-TTCAAAGCCCACAAGTCAGTGG
**
1190560 CATCCTTTCAAAGCCCACAAGTTGGTGG
1 CAT-CTTTCAAAGCCCACAAGTCAGTGG
* *
1190588 TATCTCTTC-AAGCCCACAGGTCAGTGG
1 CATCT-TTCAAAGCCCACAAGTCAGTGG
*
1190615 CATCCTTTCAAAGTCCACAAGTCAGTGG
1 CAT-CTTTCAAAGCCCACAAGTCAGTGG
1190643 CATCTTTTCAAAGCCCACAAGTCAGTGG
1 CATC-TTTCAAAGCCCACAAGTCAGTGG
** *
1190671 CATCCTTTCAAAATCCATAAGTCAGTGG
1 CAT-CTTTCAAAGCCCACAAGTCAGTGG
1190699 TACCCTTTTT
Statistics
Matches: 324, Mismatches: 27, Indels: 24
0.86 0.07 0.06
Matches are distributed among these distances:
27 29 0.09
28 286 0.88
29 9 0.03
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (27 bp):
CATCTTTCAAAGCCCACAAGTCAGTGG
Found at i:1190458 original size:84 final size:84
Alignment explanation
Indices: 1190317--1190698 Score: 540
Period size: 84 Copynumber: 4.6 Consensus size: 84
1190307 TCATCTCTTG
* *
1190317 AAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCCCATAAGTCAGTGGCATCTCTTCAAAGCCCAC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTCTTCAAAGCCCAC
1190382 AGGTCAGTGGCATCCTTTC
66 AGGTCAGTGGCATCCTTTC
* *
1190401 AAAGCCCACAAGTCAGTGGCAT-CTCTTCAAAGCCCACAGGTCAGTGCCATCTCTTCAAAGCCCA
1 AAAGCCCACAAGTCAGTGGCATCCT-TTCAAAGCCCACAAGTCAGTGGCATCTCTTCAAAGCCCA
*
1190465 CAGGTCAGTGCCAT-CTCTTC
65 CAGGTCAGTGGCATCCT-TTC
* *
1190485 AAAGCCCACAGGTCAATGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTCTTCAAAGCCCAC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTCTTCAAAGCCCAC
1190550 AGGTCAGTGGCATCCTTTC
66 AGGTCAGTGGCATCCTTTC
** * * *
1190569 AAAGCCCACAAGTTGGTGGTAT-CTCTTC-AAGCCCACAGGTCAGTGGCATC-CTTTCAAAGTCC
1 AAAGCCCACAAGTCAGTGGCATCCT-TTCAAAGCCCACAAGTCAGTGGCATCTC-TTCAAAGCCC
* *
1190631 ACAAGTCAGTGGCATCTTTTC
64 ACAGGTCAGTGGCATCCTTTC
** *
1190652 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAATCCATAAGTCAGTGG
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGG
1190699 TACCCTTTTT
Statistics
Matches: 264, Mismatches: 26, Indels: 16
0.86 0.08 0.05
Matches are distributed among these distances:
82 1 0.00
83 77 0.29
84 182 0.69
85 4 0.02
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.23
Consensus pattern (84 bp):
AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTCTTCAAAGCCCAC
AGGTCAGTGGCATCCTTTC
Found at i:1190721 original size:56 final size:56
Alignment explanation
Indices: 1190308--1190698 Score: 606
Period size: 56 Copynumber: 7.0 Consensus size: 56
1190298 CTAGAACATT
* * * *
1190308 CATCTCTTGAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCCCATAAGTCAGTGG
1 CATCTCTTCAAAGCCCACAGGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGG
1190364 CATCTCTTCAAAGCCCACAGGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGG
1 CATCTCTTCAAAGCCCACAGGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGG
* * *
1190420 CATCTCTTCAAAGCCCACAGGTCAGTGCCAT-CTCTTCAAAGCCCACAGGTCAGTGC
1 CATCTCTTCAAAGCCCACAGGTCAGTGGCATCCT-TTCAAAGCCCACAAGTCAGTGG
*
1190476 CATCTCTTCAAAGCCCACAGGTCAATGGCATCCTTTCAAAGCCCACAAGTCAGTGG
1 CATCTCTTCAAAGCCCACAGGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGG
**
1190532 CATCTCTTCAAAGCCCACAGGTCAGTGGCATCCTTTCAAAGCCCACAAGTTGGTGG
1 CATCTCTTCAAAGCCCACAGGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGG
* *
1190588 TATCTCTTC-AAGCCCACAGGTCAGTGGCATCCTTTCAAAGTCCACAAGTCAGTGG
1 CATCTCTTCAAAGCCCACAGGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGG
* * ** *
1190643 CATCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAATCCATAAGTCAGTGG
1 CATCTCTTCAAAGCCCACAGGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGG
1190699 TACCCTTTTT
Statistics
Matches: 309, Mismatches: 23, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
55 52 0.17
56 255 0.83
57 2 0.01
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (56 bp):
CATCTCTTCAAAGCCCACAGGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGG
Found at i:1191691 original size:20 final size:20
Alignment explanation
Indices: 1191663--1191734 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
1191653 TTACCCAGAC
1191663 GTATCGATACATTCTTCAAT
1 GTATCGATACATTCTTCAAT
* *
1191683 GTATTGATACATT-TATGAAT
1 GTATCGATACATTCT-TCAAT
* *
1191703 GTATCGATATATTCTTTAAT
1 GTATCGATACATTCTTCAAT
1191723 GTATCGATACAT
1 GTATCGATACAT
1191735 CTAGTTAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
19 1 0.02
20 42 0.95
21 1 0.02
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (20 bp):
GTATCGATACATTCTTCAAT
Found at i:1199032 original size:12 final size:12
Alignment explanation
Indices: 1199004--1199051 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
1198994 TTTGGCTGAC
*
1199004 ATGTGGTTGGAA
1 ATGTGGTTGAAA
*
1199016 TTGTGGTTGAAA
1 ATGTGGTTGAAA
* *
1199028 ATGTGGATAAAA
1 ATGTGGTTGAAA
*
1199040 ATGTAGTTGAAA
1 ATGTGGTTGAAA
1199052 GTAAAAGTCC
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.33
Consensus pattern (12 bp):
ATGTGGTTGAAA
Found at i:1199495 original size:20 final size:20
Alignment explanation
Indices: 1199457--1199510 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1199447 AAATTTAATT
*
1199457 GGATGTTATCGATACATTGAA
1 GGATG-TATCGATAAATTGAA
*
1199478 GGATGTATTGATAAATTGAA
1 GGATGTATCGATAAATTGAA
*
1199498 GTATGTATCGATA
1 GGATGTATCGATA
1199511 CATTAAGGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 24 0.83
21 5 0.17
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (20 bp):
GGATGTATCGATAAATTGAA
Found at i:1202364 original size:52 final size:52
Alignment explanation
Indices: 1202301--1202404 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 52
1202291 CCTAGGCGTT
* ** * **
1202301 TCTGATTGCCACCATGGCATCATCATTACT-AGTGATGCCAAGTCACCCCAAC
1 TCTGATCGCCACCATAACATCAT-ATTAATCAGTGACACCAAGTCACCCCAAC
*
1202353 TCTGATCGCCACCATAACATCATTTTAATCAGTGACACCAAGTCACCCCAAC
1 TCTGATCGCCACCATAACATCATATTAATCAGTGACACCAAGTCACCCCAAC
1202405 CCTTGAACGC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
51 4 0.09
52 40 0.91
ACGTcount: A:0.30, C:0.34, G:0.12, T:0.24
Consensus pattern (52 bp):
TCTGATCGCCACCATAACATCATATTAATCAGTGACACCAAGTCACCCCAAC
Found at i:1208692 original size:33 final size:33
Alignment explanation
Indices: 1208655--1208719 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1208645 TTACAAGCTA
1208655 TGTATCGATACATT-T-CTTCATGTATCGATACAT
1 TGTATCGATACATTATAC--CATGTATCGATACAT
1208688 TGTATCGATACATTATACCATGTATCGATACA
1 TGTATCGATACATTATACCATGTATCGATACA
1208720 AATAGTGATA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 28 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.38
Consensus pattern (33 bp):
TGTATCGATACATTATACCATGTATCGATACAT
Found at i:1208718 original size:13 final size:13
Alignment explanation
Indices: 1208675--1208701 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1208665 CATTTCTTCA
1208675 TGTATCGATACAT
1 TGTATCGATACAT
1208688 TGTATCGATACAT
1 TGTATCGATACAT
1208701 T
1 T
1208702 ATACCATGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1208775 original size:21 final size:21
Alignment explanation
Indices: 1208748--1208804 Score: 84
Period size: 19 Copynumber: 2.8 Consensus size: 21
1208738 ACTGCCAATT
1208748 TCATGTATCGATACAATTTG-
1 TCATGTATCGATACAATTTGA
1208768 TCCATGTATCGATAC-A-TTGA
1 T-CATGTATCGATACAATTTGA
1208788 TCATGTATCGATACAAT
1 TCATGTATCGATACAAT
1208805 GTATCGATAC
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
19 16 0.48
20 4 0.12
21 13 0.39
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (21 bp):
TCATGTATCGATACAATTTGA
Found at i:1208808 original size:13 final size:13
Alignment explanation
Indices: 1208790--1208816 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1208780 TACATTGATC
1208790 ATGTATCGATACA
1 ATGTATCGATACA
1208803 ATGTATCGATACA
1 ATGTATCGATACA
1208816 A
1 A
1208817 GGCAGCATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1209379 original size:17 final size:18
Alignment explanation
Indices: 1209352--1209406 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
1209342 GGTTTTCGTT
1209352 TTTCT-CCCCTT-AA-AA
1 TTTCTCCCCCTTAAACAA
1209367 TATTCTCCCCCTTAAACAA
1 T-TTCTCCCCCTTAAACAA
1209386 TTATCTCCCCCTTAAACAA
1 TT-TCTCCCCCTTAAACAA
1209405 TT
1 TT
1209407 ATCTTCTCCC
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
15 1 0.03
16 4 0.11
17 6 0.17
18 3 0.09
19 21 0.60
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.36
Consensus pattern (18 bp):
TTTCTCCCCCTTAAACAA
Found at i:1209394 original size:19 final size:19
Alignment explanation
Indices: 1209370--1209410 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
1209360 CTTAAAATAT
1209370 TCTCCCCCTTAAACAATTA
1 TCTCCCCCTTAAACAATTA
1209389 TCTCCCCCTTAAACAATTA
1 TCTCCCCCTTAAACAATTA
1209408 TCT
1 TCT
1209411 TCTCCCCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.29, C:0.37, G:0.00, T:0.34
Consensus pattern (19 bp):
TCTCCCCCTTAAACAATTA
Found at i:1211307 original size:13 final size:13
Alignment explanation
Indices: 1211289--1211330 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
1211279 AAATAGTACC
1211289 CAATGTATCGATA
1 CAATGTATCGATA
1211302 CAATGTATCGATA
1 CAATGTATCGATA
*
1211315 TAATGTATCGATA
1 CAATGTATCGATA
1211328 CAA
1 CAA
1211331 GAAATGTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1217443 original size:20 final size:20
Alignment explanation
Indices: 1217418--1217470 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
1217408 GTTACAAGCT
1217418 ATGTATCGATACATT-T-CTTC
1 ATGTATCGATACATTGTAC--C
1217438 ATGTATCGATACATTGTACC
1 ATGTATCGATACATTGTACC
1217458 ATGTATCGATACA
1 ATGTATCGATACA
1217471 AATAGTGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 29 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTGTACC
Found at i:1217538 original size:13 final size:13
Alignment explanation
Indices: 1217520--1217546 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1217510 TACATTGATC
1217520 ATGTATCGATACA
1 ATGTATCGATACA
1217533 ATGTATCGATACA
1 ATGTATCGATACA
1217546 A
1 A
1217547 GGCAGCATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1221778 original size:34 final size:35
Alignment explanation
Indices: 1221709--1221780 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 35
1221699 AGTGTTTATG
* *
1221709 GAAAGAATAAGCACAAAGGAATACAAATGAGCTTT
1 GAAAGAATAAGAACAAAGGAATACAAAAGAGCTTT
* **
1221744 GAAAGAATAATAACAAA-GAATACAAAAGCTCTTT
1 GAAAGAATAAGAACAAAGGAATACAAAAGAGCTTT
1221778 GAA
1 GAA
1221781 GTGCAGAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
34 17 0.53
35 15 0.47
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.18
Consensus pattern (35 bp):
GAAAGAATAAGAACAAAGGAATACAAAAGAGCTTT
Found at i:1222118 original size:19 final size:20
Alignment explanation
Indices: 1222094--1222144 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
1222084 TGCCAGTTTT
* *
1222094 ATGTATCGATACTATG-AAC
1 ATGTATCGATACCAAGTAAC
*
1222113 ATGTATCGATACCAAGTAAT
1 ATGTATCGATACCAAGTAAC
1222133 ATGTATCGATAC
1 ATGTATCGATAC
1222145 ATCTAGGTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACCAAGTAAC
Found at i:1228301 original size:33 final size:34
Alignment explanation
Indices: 1228253--1228320 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 34
1228243 TAGTACCCAC
* *
1228253 GTATCGGTACAAAGAACTCAATATCAATAC-TCT
1 GTATCGATACAAAGAACACAATATCAATACATCT
* * *
1228286 GTATCGATACTAAGAACACAGTATCGATACATCT
1 GTATCGATACAAAGAACACAATATCAATACATCT
1228320 G
1 G
1228321 GGTTTTCCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
33 25 0.86
34 4 0.14
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (34 bp):
GTATCGATACAAAGAACACAATATCAATACATCT
Found at i:1232350 original size:104 final size:104
Alignment explanation
Indices: 1232170--1232380 Score: 413
Period size: 104 Copynumber: 2.0 Consensus size: 104
1232160 TTATTATTAT
1232170 TTTGTATTTCATTCAATTGTTTTTCTAATTTGACCAATTTAATTTTAAGCTCATTATTCTCTAAA
1 TTTGTATTTCATTCAATTGTTTTTCTAATTTGACCAATTTAATTTTAAGCTCATTATTCTCTAAA
*
1232235 CTTATCGATTTTTCATCATTTATCTTAGAGAGAGTTTCC
66 CTTATCGATTTTTCATCATTTAGCTTAGAGAGAGTTTCC
1232274 TTTGTATTTCATTCAATTGTTTTTCTAATTTGACCAATTTAATTTTAAGCTCATTATTCTCTAAA
1 TTTGTATTTCATTCAATTGTTTTTCTAATTTGACCAATTTAATTTTAAGCTCATTATTCTCTAAA
1232339 CTTATCGATTTTTCATCATTTAGCTTAGAGAGAGTTTCC
66 CTTATCGATTTTTCATCATTTAGCTTAGAGAGAGTTTCC
1232378 TTT
1 TTT
1232381 TCTAGTTCAA
Statistics
Matches: 106, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 106 1.00
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (104 bp):
TTTGTATTTCATTCAATTGTTTTTCTAATTTGACCAATTTAATTTTAAGCTCATTATTCTCTAAA
CTTATCGATTTTTCATCATTTAGCTTAGAGAGAGTTTCC
Found at i:1235600 original size:54 final size:54
Alignment explanation
Indices: 1235541--1235647 Score: 151
Period size: 54 Copynumber: 2.0 Consensus size: 54
1235531 CCCCCATCCC
* * *
1235541 CTTTACCTTTGCCTCTCTTCACTTTCTCCCCTCATCTAGCACCAGAAACCTCCT
1 CTTTACCCTTGCCTCTCCTCACTTTCTCCCCTCATCCAGCACCAGAAACCTCCT
* * * *
1235595 CTTTACCCTTGCTTCTCCTCATTTTCTCCCGTCATCCAGCACCAGAAGCCTCC
1 CTTTACCCTTGCCTCTCCTCACTTTCTCCCCTCATCCAGCACCAGAAACCTCC
1235648 CATTTCCCTA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.16, C:0.43, G:0.07, T:0.34
Consensus pattern (54 bp):
CTTTACCCTTGCCTCTCCTCACTTTCTCCCCTCATCCAGCACCAGAAACCTCCT
Found at i:1236508 original size:28 final size:25
Alignment explanation
Indices: 1236477--1236530 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 25
1236467 ATTGAAATAT
*
1236477 TTTAGTTAATTAAATATTATTACATAAA
1 TTTA-TTAATT-AATA-TATTAAATAAA
*
1236505 TTTATTTATTAATATATTAAATAAA
1 TTTATTAATTAATATATTAAATAAA
1236530 T
1 T
1236531 AATTTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 11 0.46
26 4 0.17
27 5 0.21
28 4 0.17
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (25 bp):
TTTATTAATTAATATATTAAATAAA
Found at i:1242709 original size:20 final size:21
Alignment explanation
Indices: 1242684--1242722 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1242674 AGTTTGTATG
*
1242684 TAATTTT-TTTTTTATTTTGA
1 TAATTTTGATTTTTATTTTGA
1242704 TAATTTTGATTTTTATTTT
1 TAATTTTGATTTTTATTTT
1242723 TTAGATTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (21 bp):
TAATTTTGATTTTTATTTTGA
Found at i:1242979 original size:2 final size:2
Alignment explanation
Indices: 1242972--1243006 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1242962 ATTTACTTTC
* *
1242972 AT AT AT AT AG AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1243007 AAATAAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1249105 original size:12 final size:12
Alignment explanation
Indices: 1249088--1249174 Score: 51
Period size: 12 Copynumber: 7.6 Consensus size: 12
1249078 ATTGTACATT
*
1249088 TTATATTATATA
1 TTATATAATATA
1249100 TTATATAATATA
1 TTATATAATATA
1249112 --A-ATAATAT-
1 TTATATAATATA
* *
1249120 TTATATTACATA
1 TTATATAATATA
* *
1249132 TTTTAAAAT-TA
1 TTATATAATATA
1249143 TTATATAACTATAA
1 TTATATAA-TAT-A
* *
1249157 TTTTAT-CTATA
1 TTATATAATATA
1249168 TTATATA
1 TTATATA
1249175 TAAAATTAAA
Statistics
Matches: 55, Mismatches: 12, Indels: 16
0.66 0.14 0.19
Matches are distributed among these distances:
9 7 0.13
10 2 0.04
11 19 0.35
12 20 0.36
13 1 0.02
14 6 0.11
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (12 bp):
TTATATAATATA
Found at i:1249900 original size:16 final size:18
Alignment explanation
Indices: 1249873--1249905 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1249863 TTATTTAATA
1249873 TTAATGTTAAAA-AAATT
1 TTAATGTTAAAAGAAATT
1249890 TTAAT-TTAAAAGAAAT
1 TTAATGTTAAAAGAAAT
1249906 AATATATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (18 bp):
TTAATGTTAAAAGAAATT
Found at i:1251566 original size:150 final size:149
Alignment explanation
Indices: 1251278--1251559 Score: 359
Period size: 150 Copynumber: 1.9 Consensus size: 149
1251268 GAAATTTGAT
* * *
1251278 TTTTTTTAAAATTAACTTCAAAGTTTTAAAAATTATGTTTCGTACCCAACGGAAAACCAGGGGAT
1 TTTTTTTAAAATTAACTTCAAAGTTTCAAAAATTACGTTTCGCACCCAACGGAAAACCAGGGGAT
* * * * *
1251343 ACGAAAGGTATTGAAATTTTTCATACCCCTACAAAAAATCATAGGAATATGAAAATATGACTCGA
66 ACAAAAGGTATTAAAAATTTTCATACCCCTACAAAAAACCATAGGAATATGAAAACATGACTCGA
1251408 GTGAGCATAGCCGATCACG
131 GTGAGCATAGCCGATCACG
* * * *
1251427 TTTTTTTAAAATTTAACTTCTAA-TTTCCAAAGTTACGTTTCGCACCCAACGGAAAAATCAGGGG
1 TTTTTTTAAAA-TTAACTTCAAAGTTTCAAAAATTACGTTTCGCACCCAACGG-AAAACCAGGGG
* * * ** * * *
1251491 ATGCAAAAGGTGTTAAAAATTTTCATACCTCTACGGAAAACCATGGGAATATGAAAGCATGACTT
64 ATACAAAAGGTATTAAAAATTTTCATACCCCTACAAAAAACCATAGGAATATGAAAACATGACTC
1251556 GAGT
129 GAGT
1251560 AGGCATAAAA
Statistics
Matches: 111, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
149 35 0.32
150 76 0.68
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (149 bp):
TTTTTTTAAAATTAACTTCAAAGTTTCAAAAATTACGTTTCGCACCCAACGGAAAACCAGGGGAT
ACAAAAGGTATTAAAAATTTTCATACCCCTACAAAAAACCATAGGAATATGAAAACATGACTCGA
GTGAGCATAGCCGATCACG
Found at i:1252762 original size:122 final size:123
Alignment explanation
Indices: 1252623--1252865 Score: 337
Period size: 122 Copynumber: 2.0 Consensus size: 123
1252613 TGCTGGTTCA
* *
1252623 TGGATGCCGCTGCTGGAGTACTCGAGCTGCAAGCGCTCGTGGAAGCTGCTGCTACCGTGGATGCT
1 TGGATGCCACTGCTGGAGTACTCGAGCAGCAAGCGCTCGTGGAAGCTGCTGCTACCGTGGATGCT
1252688 GGAAGAAACTC-AAGCTGCTGG-TTTCAATACTTTGTTGGAGCTGGAAGCTGCTATTGG
66 GGAAGAAACTCTAA-CTGCTGGTTTTCAATACTTTGTTGGAGCTGGAAGCTGCTATTGG
* * * * * *
1252745 TGGATGCTACTGCTGGAGTGCTCGAGCAGTAAGCGCTCGTGGAAGCTGCTGCTGCCGTGGGTGTT
1 TGGATGCCACTGCTGGAGTACTCGAGCAGCAAGCGCTCGTGGAAGCTGCTGCTACCGTGGATGCT
* *** * *
1252810 GGAAGAAACTCTAATTGCTGGTTTTGGGTGCTTTGTTGGAGTTGGAAGCTGCTATT
66 GGAAGAAACTCTAACTGCTGGTTTTCAATACTTTGTTGGAGCTGGAAGCTGCTATT
1252866 TATTCCCTTC
Statistics
Matches: 105, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
122 74 0.70
123 31 0.30
ACGTcount: A:0.18, C:0.19, G:0.34, T:0.29
Consensus pattern (123 bp):
TGGATGCCACTGCTGGAGTACTCGAGCAGCAAGCGCTCGTGGAAGCTGCTGCTACCGTGGATGCT
GGAAGAAACTCTAACTGCTGGTTTTCAATACTTTGTTGGAGCTGGAAGCTGCTATTGG
Found at i:1252973 original size:35 final size:36
Alignment explanation
Indices: 1252871--1252985 Score: 112
Period size: 35 Copynumber: 3.3 Consensus size: 36
1252861 CTATTTATTC
* * * *
1252871 CCTTCTTTTTTGCTCCTCTCCTACTTACCGTGACTT-
1 CCTT-TTTTTTTCTCCTCTCCCACTTGCCGTGAGTTA
* *
1252907 GC--TTTATTTCTCCTCTCCCACTTGCCGTGAGTTA
1 CCTTTTTTTTTCTCCTCTCCCACTTGCCGTGAGTTA
* * *
1252941 CCTTTTTTTTTC-CCTTTCCCTCTTGCTGTGAGTTA
1 CCTTTTTTTTTCTCCTCTCCCACTTGCCGTGAGTTA
1252976 CCTTTTTTTT
1 CCTTTTTTTT
1252986 CCTTTTTTTT
Statistics
Matches: 65, Mismatches: 11, Indels: 7
0.78 0.13 0.08
Matches are distributed among these distances:
33 26 0.40
34 1 0.02
35 30 0.46
36 8 0.12
ACGTcount: A:0.08, C:0.31, G:0.10, T:0.50
Consensus pattern (36 bp):
CCTTTTTTTTTCTCCTCTCCCACTTGCCGTGAGTTA
Found at i:1253489 original size:18 final size:19
Alignment explanation
Indices: 1253466--1253537 Score: 71
Period size: 18 Copynumber: 3.8 Consensus size: 19
1253456 TTTCATGATG
*
1253466 ATTTTTTTTAC-TTCTTTT
1 ATTTTTTTTACTTTATTTT
1253484 ATTTTTTTTACTTTTATTTT
1 ATTTTTTTTAC-TTTATTTT
1253504 A-TTTTTTTA-TTT-TTTT
1 ATTTTTTTTACTTTATTTT
*
1253520 ACTTTTATTTTATTTTAT
1 A-TTTT-TTTTACTTTAT
1253538 ATCAAATAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
16 5 0.11
17 3 0.07
18 14 0.30
19 13 0.28
20 10 0.22
21 1 0.02
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (19 bp):
ATTTTTTTTACTTTATTTT
Found at i:1253503 original size:5 final size:5
Alignment explanation
Indices: 1253480--1253537 Score: 64
Period size: 5 Copynumber: 11.2 Consensus size: 5
1253470 TTTTTACTTC
* *
1253480 TTTTA TTTT- TTTTA CTTTTA TTTTA TTTTT TTATTT TTTTA CTTTTA
1 TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TT-TTA TTTTA -TTTTA
1253527 TTTTA TTTTA T
1 TTTTA TTTTA T
1253538 ATCAAATAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
4 4 0.09
5 28 0.60
6 15 0.32
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:1253532 original size:19 final size:20
Alignment explanation
Indices: 1253466--1253536 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
1253456 TTTCATGATG
*
1253466 ATTTTTTTTAC--TTCTTTT
1 ATTTTTTTTACTTTTATTTT
1253484 ATTTTTTTTACTTTTATTTT
1 ATTTTTTTTACTTTTATTTT
**
1253504 ATTTTTTTATTTTTTTACTTTT
1 ATTTTTTT-TACTTTTA-TTTT
1253526 ATTTTATTTTA
1 ATTTT-TTTTA
1253537 TATCAAATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
18 11 0.25
20 14 0.32
21 6 0.14
22 10 0.23
23 3 0.07
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (20 bp):
ATTTTTTTTACTTTTATTTT
Found at i:1253534 original size:27 final size:28
Alignment explanation
Indices: 1253467--1253535 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
1253457 TTCATGATGA
*
1253467 TTTT-TTTTACTTCTTTTATTTTTTTTAC
1 TTTTATTTTA-TTTTTTTATTTTTTTTAC
1253495 TTTTATTTTATTTTTTTA-TTTTTTTAC
1 TTTTATTTTATTTTTTTATTTTTTTTAC
1253522 TTTTATTTTATTTT
1 TTTTATTTTATTTT
1253536 ATATCAAATA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 23 0.59
28 11 0.28
29 5 0.13
ACGTcount: A:0.13, C:0.06, G:0.00, T:0.81
Consensus pattern (28 bp):
TTTTATTTTATTTTTTTATTTTTTTTAC
Found at i:1254076 original size:43 final size:43
Alignment explanation
Indices: 1254014--1254532 Score: 656
Period size: 43 Copynumber: 12.1 Consensus size: 43
1254004 TAGATAAGGC
* * *
1254014 AGTCTTTAGGGTCAAAGCTGACAGGCAGACTGAGGGATAGAAA
1 AGTCTCTAGGGTCAAAGCTGACAGGCAGACTAAGGGATAGGAA
* * *
1254057 AGTCTTTAGGGTCAGAGCTGACAGGCAGACTAAGGGATAGAAA
1 AGTCTCTAGGGTCAAAGCTGACAGGCAGACTAAGGGATAGGAA
* * * *
1254100 AGTCTCCAAGGTCAAAGCCGATAGGCAGACTAAGGGATAGGAA
1 AGTCTCTAGGGTCAAAGCTGACAGGCAGACTAAGGGATAGGAA
1254143 AGTCTCTAGGGTCAAAGCTGACAGGCAGACTAAGGGCA-AGGAA
1 AGTCTCTAGGGTCAAAGCTGACAGGCAGACTAAGGG-ATAGGAA
*
1254186 AGTCTCTAGGGTCAAAG-TCGACAGGAAGACTAAGGGATAGGAA
1 AGTCTCTAGGGTCAAAGCT-GACAGGCAGACTAAGGGATAGGAA
* * * * **
1254229 AATCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGA-AAAAA
1 AGTCTCTAGGGTCAAAGCTGACAGGCAGACTAAGGGATAGGAA
* * **
1254271 AGTCTCTAGAGTCAAAG-TCGATATACAGACTAAGGGATAGGAA
1 AGTCTCTAGGGTCAAAGCT-GACAGGCAGACTAAGGGATAGGAA
* *
1254314 AGTCTCCAGGGTCAAAG-TCGACAGGCAAACTAAGGGA-AGGAA
1 AGTCTCTAGGGTCAAAGCT-GACAGGCAGACTAAGGGATAGGAA
1254356 AGTCTCTAGGGTCAAAGCTGACAGGCAGACTAAGGGATAGGAA
1 AGTCTCTAGGGTCAAAGCTGACAGGCAGACTAAGGGATAGGAA
* * ** *
1254399 AGTCTCCACGGTCAAAGCCAACAGGCAGACTAAGGAATAGGAA
1 AGTCTCTAGGGTCAAAGCTGACAGGCAGACTAAGGGATAGGAA
*
1254442 AGTCTCTAGGGTCAAAGCCGACAGGCAGACTAAGGGATAGGAA
1 AGTCTCTAGGGTCAAAGCTGACAGGCAGACTAAGGGATAGGAA
* * * *
1254485 AGTCTCCAAGGTCAAAGCTGACTGACAGACTAAGGGATA-GAA
1 AGTCTCTAGGGTCAAAGCTGACAGGCAGACTAAGGGATAGGAA
1254527 AGTCTC
1 AGTCTC
1254533 CAGAAGTTTA
Statistics
Matches: 415, Mismatches: 53, Indels: 17
0.86 0.11 0.04
Matches are distributed among these distances:
42 80 0.19
43 334 0.80
44 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.30, T:0.15
Consensus pattern (43 bp):
AGTCTCTAGGGTCAAAGCTGACAGGCAGACTAAGGGATAGGAA
Found at i:1254443 original size:256 final size:257
Alignment explanation
Indices: 1254039--1254532 Score: 733
Period size: 256 Copynumber: 1.9 Consensus size: 257
1254029 AGCTGACAGG
* ** * *
1254039 CAGACTGAGGGATAGAAAAGTCTTTAGGGTCAGAGCTGACAGGCAGACTAAGGGATAGAAAAGTC
1 CAGACTAAGGGATAGAAAAGTCTCCAGGGTCAAAGCTGACAGGCAAACTAAGGGATAGAAAAGTC
* * * **
1254104 TCCAAGGTCAAAGCCGATAGGCAGACTAAGGGATAGGAAAGTCTCTAGGGTCAAAGCTGACAGGC
66 TCCAAGGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTCCACGGTCAAAGCCAACAGGC
* *
1254169 AGACTAAGGGCAAGGAAAGTCTCTAGGGTCAAAGTCGACAGGAAGACTAAGGGATAGGAAAATCT
131 AGACTAAGGGAAAGGAAAGTCTCTAGGGTCAAAGCCGACAGGAAGACTAAGGGATAGGAAAATCT
*
1254234 CCAAGGTCAAAGCCGACAGGCAGACTAAGGGAAAAAAAGTCTCTAGAGTCAAAGTCGATATA
196 CCAAGGTCAAAGCCGACAGACAGACTAAGGGAAAAAAAGTCTCTAGAGTCAAAGTCGATATA
* *
1254296 CAGACTAAGGGATAGGAAAGTCTCCAGGGTCAAAG-TCGACAGGCAAACTAAGGGA-AGGAAAGT
1 CAGACTAAGGGATAGAAAAGTCTCCAGGGTCAAAGCT-GACAGGCAAACTAAGGGATAGAAAAGT
* * *
1254359 CTCTAGGGTCAAAGCTGACAGGCAGACTAAGGGATAGGAAAGTCTCCACGGTCAAAGCCAACAGG
65 CTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTCCACGGTCAAAGCCAACAGG
* *
1254424 CAGACTAA-GGAATAGGAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGT
130 CAGACTAAGGGAA-AGGAAAGTCTCTAGGGTCAAAGCCGACAGGAAGACTAAGGGATAGGAAAAT
* * * *
1254488 CTCCAAGGTCAAAGCTGACTGACAGACTAAGGGATAGAAAGTCTC
194 CTCCAAGGTCAAAGCCGACAGACAGACTAAGGGAAAAAAAGTCTC
1254533 CAGAAGTTTA
Statistics
Matches: 211, Mismatches: 24, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
255 3 0.01
256 161 0.76
257 47 0.22
ACGTcount: A:0.38, C:0.18, G:0.30, T:0.15
Consensus pattern (257 bp):
CAGACTAAGGGATAGAAAAGTCTCCAGGGTCAAAGCTGACAGGCAAACTAAGGGATAGAAAAGTC
TCCAAGGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTCCACGGTCAAAGCCAACAGGC
AGACTAAGGGAAAGGAAAGTCTCTAGGGTCAAAGCCGACAGGAAGACTAAGGGATAGGAAAATCT
CCAAGGTCAAAGCCGACAGACAGACTAAGGGAAAAAAAGTCTCTAGAGTCAAAGTCGATATA
Found at i:1254806 original size:22 final size:22
Alignment explanation
Indices: 1254756--1254806 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
1254746 ATGTTCATGA
1254756 CTTGATTTTATTCTTTCTATGT
1 CTTGATTTTATTCTTTCTATGT
*
1254778 CTT-ATTTGTATT-TTTTTATAG-
1 CTTGATTT-TATTCTTTCTAT-GT
1254799 CTTGATTT
1 CTTGATTT
1254807 ACTCTACCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.16, C:0.10, G:0.10, T:0.65
Consensus pattern (22 bp):
CTTGATTTTATTCTTTCTATGT
Found at i:1261277 original size:122 final size:123
Alignment explanation
Indices: 1261138--1261393 Score: 372
Period size: 122 Copynumber: 2.1 Consensus size: 123
1261128 AAGAGGTTCG
*
1261138 AGTTGCTAGTTCGTGGATGCTG-TTGCTGAAGTGCTCGAGCTGCAAGCGCTCGTGGAAGCTACTG
1 AGTTGCT-GTTCGTGGATGCTGCTT-CTGAAGTGCTCGAGCAGCAAGCGCTCGTGGAAGCTACTG
* * *
1261202 TTGCCGTGGATGCTGGAAGAAACTCGAGCTGCTGG-TTTCGGTGCTTTGTTGGAGCTGGA
64 CTGCCGTGGATGCTGGAAGAAACTCGAACTGCTGGTTTTCGGTGCTTTGTTGAAGCTGGA
* * *
1261261 AGTTGCTGTTGGTGGATGCTGCTTCTGGAGTGCTCGAGCAGCAAGCGCTCGTGGAAGCTGCTGCT
1 AGTTGCTGTTCGTGGATGCTGCTTCTGAAGTGCTCGAGCAGCAAGCGCTCGTGGAAGCTACTGCT
* * * *
1261326 GCCGTGGGTGTTGGAAGAAACTCGAATTGCTGGTTTTGGGTGCTTTGTTGAAGCTGGA
66 GCCGTGGATGCTGGAAGAAACTCGAACTGCTGGTTTTCGGTGCTTTGTTGAAGCTGGA
*
1261384 AGCTGCTGTT
1 AGTTGCTGTT
1261394 TATTCCCTTC
Statistics
Matches: 119, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
122 79 0.66
123 40 0.34
ACGTcount: A:0.16, C:0.18, G:0.36, T:0.30
Consensus pattern (123 bp):
AGTTGCTGTTCGTGGATGCTGCTTCTGAAGTGCTCGAGCAGCAAGCGCTCGTGGAAGCTACTGCT
GCCGTGGATGCTGGAAGAAACTCGAACTGCTGGTTTTCGGTGCTTTGTTGAAGCTGGA
Found at i:1261458 original size:33 final size:34
Alignment explanation
Indices: 1261403--1261517 Score: 126
Period size: 33 Copynumber: 3.4 Consensus size: 34
1261393 TTATTCCCTT
* * * *
1261403 CTTTTTTTCTCCTCTCCTACTTGTCGTGAGTT-G
1 CTTTATTTCTCCTTTCCCACTTGTCGTGAGTTAC
1261436 CTTTATTTCTCCTTTCCCACTTGTCGTGAGTTAC
1 CTTTATTTCTCCTTTCCCACTTGTCGTGAGTTAC
* * * *
1261470 CTTTTCTTTTTCCTTTCCCTCTTGCCGTGAGTTAC
1 C-TTTATTTCTCCTTTCCCACTTGTCGTGAGTTAC
*
1261505 CTTT-TTTTTCCTT
1 CTTTATTTCTCCTT
1261518 CTTTTGTCGT
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
33 38 0.53
34 4 0.06
35 30 0.42
ACGTcount: A:0.07, C:0.29, G:0.11, T:0.53
Consensus pattern (34 bp):
CTTTATTTCTCCTTTCCCACTTGTCGTGAGTTAC
Found at i:1261999 original size:13 final size:13
Alignment explanation
Indices: 1261981--1262048 Score: 79
Period size: 13 Copynumber: 5.3 Consensus size: 13
1261971 CATGATGATT
1261981 TTTTTTACTTTTA
1 TTTTTTACTTTTA
*
1261994 TTTTTT--TATTA
1 TTTTTTACTTTTA
1262005 TTTTTTACTTTTA
1 TTTTTTACTTTTA
*
1262018 TTTTATT-TTTTTA
1 TTTT-TTACTTTTA
1262031 TTTTTTTACTTTTA
1 -TTTTTTACTTTTA
1262045 TTTT
1 TTTT
1262049 ATTTTATATC
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
11 10 0.22
13 25 0.54
14 11 0.24
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTTACTTTTA
Found at i:1262010 original size:18 final size:18
Alignment explanation
Indices: 1261989--1262053 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 18
1261979 TTTTTTTTAC
1261989 TTTTATTTTTTTATTATT
1 TTTTATTTTTTTATTATT
*
1262007 TTTTACTTTTATT-TTATTT
1 TTTTA-TTTTTTTATTA-TT
1262026 TTTTATTTTTTTACTT-TT
1 TTTTATTTTTTTA-TTATT
1262044 ATTTTATTTT
1 -TTTTATTTT
1262054 ATATCGAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
18 16 0.40
19 22 0.55
20 2 0.05
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTATTTTTTTATTATT
Found at i:1262023 original size:5 final size:5
Alignment explanation
Indices: 1261978--1262055 Score: 65
Period size: 5 Copynumber: 15.4 Consensus size: 5
1261968 TTTCATGATG
1261978 ATTTT -TTTT ACTTTT A-TTT -TTTT ATTATT -TTTT ACTTTT ATTTT
1 ATTTT ATTTT A-TTTT ATTTT ATTTT ATT-TT ATTTT A-TTTT ATTTT
* *
1262022 ATTTT TTTATT TTTTT ACTTTT ATTTT ATTTT AT
1 ATTTT ATT-TT ATTTT A-TTTT ATTTT ATTTT AT
1262056 ATCGAATAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 18
0.76 0.02 0.22
Matches are distributed among these distances:
4 12 0.19
5 28 0.45
6 22 0.35
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:1262026 original size:27 final size:27
Alignment explanation
Indices: 1261980--1262053 Score: 118
Period size: 27 Copynumber: 2.9 Consensus size: 27
1261970 TCATGATGAT
*
1261980 TTTTTTTACTTTTA-TTT-TTTTATTA
1 TTTTTTTACTTTTATTTTATTTTTTTA
1262005 -TTTTTTACTTTTATTTTATTTTTTTA
1 TTTTTTTACTTTTATTTTATTTTTTTA
1262031 TTTTTTTACTTTTATTTTATTTT
1 TTTTTTTACTTTTATTTTATTTT
1262054 ATATCGAATA
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
24 13 0.29
25 3 0.07
26 7 0.16
27 22 0.49
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.81
Consensus pattern (27 bp):
TTTTTTTACTTTTATTTTATTTTTTTA
Found at i:1267173 original size:23 final size:23
Alignment explanation
Indices: 1267142--1267205 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
1267132 GCTGGCCGAA
1267142 GTTTGGGTTATGGATTTTGATTT
1 GTTTGGGTTATGGATTTTGATTT
*
1267165 GTTTAGGTTATGGATTTTGATTT
1 GTTTGGGTTATGGATTTTGATTT
* *
1267188 GTTGGGGTTATGGGTTTT
1 GTTTGGGTTATGGATTTT
1267206 AGGTTGAGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.12, C:0.00, G:0.33, T:0.55
Consensus pattern (23 bp):
GTTTGGGTTATGGATTTTGATTT
Found at i:1267740 original size:23 final size:22
Alignment explanation
Indices: 1267714--1267784 Score: 81
Period size: 23 Copynumber: 3.1 Consensus size: 22
1267704 GTACAAAAAA
1267714 AATTTTAATATTATTTTTAATTT
1 AATTTT-ATATTATTTTTAATTT
* *
1267737 AATTATATATTAGTTTTAATATT
1 AATTTTATATTATTTTTAAT-TT
1267760 AATATATTATATTATTTTT-ATTT
1 AAT-T-TTATATTATTTTTAATTT
1267783 AA
1 AA
1267785 AAATTAAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
22 13 0.32
23 14 0.34
24 3 0.07
25 11 0.27
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (22 bp):
AATTTTATATTATTTTTAATTT
Found at i:1267746 original size:22 final size:24
Alignment explanation
Indices: 1267721--1267784 Score: 89
Period size: 22 Copynumber: 2.8 Consensus size: 24
1267711 AAAAATTTTA
1267721 ATATTATTTTTAATTTAAT-TA-T
1 ATATTATTTTTAATTTAATATATT
*
1267743 ATATTAGTTTTAATATTAATATATT
1 ATATTATTTTTAAT-TTAATATATT
1267768 ATATTATTTTT-ATTTAA
1 ATATTATTTTTAATTTAA
1267785 AAATTAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
22 13 0.35
23 9 0.24
24 4 0.11
25 11 0.30
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
ATATTATTTTTAATTTAATATATT
Found at i:1267790 original size:22 final size:22
Alignment explanation
Indices: 1267721--1267795 Score: 71
Period size: 22 Copynumber: 3.3 Consensus size: 22
1267711 AAAAATTTTA
*
1267721 ATATTATTTTTAATTTAATTA-T
1 ATATTATTTTT-ATTTAAATATT
*
1267743 ATATTAGTTTTAATATTAATATATT
1 ATATTA-TTTTTAT-TTAA-ATATT
*
1267768 ATATTATTTTTATTTAAAAATT
1 ATATTATTTTTATTTAAATATT
*
1267790 AAATTA
1 ATATTA
1267796 ATTATCATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
22 17 0.39
23 12 0.27
24 8 0.18
25 7 0.16
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (22 bp):
ATATTATTTTTATTTAAATATT
Found at i:1268060 original size:20 final size:22
Alignment explanation
Indices: 1268018--1268061 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
1268008 TCATTAAATT
*
1268018 TTTAAATAATAATAATTAATTAA
1 TTTAAATAAAAATAATT-ATTAA
1268041 TTTAAATAAAAAT-ATT-TTAA
1 TTTAAATAAAAATAATTATTAA
1268061 T
1 T
1268062 AAATTCATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
22 3 0.15
23 12 0.60
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTAAATAAAAATAATTATTAA
Found at i:1268587 original size:26 final size:26
Alignment explanation
Indices: 1268558--1268611 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
1268548 TGCAATTGAT
* *
1268558 TCGGATTGGGTTAGTTTGCTGTATTA
1 TCGGATTGGGTTAGCTTGCTGAATTA
*
1268584 TCGGCTTGGGTTAGCTTGCTGAATTA
1 TCGGATTGGGTTAGCTTGCTGAATTA
1268610 TC
1 TC
1268612 CTACTTTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.15, C:0.13, G:0.30, T:0.43
Consensus pattern (26 bp):
TCGGATTGGGTTAGCTTGCTGAATTA
Found at i:1269152 original size:2 final size:2
Alignment explanation
Indices: 1269145--1269179 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1269135 AGAAAAATAC
1269145 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1269180 GTTATATCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1276707 original size:28 final size:29
Alignment explanation
Indices: 1276666--1276726 Score: 106
Period size: 28 Copynumber: 2.1 Consensus size: 29
1276656 GGCCAAAGAG
*
1276666 TAATCCTCTTCACTAATGAATTACGATTC
1 TAATCCTCTTCACTAATGAAGTACGATTC
1276695 TAAT-CTCTTCACTAATGAAGTACGATTC
1 TAATCCTCTTCACTAATGAAGTACGATTC
1276723 TAAT
1 TAAT
1276727 ATGCTCACTC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 27 0.87
29 4 0.13
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (29 bp):
TAATCCTCTTCACTAATGAAGTACGATTC
Found at i:1283496 original size:16 final size:17
Alignment explanation
Indices: 1283467--1283499 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1283457 TTTCTTTGGC
1283467 AATTAAAAGCTTTTTATA
1 AATTAAAA-CTTTTTATA
1283485 AATTAAAA-TTTTTAT
1 AATTAAAACTTTTTAT
1283500 GCTCTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (17 bp):
AATTAAAACTTTTTATA
Found at i:1287622 original size:14 final size:15
Alignment explanation
Indices: 1287597--1287638 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
1287587 AAAAATTATA
1287597 AAAAATATAAAAAT-T
1 AAAAA-ATAAAAATCT
*
1287612 CAAAAATAAAAATCCT
1 AAAAAATAAAAAT-CT
1287628 AAAAAATAAAA
1 AAAAAATAAAA
1287639 GATATATACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 8 0.35
15 4 0.17
16 11 0.48
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAAAATAAAAATCT
Found at i:1290378 original size:14 final size:14
Alignment explanation
Indices: 1290343--1290371 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1290333 ATATGTACAT
1290343 TATAT-TATTGTTA
1 TATATATATTGTTA
1290356 TATATATATTGTTA
1 TATATATATTGTTA
1290370 TA
1 TA
1290372 ATGATATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TATATATATTGTTA
Found at i:1291297 original size:206 final size:209
Alignment explanation
Indices: 1290935--1291331 Score: 649
Period size: 206 Copynumber: 1.9 Consensus size: 209
1290925 ATTTGGGGGA
* *
1290935 TAGTGATTGTGATAAGATGAATCAATTACCATAATAAGAGAATGGCTTTCAGTAAAACTGACTCA
1 TAGTGATTGAGATAAGATGAATCAATTACCATAATAAGAGAATGGCTTTCAATAAAACTGACTCA
*
1291000 CAAGGAAAAGAATCGACTTTATAAGGACTCAATTTATTTGTTTATAAGGGAATCTGTTCATTCTA
66 CAAGGAAAAGAATCGACTTTATAAAGACTCAATTTATTTGTTTATAAGGGAATCTGTTCATTCTA
* * *
1291065 TAAAAAGGGTCGATTCTGAGTAAAAAATATATTAATTTATTTTGTTTTGAGAATGAAAAGGAAAA
131 TAAAAAGGGTCGATTCCGAATAAAAAATATATTAATTTATTTTGCTTTGAGAATGAAAAGGAAAA
1291130 GAACCGACTTTCAG
196 GAACCGACTTTCAG
* * *
1291144 TAGTGATTGAGATAAGATGAATCAATTACCATAA-AA-A-AATGGCTTTTAATAAAGCTGATTCA
1 TAGTGATTGAGATAAGATGAATCAATTACCATAATAAGAGAATGGCTTTCAATAAAACTGACTCA
* *
1291206 CAGGGAAAAGAA-CTGACTTTATAAAGACTCAATTTATTTGTTTATGAGGGAATCTGTTCATTCT
66 CAAGGAAAAGAATC-GACTTTATAAAGACTCAATTTATTTGTTTATAAGGGAATCTGTTCATTCT
*
1291270 ATAAAAAGGGTCGATTCCGAATAAAAAATATATTGATTTATTTTGCTTTGAGAATGAAAAGG
130 ATAAAAAGGGTCGATTCCGAATAAAAAATATATTAATTTATTTTGCTTTGAGAATGAAAAGG
1291332 TCAGTTCTCT
Statistics
Matches: 175, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
205 1 0.01
206 138 0.79
207 1 0.01
208 2 0.01
209 33 0.19
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.32
Consensus pattern (209 bp):
TAGTGATTGAGATAAGATGAATCAATTACCATAATAAGAGAATGGCTTTCAATAAAACTGACTCA
CAAGGAAAAGAATCGACTTTATAAAGACTCAATTTATTTGTTTATAAGGGAATCTGTTCATTCTA
TAAAAAGGGTCGATTCCGAATAAAAAATATATTAATTTATTTTGCTTTGAGAATGAAAAGGAAAA
GAACCGACTTTCAG
Found at i:1291500 original size:22 final size:22
Alignment explanation
Indices: 1291446--1291542 Score: 97
Period size: 22 Copynumber: 4.5 Consensus size: 22
1291436 TTCTTCAAAT
* *
1291446 AAAATAATATATACATACAGTA
1 AAAATAATATGTACATATAGTA
* *
1291468 AAAATAATATGTATATTTAGTA
1 AAAATAATATGTACATATAGTA
* *
1291490 AAAATAATATGTGCATATAG-C
1 AAAATAATATGTACATATAGTA
* * *
1291511 ATAATCATATGTATATATAGTA
1 AAAATAATATGTACATATAGTA
*
1291533 AAAATGATAT
1 AAAATAATAT
1291543 TTTGGCCTAA
Statistics
Matches: 59, Mismatches: 15, Indels: 2
0.78 0.20 0.03
Matches are distributed among these distances:
21 16 0.27
22 43 0.73
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.34
Consensus pattern (22 bp):
AAAATAATATGTACATATAGTA
Found at i:1292126 original size:7 final size:7
Alignment explanation
Indices: 1292109--1292144 Score: 54
Period size: 7 Copynumber: 4.9 Consensus size: 7
1292099 TCACTATAAA
1292109 TTTTAATT
1 TTTTAA-T
1292117 TTTTAAT
1 TTTTAAT
1292124 TTTTAAT
1 TTTTAAT
1292131 TTTTAAT
1 TTTTAAT
1292138 ATTTTAA
1 -TTTTAA
1292145 CGTTAATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 15 0.56
8 12 0.44
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTTAAT
Found at i:1292129 original size:15 final size:15
Alignment explanation
Indices: 1292108--1292144 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1292098 GTCACTATAA
1292108 ATTTTAATTTTTTAAT
1 ATTTTAA-TTTTTAAT
1292124 -TTTTAATTTTTAAT
1 ATTTTAATTTTTAAT
1292138 ATTTTAA
1 ATTTTAA
1292145 CGTTAATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTTAATTTTTAAT
Found at i:1292244 original size:13 final size:13
Alignment explanation
Indices: 1292205--1292244 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1292195 TAATTTTTTA
1292205 TTTTAAATAAAAT
1 TTTTAAATAAAAT
* *
1292218 ATTTAAAGAAAAT
1 TTTTAAATAAAAT
*
1292231 TTTTGAATAAAAT
1 TTTTAAATAAAAT
1292244 T
1 T
1292245 AAAATTATTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (13 bp):
TTTTAAATAAAAT
Found at i:1292546 original size:16 final size:16
Alignment explanation
Indices: 1292527--1292568 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1292517 GTTTAAGCAG
1292527 GTTTGGGTTCGGACTC
1 GTTTGGGTTCGGACTC
* *
1292543 GTTTGAGTTTGGACTC
1 GTTTGGGTTCGGACTC
*
1292559 ATTTGGGTTC
1 GTTTGGGTTC
1292569 AGGCTCATTC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.10, C:0.14, G:0.33, T:0.43
Consensus pattern (16 bp):
GTTTGGGTTCGGACTC
Found at i:1292575 original size:16 final size:16
Alignment explanation
Indices: 1292556--1292586 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1292546 TGAGTTTGGA
*
1292556 CTCATTTGGGTTCAGG
1 CTCATTCGGGTTCAGG
1292572 CTCATTCGGGTTCAG
1 CTCATTCGGGTTCAG
1292587 ACTTTTTCGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.23, G:0.29, T:0.35
Consensus pattern (16 bp):
CTCATTCGGGTTCAGG
Found at i:1292595 original size:16 final size:16
Alignment explanation
Indices: 1292576--1292627 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
1292566 TTCAGGCTCA
*
1292576 TTCGGGTTCAGACTTT
1 TTCGGATTCAGACTTT
*
1292592 TTCGGATCCAGACTTTT
1 TTCGGATTCAGAC-TTT
*
1292609 TTC-GATTCAGGCTTT
1 TTCGGATTCAGACTTT
1292624 TTCG
1 TTCG
1292628 AGTTCGGATC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 6 0.20
16 18 0.60
17 6 0.20
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.44
Consensus pattern (16 bp):
TTCGGATTCAGACTTT
Found at i:1292862 original size:18 final size:18
Alignment explanation
Indices: 1292823--1292862 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1292813 ATATTTATAT
*
1292823 ATAAAATTAATTTGTTAT
1 ATAAAATTAATTTGTTAA
1292841 ATAAAATTAATTT-TTCAA
1 ATAAAATTAATTTGTT-AA
1292859 ATAA
1 ATAA
1292863 TTTATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (18 bp):
ATAAAATTAATTTGTTAA
Found at i:1293566 original size:16 final size:15
Alignment explanation
Indices: 1293539--1293568 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1293529 ATGTTAACTT
1293539 TATATTCTATTCTAC
1 TATATTCTATTCTAC
1293554 TATATTGCTATTCTA
1 TATATT-CTATTCTA
1293569 AGTATAGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.27, C:0.17, G:0.03, T:0.53
Consensus pattern (15 bp):
TATATTCTATTCTAC
Found at i:1294052 original size:16 final size:16
Alignment explanation
Indices: 1294028--1294081 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
1294018 CAGTCTTGAA
1294028 TTCGGGTTCTTTCAGG
1 TTCGGGTTCTTTCAGG
* *
1294044 TTTGGGTTCTTTTAGG
1 TTCGGGTTCTTTCAGG
* **
1294060 TTCGGGTTTTTTTGGG
1 TTCGGGTTCTTTCAGG
1294076 TTCGGG
1 TTCGGG
1294082 CTTTCTCGGG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.04, C:0.11, G:0.35, T:0.50
Consensus pattern (16 bp):
TTCGGGTTCTTTCAGG
Found at i:1294108 original size:16 final size:16
Alignment explanation
Indices: 1294071--1294128 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
1294061 TCGGGTTTTT
*
1294071 TTGGGTTCGGGCTT-TC
1 TTGGGTTCGAG-TTATC
*
1294087 TCGGGTTCGAGTTATC
1 TTGGGTTCGAGTTATC
1294103 TTGGGTTC-AGGTTAT-
1 TTGGGTTCGA-GTTATC
1294118 TTCGGGTTCGA
1 TT-GGGTTCGA
1294129 ATTTTTAACT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
15 5 0.14
16 29 0.83
17 1 0.03
ACGTcount: A:0.09, C:0.16, G:0.34, T:0.41
Consensus pattern (16 bp):
TTGGGTTCGAGTTATC
Found at i:1296322 original size:30 final size:31
Alignment explanation
Indices: 1296287--1296345 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1296277 AAAAAAATAT
* *
1296287 ATAATT-ATTAAATTTTAAATTTTTTTAAAA
1 ATAATTGATTAAATATAAAATTTTTTTAAAA
* *
1296317 ATAATTGGTTTAATATAAAATTTTTTTAA
1 ATAATTGATTAAATATAAAATTTTTTTAA
1296346 TGATTATATG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 6 0.25
31 18 0.75
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (31 bp):
ATAATTGATTAAATATAAAATTTTTTTAAAA
Found at i:1301550 original size:54 final size:54
Alignment explanation
Indices: 1301491--1301650 Score: 268
Period size: 54 Copynumber: 3.0 Consensus size: 54
1301481 GTGGTTTGCC
* * * *
1301491 GCTTCTATTTTTCATCCTTCTTCAAAGTAGGCTTTGTTGCTTTTTATCTTTTAT
1 GCTTCTACTTTTCGTCCTTCTTCAAAGTGGGCTTGGTTGCTTTTTATCTTTTAT
1301545 GCTTCTACTTTTCGTCCTTCTTCAAAGTGGGCTTGGTTGCTTTTTATCTTTTAT
1 GCTTCTACTTTTCGTCCTTCTTCAAAGTGGGCTTGGTTGCTTTTTATCTTTTAT
*
1301599 GCTTCTACTTTTCGTCCTTCTTCAAAGTGGGCTTGGTTGC-TTTTGTCTTTTA
1 GCTTCTACTTTTCGTCCTTCTTCAAAGTGGGCTTGGTTGCTTTTTATCTTTTA
1301651 AGCGTAATGG
Statistics
Matches: 101, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 11 0.11
54 90 0.89
ACGTcount: A:0.12, C:0.20, G:0.16, T:0.53
Consensus pattern (54 bp):
GCTTCTACTTTTCGTCCTTCTTCAAAGTGGGCTTGGTTGCTTTTTATCTTTTAT
Found at i:1316126 original size:2 final size:2
Alignment explanation
Indices: 1316080--1316115 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1316070 TTATCAAATA
1316080 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
1316116 TCTAAATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1317417 original size:37 final size:37
Alignment explanation
Indices: 1317367--1317479 Score: 174
Period size: 37 Copynumber: 3.1 Consensus size: 37
1317357 ACTAATCACT
* * *
1317367 TTTATCAAAAGTAATTATTGATCC-CTCATTAAACTTA
1 TTTATCAAAAGTAACTATTGA-CCACTCAATAAACCTA
1317404 TTTATCAAAAGTAACTATTGACCACTCAATAAACCTA
1 TTTATCAAAAGTAACTATTGACCACTCAATAAACCTA
*
1317441 TTTATCAAAAGTAACTATTAACCACTCAATAAACCTA
1 TTTATCAAAAGTAACTATTGACCACTCAATAAACCTA
1317478 TT
1 TT
1317480 ATAACCTTTT
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
36 2 0.03
37 69 0.97
ACGTcount: A:0.42, C:0.19, G:0.04, T:0.35
Consensus pattern (37 bp):
TTTATCAAAAGTAACTATTGACCACTCAATAAACCTA
Found at i:1317480 original size:20 final size:20
Alignment explanation
Indices: 1317418--1317480 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
1317408 TCAAAAGTAA
*
1317418 CTATTGACCACTCAATAAAC
1 CTATTAACCACTCAATAAAC
* * *
1317438 CTATTTATCA--AAAGT-AA-
1 CTATTAACCACTCAA-TAAAC
1317455 CTATTAACCACTCAATAAAC
1 CTATTAACCACTCAATAAAC
1317475 CTATTA
1 CTATTA
1317481 TAACCTTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
17 8 0.25
18 5 0.16
19 5 0.16
20 14 0.44
ACGTcount: A:0.43, C:0.24, G:0.03, T:0.30
Consensus pattern (20 bp):
CTATTAACCACTCAATAAAC
Found at i:1318612 original size:199 final size:198
Alignment explanation
Indices: 1318261--1318657 Score: 706
Period size: 199 Copynumber: 2.0 Consensus size: 198
1318251 CTGAATCTGT
1318261 GATGCAACAATCAAGTAAAAGCAAAGATAGAATTAACAAAGAAAATAAAATACAAGTAATAAGCA
1 GATGCAACAATCAAGTAAAAGCAAAGATAGAATTAACAAAGAAAATAAAATACAAGTAATAAGCA
* *
1318326 ACACATGAAAAAAAATTAGGAAAAGAAAGTTGTAATTGCTGTAGACACCCAATTTTGTTCGGTCT
66 ACACATGAAAAAAAATTAGGAAAAGAAAGTTGTAATTGCTGTAGACACCCAATTTTGTCCGGCCT
* * *
1318391 TTTTTAGGACATTCATTTTTTTTTAAAAAAATAATAATAACAAAGAAAAAAAATAATTGAAAAAT
131 TTTTTAGGACACTCAGTTTTTTTTAAAAAAATAATAATAAAAAAGAAAAAAAA-AATTGAAAAAT
1318456 TGAG
195 TGAG
1318460 GATGCAACAATCAAGTAAAAGCAAAGATAGAATTAACAAAGAAAATAAAATACAAGTAATAAGCA
1 GATGCAACAATCAAGTAAAAGCAAAGATAGAATTAACAAAGAAAATAAAATACAAGTAATAAGCA
*
1318525 ACACATGAAAAAAAGATTAGGAAAAGAAAGTTGTAATTGCTGTAGACACTCAATTTTGTCCGGCC
66 ACACATGAAAAAAA-ATTAGGAAAAGAAAGTTGTAATTGCTGTAGACACCCAATTTTGTCCGGCC
*
1318590 TTTTTTAGGACACTC-GTTTTTTTTAAAAAAGTAATAATAAAAAAGAAAAAAAAAATTGAAAAAT
130 TTTTTTAGGACACTCAGTTTTTTTTAAAAAAATAATAATAAAAAAGAAAAAAAAAATTGAAAAAT
1318654 TGAG
195 TGAG
1318658 TGGCCTGGGT
Statistics
Matches: 190, Mismatches: 7, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
198 15 0.08
199 114 0.60
200 61 0.32
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (198 bp):
GATGCAACAATCAAGTAAAAGCAAAGATAGAATTAACAAAGAAAATAAAATACAAGTAATAAGCA
ACACATGAAAAAAAATTAGGAAAAGAAAGTTGTAATTGCTGTAGACACCCAATTTTGTCCGGCCT
TTTTTAGGACACTCAGTTTTTTTTAAAAAAATAATAATAAAAAAGAAAAAAAAAATTGAAAAATT
GAG
Found at i:1319261 original size:10 final size:10
Alignment explanation
Indices: 1319246--1319283 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
1319236 TTTCTCTTGT
*
1319246 AAATCTAGAA
1 AAATCTAAAA
1319256 AAATCTAAAA
1 AAATCTAAAA
1319266 AGAAT-TAAAA
1 A-AATCTAAAA
1319276 AAATCTAA
1 AAATCTAA
1319284 TTCCGGATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 3 0.12
10 19 0.76
11 3 0.12
ACGTcount: A:0.66, C:0.08, G:0.05, T:0.21
Consensus pattern (10 bp):
AAATCTAAAA
Found at i:1319481 original size:17 final size:15
Alignment explanation
Indices: 1319461--1319511 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 15
1319451 TTAGGTAAAA
1319461 AAGAAAGAAAGAAGATG
1 AAGAAAGAAAGAA-A-G
1319478 AAGAAA-AAAGAAAG
1 AAGAAAGAAAGAAAG
* *
1319492 AA-AAAGAAAAAAAA
1 AAGAAAGAAAGAAAG
1319506 AAGAAA
1 AAGAAA
1319512 AAATATGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 3 0.10
14 11 0.37
15 4 0.13
16 6 0.20
17 6 0.20
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (15 bp):
AAGAAAGAAAGAAAG
Found at i:1319489 original size:20 final size:17
Alignment explanation
Indices: 1319458--1319513 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
1319448 AAGTTAGGTA
1319458 AAAAAGAAAGAAAG-AAG
1 AAAAAGAAA-AAAGAAAG
**
1319475 ATGAAGAAAAAAGAAAG
1 AAAAAGAAAAAAGAAAG
*
1319492 AAAAAGAAAAAAAAAAG
1 AAAAAGAAAAAAGAAAG
1319509 AAAAA
1 AAAAA
1319514 ATATGAAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
16 4 0.12
17 29 0.88
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (17 bp):
AAAAAGAAAAAAGAAAG
Found at i:1319512 original size:11 final size:11
Alignment explanation
Indices: 1319457--1319514 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
1319447 AAAGTTAGGT
*
1319457 AAAAAAGAAAG
1 AAAAAAGAAAA
* *
1319468 AAAGAAGATGAAG
1 AAAAAAGA--AAA
1319481 AAAAAAG-AAA
1 AAAAAAGAAAA
*
1319491 GAAAAAGAAAA
1 AAAAAAGAAAA
1319502 AAAAAAGAAAA
1 AAAAAAGAAAA
1319513 AA
1 AA
1319515 TATGAAATGG
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
10 8 0.21
11 22 0.56
13 9 0.23
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:1319878 original size:2 final size:2
Alignment explanation
Indices: 1319865--1319903 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
1319855 TTATTTTATT
* *
1319865 TA TA TG TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1319904 TTTGAAAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1321434 original size:12 final size:12
Alignment explanation
Indices: 1321417--1321441 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1321407 AATTTTCTTT
1321417 TACTTGTCATTA
1 TACTTGTCATTA
1321429 TACTTGTCATTA
1 TACTTGTCATTA
1321441 T
1 T
1321442 GATGATTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (12 bp):
TACTTGTCATTA
Found at i:1327589 original size:14 final size:14
Alignment explanation
Indices: 1327570--1327629 Score: 52
Period size: 16 Copynumber: 4.1 Consensus size: 14
1327560 ATATAATAAA
1327570 AAAATTAATATATT
1 AAAATTAATATATT
* *
1327584 AAAATTTATATAAAAT
1 AAAA-TTA-ATATATT
1327600 AAATTATTAATATATT
1 AAA--ATTAATATATT
1327616 AAAATT--TATATT
1 AAAATTAATATATT
1327628 AA
1 AA
1327630 TTATATACTT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
12 8 0.21
14 7 0.18
15 3 0.08
16 16 0.42
17 3 0.08
18 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAAATTAATATATT
Found at i:1327593 original size:12 final size:10
Alignment explanation
Indices: 1327536--1327646 Score: 68
Period size: 11 Copynumber: 10.7 Consensus size: 10
1327526 AATCATATGA
1327536 AAAATA-ATT
1 AAAATATATT
1327545 AAAATATGATAT
1 AAAATAT-AT-T
*
1327557 AAAATATAAT
1 AAAATATATT
*
1327567 AAAA-AAATT
1 AAAATATATT
1327576 --AATATATT
1 AAAATATATT
*
1327584 AAAATTTATAT
1 AAAATATAT-T
*
1327595 AAAATAAATT
1 AAAATATATT
*
1327605 ATTAATATATT
1 A-AAATATATT
1327616 AAAATTTATATT
1 AAAA--TATATT
*
1327628 AATTATATACTT
1 AA-AATATA-TT
1327640 AAAATAT
1 AAAATAT
1327647 GTTTATGATA
Statistics
Matches: 78, Mismatches: 12, Indels: 22
0.70 0.11 0.20
Matches are distributed among these distances:
7 2 0.03
8 4 0.05
9 9 0.12
10 15 0.19
11 27 0.35
12 20 0.26
13 1 0.01
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.40
Consensus pattern (10 bp):
AAAATATATT
Done.