Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold40
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: 3440810
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 28138 characters in sequence are not A, C, G, or T
File 9 of 24
Found at i:1186755 original size:27 final size:27
Alignment explanation
Indices: 1186723--1186776 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
1186713 AGGAGAAAGA
* *
1186723 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACAGAATTGTGGACGTAAAAGGG
*
1186750 TGCCACGGAATTGTGGACGTAAAAGGG
1 TGCCACAGAATTGTGGACGTAAAAGGG
1186777 AAAAAGAGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.30, C:0.15, G:0.35, T:0.20
Consensus pattern (27 bp):
TGCCACAGAATTGTGGACGTAAAAGGG
Found at i:1186847 original size:34 final size:34
Alignment explanation
Indices: 1186743--1186899 Score: 166
Period size: 34 Copynumber: 4.8 Consensus size: 34
1186733 TTGTGGACTT
* *
1186743 AAAAGGGTGCCACGGAATTGTGGACGTAAAAGGGA
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAA-GGA
* * *
1186778 AAAAGAGTGCCACGGAGTTGTGGGCTT------T
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGA
* *
1186806 AAAAGGGTACCACGGAGTTGTGGACTTAGAAGGA
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGA
* *
1186840 AAAAGGGTGCCACGGAGTTGTGGGCTTAAAAAGA
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGA
*
1186874 AAAA-GGTGCCACGGAGTCGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
1186900 TGAGAAAGGA
Statistics
Matches: 101, Mismatches: 15, Indels: 14
0.78 0.12 0.11
Matches are distributed among these distances:
28 24 0.24
33 20 0.20
34 34 0.34
35 23 0.23
ACGTcount: A:0.32, C:0.13, G:0.36, T:0.18
Consensus pattern (34 bp):
AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGA
Found at i:1186872 original size:62 final size:62
Alignment explanation
Indices: 1186718--1186870 Score: 220
Period size: 62 Copynumber: 2.5 Consensus size: 62
1186708 TGAAGAGGAG
* * *
1186718 AAAGA-TGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAATTGTGGACGTAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTACCACGGAATTGTGGACGTAAAAGGGAA
* * *
1186779 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGGTACCACGGAGTTGTGGACTTAGAA-GGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAAAAGGGTACCACGGAATTGTGGACGTAAAAGGGAA
*
1186841 AAAGGGTGCCACGGAGTTGTGGGCTTAAAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAA
1186871 AGAAAAAGGT
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
61 11 0.13
62 43 0.52
63 29 0.35
ACGTcount: A:0.33, C:0.13, G:0.35, T:0.20
Consensus pattern (62 bp):
AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTACCACGGAATTGTGGACGTAAAAGGGAA
Found at i:1187882 original size:15 final size:15
Alignment explanation
Indices: 1187864--1187899 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1187854 TTTTCCTCTC
*
1187864 TTTTTTTTTGTGTGT
1 TTTTTTTTTGTGTCT
*
1187879 TTTTTTTTTGTTTCT
1 TTTTTTTTTGTGTCT
1187894 TTTTTT
1 TTTTTT
1187900 GTGAAGATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.00, C:0.03, G:0.11, T:0.86
Consensus pattern (15 bp):
TTTTTTTTTGTGTCT
Found at i:1194418 original size:52 final size:52
Alignment explanation
Indices: 1194270--1194398 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
1194260 CGAAATATGA
* *
1194270 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATATATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCAATACATCTGGGC
*
1194322 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCAATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCAATACATCTGGGC
*
1194374 AAATTTACCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1194399 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCAATACATCTGGGC
Found at i:1194498 original size:19 final size:18
Alignment explanation
Indices: 1194474--1194571 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
1194464 TAGCTTACAT
1194474 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
1194493 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1194506 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1194525 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1194538 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
1194558 TGTATCGATACAAA
1 TGTATCGATACAAA
1194572 TCGTTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 24 0.36
20 13 0.20
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1194510 original size:32 final size:32
Alignment explanation
Indices: 1194469--1194569 Score: 184
Period size: 32 Copynumber: 3.1 Consensus size: 32
1194459 TGCAGTAGCT
*
1194469 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
1194501 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
1194533 TACATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACAC-TTATGTATCGA
1194566 TACA
1 TACA
1194570 AATCGTTGAA
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
32 52 0.78
33 15 0.22
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.35
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:1194511 original size:13 final size:13
Alignment explanation
Indices: 1194493--1194549 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1194483 ACAAAACTTA
1194493 TGTATCGATACAT
1 TGTATCGATACAT
1194506 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
1194524 ATGTATCGATACAT
1 -TGTATCGATACAT
1194538 TGTATCGATACA
1 TGTATCGATACA
1194550 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1197411 original size:26 final size:26
Alignment explanation
Indices: 1197373--1197439 Score: 125
Period size: 26 Copynumber: 2.6 Consensus size: 26
1197363 ACTAGCTACA
*
1197373 TTTTGACTTGATATTGGTTTCATTGG
1 TTTTGACTCGATATTGGTTTCATTGG
1197399 TTTTGACTCGATATTGGTTTCATTGG
1 TTTTGACTCGATATTGGTTTCATTGG
1197425 TTTTGACTCGATATT
1 TTTTGACTCGATATT
1197440 ATTTTAATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.16, C:0.10, G:0.21, T:0.52
Consensus pattern (26 bp):
TTTTGACTCGATATTGGTTTCATTGG
Found at i:1199471 original size:6 final size:6
Alignment explanation
Indices: 1199460--1199492 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1199450 TTATAAATTT
*
1199460 TTTTTC TTTTTC TTTCTC TTTTTC TTTTT- TTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTT
1199493 CCAGTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTC
Found at i:1204843 original size:64 final size:64
Alignment explanation
Indices: 1204747--1204898 Score: 162
Period size: 65 Copynumber: 2.4 Consensus size: 64
1204737 CAACATTATC
* * *** * *
1204747 TTTCAAGGCTAAGATAGAAACATCTATATCTTTT-CACGGGCTAAAATAGAACCTCTTCCCTATC
1 TTTCAAGGCTAAGATAG-AACCTCCATATCTTTTACAAAAGCTAAAATAGAACCTCTACACTAT-
1204811 T
64 T
** * * *
1204812 TTTGTAGGCTAAGATAGAACCTCCCTATCTTTTACAAAAGTTAAGATAGAACCTCTACACTATT
1 TTTCAAGGCTAAGATAGAACCTCCATATCTTTTACAAAAGCTAAAATAGAACCTCTACACTATT
*
1204876 TTTCAAGGCTAAGATGGAACCTC
1 TTTCAAGGCTAAGATAGAACCTC
1204899 TCAATCACTT
Statistics
Matches: 71, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
64 34 0.48
65 37 0.52
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.32
Consensus pattern (64 bp):
TTTCAAGGCTAAGATAGAACCTCCATATCTTTTACAAAAGCTAAAATAGAACCTCTACACTATT
Found at i:1204889 original size:32 final size:32
Alignment explanation
Indices: 1204710--1204901 Score: 141
Period size: 32 Copynumber: 6.0 Consensus size: 32
1204700 AATGAATTGT
*
1204710 TATC-TTT-AAGGCTAAGATATAACCT-TACAAC
1 TATCTTTTCAAGGCTAAGATAGAACCTCT-C-AC
*
1204741 ATTATC-TTTCAAGGCTAAGATAGAAACATCT-A-
1 --TATCTTTTCAAGGCTAAGATAG-AACCTCTCAC
* * *
1204773 TATCTTTTCACGGGCTAAAATAGAACCTCTTCCC
1 TATCTTTTCA-AGGCTAAGATAGAACCTC-TCAC
**
1204807 TATCTTTTGTAGGCTAAGATAGAACCTC-C-C
1 TATCTTTTCAAGGCTAAGATAGAACCTCTCAC
* *
1204837 TATCTTTTACAAAAGTTAAGATAGAACCTCTACAC
1 TATCTTTT-C-AAGGCTAAGATAGAACCTCT-CAC
*
1204872 TAT-TTTTCAAGGCTAAGATGGAACCTCTCA
1 TATCTTTTCAAGGCTAAGATAGAACCTCTCA
1204902 ATCACTTGGA
Statistics
Matches: 129, Mismatches: 17, Indels: 28
0.74 0.10 0.16
Matches are distributed among these distances:
30 13 0.10
31 13 0.10
32 44 0.34
33 25 0.19
34 25 0.19
35 8 0.06
36 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.32
Consensus pattern (32 bp):
TATCTTTTCAAGGCTAAGATAGAACCTCTCAC
Found at i:1205429 original size:20 final size:19
Alignment explanation
Indices: 1205404--1205473 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 19
1205394 CCCAGTTTCA
1205404 TGTATCGATACAATTCAAT
1 TGTATCGATACAATTCAAT
* *
1205423 GTGTATCAATACTATGATC-A-
1 -TGTATCGATACAAT--TCAAT
*
1205443 TGTATCCATACAATTCAAT
1 TGTATCGATACAATTCAAT
1205462 CTGTATCGATAC
1 -TGTATCGATAC
1205474 TATGATCATA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
17 2 0.05
18 1 0.03
19 12 0.30
20 22 0.55
21 1 0.03
22 2 0.05
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (19 bp):
TGTATCGATACAATTCAAT
Found at i:1205448 original size:19 final size:19
Alignment explanation
Indices: 1205424--1205492 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
1205414 CAATTCAATG
*
1205424 TGTATCAATACTATGATCA
1 TGTATCGATACTATGATCA
* * *
1205443 TGTATCCATACAATTCAATC-
1 TGTATCGATACTA-T-GATCA
1205463 TGTATCGATACTATGATCA
1 TGTATCGATACTATGATCA
*
1205482 TATATCGATAC
1 TGTATCGATAC
1205493 AATGTATCGA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
18 3 0.08
19 22 0.55
20 12 0.30
21 3 0.08
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.36
Consensus pattern (19 bp):
TGTATCGATACTATGATCA
Found at i:1205455 original size:39 final size:39
Alignment explanation
Indices: 1205401--1205495 Score: 154
Period size: 39 Copynumber: 2.4 Consensus size: 39
1205391 ACTCCCAGTT
*
1205401 TCATGTATCGATACAATTCAATGTGTATCAATACTATGA
1 TCATGTATCGATACAATTCAATCTGTATCAATACTATGA
* *
1205440 TCATGTATCCATACAATTCAATCTGTATCGATACTATGA
1 TCATGTATCGATACAATTCAATCTGTATCAATACTATGA
*
1205479 TCATATATCGATACAAT
1 TCATGTATCGATACAAT
1205496 GTATCGATAC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 51 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (39 bp):
TCATGTATCGATACAATTCAATCTGTATCAATACTATGA
Found at i:1208354 original size:9 final size:10
Alignment explanation
Indices: 1208326--1208359 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
1208316 TTATAAATTT
1208326 TTAAAAGAATA
1 TTAAAA-AATA
1208337 TTAAAAAATA
1 TTAAAAAATA
1208347 TTAAAAATATA
1 TTAAAAA-ATA
1208358 TT
1 TT
1208360 TAATTATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 11 0.50
11 11 0.50
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (10 bp):
TTAAAAAATA
Found at i:1208358 original size:21 final size:22
Alignment explanation
Indices: 1208307--1208359 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
1208297 TTTTATAATG
* * * *
1208307 AAAGTTATATTATAAATTTTTA
1 AAAGATATATTAAAAAATATTA
1208329 AAAGA-ATATTAAAAAATATTA
1 AAAGATATATTAAAAAATATTA
1208350 AAA-ATATATT
1 AAAGATATATT
1208360 TAATTATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 21 0.81
22 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.40
Consensus pattern (22 bp):
AAAGATATATTAAAAAATATTA
Found at i:1209846 original size:39 final size:38
Alignment explanation
Indices: 1209824--1209923 Score: 105
Period size: 40 Copynumber: 2.5 Consensus size: 38
1209814 ATTTATATTA
1209824 TATTTTTTATTT-TTTTAAAATTTAATCTTTAATAATT
1 TATTTTTTATTTATTTTAAAATTTAATCTTTAATAATT
* * *
1209861 TATTTTTTATTTAATTTTAAAATATAAATAATTTAAT-ATA
1 TATTTTTTATTT-ATTTTAAAAT-TTAAT-CTTTAATAATT
1209901 TATTTTTAATATTTATATTTAAA
1 TATTTTT--TATTTAT-TTTAAA
1209924 TATATTTATT
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
37 12 0.23
39 9 0.17
40 13 0.25
41 8 0.15
42 11 0.21
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (38 bp):
TATTTTTTATTTATTTTAAAATTTAATCTTTAATAATT
Found at i:1209910 original size:13 final size:13
Alignment explanation
Indices: 1209892--1209930 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1209882 ATATAAATAA
1209892 TTTAATATATATT
1 TTTAATATATATT
* *
1209905 TTTAATATTTATA
1 TTTAATATATATT
1209918 TTTAA-ATATATT
1 TTTAATATATATT
1209930 T
1 T
1209931 ATTTTTTATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 6 0.27
13 16 0.73
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTAATATATATT
Found at i:1210289 original size:83 final size:85
Alignment explanation
Indices: 1210150--1210306 Score: 273
Period size: 83 Copynumber: 1.9 Consensus size: 85
1210140 GTAAAGCTGT
* *
1210150 ACCCCACTATTTTACCCGACAAGAGAAGAGAAAACGAATGTGGAAGAACACAAATTAG-AAAAAA
1 ACCCCACTATTTTACCCGAAAAGAGAAGAGAAAACGAATATGGAAGAACACAAATTAGAAAAAAA
1210214 CAA-CCGACAGACCAATAAA
66 CAAGCCGACAGACCAATAAA
*
1210233 ACCCCACTATTTTACCCGAAAAGAGAAGAGAAAACGAATATGGAAGAATACAAATTAGAAAAAAA
1 ACCCCACTATTTTACCCGAAAAGAGAAGAGAAAACGAATATGGAAGAACACAAATTAGAAAAAAA
1210298 CAAGCCGAC
66 CAAGCCGAC
1210307 TGATCACTAA
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
83 55 0.80
84 9 0.13
85 5 0.07
ACGTcount: A:0.51, C:0.20, G:0.16, T:0.13
Consensus pattern (85 bp):
ACCCCACTATTTTACCCGAAAAGAGAAGAGAAAACGAATATGGAAGAACACAAATTAGAAAAAAA
CAAGCCGACAGACCAATAAA
Found at i:1214827 original size:143 final size:144
Alignment explanation
Indices: 1214668--1214932 Score: 417
Period size: 143 Copynumber: 1.8 Consensus size: 144
1214658 TATAAATTTC
*
1214668 AAAAATCTCATTTCGTACCTTAATA-AAGAACCGAAAAGATACAAAAAATTTTAAAGATTTCTGT
1 AAAAATCTCATTTCGTACCTTAATAGAA-AACCGAAAAGATACAAAAAATTTTAAAGATTTCTAT
* * *
1214732 ACCCCTAAGAAAAATCATAGGAATATTAAAAATCTTGAAAAATTAAGATAATAATTTTTATTTAA
65 ACCCCTAAGAAAAATCATAGAAATATCAAAAATCTTAAAAAATTAAGATAATAATTTTTATTTAA
1214797 TTTTTTTAATTTATA
130 TTTTTTTAATTTATA
* * * *
1214812 AAAAAT-TCATTTCGTACCTTACTAGAAAACCGAAAAGATACGAAAAGTTTTGAAGATTTCTATA
1 AAAAATCTCATTTCGTACCTTAATAGAAAACCGAAAAGATACAAAAAATTTTAAAGATTTCTATA
* *
1214876 CCCCTACGAAAAATTATAGAAATATCAAAAATCTTAAAAAATTAAGATAATAATTTT
66 CCCCTAAGAAAAATCATAGAAATATCAAAAATCTTAAAAAATTAAGATAATAATTTT
1214933 AATTAGTGAT
Statistics
Matches: 110, Mismatches: 10, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
143 102 0.93
144 8 0.07
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (144 bp):
AAAAATCTCATTTCGTACCTTAATAGAAAACCGAAAAGATACAAAAAATTTTAAAGATTTCTATA
CCCCTAAGAAAAATCATAGAAATATCAAAAATCTTAAAAAATTAAGATAATAATTTTTATTTAAT
TTTTTTAATTTATA
Found at i:1215870 original size:12 final size:12
Alignment explanation
Indices: 1215853--1215908 Score: 69
Period size: 12 Copynumber: 4.7 Consensus size: 12
1215843 AATTTTTCTA
1215853 TTTTTTCTCTTT
1 TTTTTTCTCTTT
1215865 TTTTTTCTCTCTT
1 TTTTTTCTCT-TT
*
1215878 TTTCTT-TCTTT
1 TTTTTTCTCTTT
* *
1215889 CTTTCTCTCTTT
1 TTTTTTCTCTTT
1215901 TTTTTTCT
1 TTTTTTCT
1215909 TGCTTGCTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
11 5 0.14
12 24 0.67
13 7 0.19
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTTCTCTTT
Found at i:1215879 original size:22 final size:22
Alignment explanation
Indices: 1215845--1215909 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
1215835 TTTAGCTCAA
*
1215845 TTTTTCTAT-TTTTTCTCTT-TT
1 TTTTTCTCTCTTTTTCT-TTCTT
1215866 TTTTTCTCTCTTTTTCTTTCTT
1 TTTTTCTCTCTTTTTCTTTCTT
* *
1215888 TCTTTCTCTCTTTTTTTTTCTT
1 TTTTTCTCTCTTTTTCTTTCTT
1215910 GCTTGCTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
21 10 0.26
22 29 0.74
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTTCTCTCTTTTTCTTTCTT
Found at i:1215908 original size:14 final size:14
Alignment explanation
Indices: 1215853--1215892 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1215843 AATTTTTCTA
1215853 TTTTT-TCTCTTTT
1 TTTTTCTCTCTTTT
1215866 TTTTTCTCTCTTTT
1 TTTTTCTCTCTTTT
* *
1215880 TCTTTCTTTCTTT
1 TTTTTCTCTCTTT
1215893 CTCTCTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 5 0.21
14 19 0.79
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTCTCTCTTTT
Found at i:1215966 original size:13 final size:13
Alignment explanation
Indices: 1215948--1215973 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1215938 TTGCTCCCTA
1215948 TTTATAGTGGGAG
1 TTTATAGTGGGAG
1215961 TTTATAGTGGGAG
1 TTTATAGTGGGAG
1215974 GGGATGGCAA
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:0.23, C:0.00, G:0.38, T:0.38
Consensus pattern (13 bp):
TTTATAGTGGGAG
Found at i:1216364 original size:15 final size:15
Alignment explanation
Indices: 1216344--1216376 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1216334 TAATATTGGT
1216344 AAAATTT-TATGAAAA
1 AAAATTTGTAT-AAAA
1216359 AAAATTTGTATAAAA
1 AAAATTTGTATAAAA
1216374 AAA
1 AAA
1216377 TCAATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (15 bp):
AAAATTTGTATAAAA
Found at i:1218699 original size:12 final size:12
Alignment explanation
Indices: 1218682--1218708 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1218672 TGGAACTTGA
1218682 ATTATGAATATT
1 ATTATGAATATT
1218694 ATTATGAATATT
1 ATTATGAATATT
1218706 ATT
1 ATT
1218709 CTTGAATGTT
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:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
ATTATGAATATT
Found at i:1219173 original size:16 final size:16
Alignment explanation
Indices: 1219148--1219194 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
1219138 GACTAATTCA
1219148 AAAT-CGAAATGA-CC
1 AAATCCGAAATGATCC
1219162 TAAATCCGAAATGATCC
1 -AAATCCGAAATGATCC
*
1219179 GAATCCGAAATGATCC
1 AAATCCGAAATGATCC
1219195 GAACTTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 4 0.14
16 23 0.79
17 2 0.07
ACGTcount: A:0.43, C:0.23, G:0.15, T:0.19
Consensus pattern (16 bp):
AAATCCGAAATGATCC
Found at i:1219195 original size:16 final size:16
Alignment explanation
Indices: 1219164--1219197 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1219154 AAATGACCTA
1219164 AATCCGAAATGATCCG
1 AATCCGAAATGATCCG
1219180 AATCCGAAATGATCCG
1 AATCCGAAATGATCCG
1219196 AA
1 AA
1219198 CTTAAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.18
Consensus pattern (16 bp):
AATCCGAAATGATCCG
Found at i:1220538 original size:2 final size:2
Alignment explanation
Indices: 1220531--1220567 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1220521 AAGTTAGCAA
1220531 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1220568 ATAAACAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1220879 original size:20 final size:19
Alignment explanation
Indices: 1220854--1220921 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 19
1220844 TCAGTCAATT
*
1220854 TATTTAAATAGTATTTTAAA
1 TATTTAAATA-AATTTTAAA
*
1220874 TATTTAAATAAAAATTTAAA
1 TATTTAAAT-AAATTTTAAA
*
1220894 TA-TTAAATAAATATTAAA
1 TATTTAAATAAATTTTAAA
1220912 TATATTAAAT
1 TAT-TTAAAT
1220922 TATTAATAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 10 0.24
19 6 0.15
20 24 0.59
21 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (19 bp):
TATTTAAATAAATTTTAAA
Found at i:1220906 original size:11 final size:11
Alignment explanation
Indices: 1220870--1220921 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
1220860 AATAGTATTT
1220870 TAAATATTTAAA
1 TAAATA-TTAAA
*
1220882 TAAAAATT---
1 TAAATATTAAA
1220890 TAAATATTAAA
1 TAAATATTAAA
1220901 TAAATATTAAA
1 TAAATATTAAA
1220912 T--ATATTAAA
1 TAAATATTAAA
1220921 T
1 T
1220922 TATTAATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
8 7 0.20
9 9 0.26
11 14 0.40
12 5 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TAAATATTAAA
Found at i:1220931 original size:20 final size:20
Alignment explanation
Indices: 1220870--1220931 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
1220860 AATAGTATTT
1220870 TAAATAT-TTAAATAAA-AA
1 TAAATATATTAAATAAATAA
* *
1220888 TTTAA-ATATTAAATAAATAT
1 -TAAATATATTAAATAAATAA
* *
1220908 TAAATATATTAAATTATTAA
1 TAAATATATTAAATAAATAA
1220928 TAAA
1 TAAA
1220932 AGCATGCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
18 2 0.06
19 15 0.44
20 17 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAATATATTAAATAAATAA
Found at i:1223098 original size:34 final size:34
Alignment explanation
Indices: 1223043--1223191 Score: 147
Period size: 34 Copynumber: 4.4 Consensus size: 34
1223033 GGTTTGGTAA
* **
1223043 AAACCACCAAATCACCCATTTAATCAACAATAGC
1 AAACCACCAAATCTCTTATTTAATCAACAATAGC
* *
1223077 AAACTACCAAATCTCTTATTTAGTCAACAATAGC
1 AAACCACCAAATCTCTTATTTAATCAACAATAGC
* * ** * * *
1223111 AAACCATCAAATCACCAATTTAATCAATAATGGT
1 AAACCACCAAATCTCTTATTTAATCAACAATAGC
* * *
1223145 AAACTACCAAATCT-TTCATTTAGTCAACAATGGC
1 AAACCACCAAATCTCTT-ATTTAATCAACAATAGC
1223179 AAACCACCAAATC
1 AAACCACCAAATC
1223192 AATAATGGCA
Statistics
Matches: 91, Mismatches: 23, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
34 91 1.00
ACGTcount: A:0.44, C:0.26, G:0.05, T:0.24
Consensus pattern (34 bp):
AAACCACCAAATCTCTTATTTAATCAACAATAGC
Found at i:1223115 original size:68 final size:68
Alignment explanation
Indices: 1223043--1223192 Score: 230
Period size: 68 Copynumber: 2.2 Consensus size: 68
1223033 GGTTTGGTAA
*
1223043 AAACCACCAAATCACCCATTTAATCAACAATAGCAAACTACCAAATCTCTT-ATTTAGTCAACAA
1 AAACCACCAAATCACCAATTTAATCAACAATAGCAAACTACCAAATCT-TTCATTTAGTCAACAA
1223107 TAGC
65 TAGC
* * * *
1223111 AAACCATCAAATCACCAATTTAATCAATAATGGTAAACTACCAAATCTTTCATTTAGTCAACAAT
1 AAACCACCAAATCACCAATTTAATCAACAATAGCAAACTACCAAATCTTTCATTTAGTCAACAAT
*
1223176 GGC
66 AGC
1223179 AAACCACCAAATCA
1 AAACCACCAAATCA
1223193 ATAATGGCAA
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
67 2 0.03
68 72 0.97
ACGTcount: A:0.45, C:0.26, G:0.05, T:0.24
Consensus pattern (68 bp):
AAACCACCAAATCACCAATTTAATCAACAATAGCAAACTACCAAATCTTTCATTTAGTCAACAAT
AGC
Found at i:1223198 original size:22 final size:22
Alignment explanation
Indices: 1223168--1223214 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
1223158 TTTCATTTAG
1223168 TCAACAATGGCAAACCACCAAA
1 TCAACAATGGCAAACCACCAAA
* *
1223190 TCAATAATGGCAAACTACCAAA
1 TCAACAATGGCAAACCACCAAA
1223212 TCA
1 TCA
1223215 CTATTTAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.28, G:0.09, T:0.15
Consensus pattern (22 bp):
TCAACAATGGCAAACCACCAAA
Found at i:1227706 original size:34 final size:34
Alignment explanation
Indices: 1227668--1227814 Score: 149
Period size: 34 Copynumber: 4.4 Consensus size: 34
1227658 CAAATCACCT
* *
1227668 ATTTAATCAACAAT-AGCAAACTATCAAATTTCCC
1 ATTTAATCAACAATGA-CAAACTACCAAATTTCTC
* ** *
1227702 ATTTAGTCAACAATGACAAACTACCAAATCACTA
1 ATTTAATCAACAATGACAAACTACCAAATTTCTC
** *
1227736 ATTTAATCAACAATGGTAAACTACCAAATCTT-TT
1 ATTTAATCAACAATGACAAACTACCAAAT-TTCTC
*
1227770 ATTTAGTCAACAATGACAAACTACCAAA--TCATC
1 ATTTAATCAACAATGACAAACTACCAAATTTC-TC
1227803 ATTTAATCAACA
1 ATTTAATCAACA
1227815 TATTAGAGTA
Statistics
Matches: 92, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
31 1 0.01
33 12 0.13
34 78 0.85
35 1 0.01
ACGTcount: A:0.45, C:0.22, G:0.05, T:0.29
Consensus pattern (34 bp):
ATTTAATCAACAATGACAAACTACCAAATTTCTC
Found at i:1227740 original size:68 final size:67
Alignment explanation
Indices: 1227655--1227814 Score: 225
Period size: 68 Copynumber: 2.4 Consensus size: 67
1227645 TAGTAAAAAT
*
1227655 TACCAAATCACCTATTTAATCAACAATAGCAAACTATCAAAT-TTCCCATTTAGTCAACAATGAC
1 TACCAAATCA-CTATTTAATCAACAATAGCAAACTACCAAATCTT-CCATTTAGTCAACAATGAC
1227719 AAAC
64 AAAC
* * **
1227723 TACCAAATCACTAATTTAATCAACAATGGTAAACTACCAAATCTTTTATTTAGTCAACAATGACA
1 TACCAAATCACT-ATTTAATCAACAATAGCAAACTACCAAATCTTCCATTTAGTCAACAATGACA
1227788 AAC
65 AAC
1227791 TACCAAATCA-TCATTTAATCAACA
1 TACCAAATCACT-ATTTAATCAACA
1227815 TATTAGAGTA
Statistics
Matches: 84, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
67 15 0.18
68 67 0.80
69 2 0.02
ACGTcount: A:0.44, C:0.23, G:0.04, T:0.28
Consensus pattern (67 bp):
TACCAAATCACTATTTAATCAACAATAGCAAACTACCAAATCTTCCATTTAGTCAACAATGACAA
AC
Found at i:1231334 original size:17 final size:16
Alignment explanation
Indices: 1231312--1231345 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1231302 TAGGGATATA
1231312 TTCCTTTTAATATTTTT
1 TTCCTTTTAAT-TTTTT
*
1231329 TTCCTTTTCATTTTTT
1 TTCCTTTTAATTTTTT
1231345 T
1 T
1231346 ATAGGTGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.74
Consensus pattern (16 bp):
TTCCTTTTAATTTTTT
Found at i:1232065 original size:9 final size:10
Alignment explanation
Indices: 1232037--1232069 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
1232027 TAATTACACT
1232037 ATATAAATATA
1 ATATAAA-ATA
1232048 ATATAAAATA
1 ATATAAAATA
1232058 AT-TAAAATA
1 ATATAAAATA
1232067 ATA
1 ATA
1232070 ATATAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.43
10 5 0.24
11 7 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
ATATAAAATA
Found at i:1235027 original size:2 final size:2
Alignment explanation
Indices: 1235020--1235052 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1235010 TGCTTGAACT
1235020 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1235053 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1235305 original size:14 final size:14
Alignment explanation
Indices: 1235277--1235326 Score: 59
Period size: 13 Copynumber: 3.6 Consensus size: 14
1235267 ACCTATAATT
1235277 TTAAAATAA-ATTA
1 TTAAAATAATATTA
1235290 TTAAAATAATATTA
1 TTAAAATAATATTA
*
1235304 TTTTAAAATTAT-TTA
1 --TTAAAATAATATTA
1235319 TTAAAATA
1 TTAAAATA
1235327 TTACTATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 16 0.50
14 4 0.12
15 3 0.09
16 9 0.28
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TTAAAATAATATTA
Found at i:1235308 original size:29 final size:29
Alignment explanation
Indices: 1235274--1235337 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
1235264 AGCACCTATA
*
1235274 ATTTTAAAATAAATTATTAAAATAATATT
1 ATTTTAAAATAAATTATTAAAATAATACT
* * *
1235303 ATTTTAAAATTATTTATTAAAATATTACT
1 ATTTTAAAATAAATTATTAAAATAATACT
1235332 ATTTTA
1 ATTTTA
1235338 TTTACGTGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (29 bp):
ATTTTAAAATAAATTATTAAAATAATACT
Found at i:1236438 original size:21 final size:22
Alignment explanation
Indices: 1236396--1236438 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
1236386 ATTTTAAATT
*
1236396 TTTTAAAATATTTATCGTATAA
1 TTTTAAAATATTTATCATATAA
1236418 TTTT-AAATATTT-TCATGATAA
1 TTTTAAAATATTTATCAT-ATAA
1236439 AATACATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 3 0.16
21 12 0.63
22 4 0.21
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (22 bp):
TTTTAAAATATTTATCATATAA
Found at i:1236502 original size:170 final size:166
Alignment explanation
Indices: 1236306--1236633 Score: 410
Period size: 170 Copynumber: 2.0 Consensus size: 166
1236296 ATTAAGTTTA
* * * ** *
1236306 AAAGAAAAATATAAATTAACACTTTCGTATTAAAATATGACAGTTTCTTAATTCAAAAAATTAGT
1 AAAGAAAAAAATAAATTAACACTTTCGTATCAAAATATGACAGTTTATTAAGCCAAAAAA-TACT
* * *
1236371 -TTTACATAATTATAGATTTTAAATTTTTTAAAATATTTATCGT-ATAATTTTAAATATTTTCAT
65 CTTTACATAATTATAGATTTT-AA-TTTTTAAAATATTTAT--TAAAAATTTTAAATATTTTAAA
* *
1236434 GATAAAATACATTTA-TTAGATAAAAATTTATGATAACCCCC
126 AATAAAATACATTTAGTGA-ATAAAAATTTATGATAACCCCC
* * * *
1236475 AAAGAAAAAAAGTAAATTGATACTTTCGTATCAAGATATGACAGTTTATTAAGCCAAAAAATCCT
1 AAAGAAAAAAA-TAAATTAACACTTTCGTATCAAAATATGACAGTTTATTAAGCCAAAAAATACT
* *
1236540 CTTTACATAATTTTAGATTTTAATTTTTAAAATATTTATTAAAAATTTTATATATTTTAAAAATA
65 CTTTACATAATTATAGATTTTAATTTTTAAAATATTTATTAAAAATTTTAAATATTTTAAAAATA
*
1236605 AAATATATTTAGTGAATAAAAATTTATGA
130 AAATACATTTAGTGAATAAAAATTTATGA
1236634 AATAATAAAT
Statistics
Matches: 137, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
166 1 0.01
167 43 0.31
168 18 0.13
169 14 0.10
170 61 0.45
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (166 bp):
AAAGAAAAAAATAAATTAACACTTTCGTATCAAAATATGACAGTTTATTAAGCCAAAAAATACTC
TTTACATAATTATAGATTTTAATTTTTAAAATATTTATTAAAAATTTTAAATATTTTAAAAATAA
AATACATTTAGTGAATAAAAATTTATGATAACCCCC
Found at i:1236610 original size:18 final size:18
Alignment explanation
Indices: 1236567--1236614 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
1236557 TTTTAATTTT
1236567 TAAAATAT-TTATTAAAAA
1 TAAAATATATT-TTAAAAA
***
1236585 TTTTATATATTTTAAAAA
1 TAAAATATATTTTAAAAA
1236603 TAAAATATATTT
1 TAAAATATATTT
1236615 AGTGAATAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TAAAATATATTTTAAAAA
Found at i:1237359 original size:20 final size:20
Alignment explanation
Indices: 1237334--1237499 Score: 143
Period size: 20 Copynumber: 7.8 Consensus size: 20
1237324 TTTTACCCAG
1237334 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
1237354 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
1237374 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
*
1237394 ATGTATCGATATATTCTGTTTTTTTATCCA
1 ATGTATCG--ATA--C----ATTTT-T-CA
*
1237424 GATGTATCGATACAGTTTTCA
1 -ATGTATCGATACATTTTTCA
* * *
1237445 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
1237465 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
1237485 ATGTATCGATACATT
1 ATGTATCGATACATT
1237500 CTGTCTTTTT
Statistics
Matches: 116, Mismatches: 19, Indels: 22
0.74 0.12 0.14
Matches are distributed among these distances:
20 88 0.76
21 2 0.02
22 4 0.03
23 3 0.03
24 1 0.01
27 1 0.01
28 3 0.03
29 4 0.03
30 2 0.02
31 8 0.07
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1237394 original size:40 final size:40
Alignment explanation
Indices: 1237334--1237498 Score: 188
Period size: 40 Copynumber: 3.9 Consensus size: 40
1237324 TTTTACCCAG
*
1237334 ATGTATCGATACATTTTTCAATGTATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATGTATCGATACATGTATGA
* *
1237374 ATGTATCGATACATTCTTCAATGTATCGATATATTCTGTTTTTTTATCCA
1 ATGTATCGATACATTCTTCAATGTATCGATACA---TG------TAT-GA
1237424 GATGTATCGATACAGTT-TTCAATGTATCGATACATGTATGA
1 -ATGTATCGATACA-TTCTTCAATGTATCGATACATGTATGA
1237465 ATGTATCGATACATTCTTCAATGTATCGATACAT
1 ATGTATCGATACATTCTTCAATGTATCGATACAT
1237499 TCTGTCTTTT
Statistics
Matches: 107, Mismatches: 5, Indels: 26
0.78 0.04 0.19
Matches are distributed among these distances:
39 2 0.02
40 62 0.58
41 1 0.01
42 3 0.03
43 2 0.02
48 2 0.02
49 3 0.03
50 1 0.01
51 29 0.27
52 2 0.02
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (40 bp):
ATGTATCGATACATTCTTCAATGTATCGATACATGTATGA
Found at i:1237479 original size:91 final size:92
Alignment explanation
Indices: 1237324--1237549 Score: 402
Period size: 91 Copynumber: 2.5 Consensus size: 92
1237314 AAAGTCATAA
1237324 TTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACATT
1 TTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACATT
*
1237389 CTTCAATGTATCGATATATTCTGT-TT
66 CTTCAATGTATCGATACATTCTGTCTT
* *
1237415 TTTTATCCAGATGTATCGATACAGTTTTCAATGTATCGATACATGTATGAATGTATCGATACATT
1 TTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACATT
1237480 CTTCAATGTATCGATACATTCTGTCTT
66 CTTCAATGTATCGATACATTCTGTCTT
*
1237507 TTTT-CCCAGATGTATCGATACATTTTTTAATGTATCGATACAT
1 TTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACAT
1237550 TTCATTAAAA
Statistics
Matches: 128, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
91 122 0.95
92 6 0.05
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.42
Consensus pattern (92 bp):
TTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACATT
CTTCAATGTATCGATACATTCTGTCTT
Found at i:1238144 original size:20 final size:20
Alignment explanation
Indices: 1238119--1238311 Score: 127
Period size: 20 Copynumber: 8.7 Consensus size: 20
1238109 TTTTACTCAG
1238119 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
*
1238139 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
*
1238159 ATGTATCAATACATTTTTTTTTACCCA
1 ATGTATCGATACA----TTTTT---CA
*
1238186 GATGTATCAATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
* * * *
1238207 ATTTATCGATACATGTATAA
1 ATGTATCGATACATTTTTCA
*
1238227 ATGTATCGATGCATTCTTT-A
1 ATGTATCGATACATT-TTTCA
1238247 ATGTATCGATACATTCTGTCTTTTTTTCTA
1 ATGTATCGATACA---------TTTTTC-A
1238277 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
1238298 ATGTATCGATACAT
1 ATGTATCGATACAT
1238312 CTAGTTAAAA
Statistics
Matches: 139, Mismatches: 13, Indels: 42
0.72 0.07 0.22
Matches are distributed among these distances:
20 85 0.61
21 5 0.04
22 6 0.04
24 9 0.06
27 2 0.01
28 16 0.12
29 2 0.01
30 1 0.01
31 13 0.09
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.45
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1240586 original size:248 final size:248
Alignment explanation
Indices: 1240148--1240611 Score: 883
Period size: 248 Copynumber: 1.9 Consensus size: 248
1240138 TTTTTGGATT
*
1240148 TTTGAAATATTTTTAAATCGACCCTCATTGAGTCACCTTTTGAATAGTATCTCTTTCACCTTTTA
1 TTTGAAATATTTTTAAATCGACCCTCATTGAGTCACCTTTTGAATAATATCTCTTTCACCTTTTA
*
1240213 TAACTTCTGAATCAACCCGAAATAAACTTGGGAAGTGGGATAGCACGAAGCTGTCCCCCTGTTTT
66 TAACTTCTGAATCAACCCGAAATAAACTTGGGAAGTGGGATAGCACGAAGCTGTCCCCCTATTTT
1240278 CGGTTGTTGCCAAAATTGATTTTTTTCTCTTGATCCCATCCCAAGACATTCGGATGTCTCCGTAC
131 CGGTTGTTGCCAAAATTGATTTTTTTCTCTTGATCCCATCCCAAGACATTCGGATGTCTCCGTAC
*
1240343 AGCCCCGATCAACTTTGAAATAGTATCTCTTTCACCTTTTGAATAGTATCAAC
196 AGCCCCAATCAACTTTGAAATAGTATCTCTTTCACCTTTTGAATAGTATCAAC
1240396 TTTGAAATATTTTTAAATCGACCCTCATTGAGTCACCTTTTGAATAATATCTCTTTCACCTTTTA
1 TTTGAAATATTTTTAAATCGACCCTCATTGAGTCACCTTTTGAATAATATCTCTTTCACCTTTTA
*
1240461 TAACTTCTGAATCAACCTGAAATAAACTTGGGAAGTGGGATAGCACGAAGCTGTCCCCCTATTTT
66 TAACTTCTGAATCAACCCGAAATAAACTTGGGAAGTGGGATAGCACGAAGCTGTCCCCCTATTTT
1240526 CGGTTGTTGCCAAAATTGATTTTTTTCTCTTGATCCCATCCCAAGACATTCGGATGTCTCCGTAC
131 CGGTTGTTGCCAAAATTGATTTTTTTCTCTTGATCCCATCCCAAGACATTCGGATGTCTCCGTAC
*
1240591 AGCCCCAATCAATTTTGAAAT
196 AGCCCCAATCAACTTTGAAAT
1240612 CTTTTTGGAC
Statistics
Matches: 211, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
248 211 1.00
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.36
Consensus pattern (248 bp):
TTTGAAATATTTTTAAATCGACCCTCATTGAGTCACCTTTTGAATAATATCTCTTTCACCTTTTA
TAACTTCTGAATCAACCCGAAATAAACTTGGGAAGTGGGATAGCACGAAGCTGTCCCCCTATTTT
CGGTTGTTGCCAAAATTGATTTTTTTCTCTTGATCCCATCCCAAGACATTCGGATGTCTCCGTAC
AGCCCCAATCAACTTTGAAATAGTATCTCTTTCACCTTTTGAATAGTATCAAC
Found at i:1242751 original size:21 final size:22
Alignment explanation
Indices: 1242696--1242760 Score: 62
Period size: 24 Copynumber: 2.9 Consensus size: 22
1242686 TTAATTTTAT
*
1242696 TTTTAAAATTTTAAAATAATTA
1 TTTTAAATTTTTAAAATAATTA
* *
1242718 TTTTATATTTTTTTATAATAATTA
1 TTTTA-A-ATTTTTAAAATAATTA
1242742 -TTTAAA-TTTTAAATATAAT
1 TTTTAAATTTTTAAA-ATAAT
1242761 ATAAAATTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
20 6 0.17
21 5 0.14
22 6 0.17
23 5 0.14
24 13 0.37
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTAAATTTTTAAAATAATTA
Found at i:1242873 original size:31 final size:32
Alignment explanation
Indices: 1242812--1242896 Score: 84
Period size: 33 Copynumber: 2.5 Consensus size: 32
1242802 TATGAATCTC
1242812 ATAATATTTTATTTTATTAAATTAAATAATTTTT
1 ATAATATTTTATTTTA-TAAA-TAAATAATTTTT
1242846 ATAATTATTTTATTTTA-AAA-AAATAATTATTTT
1 ATAA-TATTTTATTTTATAAATAAATAA-T-TTTT
* *
1242879 ATTATAATTATATTTTAT
1 ATAAT-ATTTTATTTTAT
1242897 TTTGAATAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
31 6 0.14
32 2 0.05
33 20 0.45
34 4 0.09
35 12 0.27
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (32 bp):
ATAATATTTTATTTTATAAATAAATAATTTTT
Found at i:1243527 original size:16 final size:17
Alignment explanation
Indices: 1243508--1243542 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1243498 TAAAAAATTG
1243508 ATTTAAT-AATTTAAAT
1 ATTTAATAAATTTAAAT
1243524 ATTTAATAAATTTAAAT
1 ATTTAATAAATTTAAAT
1243541 AT
1 AT
1243543 CTGATAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTTAATAAATTTAAAT
Found at i:1243549 original size:17 final size:17
Alignment explanation
Indices: 1243511--1243549 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1243501 AAAATTGATT
*
1243511 TAAT-AATTTAAATATT
1 TAATAAATTTAAATATC
1243527 TAATAAATTTAAATATC
1 TAATAAATTTAAATATC
*
1243544 TGATAA
1 TAATAA
1243550 TAATTACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (17 bp):
TAATAAATTTAAATATC
Found at i:1245101 original size:2 final size:2
Alignment explanation
Indices: 1245089--1245127 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1245079 TTTGCTCCAA
*
1245089 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1245128 ACAAGGAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1245655 original size:19 final size:20
Alignment explanation
Indices: 1245614--1245666 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
1245604 CATATCAATT
1245614 TTTTATATTAATTATATTAA
1 TTTTATATTAATTATATTAA
*
1245634 TTTT-TATTAATTGATGTT-A
1 TTTTATATTAATT-ATATTAA
*
1245653 TTTTATATTGATTA
1 TTTTATATTAATTA
1245667 GCACAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (20 bp):
TTTTATATTAATTATATTAA
Found at i:1245710 original size:18 final size:18
Alignment explanation
Indices: 1245683--1245766 Score: 62
Period size: 18 Copynumber: 4.5 Consensus size: 18
1245673 AATTTTTATT
1245683 TTTTTA-TTTTTTAAATA
1 TTTTTATTTTTTTAAATA
* **
1245700 TTTTTATTTTTTCAACCA
1 TTTTTATTTTTTTAAATA
*
1245718 TTTTCTAATTTTTTTAAGATCG
1 TTTT-T-ATTTTTTTAA-AT-A
**
1245740 TTTTTATTTTTTTTCATA
1 TTTTTATTTTTTTAAATA
*
1245758 ATTTTATTT
1 TTTTTATTT
1245767 AAAAACAAAA
Statistics
Matches: 51, Mismatches: 11, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
17 6 0.12
18 20 0.39
19 3 0.06
20 17 0.33
21 1 0.02
22 4 0.08
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTTTATTTTTTTAAATA
Found at i:1248818 original size:58 final size:58
Alignment explanation
Indices: 1248728--1248837 Score: 193
Period size: 58 Copynumber: 1.9 Consensus size: 58
1248718 GAGGAGTAGA
* * *
1248728 GTTGGAGTGTTCCCGACAATGATAATTTAGGTAAAAATAAGAATGATCTTGGAATGGG
1 GTTGGAGTGCTCCCAACAATGATAATTTAGGTAAAAATAAGAATAATCTTGGAATGGG
1248786 GTTGGAGTGCTCCCAACAATGATAATTTAGGTAAAAATAAGAATAATCTTGG
1 GTTGGAGTGCTCCCAACAATGATAATTTAGGTAAAAATAAGAATAATCTTGG
1248838 CAAATATAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 49 1.00
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.29
Consensus pattern (58 bp):
GTTGGAGTGCTCCCAACAATGATAATTTAGGTAAAAATAAGAATAATCTTGGAATGGG
Found at i:1251791 original size:2 final size:2
Alignment explanation
Indices: 1251784--1251820 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1251774 TTTTCTCCAA
1251784 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1251821 AAACAAGGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1252610 original size:16 final size:16
Alignment explanation
Indices: 1252568--1252611 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
1252558 TTATTTGATG
*
1252568 TAAAAATTTAAAATAT
1 TAAAAATTTATAATAT
* *
1252584 TAAATATTTATAATTT
1 TAAAAATTTATAATAT
1252600 TAAAAATTTATA
1 TAAAAATTTATA
1252612 TTTGTATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAAAATTTATAATAT
Found at i:1253184 original size:80 final size:80
Alignment explanation
Indices: 1253051--1253210 Score: 295
Period size: 80 Copynumber: 2.0 Consensus size: 80
1253041 ACTGAGCAAT
*
1253051 GCTTTTTCGTGTTTTGGGGTTTATTGAGTAATTCAATAGGAAAGGATAGAAAGAAAAGAAAAGGA
1 GCTTTTTCGTGTTTTGGGGTTTACTGAGTAATTCAATAGGAAAGGATAGAAAGAAAAGAAAAGGA
1253116 AAGAAAAGAAATGAA
66 AAGAAAAGAAATGAA
1253131 GCTTTTGT-GTGTTTTGGGGTTTACTGAGTAATTCAATAGGAAAGGATAGAAAGAAAAGAAAAGG
1 GCTTTT-TCGTGTTTTGGGGTTTACTGAGTAATTCAATAGGAAAGGATAGAAAGAAAAGAAAAGG
1253195 AAAGAAAAGAAATGAA
65 AAAGAAAAGAAATGAA
1253211 AGGGATAGAA
Statistics
Matches: 78, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
80 77 0.99
81 1 0.01
ACGTcount: A:0.44, C:0.04, G:0.27, T:0.26
Consensus pattern (80 bp):
GCTTTTTCGTGTTTTGGGGTTTACTGAGTAATTCAATAGGAAAGGATAGAAAGAAAAGAAAAGGA
AAGAAAAGAAATGAA
Found at i:1253205 original size:20 final size:20
Alignment explanation
Indices: 1253171--1253289 Score: 66
Period size: 20 Copynumber: 5.9 Consensus size: 20
1253161 ATTCAATAGG
*
1253171 AAAGGATAG-AAAGAAAAGA
1 AAAGGAAAGAAAAGAAAAGA
*
1253190 AAAGGAAAGAAAAGAAATGA
1 AAAGGAAAGAAAAGAAAAGA
* * * *
1253210 AAGGGATAG-AAGGGAAAGA
1 AAAGGAAAGAAAAGAAAAGA
* *
1253229 AGAGGGAAAGAAGAAGGAAAGA
1 A-AAGGAAAGAA-AAGAAAAGA
*
1253251 AAA-GAAATAAGAA-AGAAAGA
1 AAAGGAAAGAA-AAGA-AAAGA
**
1253271 AAAAAAAAGAAAGAGAAAA
1 AAAGGAAAGAAA-AGAAAA
1253290 AAATTTAAAA
Statistics
Matches: 78, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
19 16 0.21
20 41 0.53
21 11 0.14
22 10 0.13
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (20 bp):
AAAGGAAAGAAAAGAAAAGA
Found at i:1253205 original size:24 final size:24
Alignment explanation
Indices: 1253168--1253292 Score: 67
Period size: 25 Copynumber: 5.0 Consensus size: 24
1253158 GTAATTCAAT
* *
1253168 AGGAAAGGATAGAAAGAAAAGAAA
1 AGGAAAGAAAAGAAAGAAAAGAAA
* * *
1253192 AGGAAAGAAAAGAAATGAAAGGGAT
1 AGGAAAGAAAAGAAA-GAAAAGAAA
* * *
1253217 A-GAAGGGAAAGAAGAGGGAAAGAAGA
1 AGGAAAGAAAAGAA-A-GAAAAGAA-A
*
1253243 AGGAAAGAAAAGAAATAAGAA-AGAA
1 AGGAAAGAAAAGAAAGAA-AAGA-AA
* *
1253268 AGAAAAAAAAAGAAAGAGAAA-AAA
1 AGGAAAGAAAAGAAAGA-AAAGAAA
1253292 A
1 A
1253293 TTTAAAAAAT
Statistics
Matches: 75, Mismatches: 19, Indels: 14
0.69 0.18 0.13
Matches are distributed among these distances:
24 26 0.35
25 33 0.44
26 6 0.08
27 10 0.13
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (24 bp):
AGGAAAGAAAAGAAAGAAAAGAAA
Found at i:1253236 original size:11 final size:11
Alignment explanation
Indices: 1253220--1253251 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1253210 AAGGGATAGA
1253220 AGGGAAAGAAG
1 AGGGAAAGAAG
1253231 AGGGAAAGAAG
1 AGGGAAAGAAG
*
1253242 AAGGAAAGAA
1 AGGGAAAGAA
1253252 AAGAAATAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (11 bp):
AGGGAAAGAAG
Found at i:1253264 original size:16 final size:15
Alignment explanation
Indices: 1253235--1253290 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 15
1253225 AAGAAGAGGG
*
1253235 AAAGAAGAAGGAAAGA
1 AAAGAA-AAAGAAAGA
1253251 AAAGAAATAAGAAAG-
1 AAAGAAA-AAGAAAGA
*
1253266 AAAGAAAAAAAAAGA
1 AAAGAAAAAGAAAGA
1253281 AAGAGAAAAA
1 AA-AGAAAAA
1253291 AATTTAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
14 6 0.17
15 10 0.29
16 19 0.54
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (15 bp):
AAAGAAAAAGAAAGA
Found at i:1253441 original size:13 final size:13
Alignment explanation
Indices: 1253414--1253451 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1253404 GAGTACATGA
1253414 TTATATT-TATTT
1 TTATATTATATTT
*
1253426 TTATATTATTTTT
1 TTATATTATATTT
1253439 TTATATTATATTT
1 TTATATTATATTT
1253452 GTATTATATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTATATTATATTT
Found at i:1253585 original size:21 final size:21
Alignment explanation
Indices: 1253546--1253585 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1253536 TATCGTGACT
* *
1253546 TAATTTATGATATTTATTTTA
1 TAATTTATGATAATAATTTTA
*
1253567 TAATTTATTATAATAATTT
1 TAATTTATGATAATAATTT
1253586 ATTTTTTTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (21 bp):
TAATTTATGATAATAATTTTA
Found at i:1253585 original size:25 final size:26
Alignment explanation
Indices: 1253557--1253608 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 26
1253547 AATTTATGAT
*
1253557 ATTTA-TTTTATAATTTATTATAATA
1 ATTTATTTTTATAATTTATCATAATA
1253582 ATTTATTTTTTTATAATTTATCATAAT
1 ATTTA--TTTTTATAATTTATCATAAT
1253609 TATTCATGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 5 0.22
28 18 0.78
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (26 bp):
ATTTATTTTTATAATTTATCATAATA
Found at i:1253599 original size:15 final size:15
Alignment explanation
Indices: 1253556--1253602 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
1253546 TAATTTATGA
1253556 TATTTATTTTATAATT
1 TATTT-TTTTATAATT
* *
1253572 TA--TTATAATAATT
1 TATTTTTTTATAATT
1253585 TATTTTTTTATAATT
1 TATTTTTTTATAATT
1253600 TAT
1 TAT
1253603 CATAATTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
13 10 0.40
14 1 0.04
15 12 0.48
16 2 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TATTTTTTTATAATT
Found at i:1254112 original size:2 final size:2
Alignment explanation
Indices: 1254105--1254145 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1254095 CCCCAAGAGC
1254105 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1254146 CCTTGACATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1256156 original size:17 final size:16
Alignment explanation
Indices: 1256132--1256167 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
1256122 TTTTAAGTTC
1256132 TTTTATTTTAAATTAT
1 TTTTATTTTAAATTAT
*
1256148 TTTTAATTTTAAATTCT
1 TTTT-ATTTTAAATTAT
1256165 TTT
1 TTT
1256168 GATTATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTATTTTAAATTAT
Found at i:1256180 original size:21 final size:20
Alignment explanation
Indices: 1256154--1256199 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1256144 TTATTTTTAA
*
1256154 TTTTAAATTCTT-TTGATTAT
1 TTTTAAATT-TTAATGATTAT
1256174 TATTTAAATTTTAATGATTAT
1 T-TTTAAATTTTAATGATTAT
1256195 TTTTA
1 TTTTA
1256200 TATAATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.63
Consensus pattern (20 bp):
TTTTAAATTTTAATGATTAT
Found at i:1256694 original size:16 final size:16
Alignment explanation
Indices: 1256675--1256730 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 16
1256665 TTTAGTTTTT
*
1256675 AATTATTTTAAATTTA
1 AATTATTTTAAGTTTA
*
1256691 AATTACTTTAAGTTTA
1 AATTATTTTAAGTTTA
* * *
1256707 AGTCATTTCAAGTTTA
1 AATTATTTTAAGTTTA
1256723 AATT-TTTT
1 AATTATTTT
1256731 CATGGTCTTT
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
15 3 0.10
16 28 0.90
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (16 bp):
AATTATTTTAAGTTTA
Found at i:1257298 original size:15 final size:15
Alignment explanation
Indices: 1257259--1257298 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
1257249 TTGTTCATTA
1257259 TATTATTAAT-TTTT
1 TATTATTAATATTTT
1257273 TATT-TTAAATATTTT
1 TATTATT-AATATTTT
1257288 TATTATTAATA
1 TATTATTAATA
1257299 AAATTTATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 2 0.09
14 7 0.30
15 12 0.52
16 2 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTATTAATATTTT
Found at i:1257398 original size:73 final size:74
Alignment explanation
Indices: 1257318--1257454 Score: 222
Period size: 73 Copynumber: 1.9 Consensus size: 74
1257308 TTACTTATAA
* * *
1257318 ATAATAAAATTTATTACATTTGTAAATAAGAATTTTAATTATATTGAAAGA-TTTGGTTAAATGA
1 ATAATAAAATTTATTACATTTGTAAATAAGAATTCTAATTATATTAAAAGACTTTGGGTAAATGA
1257382 ATTTATTGG
66 ATTTATTGG
* *
1257391 ATAATAAAATTTATTATATTTGTAAATAAGAATTCTAATTCTATTAAAAGACTTTGGGTAAATG
1 ATAATAAAATTTATTACATTTGTAAATAAGAATTCTAATTATATTAAAAGACTTTGGGTAAATG
1257455 GAAATTTTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
73 47 0.81
74 11 0.19
ACGTcount: A:0.43, C:0.03, G:0.12, T:0.42
Consensus pattern (74 bp):
ATAATAAAATTTATTACATTTGTAAATAAGAATTCTAATTATATTAAAAGACTTTGGGTAAATGA
ATTTATTGG
Found at i:1259874 original size:14 final size:14
Alignment explanation
Indices: 1259857--1259897 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 14
1259847 AGTTTACTCG
1259857 TATTTTTTAAAATT
1 TATTTTTTAAAATT
1259871 TATTTTTT--AATT
1 TATTTTTTAAAATT
*
1259883 TAATTTTTAATAATT
1 TATTTTTTAA-AATT
1259898 ACATATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
12 11 0.48
14 8 0.35
15 4 0.17
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATTTTTTAAAATT
Found at i:1259995 original size:20 final size:23
Alignment explanation
Indices: 1259972--1260020 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 23
1259962 AAAATGTTTT
1259972 AATAAATTA-AA-AATTA-ATAA
1 AATAAATTATAATAATTATATAA
1259992 AATAAAATTATAATAATTATTATAA
1 AAT-AAATTATAATAATTA-TATAA
1260017 AATA
1 AATA
1260021 TATGTAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
20 3 0.12
21 6 0.25
22 2 0.08
23 5 0.21
24 1 0.04
25 7 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
AATAAATTATAATAATTATATAA
Found at i:1260715 original size:22 final size:22
Alignment explanation
Indices: 1260674--1260716 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1260664 AAATAATATT
*
1260674 ATTAAATTTTTATTATTAATTA
1 ATTAAATTTTTATTACTAATTA
1260696 ATTAAATTATTTA-TACTAATT
1 ATTAAATT-TTTATTACTAATT
1260717 TTAATAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTAAATTTTTATTACTAATTA
Found at i:1260912 original size:16 final size:17
Alignment explanation
Indices: 1260893--1260924 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1260883 TGTTTAATGA
1260893 TATAATTTA-ATAAAAT
1 TATAATTTATATAAAAT
1260909 TATAATTTATATAAAA
1 TATAATTTATATAAAA
1260925 ATTAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TATAATTTATATAAAAT
Found at i:1262023 original size:21 final size:22
Alignment explanation
Indices: 1261985--1262026 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
1261975 ATTATCTATT
*
1261985 TTTTTTGAATATGAATGCATTAG
1 TTTTTGGAATAT-AATGCATTAG
1262008 TTTTTGGAATAT-ATGCATT
1 TTTTTGGAATATAATGCATT
1262027 CAAATTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
23 11 0.61
ACGTcount: A:0.29, C:0.05, G:0.17, T:0.50
Consensus pattern (22 bp):
TTTTTGGAATATAATGCATTAG
Found at i:1263585 original size:24 final size:24
Alignment explanation
Indices: 1263557--1263604 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
1263547 ATATCTTTTT
* *
1263557 TTATATA-T-ATTTATATTTATAA
1 TTATATATTAATTAATATTAATAA
1263579 TTATATATTAATTAATATTAATAA
1 TTATATATTAATTAATATTAATAA
1263603 TT
1 TT
1263605 TATTAAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 7 0.32
23 1 0.05
24 14 0.64
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TTATATATTAATTAATATTAATAA
Found at i:1299157 original size:15 final size:15
Alignment explanation
Indices: 1299137--1299167 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1299127 ATTTCTATGC
1299137 CTTAGTTTCAGATGT
1 CTTAGTTTCAGATGT
1299152 CTTAGTTTCAGATGT
1 CTTAGTTTCAGATGT
1299167 C
1 C
1299168 CAAACCACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.45
Consensus pattern (15 bp):
CTTAGTTTCAGATGT
Found at i:1303528 original size:15 final size:16
Alignment explanation
Indices: 1303510--1303544 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1303500 ATATTTTATA
*
1303510 TTTATTT-AATTATTT
1 TTTATTTAAAATATTT
1303525 TTTATTTAAAATATTT
1 TTTATTTAAAATATTT
1303541 TTTA
1 TTTA
1303545 ACTATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTATTTAAAATATTT
Found at i:1308210 original size:38 final size:39
Alignment explanation
Indices: 1308156--1308273 Score: 175
Period size: 39 Copynumber: 3.1 Consensus size: 39
1308146 CTGCCATCAT
*
1308156 AGTATGAAAATAAACTCTGTTAAAATCAGCTATAATTGC
1 AGTATGAAAATAAACTCTGTTAAAATCAGTTATAATTGC
* * ***
1308195 AG-ATGAAAATAAACTCTGTTAAGATCAGTTAAAATCAT
1 AGTATGAAAATAAACTCTGTTAAAATCAGTTATAATTGC
1308233 AGTATGAAAATAAACTCTGTTAAAATCAGTTATAATTGC
1 AGTATGAAAATAAACTCTGTTAAAATCAGTTATAATTGC
1308272 AG
1 AG
1308274 CCTTTTGATA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
38 32 0.48
39 35 0.52
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.31
Consensus pattern (39 bp):
AGTATGAAAATAAACTCTGTTAAAATCAGTTATAATTGC
Found at i:1308251 original size:39 final size:39
Alignment explanation
Indices: 1308151--1308264 Score: 167
Period size: 38 Copynumber: 2.9 Consensus size: 39
1308141 ATATGCTGCC
* *
1308151 ATCATAGTATGAAAATAAACTCTGTTAAAATCAGCTATA
1 ATCATAGTATGAAAATAAACTCTGTTAAAATCAGTTAAA
*** *
1308190 ATTGCAG-ATGAAAATAAACTCTGTTAAGATCAGTTAAA
1 ATCATAGTATGAAAATAAACTCTGTTAAAATCAGTTAAA
1308228 ATCATAGTATGAAAATAAACTCTGTTAAAATCAGTTA
1 ATCATAGTATGAAAATAAACTCTGTTAAAATCAGTTA
1308265 TAATTGCAGC
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
38 32 0.50
39 32 0.50
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (39 bp):
ATCATAGTATGAAAATAAACTCTGTTAAAATCAGTTAAA
Found at i:1308531 original size:17 final size:16
Alignment explanation
Indices: 1308509--1308552 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
1308499 AAATATGTGT
1308509 AAAATAAATATTTATAA
1 AAAATAAATATTT-TAA
*
1308526 AAAATAAAAATTTTAA
1 AAAATAAATATTTTAA
1308542 ATAATATAAAT
1 A-AA-ATAAAT
1308553 TTAAATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 4 0.17
17 14 0.61
18 5 0.22
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAATAAATATTTTAA
Found at i:1308550 original size:18 final size:17
Alignment explanation
Indices: 1308509--1308555 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
1308499 AAATATGTGT
*
1308509 AAAATAAATATTTATAA
1 AAAATAAAAATTTATAA
1308526 AAAATAAAAATTT-TAA
1 AAAATAAAAATTTATAA
* *
1308542 ATAATATAAATTTA
1 AAAATAAAAATTTA
1308556 AATTTATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 14 0.54
17 12 0.46
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAATAAAAATTTATAA
Found at i:1309593 original size:2 final size:2
Alignment explanation
Indices: 1309586--1309614 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1309576 GAATAAAGAG
1309586 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1309615 AGTAACTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1310310 original size:16 final size:16
Alignment explanation
Indices: 1310289--1310320 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1310279 TAATTAATTT
*
1310289 TGATTAAATTATAATA
1 TGATTAAATAATAATA
1310305 TGATTAAATAATAATA
1 TGATTAAATAATAATA
1310321 AAATATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (16 bp):
TGATTAAATAATAATA
Found at i:1310400 original size:21 final size:22
Alignment explanation
Indices: 1310376--1310421 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
1310366 TAACTATCAC
*
1310376 ATCAATATTTAATA-TATTTTT
1 ATCAATATTTAATATTAATTTT
*
1310397 ATC-ATATTTATTATTAATTTT
1 ATCAATATTTAATATTAATTTT
1310418 ATCA
1 ATCA
1310422 TTTTATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (22 bp):
ATCAATATTTAATATTAATTTT
Found at i:1310422 original size:21 final size:20
Alignment explanation
Indices: 1310380--1310428 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1310370 TATCACATCA
* *
1310380 ATATTTAATATATTTTTATC
1 ATATTTATTATAATTTTATC
1310400 ATATTTATTATTAATTTTATC
1 ATATTTATTA-TAATTTTATC
1310421 AT-TTTATT
1 ATATTTATT
1310429 TTACTTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (20 bp):
ATATTTATTATAATTTTATC
Found at i:1311311 original size:12 final size:14
Alignment explanation
Indices: 1311277--1311335 Score: 59
Period size: 15 Copynumber: 4.1 Consensus size: 14
1311267 TAAATAAAAT
1311277 TAAACTTATTTTAAA
1 TAAA-TTATTTTAAA
1311292 TAAATTATTTT-AA
1 TAAATTATTTTAAA
1311305 T-AATTATTATTTAAA
1 TAAATTA-T-TTTAAA
*
1311320 TATTATTATTTTAAA
1 TA-AATTATTTTAAA
1311335 T
1 T
1311336 TTAAAATTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
12 5 0.13
13 4 0.11
14 10 0.26
15 14 0.37
16 1 0.03
17 4 0.11
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (14 bp):
TAAATTATTTTAAA
Found at i:1311334 original size:15 final size:15
Alignment explanation
Indices: 1311282--1311335 Score: 69
Period size: 14 Copynumber: 3.7 Consensus size: 15
1311272 AAAATTAAAC
*
1311282 TTATTTTAAATA-AA
1 TTATTTTAAATATTA
1311296 TTATTTT-AATAATTA
1 TTATTTTAAAT-ATTA
1311311 TTA-TTTAAATATTA
1 TTATTTTAAATATTA
1311325 TTATTTTAAAT
1 TTATTTTAAAT
1311336 TTAAAATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
13 3 0.09
14 18 0.51
15 14 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATTTTAAATATTA
Found at i:1311344 original size:28 final size:28
Alignment explanation
Indices: 1311286--1311344 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
1311276 TTAAACTTAT
**
1311286 TTTAAATAAATTATTTTAATAATTATTA
1 TTTAAATAAATTATTTTAATAATTAAAA
* *
1311314 TTTAAATATTATTATTTTAA-ATTTAAAA
1 TTTAAATA-AATTATTTTAATAATTAAAA
1311342 TTT
1 TTT
1311345 TTTTATCGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
TTTAAATAAATTATTTTAATAATTAAAA
Found at i:1312240 original size:14 final size:14
Alignment explanation
Indices: 1312221--1312248 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1312211 TTAATTATAA
1312221 AATATAAAAATATT
1 AATATAAAAATATT
1312235 AATATAAAAATATT
1 AATATAAAAATATT
1312249 TTTAAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AATATAAAAATATT
Found at i:1312828 original size:17 final size:18
Alignment explanation
Indices: 1312806--1312844 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
1312796 AAATTTATAT
1312806 ATTAATTTT-TTAAAAAA
1 ATTAATTTTATTAAAAAA
1312823 ATTAATTTTGATTAAAAAA
1 ATTAATTTT-ATTAAAAAA
1312842 ATT
1 ATT
1312845 TTATATTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 9 0.45
19 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
ATTAATTTTATTAAAAAA
Found at i:1312902 original size:15 final size:16
Alignment explanation
Indices: 1312877--1312909 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1312867 ATTAAATTGA
1312877 AATATATTATTAATAT
1 AATATATTATTAATAT
*
1312893 AATATA-TATTTATAT
1 AATATATTATTAATAT
1312908 AA
1 AA
1312910 ATTAATTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATATATTATTAATAT
Found at i:1312955 original size:25 final size:26
Alignment explanation
Indices: 1312913--1312965 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
1312903 TATATAAATT
*
1312913 AATTTAGTTTAAAATATA-ATTTTTA
1 AATTTAGTTTAAAATATACATATTTA
*
1312938 AATTT-GTTTAAATTTATACATATTTA
1 AATTTAGTTTAAA-ATATACATATTTA
1312964 AA
1 AA
1312966 ATAAATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.29
25 9 0.38
26 8 0.33
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (26 bp):
AATTTAGTTTAAAATATACATATTTA
Found at i:1313056 original size:16 final size:17
Alignment explanation
Indices: 1313017--1313053 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1313007 TTTAAAAATA
* *
1313017 TTTTAATTTTATTTATT
1 TTTTATTTTTATATATT
1313034 TTTTATTTTTATATATT
1 TTTTATTTTTATATATT
1313051 TTT
1 TTT
1313054 ATTAAATCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTATTTTTATATATT
Found at i:1313126 original size:16 final size:17
Alignment explanation
Indices: 1313105--1313137 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1313095 ATATTTACAC
1313105 TTTAATATTT-TAAAAT
1 TTTAATATTTATAAAAT
*
1313121 TTTAATTTTTATAAAAT
1 TTTAATATTTATAAAAT
1313138 ATAAATCACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTAATATTTATAAAAT
Found at i:1313262 original size:17 final size:16
Alignment explanation
Indices: 1313239--1313278 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
1313229 ATTTGATATA
1313239 TTTTTTAAATAAATTT
1 TTTTTTAAATAAATTT
**
1313255 TATTTTTATTTAAATTT
1 T-TTTTTAAATAAATTT
1313272 TTTTTTA
1 TTTTTTA
1313279 TTTAAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTTAAATAAATTT
Found at i:1313286 original size:17 final size:17
Alignment explanation
Indices: 1313248--1313290 Score: 70
Period size: 17 Copynumber: 2.5 Consensus size: 17
1313238 ATTTTTTAAA
1313248 TAAATTTTATTTTTATT
1 TAAATTTTATTTTTATT
1313265 TAAATTTT-TTTTTATT
1 TAAATTTTATTTTTATT
1313281 TAAAATTTTA
1 T-AAATTTTA
1313291 AAATATGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TAAATTTTATTTTTATT
Found at i:1314658 original size:2 final size:2
Alignment explanation
Indices: 1314651--1314693 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1314641 TTCTTCTTCT
1314651 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1314693 T
1 T
1314694 ATATATATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1314698 original size:2 final size:2
Alignment explanation
Indices: 1314693--1314718 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1314683 TCTCTCTCTC
1314693 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
1314719 GCCTTTTTTC
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):
TA
Found at i:1315282 original size:13 final size:13
Alignment explanation
Indices: 1315246--1315287 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1315236 AAAAAATGTT
1315246 TTTTTTTTATTTCC
1 TTTTTTTT-TTTCC
* *
1315260 -CTTGTTTTTTCC
1 TTTTTTTTTTTCC
1315272 TTTTTTTTTTTCC
1 TTTTTTTTTTTCC
1315285 TTT
1 TTT
1315288 CCTTTTATCA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
12 5 0.22
13 18 0.78
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTTTCC
Found at i:1315537 original size:28 final size:28
Alignment explanation
Indices: 1315480--1315544 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
1315470 TTGAGCTTTA
* * *
1315480 TTATTTTATTTAAATAAATCTTATATTT
1 TTATTTTATCTAAATAAATCTTAAAATT
* *
1315508 TTATTTTATCTAAATAAGTTTTAAAATT
1 TTATTTTATCTAAATAAATCTTAAAATT
*
1315536 TTAATTTAT
1 TTATTTTAT
1315545 TTTCAAATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (28 bp):
TTATTTTATCTAAATAAATCTTAAAATT
Found at i:1315559 original size:30 final size:32
Alignment explanation
Indices: 1315519--1315579 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 32
1315509 TATTTTATCT
1315519 AAATAAGTTTTAAAATTTT-AATT-TATTTTC
1 AAATAAGTTTTAAAATTTTAAATTATATTTTC
* * *
1315549 AAATATGTTTTTAACTTTTAAATTATATTTT
1 AAATAAGTTTTAAAATTTTAAATTATATTTT
1315580 AAAAAAATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 16 0.62
31 4 0.15
32 6 0.23
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (32 bp):
AAATAAGTTTTAAAATTTTAAATTATATTTTC
Found at i:1315880 original size:16 final size:16
Alignment explanation
Indices: 1315848--1315909 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
1315838 CTAATCTCTC
1315848 ATTTGAAATA-AAGATTT
1 ATTT-AAATACAA-ATTT
1315865 ATTTAAATACAAATTT
1 ATTTAAATACAAATTT
** * *
1315881 A-AAAAATAAAAACTT
1 ATTTAAATACAAATTT
1315896 ATTTAAATACAAAT
1 ATTTAAATACAAAT
1315910 CAAAAATAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
15 11 0.31
16 18 0.51
17 6 0.17
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.35
Consensus pattern (16 bp):
ATTTAAATACAAATTT
Found at i:1315888 original size:31 final size:29
Alignment explanation
Indices: 1315853--1315959 Score: 99
Period size: 29 Copynumber: 3.6 Consensus size: 29
1315843 CTCTCATTTG
*
1315853 AAATAAAGATTTATTTAAATACAAATTTAAA
1 AAATAAAAATTTATTTAAATACAAA--TAAA
* *
1315884 AAATAAAAACTTATTTAAATACAAATCAA
1 AAATAAAAATTTATTTAAATACAAATAAA
** * *
1315913 AAATAATTATTTATTTAAACAC-CATATAA
1 AAATAAAAATTTATTTAAATACAAATA-AA
**
1315942 GTATAAAAATTTATTTAA
1 AAATAAAAATTTATTTAA
1315960 GTTTAAGAGT
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
28 2 0.03
29 37 0.60
31 23 0.37
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (29 bp):
AAATAAAAATTTATTTAAATACAAATAAA
Found at i:1317108 original size:43 final size:43
Alignment explanation
Indices: 1317047--1317132 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
1317037 GCATAGTTTC
1317047 TGCTGACTTTCTGCTGACGTGAATTGTCATAAGATTTGTGAGT
1 TGCTGACTTTCTGCTGACGTGAATTGTCATAAGATTTGTGAGT
1317090 TGCTGACTTTCTGCTGACGTGAATTGTCATAAGATTTGTGAGT
1 TGCTGACTTTCTGCTGACGTGAATTGTCATAAGATTTGTGAGT
1317133 GGTTGTGTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.21, C:0.14, G:0.26, T:0.40
Consensus pattern (43 bp):
TGCTGACTTTCTGCTGACGTGAATTGTCATAAGATTTGTGAGT
Found at i:1322221 original size:30 final size:30
Alignment explanation
Indices: 1322187--1322248 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
1322177 TTTTAAATCA
* *
1322187 ATAATTAAA-ATATATTAAAATATTAATTTT
1 ATAATTAAATATAAATAAAAATATT-ATTTT
*
1322217 ATAATTAAATTTAAATAAAAATATTATTTT
1 ATAATTAAATATAAATAAAAATATTATTTT
1322247 AT
1 AT
1322249 TTAATAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 16 0.57
31 12 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
ATAATTAAATATAAATAAAAATATTATTTT
Found at i:1322295 original size:2 final size:2
Alignment explanation
Indices: 1322288--1322319 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1322278 ATCAACAAAA
1322288 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
1322320 GCCCAAACCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1328381 original size:15 final size:16
Alignment explanation
Indices: 1328361--1328390 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1328351 CACCCAACAG
1328361 AAAAAAC-AAACAAAC
1 AAAAAACAAAACAAAC
1328376 AAAAAACAAAACAAA
1 AAAAAACAAAACAAA
1328391 GTGTTCTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAACAAAACAAAC
Found at i:1331719 original size:57 final size:56
Alignment explanation
Indices: 1331628--1331739 Score: 188
Period size: 57 Copynumber: 2.0 Consensus size: 56
1331618 ATTAAAAAGT
* * *
1331628 AAACCATACTAGATCTCAATATTTGCCAATCTCAATCAAGAATAAAACAATTGACAA
1 AAACCATACGAGATCTCAATATCTGCCAAACTCAATCAAGAATAAAA-AATTGACAA
1331685 AAACCATACGAGATCTCAATATCTGCCAAACTCAATCAAGAATAAAAAATTGACA
1 AAACCATACGAGATCTCAATATCTGCCAAACTCAATCAAGAATAAAAAATTGACA
1331740 CTTTATACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
56 8 0.15
57 44 0.85
ACGTcount: A:0.48, C:0.21, G:0.08, T:0.22
Consensus pattern (56 bp):
AAACCATACGAGATCTCAATATCTGCCAAACTCAATCAAGAATAAAAAATTGACAA
Found at i:1335189 original size:17 final size:19
Alignment explanation
Indices: 1335155--1335204 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 19
1335145 TAACTTTAAT
* **
1335155 TATTTCATTATATTATAAC
1 TATTTTATTATAAAATAAC
*
1335174 T-TTTT-TTATAAAATAAT
1 TATTTTATTATAAAATAAC
1335191 TATTTTATTATAAA
1 TATTTTATTATAAA
1335205 TTTATTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 10 0.40
18 7 0.28
19 8 0.32
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (19 bp):
TATTTTATTATAAAATAAC
Found at i:1335201 original size:19 final size:19
Alignment explanation
Indices: 1335151--1335215 Score: 59
Period size: 18 Copynumber: 3.7 Consensus size: 19
1335141 ATTATAACTT
* **
1335151 TAATTATTTCATTATATTA
1 TAATTATTTTATTATAAAA
*
1335170 TAACT-TTTT-TTATAAAA
1 TAATTATTTTATTATAAAA
1335187 TAATTATTTTATTAT-AAA
1 TAATTATTTTATTATAAAA
1335205 T--TTATTTTATT
1 TAATTATTTTATT
1335216 TTTATAAAGT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
16 10 0.26
17 10 0.26
18 11 0.28
19 8 0.21
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (19 bp):
TAATTATTTTATTATAAAA
Found at i:1335209 original size:16 final size:16
Alignment explanation
Indices: 1335165--1335215 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
1335155 TATTTCATTA
*
1335165 TATTATAACTTT-TTT
1 TATTATAAATTTATTT
1335180 TA-TA-AAATAATTATTT
1 TATTATAAAT--TTATTT
1335196 TATTATAAATTTATTT
1 TATTATAAATTTATTT
1335212 TATT
1 TATT
1335216 TTTATAAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
13 3 0.10
14 2 0.07
15 4 0.13
16 15 0.50
17 2 0.07
18 4 0.13
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTATAAATTTATTT
Found at i:1335220 original size:19 final size:19
Alignment explanation
Indices: 1335174--1335223 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1335164 ATATTATAAC
1335174 TTTTTTTATAAAATAATTA
1 TTTTTTTATAAAATAATTA
* * *
1335193 TTTTATTATAAATTTATT-
1 TTTTTTTATAAAATAATTA
1335211 TTATTTTTATAAA
1 TT-TTTTTATAAA
1335224 GTAAACGTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 2 0.08
19 24 0.92
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTTTTATAAAATAATTA
Found at i:1335454 original size:21 final size:21
Alignment explanation
Indices: 1335419--1335469 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1335409 TAGATTAAAA
1335419 ATATTAATAGAGATAAAATTA-
1 ATATT-ATAGAGATAAAATTAG
* *
1335440 ATTATTATAGTGATAATATTAG
1 A-TATTATAGAGATAAAATTAG
1335462 ATATTATA
1 ATATTATA
1335470 AAAATTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (21 bp):
ATATTATAGAGATAAAATTAG
Done.