Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018519.1 Corchorus olitorius cultivar O-4 contig18552, 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: 117496
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:1800 original size:19 final size:19
Alignment explanation
Indices: 1778--1828 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
1768 GGACTGAAAT
1778 TAATTAATTATTAATTAAA
1 TAATTAATTATTAATTAAA
* *
1797 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAATTAAA
1816 TAATT-ATTATTAA
1 TAATTAATTATTAA
1829 AAATCCCACA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 9 0.33
19 17 0.63
20 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TAATTAATTATTAATTAAA
Found at i:14649 original size:13 final size:13
Alignment explanation
Indices: 14631--14656 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
14621 CTTGGCATGA
14631 GTGATGATTTTTG
1 GTGATGATTTTTG
14644 GTGATGATTTTTG
1 GTGATGATTTTTG
14657 TTGTTACCTT
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:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
GTGATGATTTTTG
Found at i:15039 original size:19 final size:19
Alignment explanation
Indices: 15017--15067 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
15007 GGACTGAAAT
15017 TAATTAATTATTAATTAAA
1 TAATTAATTATTAATTAAA
* *
15036 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAATTAAA
15055 TAATT-ATTATTAA
1 TAATTAATTATTAA
15068 AAATCCCACA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 9 0.33
19 17 0.63
20 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TAATTAATTATTAATTAAA
Found at i:23391 original size:21 final size:21
Alignment explanation
Indices: 23366--23406 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
23356 AAAAAGATCA
**
23366 CATGTGGTTCACCATGTAAAG
1 CATGTGGTGAACCATGTAAAG
23387 CATGTGGTGAACCATGTAAA
1 CATGTGGTGAACCATGTAAA
23407 ATTTTGGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (21 bp):
CATGTGGTGAACCATGTAAAG
Found at i:32305 original size:1 final size:1
Alignment explanation
Indices: 32299--32328 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
32289 TCTTTTCAAG
32299 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
32329 AAATTAAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:33176 original size:155 final size:155
Alignment explanation
Indices: 32894--33203 Score: 620
Period size: 155 Copynumber: 2.0 Consensus size: 155
32884 CAACAATTTT
32894 TCTAAAAACTCAAAACTCATTTGTGCTTGTGTAACTTTGTTTTCAAAATCAAACAAAGGATTCAC
1 TCTAAAAACTCAAAACTCATTTGTGCTTGTGTAACTTTGTTTTCAAAATCAAACAAAGGATTCAC
32959 TTTCTTTAAACTATTAAAAATTATGAATAATTGCAACCAAGGATAGAAACTCACAAGTTAATTCT
66 TTTCTTTAAACTATTAAAAATTATGAATAATTGCAACCAAGGATAGAAACTCACAAGTTAATTCT
33024 AGGCTAGTCAGTGCTGTCATTTGAC
131 AGGCTAGTCAGTGCTGTCATTTGAC
33049 TCTAAAAACTCAAAACTCATTTGTGCTTGTGTAACTTTGTTTTCAAAATCAAACAAAGGATTCAC
1 TCTAAAAACTCAAAACTCATTTGTGCTTGTGTAACTTTGTTTTCAAAATCAAACAAAGGATTCAC
33114 TTTCTTTAAACTATTAAAAATTATGAATAATTGCAACCAAGGATAGAAACTCACAAGTTAATTCT
66 TTTCTTTAAACTATTAAAAATTATGAATAATTGCAACCAAGGATAGAAACTCACAAGTTAATTCT
33179 AGGCTAGTCAGTGCTGTCATTTGAC
131 AGGCTAGTCAGTGCTGTCATTTGAC
33204 ATGCGTTGTG
Statistics
Matches: 155, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
155 155 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.34
Consensus pattern (155 bp):
TCTAAAAACTCAAAACTCATTTGTGCTTGTGTAACTTTGTTTTCAAAATCAAACAAAGGATTCAC
TTTCTTTAAACTATTAAAAATTATGAATAATTGCAACCAAGGATAGAAACTCACAAGTTAATTCT
AGGCTAGTCAGTGCTGTCATTTGAC
Found at i:36578 original size:15 final size:15
Alignment explanation
Indices: 36558--36587 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
36548 ACTCACCATC
36558 ATTATTTCACCAAAA
1 ATTATTTCACCAAAA
36573 ATTATTTCACCAAAA
1 ATTATTTCACCAAAA
36588 TCAAAGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (15 bp):
ATTATTTCACCAAAA
Found at i:37293 original size:56 final size:56
Alignment explanation
Indices: 37221--37356 Score: 220
Period size: 56 Copynumber: 2.4 Consensus size: 56
37211 GGCGGGGTTG
* *
37221 ATTTTTTATCGCCCTCTACCTTTATGCTTC-GATTTTGTGGAATGGCGGGGTGTATC
1 ATTTTTTATCACCCTCTACCTTTATGCTTCAG-CTTTGTGGAATGGCGGGGTGTATC
*
37277 ATTTTTTATCACCCTCTACCTTTATGCTTCAGCTTTGTGGATTGGCGGGGTGTATC
1 ATTTTTTATCACCCTCTACCTTTATGCTTCAGCTTTGTGGAATGGCGGGGTGTATC
37333 ATTTTTTTATCACCCTCTACCTTT
1 A-TTTTTTATCACCCTCTACCTTT
37357 CCTCGAGTTC
Statistics
Matches: 75, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
56 52 0.69
57 23 0.31
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (56 bp):
ATTTTTTATCACCCTCTACCTTTATGCTTCAGCTTTGTGGAATGGCGGGGTGTATC
Found at i:37311 original size:166 final size:159
Alignment explanation
Indices: 37001--37323 Score: 540
Period size: 166 Copynumber: 2.0 Consensus size: 159
36991 ATCGGGGTGG
37001 TCTTGGCGGGGTCGATTTCTTTATCACCCTCTACCTCTCCATCGGCCTCTTGGCGGGGTTGATTT
1 TCTTGGCGGGGTCGATTTCTTTATCACCCTCTACCTCTCCATCGGCCTCTTGGCGGGGTTGATTT
*
37066 TTTTATCGCCCTATGCTTCGACTTTGTGGAATGGCGGGTTGTATCATTTTTTATCACCCTCTACC
66 TTTTATCGCCCTATGCTTCGACTTTGTGGAATGGCGGGGTGTATCATTTTTTATCACCCTCTACC
37131 TTTATGCTTCAGCTTTGTGGATTGGCGTC
131 TTTATGCTTCAGCTTTGTGGATTGGCGTC
*
37160 TCTTGGCGGGGTCGATTTTTTTATCACCCTCTACCTCTCCATCGGCCTCTTGGCGGGGTTGA-TT
1 TCTTGGCGGGGTCGATTTCTTTATCACCCTCTACCTCTCCATCGGCCTCTTGGCGGGGTTGATTT
*
37224 TTTTATCGCCCTCTACCTTTATGCTTCGATTTTGTGGAATGGCGGGGTGTATCATTTTTTATCAC
66 TTTTATCG----C--CC--TATGCTTCGACTTTGTGGAATGGCGGGGTGTATCATTTTTTATCAC
37289 CCTCTACCTTTATGCTTCAGCTTTGTGGATTGGCG
123 CCTCTACCTTTATGCTTCAGCTTTGTGGATTGGCG
37324 GGGTGTATCA
Statistics
Matches: 153, Mismatches: 3, Indels: 9
0.93 0.02 0.05
Matches are distributed among these distances:
158 10 0.07
159 61 0.40
162 1 0.01
164 2 0.01
166 79 0.52
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.41
Consensus pattern (159 bp):
TCTTGGCGGGGTCGATTTCTTTATCACCCTCTACCTCTCCATCGGCCTCTTGGCGGGGTTGATTT
TTTTATCGCCCTATGCTTCGACTTTGTGGAATGGCGGGGTGTATCATTTTTTATCACCCTCTACC
TTTATGCTTCAGCTTTGTGGATTGGCGTC
Found at i:40459 original size:42 final size:42
Alignment explanation
Indices: 40413--40497 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
40403 CTCGATGAAA
* * *
40413 TGGATATGAGAGGAATGGCCAAAGGCTTGTTATTTCTCGTTG
1 TGGATATGAGAGAAATAGCCAAAGGCTTGTTATTCCTCGTTG
* **
40455 TGGATTTGAGAGAAATAGCTGAAGGCTTGTTATTCCTCGTTG
1 TGGATATGAGAGAAATAGCCAAAGGCTTGTTATTCCTCGTTG
40497 T
1 T
40498 CAGATTTGCT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.24, C:0.12, G:0.29, T:0.35
Consensus pattern (42 bp):
TGGATATGAGAGAAATAGCCAAAGGCTTGTTATTCCTCGTTG
Found at i:47632 original size:17 final size:18
Alignment explanation
Indices: 47610--47645 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
47600 AAAGGGTAGT
*
47610 TAAAAA-AATTGTTTTCA
1 TAAAAAGAAGTGTTTTCA
47627 TAAAAAGAAGTGTTTTCA
1 TAAAAAGAAGTGTTTTCA
47645 T
1 T
47646 GTAAGACGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (18 bp):
TAAAAAGAAGTGTTTTCA
Found at i:53511 original size:21 final size:21
Alignment explanation
Indices: 53473--53512 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
53463 GGCGCCCAAA
* *
53473 TGGTTTGTCTGAAGACCCATG
1 TGGTTTGCCTGAACACCCATG
*
53494 TGGTTTGCCTGATCACCCA
1 TGGTTTGCCTGAACACCCA
53513 GGTAGGCAGT
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:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (21 bp):
TGGTTTGCCTGAACACCCATG
Found at i:58213 original size:21 final size:21
Alignment explanation
Indices: 58187--58229 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
58177 AGCTTTGGAA
58187 GAGATAAATACAGAAATGATG
1 GAGATAAATACAGAAATGATG
58208 GAGATAAATACAGAAATGATG
1 GAGATAAATACAGAAATGATG
58229 G
1 G
58230 CTTCAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.51, C:0.05, G:0.26, T:0.19
Consensus pattern (21 bp):
GAGATAAATACAGAAATGATG
Found at i:71700 original size:171 final size:171
Alignment explanation
Indices: 71415--71758 Score: 670
Period size: 171 Copynumber: 2.0 Consensus size: 171
71405 ATGAAAAAGG
71415 CTTTAACATTGTTGGCATAAGAAGTGGTGACCATGGTGGTGAGTTTGATAGCCATGCTTTTGAAA
1 CTTTAACATTGTTGGCATAAGAAGTGGTGACCATGGTGGTGAGTTTGATAGCCATGCTTTTGAAA
71480 GTTTTTGTAATGAAAATGGTTTCATTCACAATTTTTCTGTTCCTAGAACACCACAACAGAATGGT
66 GTTTTTGTAATGAAAATGGTTTCATTCACAATTTTTCTGTTCCTAGAACACCACAACAGAATGGT
*
71545 GTGGTGGAAAGAAAAAACAGAACATTGAAGACATGGCAGAA
131 GTGGTGGAAAGAAAAAACAGAACATTAAAGACATGGCAGAA
71586 CTTTAACATTGTTGGCATAAGAAGTGGTGACCATGGTGGTGAGTTTGATAGCCATGCTTTTGAAA
1 CTTTAACATTGTTGGCATAAGAAGTGGTGACCATGGTGGTGAGTTTGATAGCCATGCTTTTGAAA
71651 GTTTTTGTAATGAAAATGGTTTCATTCACAATTTTTCTGTTCCTAGAACACCACAACAGAATGGT
66 GTTTTTGTAATGAAAATGGTTTCATTCACAATTTTTCTGTTCCTAGAACACCACAACAGAATGGT
*
71716 GTGGTGGAAAGAAAAAACAGAACATTAAAGACATGGTAGAA
131 GTGGTGGAAAGAAAAAACAGAACATTAAAGACATGGCAGAA
71757 CT
1 CT
71759 ATGACATGGC
Statistics
Matches: 171, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
171 171 1.00
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.30
Consensus pattern (171 bp):
CTTTAACATTGTTGGCATAAGAAGTGGTGACCATGGTGGTGAGTTTGATAGCCATGCTTTTGAAA
GTTTTTGTAATGAAAATGGTTTCATTCACAATTTTTCTGTTCCTAGAACACCACAACAGAATGGT
GTGGTGGAAAGAAAAAACAGAACATTAAAGACATGGCAGAA
Found at i:81449 original size:3 final size:3
Alignment explanation
Indices: 81443--81492 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
81433 AAATAATATG
81443 TAA TAA TAA TAA TAA TAA TAA 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
81491 TA
1 TA
81493 TATATTATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:81507 original size:7 final size:7
Alignment explanation
Indices: 81495--81520 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
81485 TAATAATATA
81495 TATTATT
1 TATTATT
81502 TATTATT
1 TATTATT
81509 TATTATT
1 TATTATT
81516 TATTA
1 TATTA
81521 GTATTAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TATTATT
Found at i:81554 original size:34 final size:32
Alignment explanation
Indices: 81516--81584 Score: 120
Period size: 34 Copynumber: 2.1 Consensus size: 32
81506 ATTTATTATT
81516 TATTAGTATTAGTATTAGTATTAGTATAGTATAG
1 TATTAGTATTAGTATTAGTATTAGTATA-TA-AG
81550 TATTAGTATTAGTATTAGTATTAGTATATAAG
1 TATTAGTATTAGTATTAGTATTAGTATATAAG
81582 TAT
1 TAT
81585 ATATATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
32 5 0.14
33 2 0.06
34 28 0.80
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (32 bp):
TATTAGTATTAGTATTAGTATTAGTATATAAG
Found at i:81585 original size:6 final size:6
Alignment explanation
Indices: 81516--81576 Score: 108
Period size: 6 Copynumber: 10.5 Consensus size: 6
81506 ATTTATTATT
81516 TATTAG TATTAG TATTAG TATTAG TA-TAG TA-TAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
81562 TATTAG TATTAG TAT
1 TATTAG TATTAG TAT
81577 ATAAGTATAT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
5 10 0.19
6 44 0.81
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.49
Consensus pattern (6 bp):
TATTAG
Found at i:85021 original size:16 final size:15
Alignment explanation
Indices: 85000--85029 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
84990 TTACTATATA
85000 ATATATAT-TTATGT
1 ATATATATATTATGT
85014 ATATATATATTATGT
1 ATATATATATTATGT
85029 A
1 A
85030 ATACGTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (15 bp):
ATATATATATTATGT
Found at i:85059 original size:12 final size:12
Alignment explanation
Indices: 85042--85066 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
85032 ACGTATATCT
85042 ATATTATTTCTA
1 ATATTATTTCTA
85054 ATATTATTTCTA
1 ATATTATTTCTA
85066 A
1 A
85067 ATAATATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (12 bp):
ATATTATTTCTA
Found at i:87822 original size:40 final size:38
Alignment explanation
Indices: 87754--87830 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
87744 CATGTTTTCC
*
87754 GCTAGATCATGCAATTTTTTAGACAAAAAAAATGTTTA
1 GCTAGATCATGCAATTTTTTAGAAAAAAAAAATGTTTA
87792 GCTAGATCATGCAATTTTTTAGGCAAAAAAAAAATGTTT
1 GCTAGATCATGCAATTTTTTA-G-AAAAAAAAAATGTTT
87831 TGTTTGATGG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 21 0.58
39 1 0.03
40 14 0.39
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (38 bp):
GCTAGATCATGCAATTTTTTAGAAAAAAAAAATGTTTA
Found at i:91328 original size:28 final size:28
Alignment explanation
Indices: 91289--91344 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
91279 GCTACTGCTT
*
91289 AACAACAATTTTTTTTTCTCTCCATCTC
1 AACAACAATTTTTTTTTATCTCCATCTC
*
91317 AACAGCAATTTTTTTTTATCTCCATCTC
1 AACAACAATTTTTTTTTATCTCCATCTC
91345 TATACTTTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.25, C:0.27, G:0.02, T:0.46
Consensus pattern (28 bp):
AACAACAATTTTTTTTTATCTCCATCTC
Found at i:105098 original size:21 final size:21
Alignment explanation
Indices: 105072--105114 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
105062 CAAGTGCCCA
*
105072 TCTTTTGACTAATACAATTAG
1 TCTTTTAACTAATACAATTAG
* *
105093 TCTTTTAACTAATCCCATTAG
1 TCTTTTAACTAATACAATTAG
105114 T
1 T
105115 AGGAGAATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.44
Consensus pattern (21 bp):
TCTTTTAACTAATACAATTAG
Found at i:107056 original size:22 final size:22
Alignment explanation
Indices: 106983--107194 Score: 125
Period size: 22 Copynumber: 9.5 Consensus size: 22
106973 TCTTGTCTCT
*
106983 GTGTGGTTATCAAAATTTCGAAA
1 GTGTGGTTATCAAAATTTC-ATA
* * **
107006 G-ATGGTTATTATCATTTCATGA
1 GTGTGGTTATCAAAATTTCAT-A
* *
107028 G-GAGGTTATCAAAATTCCATA
1 GTGTGGTTATCAAAATTTCATA
*
107049 GTGTGGTTACCAAAATTTCATA
1 GTGTGGTTATCAAAATTTCATA
107071 -TG-GAAGTTATCAAAATTTCATGA
1 GTGTG--GTTATCAAAATTTCAT-A
** *
107094 G-AAGATTATCAAAATTTCATA
1 GTGTGGTTATCAAAATTTCATA
* *
107115 GTGTGGTTACCAAAATTTCAAA
1 GTGTGGTTATCAAAATTTCATA
* **
107137 G-GATCGGGTTATTAAAATTTTTTA
1 GTG-T--GGTTATCAAAATTTCATA
*
107161 G-GAAGGTTATTC-AAATTTCATA
1 GTG-TGGTTA-TCAAAATTTCATA
107183 GTGTGGTTATCA
1 GTGTGGTTATCA
107195 CTATTTTATA
Statistics
Matches: 143, Mismatches: 32, Indels: 29
0.70 0.16 0.14
Matches are distributed among these distances:
20 1 0.01
21 10 0.07
22 111 0.78
23 4 0.03
24 17 0.12
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (22 bp):
GTGTGGTTATCAAAATTTCATA
Found at i:107259 original size:22 final size:21
Alignment explanation
Indices: 107223--107344 Score: 86
Period size: 22 Copynumber: 5.5 Consensus size: 21
107213 ATCAAAGAGA
* *
107223 TTATCAAAATGTCATAACGAGG
1 TTAT-AAAATTTCATAAGGAGG
*
107245 TTATAAGAATTTCAT-AGTGTGG
1 TTATAA-AATTTCATAAG-GAGG
* *
107267 TTAACAAAATTTTATAAGGAGG
1 TT-ATAAAATTTCATAAGGAGG
* *
107289 TTACTAATATTTCATAGGGAGG
1 TTA-TAAAATTTCATAAGGAGG
*
107311 TTATCAAAATTTCAT-AGTGTGG
1 TTAT-AAAATTTCATAAG-GAGG
107333 TTATTAAAATTT
1 TTA-TAAAATTT
107345 TTTAGTGTGG
Statistics
Matches: 79, Mismatches: 13, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
21 6 0.08
22 67 0.85
23 6 0.08
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.38
Consensus pattern (21 bp):
TTATAAAATTTCATAAGGAGG
Found at i:107289 original size:44 final size:44
Alignment explanation
Indices: 107223--107370 Score: 156
Period size: 44 Copynumber: 3.4 Consensus size: 44
107213 ATCAAAGAGA
* *
107223 TTATCAAAATGTCATAACGAGGTTA-TAAGAATTTCATAGTGTGG
1 TTATCAAAATTTCATAAGGAGGTTACTAA-AATTTCATAGTGTGG
* * * * *
107267 TTAACAAAATTTTATAAGGAGGTTACTAATATTTCATAGGGAGG
1 TTATCAAAATTTCATAAGGAGGTTACTAAAATTTCATAGTGTGG
* * **
107311 TTATCAAAATTTCAT-AGTGTGGTTATTAAAATTTTTTAGTGTGG
1 TTATCAAAATTTCATAAG-GAGGTTACTAAAATTTCATAGTGTGG
*
107355 TTATCAAATTTTCATA
1 TTATCAAAATTTCATA
107371 TGAAAGTTAT
Statistics
Matches: 84, Mismatches: 17, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
43 2 0.02
44 79 0.94
45 3 0.04
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.40
Consensus pattern (44 bp):
TTATCAAAATTTCATAAGGAGGTTACTAAAATTTCATAGTGTGG
Found at i:107350 original size:22 final size:22
Alignment explanation
Indices: 107243--107366 Score: 92
Period size: 22 Copynumber: 5.7 Consensus size: 22
107233 GTCATAACGA
*
107243 GGTTA-TAAGAATTTCATAGTGT
1 GGTTATTAA-AATTTTATAGTGT
** *
107265 GGTTAACAAAATTTTATAAG-GA
1 GGTTATTAAAATTTTAT-AGTGT
* * * * *
107287 GGTTACTAATATTTCATAGGGA
1 GGTTATTAAAATTTTATAGTGT
* *
107309 GGTTATCAAAATTTCATAGTGT
1 GGTTATTAAAATTTTATAGTGT
*
107331 GGTTATTAAAATTTTTTAGTGT
1 GGTTATTAAAATTTTATAGTGT
*
107353 GGTTA-TCAAATTTT
1 GGTTATTAAAATTTT
107367 CATATGAAAG
Statistics
Matches: 83, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
21 10 0.12
22 69 0.83
23 4 0.05
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (22 bp):
GGTTATTAAAATTTTATAGTGT
Found at i:107357 original size:66 final size:66
Alignment explanation
Indices: 107223--107370 Score: 167
Period size: 66 Copynumber: 2.2 Consensus size: 66
107213 ATCAAAGAGA
* * **
107223 TTATCAAAATGTCATAACGAGGTTATAAGAATTTCATAGTGTGGTTAACAAAATTTTATAAGGAG
1 TTATCAAATTTTCATAGGGAGGTTATAAGAATTTCATAGTGTGGTTAACAAAATTTTATAAGGAG
107288 G
66 G
* ** *
107289 TTA-CTAATATTTCATAGGGAGGTTATCAA-AATTTCATAGTGTGGTTATTAAAATTTT-TTAGT
1 TTATCAAAT-TTTCATAGGGAGGTTAT-AAGAATTTCATAGTGTGGTTAACAAAATTTTATAAG-
*
107351 GTGG
63 GAGG
107355 TTATCAAATTTTCATA
1 TTATCAAATTTTCATA
107371 TGAAAGTTAT
Statistics
Matches: 68, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
65 6 0.09
66 56 0.82
67 6 0.09
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.40
Consensus pattern (66 bp):
TTATCAAATTTTCATAGGGAGGTTATAAGAATTTCATAGTGTGGTTAACAAAATTTTATAAGGAG
G
Found at i:107461 original size:22 final size:22
Alignment explanation
Indices: 107390--107641 Score: 176
Period size: 22 Copynumber: 11.5 Consensus size: 22
107380 TAAAAGTCTT
* *
107390 AATTTCATA-AG-GAGTACCAA
1 AATTTCATAGAGAGATTATCAA
* * *
107410 AATTTGATATAGAAGGTTATC-A
1 AATTTCATAGAG-AGATTATCAA
* * *
107432 AATCTCATAGAGTGATTATCGA
1 AATTTCATAGAGAGATTATCAA
107454 AATTTCATAGAGATCGGATTATCAA
1 AATTTCATAGAGA---GATTATCAA
*
107479 AATTT-ATAG-GAAGATCATCAA
1 AATTTCATAGAG-AGATTATCAA
* *
107500 AATTTCATAGTGTTG-TTATCAA
1 AATTTCATAGAG-AGATTATCAA
* * *
107522 AATTTCAAAGCGAGGTTATCAA
1 AATTTCATAGAGAGATTATCAA
* * *
107544 AATTTCATAGAGAGGTCAACAA
1 AATTTCATAGAGAGATTATCAA
* *
107566 AATTTTATAGAGAGTTTATCAA
1 AATTTCATAGAGAGATTATCAA
*
107588 AATTTCATAAAGAGATTATCAA
1 AATTTCATAGAGAGATTATCAA
* * * *
107610 ATTTTCA-AAATGTGATTACCAA
1 AATTTCATAGA-GAGATTATCAA
107632 AATTTCATAG
1 AATTTCATAG
107642 TGGTATTTAT
Statistics
Matches: 184, Mismatches: 35, Indels: 23
0.76 0.14 0.10
Matches are distributed among these distances:
20 8 0.04
21 25 0.14
22 125 0.68
23 8 0.04
24 5 0.03
25 13 0.07
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.33
Consensus pattern (22 bp):
AATTTCATAGAGAGATTATCAA
Found at i:107672 original size:34 final size:34
Alignment explanation
Indices: 107624--107746 Score: 117
Period size: 34 Copynumber: 3.6 Consensus size: 34
107614 TCAAAATGTG
107624 ATTACCAAAATTTCATAGTGGTATTTATGGGGAA
1 ATTACCAAAATTTCATAGTGGTATTTATGGGGAA
* *** *
107658 ATTATCAAAATTTCATAGTATGGTTACCAAAAT-GTG--
1 ATTACCAAAATTTCATAG--TGG-TA--TTTATGGGGAA
*
107694 ATTGCCAAAATTTCATAGTGGTATTTATGGGGAA
1 ATTACCAAAATTTCATAGTGGTATTTATGGGGAA
*
107728 ATTATCAAAATTTCATAGT
1 ATTACCAAAATTTCATAGT
107747 ATGATTACCA
Statistics
Matches: 68, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
31 2 0.03
32 2 0.03
33 2 0.03
34 37 0.54
36 19 0.28
37 2 0.03
38 2 0.03
39 2 0.03
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (34 bp):
ATTACCAAAATTTCATAGTGGTATTTATGGGGAA
Found at i:107692 original size:70 final size:70
Alignment explanation
Indices: 107615--107758 Score: 270
Period size: 70 Copynumber: 2.1 Consensus size: 70
107605 ATCAAATTTT
107615 CAAAATGTGATTACCAAAATTTCATAGTGGTATTTATGGGGAAATTATCAAAATTTCATAGTATG
1 CAAAATGTGATTACCAAAATTTCATAGTGGTATTTATGGGGAAATTATCAAAATTTCATAGTATG
*
107680 GTTAC
66 ATTAC
*
107685 CAAAATGTGATTGCCAAAATTTCATAGTGGTATTTATGGGGAAATTATCAAAATTTCATAGTATG
1 CAAAATGTGATTACCAAAATTTCATAGTGGTATTTATGGGGAAATTATCAAAATTTCATAGTATG
107750 ATTAC
66 ATTAC
107755 CAAA
1 CAAA
107759 TTAGGAAGGT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (70 bp):
CAAAATGTGATTACCAAAATTTCATAGTGGTATTTATGGGGAAATTATCAAAATTTCATAGTATG
ATTAC
Found at i:108074 original size:20 final size:22
Alignment explanation
Indices: 108041--108100 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 22
108031 AACTTTTACT
*
108041 ATGAAGTA-ATCAAAATTTCAG
1 ATGAAGGATATCAAAATTTCAG
*
108062 A-G-AGGATATCAAAATTTCAT
1 ATGAAGGATATCAAAATTTCAG
*
108082 ATGAAGGTTATCAAAATTT
1 ATGAAGGATATCAAAATTT
108101 TATAGTTTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
19 3 0.09
20 14 0.42
21 2 0.06
22 14 0.42
ACGTcount: A:0.45, C:0.08, G:0.15, T:0.32
Consensus pattern (22 bp):
ATGAAGGATATCAAAATTTCAG
Found at i:108096 original size:22 final size:22
Alignment explanation
Indices: 108049--108527 Score: 225
Period size: 22 Copynumber: 22.0 Consensus size: 22
108039 CTATGAAGTA
* *
108049 ATCAAAATTTCAGA--GAGGAT
1 ATCAAAATTTCATATGGAGGTT
*
108069 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATATGGAGGTT
* **
108091 ATCAAAATTTTATAGTTTA-GTT
1 ATCAAAATTTCATA-TGGAGGTT
* * * *
108113 TTCAAAATGTGATA-AGAGGGTT
1 ATCAAAATTTCATATGGA-GGTT
* * *
108135 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATATGGAGGT-T
* * *
108157 ATCAATATTTCATAGGGAGATT
1 ATCAAAATTTCATATGGAGGTT
*
108179 AACAAAATTTCATTAT-GAGGTT
1 ATCAAAATTTCA-TATGGAGGTT
**
108201 ATCAAAAAATCAT-TGGGAGGTT
1 ATCAAAATTTCATAT-GGAGGTT
*
108223 ATCAAAA--T--T-TGTA-GTT
1 ATCAAAATTTCATATGGAGGTT
*
108239 ATCAAAGATTTCATAAGGAGGTT
1 ATCAAA-ATTTCATATGGAGGTT
* *
108262 ATCAAAATTTTATAAGGAGGTTT
1 ATCAAAATTTCATATGGAGG-TT
*
108285 ATCAAAATTTTATA-GCGAGGTT
1 ATCAAAATTTCATATG-GAGGTT
*
108307 ATCACAATTTCATAATGTGA--TT
1 ATCAAAATTTCAT-ATG-GAGGTT
*
108329 ATCAAAATTTCAGAGTGTGA--TT
1 ATCAAAATTTCATA-TG-GAGGTT
108351 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATATGGAGGTT
* * ** * *
108373 TTCAAATTTTCATAACGTGGGT
1 ATCAAAATTTCATATGGAGGTT
* *
108395 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATATGGAGGTT
* * **
108417 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATA-TGGAGGTT
*
108440 ATCAAAATTTCAT-TCGGAAGTT
1 ATCAAAATTTCATAT-GGAGGTT
108462 ATCAAAATTTCATA-GTGAGGTCT
1 ATCAAAATTTCATATG-GAGGT-T
*
108485 -TCAAAA-TTCCT-TGGGAGGTT
1 ATCAAAATTTCATAT-GGAGGTT
* * *
108505 AACAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATATGGAGGTT
108527 A
1 A
108528 AAAATAATTT
Statistics
Matches: 352, Mismatches: 69, Indels: 74
0.71 0.14 0.15
Matches are distributed among these distances:
16 9 0.03
17 3 0.01
18 2 0.01
19 1 0.00
20 19 0.05
21 25 0.07
22 232 0.66
23 58 0.16
24 3 0.01
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATATGGAGGTT
Found at i:108548 original size:22 final size:22
Alignment explanation
Indices: 108500--108545 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
108490 ATTCCTTGGG
*
108500 AGGTTAACAAAATTTCATAAGA
1 AGGTTAAAAAAATTTCATAAGA
108522 AGGTTAAAAATAATTT-ATAA-A
1 AGGTTAAAAA-AATTTCATAAGA
108543 AGG
1 AGG
108546 GTTCTCGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 4 0.18
22 13 0.59
23 5 0.23
ACGTcount: A:0.52, C:0.04, G:0.15, T:0.28
Consensus pattern (22 bp):
AGGTTAAAAAAATTTCATAAGA
Found at i:108672 original size:2 final size:2
Alignment explanation
Indices: 108665--108693 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
108655 ATCATGATTC
108665 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
108694 GGATATTCTT
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:114833 original size:30 final size:30
Alignment explanation
Indices: 114797--114869 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
114787 CCTTCTCCTT
* *
114797 CTCCACCACCGCCGTATGTGTACAAGTCTC
1 CTCCACCACCACCGTATGAGTACAAGTCTC
*
114827 CTCCACCACCACCTTATGAGTACAAGTCTC
1 CTCCACCACCACCGTATGAGTACAAGTCTC
*
114857 CTCCTCCACCACC
1 CTCCACCACCACC
114870 AAAGCATGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.22, C:0.45, G:0.11, T:0.22
Consensus pattern (30 bp):
CTCCACCACCACCGTATGAGTACAAGTCTC
Found at i:114939 original size:15 final size:15
Alignment explanation
Indices: 114911--114940 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
114901 AAATCACCAC
*
114911 CACCTCCATCACCTT
1 CACCTCCACCACCTT
114926 CACCTCCACCACCTT
1 CACCTCCACCACCTT
114941 ATGAGTACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.57, G:0.00, T:0.23
Consensus pattern (15 bp):
CACCTCCACCACCTT
Found at i:115013 original size:96 final size:96
Alignment explanation
Indices: 114886--115327 Score: 449
Period size: 96 Copynumber: 4.6 Consensus size: 96
114876 TGAGGAACAA
* * *
114886 CCTCCATACTACTACAAATCACCACCACCTCCATCACCTTCACCTCCACCACCTTATGAGTACAA
1 CCTCCATACTACTACAAATCACCACCTCCTCCATCACCTTCACCACCACCTCCTTATGAGTACAA
114951 GTCTCCGCCCCCACCATCTCCCTCACCACCT
66 GTCTCCGCCCCCACCATCTCCCTCACCACCT
* * *
114982 CCTCCATACTACTATAAATCACCACCTCCTCCATCACCCTCACCACCACCTCCTTATGAATACAA
1 CCTCCATACTACTACAAATCACCACCTCCTCCATCACCTTCACCACCACCTCCTTATGAGTACAA
* *
115047 GTCTCCTCCTCCACCATCTCCCTCACCACCT
66 GTCTCCGCCCCCACCATCTCCCTCACCACCT
* *
115078 CCTCCATACTACTACAAATCCCCACCTCCTCCATCACCTTCACCACCACCTCCATATGAGTACAA
1 CCTCCATACTACTACAAATCACCACCTCCTCCATCACCTTCACCACCACCTCCTTATGAGTACAA
* * * * * ** ***
115143 GTCTCCTCCTCCTCC-TCCACCAAAGCATGAGGAAAAG
66 GTCTCCGCCCCCACCAT-CTCC----C-TCA-CCACCT
* * * * * * *
115180 CCCCCATACTACTACAAATCGCCACCTCCTCCGTCTCCATCCCCACC-CCTCCTTACT-ACTACA
1 CCTCCATACTACTACAAATCACCACCTCCTCCATCACCTTCACCACCACCTCCTTA-TGAGTACA
* * * *
115243 AATCTCCTCCACCACCATCCCCCTCACCACCT
65 AGTCTCCGCCCCCACCATCTCCCTCACCACCT
* * * * * * *
115275 CCTCCATACTACTACAAGTCCCCACCACCACCATCTCCTTCCCCACCTCCTCC
1 CCTCCATACTACTACAAATCACCACCTCCTCCATCACCTTCACCACCACCTCC
115328 ATACTACTAC
Statistics
Matches: 290, Mismatches: 46, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
95 42 0.14
96 172 0.59
97 1 0.00
100 1 0.00
101 30 0.10
102 44 0.15
ACGTcount: A:0.25, C:0.50, G:0.04, T:0.21
Consensus pattern (96 bp):
CCTCCATACTACTACAAATCACCACCTCCTCCATCACCTTCACCACCACCTCCTTATGAGTACAA
GTCTCCGCCCCCACCATCTCCCTCACCACCT
Found at i:115299 original size:27 final size:27
Alignment explanation
Indices: 115269--115348 Score: 91
Period size: 27 Copynumber: 3.2 Consensus size: 27
115259 ATCCCCCTCA
115269 CCACCTCCTCCATACTACTACAAGTCC
1 CCACCTCCTCCATACTACTACAAGTCC
* * *
115296 CCACCACCACCAT-CT-C--C--TTCC
1 CCACCTCCTCCATACTACTACAAGTCC
115317 CCACCTCCTCCATACTACTACAAGTCC
1 CCACCTCCTCCATACTACTACAAGTCC
115344 CCACC
1 CCACC
115349 ACCACCACCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
21 14 0.34
22 2 0.05
23 2 0.05
25 2 0.05
26 2 0.05
27 19 0.46
ACGTcount: A:0.24, C:0.54, G:0.03, T:0.20
Consensus pattern (27 bp):
CCACCTCCTCCATACTACTACAAGTCC
Found at i:115303 original size:48 final size:48
Alignment explanation
Indices: 114885--115498 Score: 374
Period size: 48 Copynumber: 12.6 Consensus size: 48
114875 ATGAGGAACA
* * * * *
114885 ACCTCCATACTACTACAAATCACCACCACCTCCATCACCTTCACCTCC
1 ACCTCCATACTACTACAAGTCTCCACCACCTCCATCTCCCTCACCACC
* * * * * *
114933 ACCACCTTA-TGAGTACAAGTCTCCGCCCCCACCATCTCCCTCACCACC
1 ACCTCCATACT-ACTACAAGTCTCCACCACCTCCATCTCCCTCACCACC
* * * * * *
114981 TCCTCCATACTACTATAAATCACCACCTCCTCCATCACCCTCACCACC
1 ACCTCCATACTACTACAAGTCTCCACCACCTCCATCTCCCTCACCACC
* * * * *
115029 ACCTCCTTA-TGAATACAAGTCTCCTCCTCCACCATCTCCCTCACCACC
1 ACCTCCATACT-ACTACAAGTCTCCACCACCTCCATCTCCCTCACCACC
* * * * * *
115077 TCCTCCATACTACTACAAATCCCCACCTCCTCCATCACCTTCACCACC
1 ACCTCCATACTACTACAAGTCTCCACCACCTCCATCTCCCTCACCACC
* * * * * ** **
115125 ACCTCCATA-TGAGTACAAGTCTCCTCCTCCTCC-TCCACCAAAGCATGAGGAAA
1 ACCTCCATACT-ACTACAAGTCTCCACCACCTCCAT-CTCC----C-TCACCACC
* * * * * * *
115178 AGCCCCCATACTACTACAAATCGCCACCTCCTCCGTCTCCATCCCCACC
1 A-CCTCCATACTACTACAAGTCTCCACCACCTCCATCTCCCTCACCACC
* * * * *
115227 -CCTCCTTACTACTACAAATCTCCTCCACCACCATCCCCCTCACCACC
1 ACCTCCATACTACTACAAGTCTCCACCACCTCCATCTCCCTCACCACC
* * * * *
115274 TCCTCCATACTACTACAAGTCCCCACCACCACCATCTCCTTCCCCACC
1 ACCTCCATACTACTACAAGTCTCCACCACCTCCATCTCCCTCACCACC
* * * * ** * * ** *
115322 TCCTCCATACTACTACAAGTCCCCACCACCACCACCAAAGCATGAAGAGCA
1 ACCTCCATACTACTACAAGTCTCCACCACCTCCATC--TCCCTCACCA-CC
* * *
115373 ACCCCCATACTACTACAAGTCTCCTCCACCTCCCTCTCCCTCACCACC
1 ACCTCCATACTACTACAAGTCTCCACCACCTCCATCTCCCTCACCACC
* * * * * * * *
115421 TCCACCATACTACTACAAGTCACCACCTCCTCCTTCACCATCTCCACC
1 ACCTCCATACTACTACAAGTCTCCACCACCTCCATCTCCCTCACCACC
* *
115469 ACCTCCATACTACTACAAGTCCCCTCCACC
1 ACCTCCATACTACTACAAGTCTCCACCACC
115499 ACCTAAACAC
Statistics
Matches: 430, Mismatches: 118, Indels: 36
0.74 0.20 0.06
Matches are distributed among these distances:
47 41 0.10
48 314 0.73
49 8 0.02
50 3 0.01
51 30 0.07
53 4 0.01
54 28 0.07
55 2 0.00
ACGTcount: A:0.26, C:0.50, G:0.04, T:0.21
Consensus pattern (48 bp):
ACCTCCATACTACTACAAGTCTCCACCACCTCCATCTCCCTCACCACC
Found at i:115392 original size:99 final size:98
Alignment explanation
Indices: 115081--115447 Score: 312
Period size: 99 Copynumber: 3.7 Consensus size: 98
115071 ACCACCTCCT
* * * *
115081 CCATACTACTACAAATCCCCACCTCCTCCATCACCTTCACCACCACCTCCATA-TGAGTACAAGT
1 CCATACTACTACAAATCCCCACCACCTCCATCTCCTTCACCACCTCCTCCATACT-ACTACAAG-
* * * * *
115145 CTCCTCCTCCTCCTCCACCAAAGCATGAGGAAAAGCCC
64 -TCC-CCACCACCACCACCAAAGCATGAAGACAA-CCC
* * * * * * *
115183 CCATACTACTACAAATCGCCACCTCCTCCGTCTCCATCCCCACC-CCTCCTTACTACTACAAATC
1 CCATACTACTACAAATCCCCACCACCTCCATCTCCTTCACCACCTCCTCCATACTACTACAAGTC
* * * * * ** ** *
115247 TCCTCCACCACCATCC---CCCTCACCACCTCCT
66 CCCACCACCACCA-CCAAAGCATGAAGACAACCC
* * *
115278 CCATACTACTACAAGTCCCCACCACCACCATCTCCTTCCCCACCTCCTCCATACTACTACAAGTC
1 CCATACTACTACAAATCCCCACCACCTCCATCTCCTTCACCACCTCCTCCATACTACTACAAGTC
115343 CCCACCACCACCACCAAAGCATGAAGAGCAACCC
66 CCCACCACCACCACCAAAGCATGAAGA-CAACCC
* * * * * *
115377 CCATACTACTACAAGTCTCCTCCACCTCCCTCTCCCTCACCACCTCCACCATACTACTACAAGTC
1 CCATACTACTACAAATCCCCACCACCTCCATCTCCTTCACCACCTCCTCCATACTACTACAAGTC
*
115442 ACCACC
66 CCCACC
115448 TCCTCCTTCA
Statistics
Matches: 212, Mismatches: 46, Indels: 17
0.77 0.17 0.06
Matches are distributed among these distances:
95 42 0.20
96 33 0.16
98 14 0.07
99 70 0.33
101 13 0.06
102 40 0.19
ACGTcount: A:0.27, C:0.49, G:0.05, T:0.19
Consensus pattern (98 bp):
CCATACTACTACAAATCCCCACCACCTCCATCTCCTTCACCACCTCCTCCATACTACTACAAGTC
CCCACCACCACCACCAAAGCATGAAGACAACCC
Found at i:115528 original size:144 final size:147
Alignment explanation
Indices: 115233--115645 Score: 521
Period size: 147 Copynumber: 2.8 Consensus size: 147
115223 CACCCCTCCT
* * * *
115233 TACTACTACAAATCTCCTCCACCACCATCCCCCTCACCACCTCCTCCATACTACTACAAGTCCCC
1 TACTACTACAAGTCTCCTCCACCACCCTCACCCTCACCACCTCCACCATACTACTACAAGTCCCC
* * * * *
115298 ACCACCACCATCTCCTTCCCCACCTCCTCCATACTACTACAAGTCCCCACCACCACCACCAAAGC
66 ACCACCTCCATCACCATCTCCACCACCTCCATACTACTACAAGTCCCCACCACCACCACCAAAGC
*
115363 ATGAAGAGCAACCCCCA
131 ACGAAGAGCAACCCCCA
* * *
115380 TACTACTACAAGTCTCCTCCACCTCCCTCTCCCTCACCACCTCCACCATACTACTACAAGTCACC
1 TACTACTACAAGTCTCCTCCACCACCCTCACCCTCACCACCTCCACCATACTACTACAAGTCCCC
* * * *
115445 ACCTCCTCCTTCACCATCTCCACCACCTCCATACTACTACAAGTCCCCTCCACCA-C-CTAAA-C
66 ACCACCTCCATCACCATCTCCACCACCTCCATACTACTACAAGTCCCCACCACCACCACCAAAGC
*
115507 ACGAAGAGCAACCCCCG
131 ACGAAGAGCAACCCCCA
* * * * *
115524 TACTACTACAAGTCTCCTCCACCACCCTCACCCGCACCGCCACCACCTTACTACTACAAATCCCC
1 TACTACTACAAGTCTCCTCCACCACCCTCACCCTCACCACCTCCACCATACTACTACAAGTCCCC
* *
115589 ACCACCTCCAGT-A-AAGTCTCCACCACCACCAGTTTACTACTACAAGTCCCCACCACC
66 ACCACCTCCA-TCACCA-TCTCCACCACCTCCA---TACTACTACAAGTCCCCACCACC
115646 TCCTCCACAT
Statistics
Matches: 231, Mismatches: 30, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
143 1 0.00
144 96 0.42
145 5 0.02
146 1 0.00
147 128 0.55
ACGTcount: A:0.28, C:0.49, G:0.05, T:0.18
Consensus pattern (147 bp):
TACTACTACAAGTCTCCTCCACCACCCTCACCCTCACCACCTCCACCATACTACTACAAGTCCCC
ACCACCTCCATCACCATCTCCACCACCTCCATACTACTACAAGTCCCCACCACCACCACCAAAGC
ACGAAGAGCAACCCCCA
Found at i:115594 original size:48 final size:48
Alignment explanation
Indices: 114885--115594 Score: 320
Period size: 48 Copynumber: 14.6 Consensus size: 48
114875 ATGAGGAACA
* * * * * *
114885 ACCTCCATACTACTACAAATCACCACCACCTCCATCACCTTCACCTCC
1 ACCTCCATACTACTACAAGTCCCCACCACCACCCTCACCCTCACCACC
* * * * * * * *
114933 ACCACCTTA-TGAGTACAAGTCTCCGCCCCCACCATCTCCCTCACCACC
1 ACCTCCATACT-ACTACAAGTCCCCACCACCACCCTCACCCTCACCACC
* * * * * * *
114981 TCCTCCATACTACTATAAATCACCACCTCCTCCATCACCCTCACCACC
1 ACCTCCATACTACTACAAGTCCCCACCACCACCCTCACCCTCACCACC
* * * * * * *
115029 ACCTCCTTA-TGAATACAAGTCTCCTCCTCCACCATCTCCCTCACCACC
1 ACCTCCATACT-ACTACAAGTCCCCACCACCACCCTCACCCTCACCACC
* * * * * *
115077 TCCTCCATACTACTACAAATCCCCACCTCCTCCATCACCTTCACCACC
1 ACCTCCATACTACTACAAGTCCCCACCACCACCCTCACCCTCACCACC
* * * * * * ** **
115125 ACCTCCATA-TGAGTACAAGTCTCCTCCTCC-TCCTCCACCAAAGCATGAGGAAA
1 ACCTCCATACT-ACTACAAGTCCCCACCACCACCCT-CACC----C-TCACCACC
* * * * * * * * *
115178 AGCCCCCATACTACTACAAATCGCCACCTCCTCCGTCTCCATCCCCACC
1 A-CCTCCATACTACTACAAGTCCCCACCACCACCCTCACCCTCACCACC
* * * * * *
115227 -CCTCCTTACTACTACAAATCTCCTCCACCACCATCCCCCTCACCACC
1 ACCTCCATACTACTACAAGTCCCCACCACCACCCTCACCCTCACCACC
* * * * *
115274 TCCTCCATACTACTACAAGTCCCCACCACCACCATCTCCTTCCCCACC
1 ACCTCCATACTACTACAAGTCCCCACCACCACCCTCACCCTCACCACC
* * * * ** *
115322 TCCTCCATACTACTACAAGTCCCCACCACCACCAC-CAAAGCATGAAGAGCA
1 ACCTCCATACTACTACAAGTCCCCACCACCACC-CTC--ACCCTCACCA-CC
* * * * *
115373 ACCCCCATACTACTACAAGTCTCCTCCACCTCCCTCTCCCTCACCACC
1 ACCTCCATACTACTACAAGTCCCCACCACCACCCTCACCCTCACCACC
* * * * * * * *
115421 TCCACCATACTACTACAAGTCACCACCTCCTCCTTCACCATCTCCACC
1 ACCTCCATACTACTACAAGTCCCCACCACCACCCTCACCCTCACCACC
* * * * ** *
115469 ACCTCCATACTACTACAAGTCCCCTCCACCA-CCTAAACAC-GAAGAGCA
1 ACCTCCATACTACTACAAGTCCCCACCACCACCCT-CACCCTCACCA-CC
* * * * * *
115517 ACCCCCGTACTACTACAAGTCTCCTCCACCACCCTCACCCGCACCGCC
1 ACCTCCATACTACTACAAGTCCCCACCACCACCCTCACCCTCACCACC
* * *
115565 ACCACCTTACTACTACAAATCCCCACCACC
1 ACCTCCATACTACTACAAGTCCCCACCACC
115595 TCCAGTAAAG
Statistics
Matches: 493, Mismatches: 145, Indels: 48
0.72 0.21 0.07
Matches are distributed among these distances:
47 45 0.09
48 370 0.75
49 12 0.02
50 4 0.01
51 30 0.06
53 4 0.01
54 25 0.05
55 3 0.01
ACGTcount: A:0.26, C:0.49, G:0.05, T:0.20
Consensus pattern (48 bp):
ACCTCCATACTACTACAAGTCCCCACCACCACCCTCACCCTCACCACC
Found at i:115764 original size:6 final size:6
Alignment explanation
Indices: 115750--115783 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
115740 ACTCCTTACT
* *
115750 ACCCAC ACCCCC ACCCCC ACCCCC ACCACC ACCC
1 ACCCCC ACCCCC ACCCCC ACCCCC ACCCCC ACCC
115784 ATTCATTGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.24, C:0.76, G:0.00, T:0.00
Consensus pattern (6 bp):
ACCCCC
Found at i:117064 original size:36 final size:36
Alignment explanation
Indices: 117024--117288 Score: 225
Period size: 36 Copynumber: 7.7 Consensus size: 36
117014 CTCCTTACTA
* * *
117024 CTACAAATCTCCTCCACCACCAACACCCACCTACGT
1 CTACAAGTCTCCACCACCACCACCACCCACCTACGT
* *
117060 CTACAAG--T-CGCCACCACCTCCA-CCA--TACGT
1 CTACAAGTCTCCACCACCACCACCACCCACCTACGT
* * **
117090 CTACAAGTCTCCACCACCACCACCTCCAAAGTAC-T
1 CTACAAGTCTCCACCACCACCACCACCCACCTACGT
* * *
117125 ACTACAAGTCCCCTCCACCACCATCACCCACCTACGT
1 -CTACAAGTCTCCACCACCACCACCACCCACCTACGT
*
117162 CTACAAG--T-CACCACCACCTCCA-CCA--TACGT
1 CTACAAGTCTCCACCACCACCACCACCCACCTACGT
* * **
117192 CTACAAGTCCCCACCACCACCACCACCAAAATAC-T
1 CTACAAGTCTCCACCACCACCACCACCCACCTACGT
* * *
117227 ACTACAAGTCCCCTCCACCACCATCACCCACCTACGT
1 -CTACAAGTCTCCACCACCACCACCACCCACCTACGT
*
117264 CTACAAGTCTCCACCACCTCCACCA
1 CTACAAGTCTCCACCACCACCACCA
117289 TACGTCTACA
Statistics
Matches: 182, Mismatches: 31, Indels: 32
0.74 0.13 0.13
Matches are distributed among these distances:
30 24 0.13
32 7 0.04
33 46 0.25
34 5 0.03
35 2 0.01
36 96 0.53
37 2 0.01
ACGTcount: A:0.30, C:0.49, G:0.05, T:0.16
Consensus pattern (36 bp):
CTACAAGTCTCCACCACCACCACCACCCACCTACGT
Found at i:117101 original size:66 final size:67
Alignment explanation
Indices: 117024--117315 Score: 246
Period size: 66 Copynumber: 4.3 Consensus size: 67
117014 CTCCTTACTA
* * * *
117024 CTACAAATCTCCTCCACCACCAACACCCACCTACGTCTACAAGT-CGCCACCACCTCCACCATAC
1 CTACAAGTCTCCACCACCACCACCACCCACCTACGTCTACAAGTCCTCCACCACCTCCACCATAC
117088 GT
66 GT
* * **
117090 CTACAAGTCTCCACCACCACCACCTCCAAAGTAC-TACTACAAGTCCCCTCCACCACCAT-CACC
1 CTACAAGTCTCCACCACCACCACCACCCACCTACGT-CTACAAGT--CCTCCACCACC-TCCA-C
117153 CACCTACGT
61 CA--TACGT
* * *
117162 CTACAAG--T-CACCACCACCTCCA-CCA--TACGTCTACAAGTCCCCACCACCACCACCACCAA
1 CTACAAGTCTCCACCACCACCACCACCCACCTACGTCTACAAGT--CCTCCACCACCTCCACC--
117221 AATAC-T
62 -ATACGT
* * *
117227 ACTACAAGTCCCCTCCACCACCATCACCCACCTACGTCTACAAGT-CTCCACCACCTCCACCATA
1 -CTACAAGTCTCCACCACCACCACCACCCACCTACGTCTACAAGTCCTCCACCACCTCCACCATA
117291 CGT
65 CGT
* *
117294 CTACAAATCCCCACCACCACCA
1 CTACAAGTCTCCACCACCACCA
117316 GTCCACTCTC
Statistics
Matches: 184, Mismatches: 21, Indels: 42
0.74 0.09 0.17
Matches are distributed among these distances:
65 4 0.02
66 94 0.51
67 2 0.01
68 3 0.02
69 48 0.26
70 8 0.04
72 25 0.14
ACGTcount: A:0.30, C:0.49, G:0.05, T:0.16
Consensus pattern (67 bp):
CTACAAGTCTCCACCACCACCACCACCCACCTACGTCTACAAGTCCTCCACCACCTCCACCATAC
GT
Found at i:117168 original size:102 final size:102
Alignment explanation
Indices: 117019--117315 Score: 513
Period size: 102 Copynumber: 2.9 Consensus size: 102
117009 ACCGGCTCCT
* * * *
117019 TACTACTACAAATCTCCTCCACCACCAACACCCACCTACGTCTACAAGTCGCCACCACCTCCACC
1 TACTACTACAAGTCCCCTCCACCACCATCACCCACCTACGTCTACAAGTCACCACCACCTCCACC
* * *
117084 ATACGTCTACAAGTCTCCACCACCACCACCTCCAAAG
66 ATACGTCTACAAGTCCCCACCACCACCACCACCAAAA
117121 TACTACTACAAGTCCCCTCCACCACCATCACCCACCTACGTCTACAAGTCACCACCACCTCCACC
1 TACTACTACAAGTCCCCTCCACCACCATCACCCACCTACGTCTACAAGTCACCACCACCTCCACC
117186 ATACGTCTACAAGTCCCCACCACCACCACCACCAAAA
66 ATACGTCTACAAGTCCCCACCACCACCACCACCAAAA
*
117223 TACTACTACAAGTCCCCTCCACCACCATCACCCACCTACGTCTACAAGTCTCCACCACCTCCACC
1 TACTACTACAAGTCCCCTCCACCACCATCACCCACCTACGTCTACAAGTCACCACCACCTCCACC
*
117288 ATACGTCTACAAATCCCCACCACCACCA
66 ATACGTCTACAAGTCCCCACCACCACCA
117316 GTCCACTCTC
Statistics
Matches: 186, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 186 1.00
ACGTcount: A:0.30, C:0.48, G:0.05, T:0.16
Consensus pattern (102 bp):
TACTACTACAAGTCCCCTCCACCACCATCACCCACCTACGTCTACAAGTCACCACCACCTCCACC
ATACGTCTACAAGTCCCCACCACCACCACCACCAAAA
Found at i:117314 original size:36 final size:36
Alignment explanation
Indices: 117070--117315 Score: 215
Period size: 36 Copynumber: 7.2 Consensus size: 36
117060 CTACAAGTCG
*
117070 CCACCACCTCCACCATACGTCTACAAGTCTCCACCA
1 CCACCACCTCCACCATACGTCTACAAGTCCCCACCA
* *
117106 CCACCACCTCCA-AAGTAC-TACTACAAGTCCCCTCCA
1 CCACCACCTCCACCA-TACGT-CTACAAGTCCCCACCA
117142 CCACCATCAC-CCACC-TACGTCTACAAGT------CA
1 CCACCA-C-CTCCACCATACGTCTACAAGTCCCCACCA
117172 CCACCACCTCCACCATACGTCTACAAGTCCCCACCA
1 CCACCACCTCCACCATACGTCTACAAGTCCCCACCA
* ** *
117208 CCACCACCACCAAAATAC-TACTACAAGTCCCCTCCA
1 CCACCACCTCCACCATACGT-CTACAAGTCCCCACCA
*
117244 CCACCATCAC-CCACC-TACGTCTACAAGT------CT
1 CCACCA-C-CTCCACCATACGTCTACAAGTCCCCACCA
*
117274 CCACCACCTCCACCATACGTCTACAAATCCCCACCA
1 CCACCACCTCCACCATACGTCTACAAGTCCCCACCA
117310 CCACCA
1 CCACCA
117316 GTCCACTCTC
Statistics
Matches: 171, Mismatches: 13, Indels: 52
0.72 0.06 0.22
Matches are distributed among these distances:
28 2 0.01
29 12 0.07
30 40 0.23
35 3 0.02
36 102 0.60
37 10 0.06
38 2 0.01
ACGTcount: A:0.30, C:0.50, G:0.05, T:0.15
Consensus pattern (36 bp):
CCACCACCTCCACCATACGTCTACAAGTCCCCACCA
Found at i:117489 original size:48 final size:48
Alignment explanation
Indices: 117275--117494 Score: 194
Period size: 48 Copynumber: 4.6 Consensus size: 48
117265 TACAAGTCTC
* *
117275 CACCACCTCCACCATACGT-CTACAAATCCCCACCACCACCAGTCCACT
1 CACCACCACCACCATAC-TACTACAAATCTCCACCACCACCAGTCCACT
* * * *
117323 CTCCACCACCACCATACTATTACAAGTCTCCACCACCACCAGTTCACT
1 CACCACCACCACCATACTACTACAAATCTCCACCACCACCAGTCCACT
* * * * ** **
117371 CCCCTCCACCACCATACTACTACAAATCACCACCACCTCCAGTAGAGG
1 CACCACCACCACCATACTACTACAAATCTCCACCACCACCAGTCCACT
** * * * * *
117419 CACCGGCACCAACC-TACCACTACAAGTCTCCACCTCCTCCATCTCCA-T
1 CACCACCACC-ACCATACTACTACAAATCTCCACCACCACCA-GTCCACT
*
117467 CACCACCTCCACCATACTACTACAAATC
1 CACCACCACCACCATACTACTACAAATC
117495 CC
Statistics
Matches: 136, Mismatches: 32, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
47 4 0.03
48 127 0.93
49 5 0.04
ACGTcount: A:0.30, C:0.48, G:0.05, T:0.17
Consensus pattern (48 bp):
CACCACCACCACCATACTACTACAAATCTCCACCACCACCAGTCCACT
Done.