Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002197.1 Hibiscus syriacus cultivar Beakdansim tig00004477_pilon, whole genome shotgun sequence
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: 153799
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1426 original size:19 final size:19
Alignment explanation
Indices: 1402--1468 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
1392 GAAACTTAAA
1402 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
* *
1421 ATCGCAACACGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
1441 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
1460 ATCGCAACG
1 ATCGCAACG
1469 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 23 0.59
20 16 0.41
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1437 original size:20 final size:19
Alignment explanation
Indices: 1383--1467 Score: 71
Period size: 20 Copynumber: 4.4 Consensus size: 19
1373 TAGTTTACTT
* **
1383 TCGCAACACGAAACTTAAAA
1 TCGCAACACGAAA-TGACTA
*
1403 TCGCAACGCGAAATGACTA
1 TCGCAACACGAAATGACTA
*
1422 TCGCAACACGGAAATGGCTA
1 TCGCAACAC-GAAATGACTA
** **
1442 TCGCAATGCGAAATGAAAA
1 TCGCAACACGAAATGACTA
1461 TCGCAAC
1 TCGCAAC
1468 GACAAAATCG
Statistics
Matches: 52, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
19 24 0.46
20 28 0.54
ACGTcount: A:0.41, C:0.25, G:0.19, T:0.15
Consensus pattern (19 bp):
TCGCAACACGAAATGACTA
Found at i:1476 original size:14 final size:14
Alignment explanation
Indices: 1457--1496 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
1447 ATGCGAAATG
1457 AAAATCGCAACGAC
1 AAAATCGCAACGAC
1471 AAAATCGCAACGAC
1 AAAATCGCAACGAC
1485 AAAATCGCAACG
1 AAAATCGCAACG
1497 CGAAACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.50, C:0.28, G:0.15, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1530 original size:19 final size:18
Alignment explanation
Indices: 1508--1572 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
1498 GAAACACAAA
*
1508 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
*
1527 TCGCGTTGCGATTT--TG
1 TCGCGTTGCGATTTCATT
1543 T--CGTTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
1559 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
1573 TGTTTGCGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 11 0.28
16 4 0.10
18 14 0.36
19 10 0.26
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:1549 original size:14 final size:14
Alignment explanation
Indices: 1530--1585 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
1520 TTTCATTTCG
1530 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1544 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1560 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
1576 --TTGCGATTTT
1 CGTTGCGATTTT
1586 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
12 10 0.28
14 11 0.31
16 4 0.11
18 11 0.31
ACGTcount: A:0.09, C:0.16, G:0.25, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1560 original size:32 final size:31
Alignment explanation
Indices: 1513--1600 Score: 142
Period size: 32 Copynumber: 2.8 Consensus size: 31
1503 ACAAATCGCA
1513 TTGCGATTTTCATTTCGCGTTGCGATTTTGT
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGT
1544 CGTTGCGA-TTTCATTTCGCGTTGCGATTTTGT
1 --TTGCGATTTTCATTTCGCGTTGCGATTTTGT
*
1576 TTGCGATTTTCATTTCGCATTGCGA
1 TTGCGATTTTCATTTCGCGTTGCGA
1601 AAGCCATTTC
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
30 6 0.11
31 17 0.32
32 24 0.45
33 6 0.11
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (31 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGT
Found at i:1620 original size:20 final size:19
Alignment explanation
Indices: 1586--1642 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
1576 TTGCGATTTT
*
1586 CATTTCGCATTGCGAAAGC
1 CATTTCGCGTTGCGAAAGC
* *
1605 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGAAAGC
*
1625 CATTTCGTGTTGCGAAAG
1 CATTTCGCGTTGCGAAAG
1643 TAAACTATTC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.32
Consensus pattern (19 bp):
CATTTCGCGTTGCGAAAGC
Found at i:2126 original size:18 final size:18
Alignment explanation
Indices: 2100--2144 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
2090 GTCGATCAGA
* *
2100 TGATGGCTCTGGGTGGGG
1 TGATGGCTCTGGGCGAGG
*
2118 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
2136 TGATGGCTC
1 TGATGGCTC
2145 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.11, C:0.16, G:0.47, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:3693 original size:21 final size:21
Alignment explanation
Indices: 3669--3711 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3659 GATTTAGATA
3669 GACGGATTTCGCCGGAGATGG
1 GACGGATTTCGCCGGAGATGG
*
3690 GACGGATTTCGTCGGAGATGG
1 GACGGATTTCGCCGGAGATGG
3711 G
1 G
3712 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.16, G:0.44, T:0.21
Consensus pattern (21 bp):
GACGGATTTCGCCGGAGATGG
Found at i:3967 original size:41 final size:41
Alignment explanation
Indices: 3915--3992 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
3905 CGAAAGTCAG
* * *
3915 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTGTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTGTAT
*
3956 TATCGCATTGCGATAGTAAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
3993 CCCAATTCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTGTAT
Found at i:3989 original size:20 final size:20
Alignment explanation
Indices: 3876--3989 Score: 90
Period size: 20 Copynumber: 5.7 Consensus size: 20
3866 CGCTTTGAAA
3876 ATCGCATTGCGATTATGTAA--
1 ATCGCATTGCGA-TA-GTAAGT
* * *
3896 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* *
3916 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* * * *
3936 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTAAGT
3957 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
3977 ATCGCATTGCGAT
1 ATCGCATTGCGAT
3990 TTTCCCAATT
Statistics
Matches: 77, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
18 3 0.04
19 4 0.05
20 56 0.73
21 12 0.16
22 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:4008 original size:41 final size:41
Alignment explanation
Indices: 3915--4010 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
3905 CGAAAGTCAG
* * * ** *
3915 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
*
3956 TATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAA
3998 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
4011 TTACTTATTC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 44 0.96
42 2 0.04
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
Found at i:5170 original size:16 final size:18
Alignment explanation
Indices: 5129--5171 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
5119 TCACGGAACG
*
5129 TAAGATTATCAATGAGAA
1 TAAGATTATCAATGAAAA
5147 TAAAGATTATC-A-GAAAA
1 T-AAGATTATCAATGAAAA
5164 TAAGATTA
1 TAAGATTA
5172 CTAGGAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 7 0.30
17 5 0.22
18 2 0.09
19 9 0.39
ACGTcount: A:0.53, C:0.05, G:0.14, T:0.28
Consensus pattern (18 bp):
TAAGATTATCAATGAAAA
Found at i:7160 original size:57 final size:57
Alignment explanation
Indices: 7095--7230 Score: 188
Period size: 57 Copynumber: 2.4 Consensus size: 57
7085 GGGGTTGTCT
*
7095 GCTTAGTTATTTTTCATTGTTTGGTACT-CTGTGTACAGGG-AGGGAGT-TTCTGTTTAA
1 GCTTAGTTATTTTTCATTGTTTGGT-CTCCTGTGTACAGGGAAGGG-GTCGT-TGTTTAA
* *
7152 GCTTAGTTATTTTTCATTGTTTGGTGTCCTGTGTATAGGGAAGGGGTCGTTGTTTAA
1 GCTTAGTTATTTTTCATTGTTTGGTCTCCTGTGTACAGGGAAGGGGTCGTTGTTTAA
7209 GCTTAGTTATTTTTTCATTGTT
1 GCTTAGTTA-TTTTTCATTGTT
7231 GGGTTTTTCT
Statistics
Matches: 72, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
56 1 0.01
57 54 0.75
58 17 0.24
ACGTcount: A:0.16, C:0.10, G:0.26, T:0.49
Consensus pattern (57 bp):
GCTTAGTTATTTTTCATTGTTTGGTCTCCTGTGTACAGGGAAGGGGTCGTTGTTTAA
Found at i:10122 original size:18 final size:18
Alignment explanation
Indices: 10074--10115 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
10064 ATCCAACTAC
10074 GCTTAGCAGTGTAGGTAA
1 GCTTAGCAGTGTAGGTAA
*
10092 GCTTAGCAGTGTAGGTAT
1 GCTTAGCAGTGTAGGTAA
10110 GCTTAG
1 GCTTAG
10116 TCGTGTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.24, C:0.12, G:0.33, T:0.31
Consensus pattern (18 bp):
GCTTAGCAGTGTAGGTAA
Found at i:10474 original size:29 final size:29
Alignment explanation
Indices: 10441--10509 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 29
10431 TCCTCAAACA
* *
10441 TAGGTCGTCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
*
10470 TAGGTTGCCATGCACTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
*
10499 TAGGTCACCAT
1 TAGGTCGCCAT
10510 AAACTCCTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.14, C:0.32, G:0.29, T:0.25
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:10515 original size:29 final size:29
Alignment explanation
Indices: 10455--10516 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
10445 TCGTCATGCC
** **
10455 CTCCGGGCGACCTTGTAGGTTGCCATGCA
1 CTCCGGGCGACCTTGTAGGTCACCATAAA
10484 CTCCGGGCGACCTTGTAGGTCACCATAAA
1 CTCCGGGCGACCTTGTAGGTCACCATAAA
10513 CTCC
1 CTCC
10517 TTCCTACTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.18, C:0.34, G:0.26, T:0.23
Consensus pattern (29 bp):
CTCCGGGCGACCTTGTAGGTCACCATAAA
Found at i:14619 original size:14 final size:15
Alignment explanation
Indices: 14594--14624 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
14584 TAGATACTTT
14594 ATGAATTAAAATAAA
1 ATGAATTAAAATAAA
14609 ATGAA-TAAAATAAA
1 ATGAATTAAAATAAA
14623 AT
1 AT
14625 AGATGTACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (15 bp):
ATGAATTAAAATAAA
Found at i:14879 original size:33 final size:32
Alignment explanation
Indices: 14842--14916 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 32
14832 GTAAAAGAAT
14842 ATATGTACATATAATACATAAACAAATAAATAA
1 ATATGTACATATAATACATAAACAAAT-AATAA
* *
14875 ATATGTACATATAATACATAGATAAATAATAA
1 ATATGTACATATAATACATAAACAAATAATAA
14907 ATATGTACAT
1 ATATGTACAT
14917 TACACATAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 15 0.38
33 25 0.62
ACGTcount: A:0.56, C:0.08, G:0.05, T:0.31
Consensus pattern (32 bp):
ATATGTACATATAATACATAAACAAATAATAA
Found at i:15994 original size:20 final size:20
Alignment explanation
Indices: 15957--15999 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
15947 TTTTAATGGG
*
15957 TTAGATTTGGTTTTATTTTA
1 TTAGATTTGGTTTTATTTCA
*
15977 TTAGATTT-TTTTTGATTTCA
1 TTAGATTTGGTTTT-ATTTCA
15997 TTA
1 TTA
16000 TTGATGTGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.21, C:0.02, G:0.12, T:0.65
Consensus pattern (20 bp):
TTAGATTTGGTTTTATTTCA
Found at i:16246 original size:3 final size:3
Alignment explanation
Indices: 16240--16280 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
16230 ATATTATTAA
16240 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
16281 AAAACGTTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17975 original size:25 final size:24
Alignment explanation
Indices: 17937--18004 Score: 82
Period size: 25 Copynumber: 2.8 Consensus size: 24
17927 GTTGAACAAG
* *
17937 TTTTGAAAATGTTTTAAGAAAGGA
1 TTTTGAAAATGTTTGAAGAAAGAA
*
17961 TTTTGAATAATGTTTGATGAAAGAA
1 TTTTGAA-AATGTTTGAAGAAAGAA
*
17986 TTTAGAAAAATGTTTGAAG
1 TTTTG-AAAATGTTTGAAG
18005 TTTTAAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
24 7 0.19
25 28 0.76
26 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (24 bp):
TTTTGAAAATGTTTGAAGAAAGAA
Found at i:19326 original size:20 final size:20
Alignment explanation
Indices: 19301--19371 Score: 142
Period size: 20 Copynumber: 3.5 Consensus size: 20
19291 AAAATGACTG
19301 GTATCGATACTCTTTCTTGA
1 GTATCGATACTCTTTCTTGA
19321 GTATCGATACTCTTTCTTGA
1 GTATCGATACTCTTTCTTGA
19341 GTATCGATACTCTTTCTTGA
1 GTATCGATACTCTTTCTTGA
19361 GTATCGATACT
1 GTATCGATACT
19372 TCTGGCATGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.21, C:0.20, G:0.15, T:0.44
Consensus pattern (20 bp):
GTATCGATACTCTTTCTTGA
Found at i:19396 original size:40 final size:38
Alignment explanation
Indices: 19299--19403 Score: 131
Period size: 40 Copynumber: 2.6 Consensus size: 38
19289 ACAAAATGAC
**
19299 TGGTATCGATACTCTTTCTTGAGTATCGATACTCTTTCT
1 TGGTATCGATAC-CTTTCTTGAGTATCGATACTCTGGCT
19338 TGAGTATCGATACTCTTTCTTGAGTATCGATACTTCTGGCAT
1 TG-GTATCGATAC-CTTTCTTGAGTATCGATAC-TCTGGC-T
19380 GTGGTATCGATA-CTTTCTTGAGTA
1 -TGGTATCGATACCTTTCTTGAGTA
19404 CATATATTAA
Statistics
Matches: 60, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
39 2 0.03
40 42 0.70
41 4 0.07
42 10 0.17
43 2 0.03
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.43
Consensus pattern (38 bp):
TGGTATCGATACCTTTCTTGAGTATCGATACTCTGGCT
Found at i:25880 original size:192 final size:192
Alignment explanation
Indices: 25553--25936 Score: 750
Period size: 192 Copynumber: 2.0 Consensus size: 192
25543 TTGGTGAGAA
25553 ATTTTTATTAGATATCATTAAGGTATCCTTAGAACTTAGAAGATTCTTGGCTATTTCATAATAGC
1 ATTTTTATTAGATATCATTAAGGTATCCTTAGAACTTAGAAGATTCTTGGCTATTTCATAATAGC
*
25618 ATAATAGATTGGCTCTCTTTTAAAAGTTGGCCATTTAAGAATATGCTTGTGGAAGGAGTAAATAA
66 ATAATAGATTGGCTATCTTTTAAAAGTTGGCCATTTAAGAATATGCTTGTGGAAGGAGTAAATAA
*
25683 AGTATGCACTGGTGGAACAAGTTGAAAGTAGATCATACGTTAGATTGAATAATCATATTCAG
131 AGTATGCACTGGTGGAACAAGTTGAAAGTAGATCATACGTGAGATTGAATAATCATATTCAG
25745 ATTTTTATTAGATATCATTAAGGTATCCTTAGAACTTAGAAGATTCTTGGCTATTTCATAATAGC
1 ATTTTTATTAGATATCATTAAGGTATCCTTAGAACTTAGAAGATTCTTGGCTATTTCATAATAGC
25810 ATAATAGATTGGCTATCTTTTAAAAGTTGGCCATTTAAGAATATGCTTGTGGAAGGAGTAAATAA
66 ATAATAGATTGGCTATCTTTTAAAAGTTGGCCATTTAAGAATATGCTTGTGGAAGGAGTAAATAA
25875 AGTATGCACTGGTGGAACAAGTTGAAAGTAGATCATACGTGAGATTGAATAATCATATTCAG
131 AGTATGCACTGGTGGAACAAGTTGAAAGTAGATCATACGTGAGATTGAATAATCATATTCAG
25937 GCATTTGTTC
Statistics
Matches: 190, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
192 190 1.00
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.35
Consensus pattern (192 bp):
ATTTTTATTAGATATCATTAAGGTATCCTTAGAACTTAGAAGATTCTTGGCTATTTCATAATAGC
ATAATAGATTGGCTATCTTTTAAAAGTTGGCCATTTAAGAATATGCTTGTGGAAGGAGTAAATAA
AGTATGCACTGGTGGAACAAGTTGAAAGTAGATCATACGTGAGATTGAATAATCATATTCAG
Found at i:27312 original size:25 final size:24
Alignment explanation
Indices: 27257--27313 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
27247 TGTGCATCTG
*
27257 ACCCTTTTTTTCATTCTTTTGCTC
1 ACCCTGTTTTTCATTCTTTTGCTC
* **
27281 ACACTGTTTTTCATTCTCTTTTTTC
1 ACCCTGTTTTTCATTCT-TTTGCTC
27306 ACCCTGTT
1 ACCCTGTT
27314 GTTCTGCCAC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 15 0.56
25 12 0.44
ACGTcount: A:0.11, C:0.28, G:0.05, T:0.56
Consensus pattern (24 bp):
ACCCTGTTTTTCATTCTTTTGCTC
Found at i:31626 original size:21 final size:21
Alignment explanation
Indices: 31593--31633 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
31583 TTCTGGGCAA
* *
31593 GGGAATCGGTACCCATTCAAG
1 GGGAACCGATACCCATTCAAG
*
31614 GGGAACCGATACCCCTTCAA
1 GGGAACCGATACCCATTCAA
31634 ACGACAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCATTCAAG
Found at i:32238 original size:18 final size:18
Alignment explanation
Indices: 32215--32249 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
32205 CTAGGAGATT
32215 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
32233 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
32250 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:32335 original size:21 final size:22
Alignment explanation
Indices: 32306--32349 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
32296 GTTGTATGAT
32306 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
32327 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
32349 A
1 A
32350 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:33735 original size:149 final size:149
Alignment explanation
Indices: 33123--33724 Score: 1177
Period size: 149 Copynumber: 4.0 Consensus size: 149
33113 GAGTCGAGGG
33123 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
33188 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
33253 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
33272 TCTACGCGGTTCTTCCGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
33337 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
33402 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
33421 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
33486 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
*
33551 TATGGTACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
33570 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
33635 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
33700 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
33719 TCTACG
1 TCTACG
33725 GGGCACTTCG
Statistics
Matches: 448, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 448 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:33747 original size:23 final size:23
Alignment explanation
Indices: 33703--33747 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
33693 ATCATTATAT
*
33703 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
33726 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
33748 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:37407 original size:3 final size:3
Alignment explanation
Indices: 37399--37597 Score: 265
Period size: 3 Copynumber: 65.7 Consensus size: 3
37389 TTTATCCATT
* *
37399 TTA TTA TTA TTA TTA TTA ATA TTA ATA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* **
37447 TTA TTA GTA TTA TTA TTA TTA TTA GCA TT- TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
37494 ATA TTA TTA TTA TCA TTA TTA ATA TTA TTA TTA TTA TTA TTA TTA GTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
37542 TTTA TTA TTA TTA TTA ATA TTA ATA TTA TATA TTA TTA TTA TATA TTA
1 -TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T-TA TTA
37590 TTA TTA TT
1 TTA TTA TT
37598 TAATAAATAA
Statistics
Matches: 170, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
2 2 0.01
3 160 0.94
4 8 0.05
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:50230 original size:6 final size:6
Alignment explanation
Indices: 50213--50307 Score: 74
Period size: 6 Copynumber: 15.5 Consensus size: 6
50203 ATTATGCTTG
*
50213 AAGAAA AA-AAA AAGAAA AAGAAA AA-AGAA AAGAAA AAG-AA GAGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGA-AA AAGAAA AAGAAA AAGAAA
*
50259 GAAGAGAA AA-AAA AGGGAAAA GAAGAAA AAGAAA AAGAAGA AA-AAA
1 -AAGA-AA AAGAAA A-AG-AAA -AAGAAA AAGAAA AAGAA-A AAGAAA
50305 AAG
1 AAG
50308 GGGTCAAGGT
Statistics
Matches: 73, Mismatches: 4, Indels: 24
0.72 0.04 0.24
Matches are distributed among these distances:
5 16 0.22
6 38 0.52
7 12 0.16
8 6 0.08
9 1 0.01
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:50288 original size:9 final size:9
Alignment explanation
Indices: 50213--50307 Score: 70
Period size: 9 Copynumber: 10.3 Consensus size: 9
50203 ATTATGCTTG
50213 AAGAA-AAA
1 AAGAAGAAA
*
50221 AAAAAGAAA
1 AAGAAGAAA
50230 AAGAA-AAA
1 AAGAAGAAA
*
50238 AGAAAAGAAA
1 A-AGAAGAAA
*
50248 AAGAAGAGA
1 AAGAAGAAA
50257 AAGAAGAGAAA
1 AAG-A-AGAAA
* *
50268 AAAAAGGGAA
1 AAGAA-GAAA
50278 AAGAAGAAA
1 AAGAAGAAA
50287 AAGAA-AAA
1 AAGAAGAAA
*
50295 GAAGAAAAAA
1 -AAGAAGAAA
50305 AAG
1 AAG
50308 GGGTCAAGGT
Statistics
Matches: 69, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
8 11 0.16
9 36 0.52
10 16 0.23
11 6 0.09
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (9 bp):
AAGAAGAAA
Found at i:50296 original size:36 final size:36
Alignment explanation
Indices: 50222--50306 Score: 50
Period size: 38 Copynumber: 2.2 Consensus size: 36
50212 GAAGAAAAAA
*
50222 AAAAGAAAAAGAAAAAAGAA-AAGAAAAAGAAGAGAA-AG
1 AAAAGAAAAA-AAAAAAAAAGAAGAAAAA-AA-A-AAGAG
* **
50260 AAGAGAAAAAAAAGGGAAAAGAAGAAAAAGAAAAAGAAG
1 AAAAGAAAAAAAA-AAAAAAGAAGAAAAA-AAAAAG-AG
50299 AAAA-AAAA
1 AAAAGAAAA
50307 GGGGTCAAGG
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
37 5 0.13
38 17 0.45
39 16 0.42
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (36 bp):
AAAAGAAAAAAAAAAAAAAGAAGAAAAAAAAAAGAG
Found at i:51321 original size:52 final size:52
Alignment explanation
Indices: 51243--51539 Score: 474
Period size: 52 Copynumber: 5.7 Consensus size: 52
51233 TATGTGCTCA
51243 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
51295 ATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* *
51347 ATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTAGA-AGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* * *
51398 ATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCT-GTTTGATCATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAGAAC
* *
51450 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GTTTGATCATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAGAAC
*
51502 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
51540 CGAAGAAGTG
Statistics
Matches: 233, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
50 5 0.02
51 42 0.18
52 186 0.80
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.40
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
Found at i:51525 original size:155 final size:155
Alignment explanation
Indices: 51243--51539 Score: 490
Period size: 155 Copynumber: 1.9 Consensus size: 155
51233 TATGTGCTCA
*
51243 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATTTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
51308 GAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTATTCTTTG
66 GAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTATTCTTTG
51373 AGTTATCTGATCTGGTTAGAAGAAC
131 AGTTATCTGATCTGGTTAGAAGAAC
* * *
51398 ATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCT-GTTTGATCATAACATAGCATCTTCT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAGAACATAGCATCTTCT
* * *
51462 GGAAGTGTTCTTTGAGTTATCTGATCT-GTTTGATCATAACATAGCATCTTCTGGAAGTGTTCTT
65 GGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAGAACATAGCATCTTCTGGAAGTATTCTT
*
51526 TGAGTTATTTGATC
129 TGAGTTATCTGATC
51540 CGAAGAAGTG
Statistics
Matches: 132, Mismatches: 8, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
154 10 0.08
155 122 0.92
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.40
Consensus pattern (155 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
GAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTATTCTTTG
AGTTATCTGATCTGGTTAGAAGAAC
Found at i:52295 original size:113 final size:113
Alignment explanation
Indices: 52097--52858 Score: 1164
Period size: 113 Copynumber: 6.6 Consensus size: 113
52087 CAAAGATTCA
* *
52097 AATTCATCATTTGATGGATCATCATTACCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCATTTGATGGATCATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
*
52162 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTG
* * * *
52210 AATTCATCACTTGATGGATCAACATTACCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCATTTGATGGATCATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
*
52275 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTG
* * *
52323 AATTCATCACTTGATGGATCAACATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCATCATCT
1 AATTCATCATTTGATGGATCATCTTTTCCAGAG-AAG-GTTCATAATGAGAAGAA--C-TCATCT
* * * *
52388 GAAGAAGAAAGAAGAAGTTCATAATGGGAAGAACTTGTTCAACTTTTTGCTTG
61 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTG
*
52441 AATTCATCACTTGATGGATCATTCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC
1 AATTCATCATTTGATGGATCA-TCTTTTCCAGA-GAAG-GTTCATAATGAGAAGAA--C-TCATC
52506 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTG
60 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTG
* *
52560 AATCCATCATTTGGTGGATCATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCATTTGATGGATCATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
* *
52625 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTG
* * *
52673 AATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCATTTGATGGATCATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
* *
52738 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTG
* * * *
52786 AATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATTTGAAGA
1 AATTCATCATTTGATGGATCATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
52851 AGGAAGAA
66 AGGAAGAA
52859 TTTGTTCAAC
Statistics
Matches: 622, Mismatches: 20, Indels: 14
0.95 0.03 0.02
Matches are distributed among these distances:
113 384 0.62
114 4 0.01
115 17 0.03
116 17 0.03
117 5 0.01
118 88 0.14
119 106 0.17
120 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (113 bp):
AATTCATCATTTGATGGATCATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTG
Found at i:52891 original size:206 final size:204
Alignment explanation
Indices: 52647--53062 Score: 681
Period size: 206 Copynumber: 2.0 Consensus size: 204
52637 TTCATAATGA
52647 GAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTT
1 GAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTT
*
52712 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC
66 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-C
* * * * ** *
52777 TTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCAT-AATGAGAAGAACT
130 TTTT--CTAAATCCATCATTTGATGGATCAACATGGCCAAAGAAAGTTCATGAATGAGAAGAACT
*
52841 CATTTGAAGAAG
193 CATCTGAAGAAG
52853 GAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTT
1 GAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTT
52918 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACT
66 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACT
* * * *
52983 TTTTTAAATTCATCATTTGATGGATCAACATGGCCAAAGAAAGTTTATGAATGAGAAGAACTCGT
131 TTTCTAAATCCATCATTTGATGGATCAACATGGCCAAAGAAAGTTCATGAATGAGAAGAACTCAT
53048 CTGAAGAAG
196 CTGAAGAAG
53057 GAAGAA
1 GAAGAA
53063 GAAGTTCATA
Statistics
Matches: 196, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
203 35 0.18
204 29 0.15
205 5 0.03
206 127 0.65
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (204 bp):
GAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTT
CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACT
TTTCTAAATCCATCATTTGATGGATCAACATGGCCAAAGAAAGTTCATGAATGAGAAGAACTCAT
CTGAAGAAG
Found at i:52933 original size:93 final size:93
Alignment explanation
Indices: 52760--52951 Score: 375
Period size: 93 Copynumber: 2.1 Consensus size: 93
52750 TTCATAATGA
52760 GAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTT
1 GAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTT
*
52825 CATAATGAGAAGAACTCATTTGAAGAAG
66 CATAATGAGAAGAACTCATCTGAAGAAG
52853 GAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTT
1 GAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTT
52918 CATAATGAGAAGAACTCATCTGAAGAAG
66 CATAATGAGAAGAACTCATCTGAAGAAG
52946 GAAGAA
1 GAAGAA
52952 GAAGTTCATA
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 98 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (93 bp):
GAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTT
CATAATGAGAAGAACTCATCTGAAGAAG
Found at i:53056 original size:111 final size:112
Alignment explanation
Indices: 52883--53101 Score: 334
Period size: 111 Copynumber: 2.0 Consensus size: 112
52873 TACCTGAATC
* * * ** *
52883 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCAACATGGCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
52948 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTT-TTTAAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGTTTAAATT
* *
52993 CATCATTTGATGGATCAACATGGCCAAAGAAAGTTTATGAATGAGAAGAACTCGTCTGAAGAAGG
1 CATCATTTGATGGATCAACATGGCCAAAGAAAGTTCAT-AATGAGAAGAACTCATCTGAAGAAGG
*
53058 AAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTGTTTA
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGTTTA
53102 TCATCTCATC
Statistics
Matches: 97, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
110 31 0.32
111 58 0.60
112 4 0.04
113 4 0.04
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (112 bp):
CATCATTTGATGGATCAACATGGCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGTTTAAATT
Found at i:53383 original size:3 final size:3
Alignment explanation
Indices: 53375--53559 Score: 248
Period size: 3 Copynumber: 61.7 Consensus size: 3
53365 TTTATCCATT
* *
53375 TTA TTA TTA TTA TTA TTA ATA TTA ATA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* **
53423 TTA TTA GTA TTA TTA TTA TTA TTA GCA TT- TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
53470 ATA TTA TTA TTA TCA TTA TTA ATA TTA TTA TTA TTA TTA TTA GTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
53518 TTA TTA TTA TTA ATA TTA TATA TTA TTA -TA TATA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T-TA TTA TTA TT
53560 TAATAAATAA
Statistics
Matches: 158, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
2 4 0.03
3 148 0.94
4 6 0.04
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:79364 original size:21 final size:22
Alignment explanation
Indices: 79318--79375 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 22
79308 TATGATCTTT
*
79318 TAATTAGTTTTATTTT-TATAA
1 TAATTAGTTATATTTTATATAA
*
79339 TAATTAGTTATATTTTATTTAA
1 TAATTAGTTATATTTTATATAA
79361 -AATTA-TTATATTTTA
1 TAATTAGTTATATTTTA
79376 CTGATTAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 10 0.29
21 20 0.59
22 4 0.12
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.60
Consensus pattern (22 bp):
TAATTAGTTATATTTTATATAA
Found at i:82024 original size:30 final size:31
Alignment explanation
Indices: 81967--82029 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 31
81957 TTATTTAAAG
81967 TTTAAGAGTCAAATTAATATCTTATCTAAAAT
1 TTTAAGAGTCAAATTAATA-CTTATCTAAAAT
81999 TTTAAGAGTTC-AATTAATA-TTATCTAAAAT
1 TTTAAGAG-TCAAATTAATACTTATCTAAAAT
82029 T
1 T
82030 CAAATATCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 12 0.40
32 16 0.53
33 2 0.07
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (31 bp):
TTTAAGAGTCAAATTAATACTTATCTAAAAT
Found at i:86350 original size:17 final size:17
Alignment explanation
Indices: 86330--86366 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
86320 CCGATTGGTG
* *
86330 AAAAAATATATTAAATT
1 AAAAAATAAATTAAAAT
86347 AAAAAATAAATTAAAAT
1 AAAAAATAAATTAAAAT
86364 AAA
1 AAA
86367 TTTAATTGTC
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:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAAAATAAATTAAAAT
Found at i:86683 original size:21 final size:21
Alignment explanation
Indices: 86657--86703 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
86647 ACTGATATAG
86657 TTTACCCTTT-ATTTTAAATAA
1 TTTA-CCTTTAATTTTAAATAA
*
86678 TTTACCTTTAAATTTTAACTAA
1 TTTACCTTT-AATTTTAAATAA
86700 TTTA
1 TTTA
86704 TAATTATACG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 5 0.22
21 4 0.17
22 14 0.61
ACGTcount: A:0.34, C:0.13, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTACCTTTAATTTTAAATAA
Found at i:93906 original size:34 final size:35
Alignment explanation
Indices: 93866--93931 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 35
93856 AATCTCACTA
*
93866 GGGTGTGTTTGGTTGGGGGAACGT-AGATTCCATT
1 GGGTGTGTTTGGTTGGGAGAACGTGAGATTCCATT
*
93900 GGGTGTGTTTGGTTGGGAGAATGTGAGATTCC
1 GGGTGTGTTTGGTTGGGAGAACGTGAGATTCC
93932 CATGGGAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 22 0.76
35 7 0.24
ACGTcount: A:0.15, C:0.08, G:0.42, T:0.35
Consensus pattern (35 bp):
GGGTGTGTTTGGTTGGGAGAACGTGAGATTCCATT
Found at i:94513 original size:18 final size:18
Alignment explanation
Indices: 94490--94533 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
94480 CTCAGTAATC
*
94490 TTATTCTCTGGTAATCTT
1 TTATTCACTGGTAATCTT
94508 TTATTCCCACTGGTAATCTT
1 TTATT--CACTGGTAATCTT
*
94528 ATATTC
1 TTATTC
94534 CGTGAACCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 6 0.27
20 16 0.73
ACGTcount: A:0.20, C:0.20, G:0.09, T:0.50
Consensus pattern (18 bp):
TTATTCACTGGTAATCTT
Found at i:94522 original size:20 final size:20
Alignment explanation
Indices: 94497--94534 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
94487 ATCTTATTCT
*
94497 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTATATTCCCA
94517 CTGGTAATCTTATATTCC
1 CTGGTAATCTTATATTCC
94535 GTGAACCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTATATTCCCA
Found at i:100480 original size:23 final size:23
Alignment explanation
Indices: 100411--100484 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 23
100401 TAAAGTGGAT
* * *
100411 AAAAATTAATATTAATGTGAAAA
1 AAAAATTGATACTAATGTAAAAA
* * **
100434 AAAAATTGGGTACCAAT-TTTAAA
1 AAAAATT-GATACTAATGTAAAAA
100457 AAAAATTGATACTAATGTAAAAA
1 AAAAATTGATACTAATGTAAAAA
100480 AAAAA
1 AAAAA
100485 GACAGAAAAT
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
22 7 0.18
23 27 0.69
24 5 0.13
ACGTcount: A:0.59, C:0.04, G:0.09, T:0.27
Consensus pattern (23 bp):
AAAAATTGATACTAATGTAAAAA
Found at i:102248 original size:34 final size:34
Alignment explanation
Indices: 102205--102274 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
102195 ACCTGTTTCA
102205 GTCATCTAAACCTTCTTTATATACAAATGATAAT
1 GTCATCTAAACCTTCTTTATATACAAATGATAAT
102239 GTCATCTAAACCTTCTTTATATACAAATGATAAT
1 GTCATCTAAACCTTCTTTATATACAAATGATAAT
102273 GT
1 GT
102275 ACTTGTAGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (34 bp):
GTCATCTAAACCTTCTTTATATACAAATGATAAT
Found at i:103317 original size:2 final size:2
Alignment explanation
Indices: 103310--103354 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
103300 AAATGAAAAT
103310 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
103352 TA T
1 TA T
103355 GAAAATTCTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:103725 original size:18 final size:18
Alignment explanation
Indices: 103702--103742 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
103692 AGCAATATCA
103702 GACTTGATTGTTTCTATG
1 GACTTGATTGTTTCTATG
103720 GACTTGATTGTTTCTATG
1 GACTTGATTGTTTCTATG
103738 GACTT
1 GACTT
103743 TTAGTCGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.12, G:0.22, T:0.49
Consensus pattern (18 bp):
GACTTGATTGTTTCTATG
Found at i:113112 original size:16 final size:17
Alignment explanation
Indices: 113081--113115 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
113071 TATATTAACA
*
113081 TATATACGTAAATAAGT
1 TATATACATAAATAAGT
113098 TATATACAT-AATAAGT
1 TATATACATAAATAAGT
113114 TA
1 TA
113116 CAAAGCATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.37
Consensus pattern (17 bp):
TATATACATAAATAAGT
Found at i:113149 original size:2 final size:2
Alignment explanation
Indices: 113142--113180 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
113132 GAAGCAAACC
113142 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
113181 CCATAAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:113659 original size:16 final size:16
Alignment explanation
Indices: 113634--113664 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
113624 CTCTCTTCAC
113634 TCATTCTCTTTCTTTT
1 TCATTCTCTTTCTTTT
*
113650 TCATTTTCTTTCTTT
1 TCATTCTCTTTCTTT
113665 CATATAACAT
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:0.06, C:0.23, G:0.00, T:0.71
Consensus pattern (16 bp):
TCATTCTCTTTCTTTT
Found at i:114830 original size:3 final size:3
Alignment explanation
Indices: 114822--114854 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
114812 TATATAATTA
114822 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
114855 TTAAAAGACG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:115181 original size:111 final size:113
Alignment explanation
Indices: 115011--115254 Score: 377
Period size: 111 Copynumber: 2.2 Consensus size: 113
115001 GCTGTACCTC
* ** * *
115011 AGGGAATATCAGATCTGGGGATGTTGGTTTATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCA
1 AGGGAATATCAGATCTGGGAAAATTGATTCATTGAATCAGGGTAGACTTGTTCCGCTGTCAC-CA
* *
115076 AG-GAATATCAAATCTTGAAA-A-AGAGGGATTTGTTCCGCTTCCTCTA
65 AGAGAATATCAAATCTTGAAAGAGAGAGAGATCTGTTCCGCTTCCTCTA
*
115122 AGGGAATATCAGATCTGGGAAAATTGATTCATTGAATCAGGGTAGACTTGTTCCGCTGTCACCCA
1 AGGGAATATCAGATCTGGGAAAATTGATTCATTGAATCAGGGTAGACTTGTTCCGCTGTCACCAA
*
115187 GAGAATATCAAATCTTGAAAGAGAGAGAGATCTGTTCCGCTTCCTCTG
66 GAGAATATCAAATCTTGAAAGAGAGAGAGATCTGTTCCGCTTCCTCTA
115235 AGGGAATATCAGATCTGGGA
1 AGGGAATATCAGATCTGGGA
115255 GAGTTGATCC
Statistics
Matches: 121, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
110 3 0.02
111 75 0.62
112 1 0.01
113 42 0.35
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (113 bp):
AGGGAATATCAGATCTGGGAAAATTGATTCATTGAATCAGGGTAGACTTGTTCCGCTGTCACCAA
GAGAATATCAAATCTTGAAAGAGAGAGAGATCTGTTCCGCTTCCTCTA
Found at i:115831 original size:13 final size:13
Alignment explanation
Indices: 115787--115833 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
115777 CTGTTCTTTG
*
115787 ATATTGAAAACTAA
1 ATATTTAAAA-TAA
115801 ATA-TTAAAATAA
1 ATATTTAAAATAA
*
115813 TTTATTTAAAATAA
1 -ATATTTAAAATAA
115827 ATATTTA
1 ATATTTA
115834 TTTATTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 3 0.11
13 13 0.46
14 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:117263 original size:3 final size:3
Alignment explanation
Indices: 117255--117306 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
117245 TTAATATATT
* *
117255 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
117303 TAA T
1 TAA T
117307 TAATTAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:117863 original size:113 final size:112
Alignment explanation
Indices: 117631--118531 Score: 1166
Period size: 113 Copynumber: 7.9 Consensus size: 112
117621 GATAGAATTA
* * *
117631 TTGAACAAGTTCTTATTATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTAT
* * * * ** * *
117696 GAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAAG
63 GAACT-TTCTCTGGAAAAGCTGATCCATCAAATGATG-ATTTGATCAAAAGG
*
117747 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* *
117812 CTTTCTCTGGAAAAGCTGATCCATCAAGTAATAGATTTGATCAAAAGG
66 CTTTCTCTGGAAAAGCTGATCCATCAAATGAT-GATTTGATCAAAAGG
* * *
117860 TTGAGCAAATTCTTCTCATTATGGACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* *
117925 CTTTCTCTGGAAAAGCTGATCCATCAAGTAATAGATTTGATCAAAAGG
66 CTTTCTCTGGAAAAGCTGATCCATCAAATGAT-GATTTGATCAAAAGG
* * * *
117973 TTGAGCAAATTCTTCTCATTAGGGACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * * * *
118038 CTTTCTCTGGAAAAGATAATCCATCAATTAATGAATTCAGGT-AAAAGG
66 CTTTCTCTGGAAAAGCTGATCCATCAAATGATG-ATT-TGATCAAAAGG
118086 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * **
118151 CTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGT-AAAAGG
66 CTTTCTCTGGAAAAGCTGATCCATCAAATGAT-GATTTGA-TCAAAAGG
118199 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* **
118264 CTTTCTCTGGAAATGAC-GATCCATCAAATGATGGATTCAAGT-AAAAGG
66 CTTTCTCTGGAAAAG-CTGATCCATCAAATGAT-GATTTGA-TCAAAAGG
118312 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * * * *
118377 CCTTCTCTGGAAATA-CTAATCCATCAATTTGATGAATTCAGGCAAAAGG
66 CTTTCTCTGGAAA-AGCTGATCCATCAA-ATGATGATTTGA-TCAAAAGG
*
118426 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * *
118491 CCTTCTCTGGAAATGCTAATCCATCAATTTGATAGATTTGA
66 CTTTCTCTGGAAAAGCTGATCCATCAA-ATGAT-GATTTGA
118532 ATCTTTGCTA
Statistics
Matches: 726, Mismatches: 46, Indels: 27
0.91 0.06 0.03
Matches are distributed among these distances:
112 4 0.01
113 564 0.78
114 109 0.15
115 5 0.01
116 44 0.06
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (112 bp):
TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTTTCTCTGGAAAAGCTGATCCATCAAATGATGATTTGATCAAAAGG
Found at i:118287 original size:339 final size:339
Alignment explanation
Indices: 117631--118517 Score: 1289
Period size: 339 Copynumber: 2.6 Consensus size: 339
117621 GATAGAATTA
* * * *
117631 TTGAACAAGTTCTTATTATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
1 TTGAACAAATTCTTCTCATTAGGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTAT
* * * * * * ** * *
117696 GAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTTCT
63 GAACT-TTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAGGCAAAAGGTTGAACAAATTCT
117760 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
127 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
* * ** * *
117825 AGCTGATCCATCAAGTAATAGATTTGATCAAAAGGTTGAGCAAATTCTTCTCATTATGGACTTCT
192 TGCTGATCCATCAAATAATAGATTCAATCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCT
* *
117890 TCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTA
257 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATA
**
117955 ATAGATTTGA-TCAAAAGG
322 ATAGATTCAAGT-AAAAGG
* * *
117973 TTGAGCAAATTCTTCTCATTAGGGACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTAGGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* *
118038 CTTTCTCTGGAAAAGATAATCCATCAATTAATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTC
66 CTTTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTC
*
118103 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGAT
131 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGCT
* *
118168 GATCCATCAAATGATGGATTCAAGT-AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
196 GATCCATCAAATAATAGATTCAA-TCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
* *
118232 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGAC-GATCCATCAAATGAT
260 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAG-CTGATCCATCAAATAAT
*
118296 GGATTCAAGTAAAAGG
324 AGATTCAAGTAAAAGG
*
118312 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTAGGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* *
118377 CCTTCTCTGGAAATA-CTAATCCATCAATTTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTC
66 CTTTCTCTGGAAA-AGATAATCCATCAA-TTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTC
* *
118441 TCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAATG
129 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATG
*
118506 CTAATCCATCAA
194 CTGATCCATCAA
118518 TTTGATAGAT
Statistics
Matches: 492, Mismatches: 47, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
338 2 0.00
339 340 0.69
340 111 0.23
342 39 0.08
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Consensus pattern (339 bp):
TTGAACAAATTCTTCTCATTAGGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTTTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTC
ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGCT
GATCCATCAAATAATAGATTCAATCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT
CCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATAATAG
ATTCAAGTAAAAGG
Found at i:119399 original size:83 final size:83
Alignment explanation
Indices: 119260--119728 Score: 843
Period size: 83 Copynumber: 5.7 Consensus size: 83
119250 CCTACCAAAA
* *
119260 CAGATCAGATAACTCAAAGAACATTTTCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAA
*
119325 TGATTGGTTTTGTCCAAC
66 TGATTGGTTCTGTCCAAC
*
119343 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGAAAATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAA
*
119408 TGATTGGTTCTGTCAAAC
66 TGATTGGTTCTGTCCAAC
*
119426 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGAAAATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAA
*
119491 TGATTGGTTTTGTCCAAC
66 TGATTGGTTCTGTCCAAC
119509 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAA
119574 TGATTGGTTCTG-CCAAAC
66 TGATTGGTTCTGTCC-AAC
119592 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAA
119657 TGATTGGTTCTG-CCAAAC
66 TGATTGGTTCTGTCC-AAC
119675 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCT
119729 GTTCCAGTTA
Statistics
Matches: 376, Mismatches: 9, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
82 2 0.01
83 374 0.99
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.29
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAA
TGATTGGTTCTGTCCAAC
Found at i:131577 original size:19 final size:18
Alignment explanation
Indices: 131527--131579 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
131517 AAATACTTGC
*
131527 AAATAAAATAAAAACATAT
1 AAAT-AAATAAAAAAATAT
* *
131546 AAAT-ATTATAAAAATAAT
1 AAATAAATAAAAAAAT-AT
131564 AAATAAATAAAAAAAT
1 AAATAAATAAAAAAAT
131580 TGAAAAGAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
17 8 0.30
18 6 0.22
19 13 0.48
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.25
Consensus pattern (18 bp):
AAATAAATAAAAAAATAT
Found at i:132257 original size:13 final size:13
Alignment explanation
Indices: 132213--132259 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
132203 ATGTTCTTTG
*
132213 ATATTGAAAACTAA
1 ATATTTAAAA-TAA
132227 ATA-TTAAAATAA
1 ATATTTAAAATAA
*
132239 TTTATTTAAAATAA
1 -ATATTTAAAATAA
132253 ATATTTA
1 ATATTTA
132260 TTTATATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 3 0.11
13 13 0.46
14 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:133688 original size:3 final size:3
Alignment explanation
Indices: 133680--133743 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
133670 TTAATATATT
*
133680 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
133728 TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
133744 TAATTAATTA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:133875 original size:37 final size:37
Alignment explanation
Indices: 133825--133935 Score: 195
Period size: 37 Copynumber: 3.0 Consensus size: 37
133815 TCAGATCTGA
**
133825 ATTTGCTTCACTACTCTTTTGTGAAGGCTTAAGATTG
1 ATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTG
133862 ATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTG
1 ATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTG
*
133899 ATTTGCTTCACTACTCTTCGGTGAAGGCTTTAGATTG
1 ATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTG
133936 CCCGTTGGAC
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 71 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (37 bp):
ATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTG
Found at i:134379 original size:43 final size:41
Alignment explanation
Indices: 134321--134442 Score: 154
Period size: 43 Copynumber: 2.9 Consensus size: 41
134311 GCTTGTGTGT
* * * *
134321 ACGATTTCCTTCGTCGTGAAGTTGAAACCGTGGATGTGTGAGC
1 ACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGT-TG-GC
*
134364 ACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATCCGTTGGT
1 ACGATATCCTCCGTCGTGGAGTTGAAATCGTGGAT--GTTGGC
*
134407 ACGATATCCTCCGTCGTGGAGTTGAAATTGTGGATG
1 ACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATG
134443 GCCCCTTCGT
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
41 1 0.01
43 66 0.93
44 2 0.03
45 2 0.03
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.30
Consensus pattern (41 bp):
ACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGTTGGC
Found at i:134793 original size:33 final size:32
Alignment explanation
Indices: 134718--134780 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
134708 TTGCATCAGG
* * *
134718 ATGTTGAATCCCCAAATATACCCCAATATTCA
1 ATGTTGAATCTCCAAATATACCCAAACATTCA
134750 ATGTTGAATCTCCAAATATTACCCAAACATT
1 ATGTTGAATCTCCAAATA-TACCCAAACATT
134781 TGTTGTTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 17 0.63
33 10 0.37
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.30
Consensus pattern (32 bp):
ATGTTGAATCTCCAAATATACCCAAACATTCA
Found at i:135850 original size:20 final size:18
Alignment explanation
Indices: 135825--135899 Score: 60
Period size: 19 Copynumber: 3.9 Consensus size: 18
135815 TTATCGTCCC
135825 CTTTTTTTCTCTTTGTTTCT
1 CTTTTTTT-TCTTT-TTTCT
*
135845 CTTTTTTTTCTTTTTTTT
1 CTTTTTTTTCTTTTTTCT
** *
135863 CTTTTCTTTAATTTTTTTT
1 CTTTT-TTTTCTTTTTTCT
*
135882 ATTCTTTTATTCTTTTTT
1 CTT-TTTT-TTCTTTTTT
135900 TTTGCTCTGT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
18 9 0.20
19 20 0.43
20 17 0.37
ACGTcount: A:0.05, C:0.13, G:0.01, T:0.80
Consensus pattern (18 bp):
CTTTTTTTTCTTTTTTCT
Found at i:135858 original size:9 final size:9
Alignment explanation
Indices: 135825--135901 Score: 73
Period size: 9 Copynumber: 8.0 Consensus size: 9
135815 TTATCGTCCC
135825 CTTTTTTTCT
1 CTTTTTTT-T
*
135835 CTTTGTTTCT
1 CTTT-TTTTT
135845 CTTTTTTTT
1 CTTTTTTTT
135854 CTTTTTTTT
1 CTTTTTTTT
*
135863 CTTTTCTTTA
1 CTTTT-TTTT
*
135873 ATTTTTTTT
1 CTTTTTTTT
*
135882 ATTCTTTTATT
1 CTT-TTTT-TT
135893 CTTTTTTTT
1 CTTTTTTTT
135902 TGCTCTGTGT
Statistics
Matches: 57, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
9 26 0.46
10 24 0.42
11 7 0.12
ACGTcount: A:0.05, C:0.13, G:0.01, T:0.81
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:142845 original size:16 final size:17
Alignment explanation
Indices: 142814--142848 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
142804 TATATTAACA
*
142814 TATATACGTAAATAAGT
1 TATATACATAAATAAGT
142831 TATATACAT-AATAAGT
1 TATATACATAAATAAGT
142847 TA
1 TA
142849 CAAAGCATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.37
Consensus pattern (17 bp):
TATATACATAAATAAGT
Found at i:142882 original size:2 final size:2
Alignment explanation
Indices: 142875--142904 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
142865 GAAGCAAACC
142875 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
142905 TACCATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:143380 original size:16 final size:16
Alignment explanation
Indices: 143361--143391 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
143351 TTCTCTTCAC
143361 TCATTCTCTTTCTTTT
1 TCATTCTCTTTCTTTT
*
143377 TCATTTTCTTTCTTT
1 TCATTCTCTTTCTTT
143392 CATATAACAT
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:0.06, C:0.23, G:0.00, T:0.71
Consensus pattern (16 bp):
TCATTCTCTTTCTTTT
Found at i:150896 original size:48 final size:47
Alignment explanation
Indices: 150821--150915 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 47
150811 ATTACTCTCC
150821 ATAGAGGATTCAAATTCAAGCCCATGTGTGTTGTAGGGTGTATGTGCA
1 ATAGAGGATTCAAATTCAAGCCCATGTGT-TTGTAGGGTGTATGTGCA
*
150869 ATAGAGGATTCAAATTCAAGCCTATGTGTTTGTAGGGTGTATGTGCA
1 ATAGAGGATTCAAATTCAAGCCCATGTGTTTGTAGGGTGTATGTGCA
150916 TATATCAATT
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 18 0.39
48 28 0.61
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.33
Consensus pattern (47 bp):
ATAGAGGATTCAAATTCAAGCCCATGTGTTTGTAGGGTGTATGTGCA
Done.