Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002886.1 Hibiscus syriacus cultivar Beakdansim tig00005968_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: 85199
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:4641 original size:19 final size:20
Alignment explanation
Indices: 4608--4652 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
4598 TAAGTTTTAT
4608 AGGGAAGATTTATATACTTA
1 AGGGAAGATTTATATACTTA
4628 AGGGAAGA-TTATATACTTA
1 AGGGAAGATTTATATACTTA
*
4647 AAGGAA
1 AGGGAA
4653 ACTATAGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.44, C:0.04, G:0.22, T:0.29
Consensus pattern (20 bp):
AGGGAAGATTTATATACTTA
Found at i:5545 original size:23 final size:23
Alignment explanation
Indices: 5512--5579 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
5502 AACCTTATAT
5512 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
5535 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
5558 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
5580 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:7674 original size:15 final size:15
Alignment explanation
Indices: 7654--7684 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
7644 TAATAGATAG
7654 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
7669 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
7684 A
1 A
7685 TTTAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:7874 original size:20 final size:20
Alignment explanation
Indices: 7838--7875 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
7828 ATCCTATTCC
**
7838 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
7858 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
7876 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:9140 original size:30 final size:28
Alignment explanation
Indices: 9074--9239 Score: 120
Period size: 30 Copynumber: 5.6 Consensus size: 28
9064 TATTAATACC
* **
9074 ATTTTAGTTCCTTAAGTTTCTGTTTTTACA
1 ATTTTAG-TCCTTAAGTTTCTATTTTT-GT
* *
9104 AATTTAGTCCATTAATTTTCTATTTTTGT
1 ATTTTAGTCC-TTAAGTTTCTATTTTTGT
* *
9133 CGTTTTAGTCCTTTAGTTT-TAGTTTTTGAT
1 -ATTTTAGTCCTTAAGTTTCTA-TTTTTG-T
* * *
9163 ATTTTAGTCCTTTAACTTTATGTTTTTGTT
1 ATTTTAGTCC-TTAAGTTTCTATTTTTG-T
9193 ATTTTAGTCCCTTAAGTTTCTA-TTTTGCT
1 ATTTTAGT-CCTTAAGTTTCTATTTTTG-T
* *
9222 ATTTTTGTCCTCAAGTTT
1 ATTTTAGTCCTTAAGTTT
9240 TTGTAAATTT
Statistics
Matches: 109, Mismatches: 20, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
28 11 0.10
29 37 0.34
30 58 0.53
31 3 0.03
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (28 bp):
ATTTTAGTCCTTAAGTTTCTATTTTTGT
Found at i:9167 original size:29 final size:29
Alignment explanation
Indices: 9135--9232 Score: 101
Period size: 29 Copynumber: 3.3 Consensus size: 29
9125 ATTTTTGTCG
9135 TTTTAGTCCTTTAGTTTTAGTTTTTGATA
1 TTTTAGTCCTTTAGTTTTAGTTTTTGATA
** *
9164 TTTTAGTCCTTTAACTTTATGTTTTTGTTA
1 TTTTAGTCCTTTAGTTTTA-GTTTTTGATA
* *
9194 TTTTAGTCCCTTAAGTTTCTA--TTTTGCTA
1 TTTTAGT-CCTTTAGTTT-TAGTTTTTGATA
*
9223 TTTTTGTCCT
1 TTTTAGTCCT
9233 CAAGTTTTTG
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
28 3 0.05
29 30 0.52
30 16 0.28
31 7 0.12
32 2 0.03
ACGTcount: A:0.15, C:0.12, G:0.11, T:0.61
Consensus pattern (29 bp):
TTTTAGTCCTTTAGTTTTAGTTTTTGATA
Found at i:9219 original size:59 final size:58
Alignment explanation
Indices: 9073--9232 Score: 151
Period size: 59 Copynumber: 2.7 Consensus size: 58
9063 CTATTAATAC
* * * * * * *
9073 CATTTTAGTTCCTTAAGTTTCTGTTTTTACAAATTTAGTCCATTAATTTTCTATTTTTGT
1 CATTTTAG-TCCTTAAGTTTCTATTTTGA-TATTTTAGTCCTTTAACTTTATATTTTTGT
* * *
9133 CGTTTTAGTCCTTTAGTTT-TAGTTTTTGATATTTTAGTCCTTTAACTTTATGTTTTTGT
1 CATTTTAGTCCTTAAGTTTCTA--TTTTGATATTTTAGTCCTTTAACTTTATATTTTTGT
* * *
9192 TATTTTAGTCCCTTAAGTTTCTATTTTGCTATTTTTGTCCT
1 CATTTTAGT-CCTTAAGTTTCTATTTTGATATTTTAGTCCT
9233 CAAGTTTTTG
Statistics
Matches: 81, Mismatches: 15, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
58 1 0.01
59 57 0.70
60 21 0.26
61 2 0.02
ACGTcount: A:0.17, C:0.13, G:0.11, T:0.59
Consensus pattern (58 bp):
CATTTTAGTCCTTAAGTTTCTATTTTGATATTTTAGTCCTTTAACTTTATATTTTTGT
Found at i:9399 original size:25 final size:29
Alignment explanation
Indices: 9370--9430 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
9360 TTGTAAATAT
*
9370 TTTATTT-CA-CATA-TT-TTTATTTGAA
1 TTTATTTCCATCATATTTCTTTATTTAAA
9395 TTTATTTCCATCATATTTCTTTATTTAAA
1 TTTATTTCCATCATATTTCTTTATTTAAA
9424 TATTATT
1 T-TTATT
9431 CGAATATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 7 0.23
26 2 0.07
27 4 0.13
28 2 0.07
29 10 0.33
30 5 0.17
ACGTcount: A:0.28, C:0.10, G:0.02, T:0.61
Consensus pattern (29 bp):
TTTATTTCCATCATATTTCTTTATTTAAA
Found at i:10207 original size:23 final size:24
Alignment explanation
Indices: 10157--10207 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
10147 ATGGTTATGA
** *
10157 CAATTTTCGTTTCAATTTTTTTTTT
1 CAATTTTCG-TTCAATTTTCATTAT
10182 CAATTTTC-TTCAATTTTCATTAT
1 CAATTTTCGTTCAATTTTCATTAT
10205 CAA
1 CAA
10208 ATTTAGTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 15 0.65
25 8 0.35
ACGTcount: A:0.24, C:0.16, G:0.02, T:0.59
Consensus pattern (24 bp):
CAATTTTCGTTCAATTTTCATTAT
Found at i:10236 original size:15 final size:15
Alignment explanation
Indices: 10216--10273 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
10206 AAATTTAGTA
10216 ATTTTAGTTTTTGAT
1 ATTTTAGTTTTTGAT
**
10231 ATTTTAGTTTTAGTCCTTT
1 ATTTTAGTTTT--T--GAT
10250 AGTTTTAGTTTTTGAT
1 A-TTTTAGTTTTTGAT
10266 ATTTTAGT
1 ATTTTAGT
10274 CCTTTAACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
15 18 0.53
16 2 0.06
17 1 0.03
18 1 0.03
19 2 0.06
20 10 0.29
ACGTcount: A:0.19, C:0.03, G:0.14, T:0.64
Consensus pattern (15 bp):
ATTTTAGTTTTTGAT
Found at i:10285 original size:29 final size:29
Alignment explanation
Indices: 10238--10332 Score: 88
Period size: 28 Copynumber: 3.3 Consensus size: 29
10228 GATATTTTAG
**
10238 TTTTAGTCCTTTAGTTTTA-GTTTTTGATA
1 TTTTAGTCCTTTAACTTTATG-TTTTGATA
*
10267 TTTTAGTCCTTTAACTTTATGTTTTGTTA
1 TTTTAGTCCTTTAACTTTATGTTTTGATA
* * * * *
10296 -TTTAGTCCCTTAAGTTTCTATTTTGCTA
1 TTTTAGTCCTTTAACTTTATGTTTTGATA
10324 TTTT-GTCCT
1 TTTTAGTCCT
10333 CAAGTTTTTG
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
28 27 0.49
29 27 0.49
30 1 0.02
ACGTcount: A:0.16, C:0.13, G:0.12, T:0.60
Consensus pattern (29 bp):
TTTTAGTCCTTTAACTTTATGTTTTGATA
Found at i:10285 original size:35 final size:35
Alignment explanation
Indices: 10217--10291 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 35
10207 AATTTAGTAA
*
10217 TTTTAGTTTTTGATATTTTAGTTTTAGTCCTTTA-G
1 TTTTAGTTTTTGATATTTTAGTTTTAG-ACTTTATG
10252 TTTTAGTTTTTGATATTTTAGTCCTTTA-ACTTTATG
1 TTTTAGTTTTTGATATTTTAGT--TTTAGACTTTATG
10288 TTTT
1 TTTT
10292 GTTATTTAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
35 27 0.75
36 5 0.14
37 4 0.11
ACGTcount: A:0.17, C:0.07, G:0.12, T:0.64
Consensus pattern (35 bp):
TTTTAGTTTTTGATATTTTAGTTTTAGACTTTATG
Found at i:10496 original size:25 final size:29
Alignment explanation
Indices: 10467--10527 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
10457 TTGTAAATAT
*
10467 TTTATTT-CA-CATA-TT-TTTATTTGAA
1 TTTATTTCCATCATATTTCTTTATTTAAA
10492 TTTATTTCCATCATATTTCTTTATTTAAA
1 TTTATTTCCATCATATTTCTTTATTTAAA
10521 TGTTATT
1 T-TTATT
10528 CGAATATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 7 0.23
26 2 0.07
27 4 0.13
28 2 0.07
29 10 0.33
30 5 0.17
ACGTcount: A:0.26, C:0.10, G:0.03, T:0.61
Consensus pattern (29 bp):
TTTATTTCCATCATATTTCTTTATTTAAA
Found at i:12906 original size:18 final size:18
Alignment explanation
Indices: 12885--12927 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
12875 GACTGTTTAA
*
12885 CCGACCCGACCCGTTGAC
1 CCGACCCGACCCGATGAC
12903 CCGACCCGACCCGATGAC
1 CCGACCCGACCCGATGAC
*
12921 CTGACCC
1 CCGACCC
12928 ATCGTTGACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.19, C:0.51, G:0.21, T:0.09
Consensus pattern (18 bp):
CCGACCCGACCCGATGAC
Found at i:13625 original size:43 final size:43
Alignment explanation
Indices: 13577--13718 Score: 241
Period size: 43 Copynumber: 3.3 Consensus size: 43
13567 GGAAGTATTA
*
13577 CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTTCC
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTTCC
13620 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAG-TTTCC
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTTCC
13662 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTTCC
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTTCC
* * *
13705 TAGGCTCCTCTGCT
1 CAGGTTCCTTTGCT
13719 TAGGTTAAGC
Statistics
Matches: 94, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
42 42 0.45
43 52 0.55
ACGTcount: A:0.15, C:0.24, G:0.25, T:0.35
Consensus pattern (43 bp):
CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTTCC
Found at i:13674 original size:42 final size:42
Alignment explanation
Indices: 13577--13701 Score: 232
Period size: 42 Copynumber: 3.0 Consensus size: 42
13567 GGAAGTATTA
*
13577 CAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTTCC
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAG-TTTCC
13620 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
13662 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT
13702 TCCTAGGCTC
Statistics
Matches: 81, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
42 45 0.56
43 36 0.44
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.35
Consensus pattern (42 bp):
CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
Found at i:16483 original size:31 final size:31
Alignment explanation
Indices: 16411--16471 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
16401 TGAGCTGATG
* *
16411 AGTTAAATTAATATTTTATCTAATATTTAAA
1 AGTTAAATTAATATTTTATCTAAAATATAAA
16442 AGTTAAATTAATATTTTATCTAAAATATAA
1 AGTTAAATTAATATTTTATCTAAAATATAA
16472 GATTCAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (31 bp):
AGTTAAATTAATATTTTATCTAAAATATAAA
Found at i:16597 original size:31 final size:32
Alignment explanation
Indices: 16547--16611 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 32
16537 TCTAGTGATC
* *
16547 AAAACGTTACAAATCAATAACGTAAGTAACCA
1 AAAACGTTACAAATAAATAACATAAGTAACCA
* * *
16579 AAAAC-TTATAAATAAATAATATAAGTGACCA
1 AAAACGTTACAAATAAATAACATAAGTAACCA
16610 AA
1 AA
16612 GCATTACATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.57, C:0.14, G:0.08, T:0.22
Consensus pattern (32 bp):
AAAACGTTACAAATAAATAACATAAGTAACCA
Found at i:20232 original size:19 final size:20
Alignment explanation
Indices: 20210--20252 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
20200 TATTTTTATA
20210 TTTTT-GATTGAAAATCTTT
1 TTTTTCGATTGAAAATCTTT
**
20229 TTTTTCTTTTGAAAATCTTT
1 TTTTTCGATTGAAAATCTTT
20249 TTTT
1 TTTT
20253 ATTCACTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.65
Consensus pattern (20 bp):
TTTTTCGATTGAAAATCTTT
Found at i:22745 original size:2 final size:2
Alignment explanation
Indices: 22738--22762 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22728 CAACATATCA
22738 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 A
22763 CACCTTAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26572 original size:60 final size:60
Alignment explanation
Indices: 26472--26638 Score: 221
Period size: 60 Copynumber: 2.8 Consensus size: 60
26462 ATTATAACAG
* * *
26472 TTATTTTAAATTAGTCCTTAAACTTTTGAATATTCAAATTTCATCCTTAAACTATGACTC
1 TTATTTTAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATCCCTAAACTATGACCC
* *
26532 TTATTTTAAATTAGTCCTTAAACTTTTG-ATCATTCTAATTTCATCCCTAAATTGTGACCC
1 TTATTTTAAATTAGTCCTTAAACTTTTGAAT-ATTCTAATTTCATCCCTAAACTATGACCC
* ** *
26592 TCT-TTCTAAATTAGTCCCCAAACTTTTGAATATTCTAATTTTATCCC
1 T-TATTTTAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATCCC
26639 CAAATTCATT
Statistics
Matches: 95, Mismatches: 9, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
59 2 0.02
60 90 0.95
61 3 0.03
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (60 bp):
TTATTTTAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATCCCTAAACTATGACCC
Found at i:26859 original size:60 final size:58
Alignment explanation
Indices: 26767--26917 Score: 171
Period size: 58 Copynumber: 2.6 Consensus size: 58
26757 GTATATATGT
* **
26767 ATAGTTTGGGATGTAATTTGAATATTCAAAAAGTTTAAGGACCAAATTAGAATGA-AGGTC
1 ATAGTTTGGGATGAAATTAAAATATTCAAAAAGTTTAAGGA--AAATTAGAATGATA-GTC
* * *
26827 ATAGTTTGGAGATGAAATTAAAATGTTC-AAAAGTTTAAGGATATTTAGAATGATAGTC
1 ATAGTTTGG-GATGAAATTAAAATATTCAAAAAGTTTAAGGAAAATTAGAATGATAGTC
* *
26885 ATAGTTTATGGATGAAATTAAAATATTTAAAAA
1 ATAGTTT-GGGATGAAATTAAAATATTCAAAAA
26918 CTTAGGGATA
Statistics
Matches: 78, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
58 36 0.46
59 6 0.08
60 22 0.28
61 14 0.18
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (58 bp):
ATAGTTTGGGATGAAATTAAAATATTCAAAAAGTTTAAGGAAAATTAGAATGATAGTC
Found at i:27645 original size:11 final size:11
Alignment explanation
Indices: 27629--27653 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
27619 GTAAATACGG
27629 GTTTTTTCATT
1 GTTTTTTCATT
27640 GTTTTTTCATT
1 GTTTTTTCATT
27651 GTT
1 GTT
27654 AGTGTGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.12, T:0.72
Consensus pattern (11 bp):
GTTTTTTCATT
Found at i:29406 original size:26 final size:26
Alignment explanation
Indices: 29368--29417 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
29358 GATTATGAAA
*
29368 AAAATTAAAAGTTTATATACTAAAAT
1 AAAATTAAAAGTTTAGATACTAAAAT
* *
29394 AAAATTAATAGTTTAGGTACTAAA
1 AAAATTAAAAGTTTAGATACTAAA
29418 CACATAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.34
Consensus pattern (26 bp):
AAAATTAAAAGTTTAGATACTAAAAT
Found at i:29768 original size:27 final size:27
Alignment explanation
Indices: 29738--29829 Score: 76
Period size: 27 Copynumber: 3.3 Consensus size: 27
29728 TAACAGTAAT
* * * * *
29738 AACAATAACATCAACATCAGTAATAGC
1 AACAATAACAACAACACCAATAACAAC
*
29765 AACAATGACAACAACACCAATAACAAC
1 AACAATAACAACAACACCAATAACAAC
* * *
29792 AACAATAATGAAAACAACAACAATGACAAC
1 AACAAT-A--ACAACAACACCAATAACAAC
29822 AACAATAA
1 AACAATAA
29830 TAGTGACAAG
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
27 28 0.54
29 1 0.02
30 23 0.44
ACGTcount: A:0.60, C:0.23, G:0.05, T:0.12
Consensus pattern (27 bp):
AACAATAACAACAACACCAATAACAAC
Found at i:29785 original size:15 final size:15
Alignment explanation
Indices: 29764--29826 Score: 90
Period size: 15 Copynumber: 4.2 Consensus size: 15
29754 TCAGTAATAG
29764 CAACAATGACAACAA
1 CAACAATGACAACAA
* *
29779 CACCAATAACAACAA
1 CAACAATGACAACAA
* *
29794 CAATAATGAAAACAA
1 CAACAATGACAACAA
29809 CAACAATGACAACAA
1 CAACAATGACAACAA
29824 CAA
1 CAA
29827 TAATAGTGAC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.62, C:0.25, G:0.05, T:0.08
Consensus pattern (15 bp):
CAACAATGACAACAA
Found at i:29836 original size:18 final size:17
Alignment explanation
Indices: 29769--29845 Score: 58
Period size: 15 Copynumber: 4.8 Consensus size: 17
29759 AATAGCAACA
**
29769 ATGACAACAACACCAAT
1 ATGACAACAACAATAAT
29786 A--ACAACAACAAT-A-
1 ATGACAACAACAATAAT
* *
29799 ATGAAAACAACAA-CA-
1 ATGACAACAACAATAAT
29814 ATGACAACAACAATAAT
1 ATGACAACAACAATAAT
*
29831 AGTGACAAGAACAAT
1 A-TGACAACAACAAT
29846 GTTAACAATA
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
13 1 0.02
14 1 0.02
15 31 0.65
16 1 0.02
17 2 0.04
18 12 0.25
ACGTcount: A:0.60, C:0.21, G:0.08, T:0.12
Consensus pattern (17 bp):
ATGACAACAACAATAAT
Found at i:29887 original size:21 final size:22
Alignment explanation
Indices: 29849--29899 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
29839 GAACAATGTT
29849 AACAATAACATCAACAATGATAAC
1 AACAATAACAT--ACAATGATAAC
*
29873 AACAATAACAT-CAATGGTAAC
1 AACAATAACATACAATGATAAC
*
29894 ATCAAT
1 AACAAT
29900 GATATCAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 14 0.56
24 11 0.44
ACGTcount: A:0.55, C:0.20, G:0.06, T:0.20
Consensus pattern (22 bp):
AACAATAACATACAATGATAAC
Found at i:29913 original size:3 final size:3
Alignment explanation
Indices: 29905--30159 Score: 71
Period size: 3 Copynumber: 85.0 Consensus size: 3
29895 TCAATGATAT
* * * * * * * * *
29905 CAA CAA CAA CAA CAT TAA CAA CAT CGA TAA TAA TAA CAA CGA CGA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
** * * * * **
29953 CAA CAA TGA CAA CAA CAA CAA CAA AAA CAA TAA CAA CAA CAT CGA TGA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
* * * * **
30001 CAA TAA CAA CAA CGA CAA TAA CAA CAA -AA GCAG TGA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA -CAA CAA CAA CAA CAA
* * * * * * ** ** *
30046 CAT CAA CGA GAG CAA CAA CAA TAA TAA TGA TGA CAA TAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
* ** * * * * ** *
30094 TAA CAA TGA TAA CAA TAA CAA CAA TAT TGA CAA CAA CAA TAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
** *
30142 CAA TGA TAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA
30160 AAATAGTAGA
Statistics
Matches: 178, Mismatches: 72, Indels: 4
0.70 0.28 0.02
Matches are distributed among these distances:
2 2 0.01
3 175 0.98
4 1 0.01
ACGTcount: A:0.59, C:0.23, G:0.07, T:0.11
Consensus pattern (3 bp):
CAA
Found at i:29976 original size:24 final size:24
Alignment explanation
Indices: 29939--30159 Score: 114
Period size: 24 Copynumber: 9.5 Consensus size: 24
29929 CGATAATAAT
* *
29939 AACAACGACGACAACAACAATGAC
1 AACAACAACAACAACAACAATGAC
*
29963 AACAACAACAACAAAAACAAT---
1 AACAACAACAACAACAACAATGAC
* * ** *
29984 AACAACAACATCGATGACAATAAC
1 AACAACAACAACAACAACAATGAC
* * *
30008 AACAACGACAATAACAACAA-AAGC
1 AACAACAACAACAACAACAATGA-C
*** * * *
30032 AGTGACAACAACAACATCAACGAG
1 AACAACAACAACAACAACAATGAC
* * * **
30056 AGCAACAACAATAATAATGATGAC
1 AACAACAACAACAACAACAATGAC
* *
30080 AATAACAACAACAATAACAATG--
1 AACAACAACAACAACAACAATGAC
* * * *
30102 -ATAACAATAACAACAATATTGAC
1 AACAACAACAACAACAACAATGAC
* *
30125 AACAACAATAACAACAACAATGAT
1 AACAACAACAACAACAACAATGAC
30149 AACAACAACAA
1 AACAACAACAA
30160 AAATAGTAGA
Statistics
Matches: 145, Mismatches: 44, Indels: 16
0.71 0.21 0.08
Matches are distributed among these distances:
21 34 0.23
23 2 0.01
24 108 0.74
25 1 0.01
ACGTcount: A:0.59, C:0.23, G:0.08, T:0.10
Consensus pattern (24 bp):
AACAACAACAACAACAACAATGAC
Found at i:29987 original size:21 final size:21
Alignment explanation
Indices: 29921--30144 Score: 83
Period size: 21 Copynumber: 10.1 Consensus size: 21
29911 CAACAACATT
* * *
29921 AACAACATCGATAATAATAAC
1 AACAACAACAATAACAATAAC
* * *
29942 AACGACGACAACAACAATGACAAC
1 AACAACAACAATAACAAT---AAC
*
29966 AACAACAACAAAAACAATAAC
1 AACAACAACAATAACAATAAC
* * *
29987 AACAACATCGATGACAATAAC
1 AACAACAACAATAACAATAAC
* *
30008 AACAACGACAATAACAACAA-
1 AACAACAACAATAACAATAAC
*
30028 AAGCAGTGACAACAACAAC-ATCAAC
1 AA-CA---ACAACAATAACAAT-AAC
* * *
30053 GAGAGCAACAACAATAATAATGAT
1 -A-A-CAACAACAATAACAATAAC
* * *
30077 GACAATAACAACAACAATAAC
1 AACAACAACAATAACAATAAC
** * * *
30098 AATGATAACAATAACAACAAT
1 AACAACAACAATAACAATAAC
*
30119 ATTGACAACAACAATAACAACAAC
1 A---ACAACAACAATAACAATAAC
30143 AA
1 AA
30145 TGATAACAAC
Statistics
Matches: 147, Mismatches: 41, Indels: 30
0.67 0.19 0.14
Matches are distributed among these distances:
20 2 0.01
21 80 0.54
22 1 0.01
23 1 0.01
24 56 0.38
25 2 0.01
26 1 0.01
27 4 0.03
ACGTcount: A:0.59, C:0.22, G:0.08, T:0.11
Consensus pattern (21 bp):
AACAACAACAATAACAATAAC
Found at i:30088 original size:27 final size:27
Alignment explanation
Indices: 30058--30117 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
30048 TCAACGAGAG
* *
30058 CAACAACAATAATAATGATGACAATAA
1 CAACAACAATAACAATGATAACAATAA
30085 CAACAACAATAACAATGATAACAATAA
1 CAACAACAATAACAATGATAACAATAA
30112 CAACAA
1 CAACAA
30118 TATTGACAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.62, C:0.18, G:0.05, T:0.15
Consensus pattern (27 bp):
CAACAACAATAACAATGATAACAATAA
Found at i:30093 original size:12 final size:12
Alignment explanation
Indices: 30078--30280 Score: 97
Period size: 12 Copynumber: 16.4 Consensus size: 12
30068 AATAATGATG
30078 ACAATAACAACA
1 ACAATAACAACA
*
30090 ACAATAACAATGATA
1 ACAATAAC-A--ACA
30105 ACAATAACAACA
1 ACAATAACAACA
* * *
30117 ATATTGACAACA
1 ACAATAACAACA
30129 ACAATAACAACA
1 ACAATAACAACA
* *
30141 ACAATGATAACA
1 ACAATAACAACA
* * *
30153 ACAACAAAAATA
1 ACAATAACAACA
*
30165 GTAGAGATAACAACA
1 --ACA-ATAACAACA
*** *
30180 ATGGTGACAACA
1 ACAATAACAACA
* * *
30192 TCAACAACAAAA
1 ACAATAACAACA
30204 ACAAT---AACA
1 ACAATAACAACA
* * * *
30213 ACGATGACGACG
1 ACAATAACAACA
30225 ACAATAACAACA
1 ACAATAACAACA
*
30237 ACATTAACAACA
1 ACAATAACAACA
*
30249 ACGAGAATAACAACG
1 AC---AATAACAACA
30264 ACAATAACAACA
1 ACAATAACAACA
30276 ACAAT
1 ACAAT
30281 GATAGGCAAC
Statistics
Matches: 136, Mismatches: 43, Indels: 24
0.67 0.21 0.12
Matches are distributed among these distances:
9 7 0.05
12 98 0.72
13 2 0.01
14 3 0.02
15 26 0.19
ACGTcount: A:0.59, C:0.21, G:0.08, T:0.12
Consensus pattern (12 bp):
ACAATAACAACA
Found at i:30252 original size:27 final size:27
Alignment explanation
Indices: 30222--30277 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
30212 AACGATGACG
*
30222 ACGACAATAACAACAACATTAACAACA
1 ACGACAATAACAACAACAATAACAACA
* *
30249 ACGAGAATAACAACGACAATAACAACA
1 ACGACAATAACAACAACAATAACAACA
30276 AC
1 AC
30278 AATGATAGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.59, C:0.25, G:0.07, T:0.09
Consensus pattern (27 bp):
ACGACAATAACAACAACAATAACAACA
Found at i:33875 original size:18 final size:18
Alignment explanation
Indices: 33851--33902 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
33841 GAGGGATTAT
33851 CAGTGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
*
33869 TAGTGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
*
33887 CAGTGGTCCTACGGGA
1 CAGTGGTCCTTCGGGA
33903 TAAATTCTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.17, C:0.25, G:0.35, T:0.23
Consensus pattern (18 bp):
CAGTGGTCCTTCGGGACA
Found at i:40240 original size:13 final size:13
Alignment explanation
Indices: 40222--40254 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
40212 ATAATAAAAG
*
40222 AATCATTTTTTTC
1 AATCATTTCTTTC
40235 AATCATTTCTTTC
1 AATCATTTCTTTC
40248 AATCATT
1 AATCATT
40255 CACCCCTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.27, C:0.18, G:0.00, T:0.55
Consensus pattern (13 bp):
AATCATTTCTTTC
Found at i:42074 original size:79 final size:80
Alignment explanation
Indices: 41810--42064 Score: 361
Period size: 79 Copynumber: 3.2 Consensus size: 80
41800 TTGGGGTCTA
* * * * * *
41810 TGGGCCTACTCAAGGATATCCTTAGATCCATAGGGTAACCTTAAGCACACAACAAAAAGGGAACC
1 TGGGCCTACCCAAGGACATCCTTAGATCCGTAGGGTTACCTTATGCACACAGC--AAAGGGAACC
*
41875 AACCTAAGGATATACCT
64 AACCTAAGGATATGCCT
**
41892 TGGTTCTACCCAAGGACATCCTTAGATCCGTAGGGTTACCTTAAT-CACACAGCAAAGGGAACCA
1 TGGGCCTACCCAAGGACATCCTTAGATCCGTAGGGTTACCTT-ATGCACACAGCAAAGGGAACCA
*
41956 ACCTAAAGATATGCCT
65 ACCTAAGGATATGCCT
* *
41972 T-GGCCTACCCAAGGACATCCTTAGATCCGTAGGGTTACCTTATGCACATAGCAAAGGAAACCAA
1 TGGGCCTACCCAAGGACATCCTTAGATCCGTAGGGTTACCTTATGCACACAGCAAAGGGAACCAA
42036 CCTAAGGATATGCCT
66 CCTAAGGATATGCCT
42051 TGGGCCTACCCAAG
1 TGGGCCTACCCAAG
42065 ATATTCTTAG
Statistics
Matches: 155, Mismatches: 15, Indels: 8
0.87 0.08 0.04
Matches are distributed among these distances:
78 2 0.01
79 71 0.46
80 38 0.25
82 43 0.28
83 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (80 bp):
TGGGCCTACCCAAGGACATCCTTAGATCCGTAGGGTTACCTTATGCACACAGCAAAGGGAACCAA
CCTAAGGATATGCCT
Found at i:45800 original size:21 final size:20
Alignment explanation
Indices: 45733--45807 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 20
45723 CAGTTTCCAA
* * *
45733 AATCGCAACGCGATTCTTGAC
1 AATCGCAATGCGATT-TTCAT
45754 AATCGCAATGCGATTTTCAT
1 AATCGCAATGCGATTTTCAT
* *
45774 ATTCGCATTGCGATTTTCCAT
1 AATCGCAATGCGATTTT-CAT
*
45795 AATCGCAACGCGA
1 AATCGCAATGCGA
45808 ATATGAAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 18 0.40
21 27 0.60
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.29
Consensus pattern (20 bp):
AATCGCAATGCGATTTTCAT
Found at i:45889 original size:20 final size:20
Alignment explanation
Indices: 45795--46023 Score: 248
Period size: 20 Copynumber: 11.4 Consensus size: 20
45785 GATTTTCCAT
* ** *
45795 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
45815 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
45835 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
45855 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
45875 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
45895 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
45915 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
45935 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
45955 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
45975 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
45995 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
46015 AATCACAAC
1 AATCGCAAC
46024 ACTGAAATTT
Statistics
Matches: 179, Mismatches: 24, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.01
20 175 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:46954 original size:12 final size:12
Alignment explanation
Indices: 46937--46961 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
46927 ATATAATCCT
46937 GAAGAAGAAAAA
1 GAAGAAGAAAAA
46949 GAAGAAGAAAAA
1 GAAGAAGAAAAA
46961 G
1 G
46962 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:49295 original size:33 final size:33
Alignment explanation
Indices: 49244--49494 Score: 168
Period size: 33 Copynumber: 7.2 Consensus size: 33
49234 CGGAAATTAC
* *
49244 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGCGAAATGAA
* *
49277 AATCCCAACAAGAAAATCGAAATGCGGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGC-GAAATGAA
* * *
49311 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AA-GAAAATCGCAATGCGA-AAT-GAA
* *
49350 AATGCGGAA-ATGAAAATCGCAATGCGAAATGAA
1 AAT-CGCAACAAGAAAATCGCAATGCGAAATGAA
* * *
49383 AATCACAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGCGAAATGAA
* * *
49416 AATCGCAATACGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGC-A-AC--AA-GAAAATCGCAATGCGA-AAT-GAA
* *
49455 AATGCGGAA-ATGAAAATCGCAATGCGAAATGAA
1 AAT-CGCAACAAGAAAATCGCAATGCGAAATGAA
49488 AATCGCA
1 AATCGCA
49495 TTGCGATTCT
Statistics
Matches: 167, Mismatches: 31, Indels: 41
0.70 0.13 0.17
Matches are distributed among these distances:
32 8 0.05
33 59 0.35
34 44 0.26
35 4 0.02
36 1 0.01
37 1 0.01
38 18 0.11
39 24 0.14
40 8 0.05
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (33 bp):
AATCGCAACAAGAAAATCGCAATGCGAAATGAA
Found at i:49321 original size:53 final size:53
Alignment explanation
Indices: 49258--49494 Score: 413
Period size: 53 Copynumber: 4.5 Consensus size: 53
49248 GCAACGAGAG
* * * *
49258 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGAAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
49311 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
*
49364 AATCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGC-GAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
*
49416 AATCGCAATACGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
49469 AATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
49495 TTGCGATTCT
Statistics
Matches: 175, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
52 50 0.29
53 125 0.71
ACGTcount: A:0.48, C:0.17, G:0.22, T:0.14
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
Found at i:49327 original size:19 final size:19
Alignment explanation
Indices: 49258--49500 Score: 247
Period size: 19 Copynumber: 13.7 Consensus size: 19
49248 GCAACGAGAG
49258 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
49277 AATCCCAA--C--AA-GAA
1 AATCGCAATGCGAAATGAA
*
49291 AATCGAAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
49311 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
49330 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
49344 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
49364 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
49383 AATCACAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
49397 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
49416 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
*
49435 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
49449 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
49469 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
49488 AATCGCATTGCGA
1 AATCGCAATGCGA
49501 TTCTCTCGTT
Statistics
Matches: 187, Mismatches: 14, Indels: 46
0.76 0.06 0.19
Matches are distributed among these distances:
14 38 0.20
15 5 0.03
16 5 0.03
17 9 0.05
18 1 0.01
19 90 0.48
20 39 0.21
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:49401 original size:86 final size:85
Alignment explanation
Indices: 49244--49423 Score: 233
Period size: 86 Copynumber: 2.1 Consensus size: 85
49234 CGGAAATTAC
*
49244 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGAAATGCGGAAATG
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGAAATGC-GAAACG
49309 AAAATCGCAATGCGAAATGAA
65 AAAATCGCAATGCGAAATGAA
* ***
49330 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG-AAAT-GAAAAT-C-ACAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAACAAGAAAATCG-AAATGCGA-AA
49391 CGAGAGAATCGCAATGCGAAATGAA
63 CGA-A-AATCGCAATGCGAAATGAA
49416 AATCGCAA
1 AATCGCAA
49424 TACGAAATGA
Statistics
Matches: 84, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
83 1 0.01
84 4 0.05
85 3 0.04
86 60 0.71
87 16 0.19
ACGTcount: A:0.48, C:0.18, G:0.22, T:0.13
Consensus pattern (85 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGAAATGCGAAACGA
AAATCGCAATGCGAAATGAA
Found at i:49444 original size:105 final size:106
Alignment explanation
Indices: 49258--49491 Score: 416
Period size: 105 Copynumber: 2.2 Consensus size: 106
49248 GCAACGAGAG
* *
49258 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGAAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCACAACAAGAAAATCGAAATGCGGAAATGAAAATCGCAATACG
49323 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
66 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
* * *
49364 AATCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATACG
1 AATCGCAATGCGAAATGAAAATCACAACAAGAAAATCGAAATGCGGAAATGAAAATCGCAATACG
49428 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
66 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
49469 AATCGCAATGCGAAATGAAAATC
1 AATCGCAATGCGAAATGAAAATC
49492 GCATTGCGAT
Statistics
Matches: 123, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
105 83 0.67
106 40 0.33
ACGTcount: A:0.48, C:0.17, G:0.21, T:0.14
Consensus pattern (106 bp):
AATCGCAATGCGAAATGAAAATCACAACAAGAAAATCGAAATGCGGAAATGAAAATCGCAATACG
AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
Found at i:49534 original size:53 final size:52
Alignment explanation
Indices: 49471--49586 Score: 151
Period size: 53 Copynumber: 2.2 Consensus size: 52
49461 GAAATGAAAA
* *
49471 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTATCTCGTTGCGATTTTCATT
** ** **
49523 TCCGCATTGCGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTATCTCGTTGCGATTTTCATT
49576 TCGCATTGCGA
1 TCGCATTGCGA
49587 TTTTCATTTC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
52 11 0.20
53 44 0.80
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTATCTCGTTGCGATTTTCATT
Found at i:49549 original size:19 final size:19
Alignment explanation
Indices: 49509--49596 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
49499 GATTCTCTCG
49509 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
49529 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
49548 TTGCGA--TT-ATCTCG--
1 TTGCGATTTTCATTTCGCA
49562 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
49581 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
49597 AACATAATGC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.10
16 7 0.11
17 7 0.11
19 26 0.43
20 15 0.25
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:49706 original size:14 final size:14
Alignment explanation
Indices: 49687--49723 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
49677 CATCAATTGC
49687 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
49701 ACAAATCATCTTTT
1 ACAAATCAACTTTT
49715 ACAAATCAA
1 ACAAATCAA
49724 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:50474 original size:14 final size:14
Alignment explanation
Indices: 50455--50511 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
50445 TTTGGTTTCG
50455 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
50469 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
50488 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
50502 CGTTGCGATT
1 CGTTGCGATT
50512 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:50487 original size:33 final size:33
Alignment explanation
Indices: 50450--50526 Score: 154
Period size: 33 Copynumber: 2.3 Consensus size: 33
50440 AGTATTTTGG
50450 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
50483 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
50516 TTTCGCGTTGC
1 TTTCGCGTTGC
50527 AGATAGTCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.08, C:0.25, G:0.22, T:0.45
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
Found at i:50556 original size:20 final size:20
Alignment explanation
Indices: 50502--50558 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
50492 GCGATTCTCT
*
50502 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCA
**
50521 CGTTGCAGATAGTCATTTTCA
1 CGTTGC-GATTTTCATTTTCA
50542 CGTTGCGATTTTCATTT
1 CGTTGCGATTTTCATTT
50559 ATCTCATTGC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 6 0.19
20 15 0.48
21 10 0.32
ACGTcount: A:0.16, C:0.19, G:0.19, T:0.46
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCA
Found at i:50692 original size:33 final size:33
Alignment explanation
Indices: 50650--50720 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
50640 AATACTAACT
50650 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
50683 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
50716 TGAAA
1 TGAAA
50721 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:51125 original size:20 final size:20
Alignment explanation
Indices: 51100--51231 Score: 192
Period size: 20 Copynumber: 6.6 Consensus size: 20
51090 CTTTAAAAAT
*
51100 CGCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
*
51120 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
51140 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
51160 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
51180 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* ** *
51200 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
51220 CGCGTTGCGATT
1 CGCGTTGCGATT
51232 ATGGAAAATC
Statistics
Matches: 101, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 101 1.00
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:51249 original size:21 final size:20
Alignment explanation
Indices: 51225--51272 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
51215 ATATTCGCGT
51225 TGCGATTATGGAAAATCGCAA
1 TGCGATTAT-GAAAATCGCAA
* *
51246 TGCGAATATGAAAATCGCAT
1 TGCGATTATGAAAATCGCAA
51266 TGCGATT
1 TGCGATT
51273 GTCAAGAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (20 bp):
TGCGATTATGAAAATCGCAA
Found at i:52235 original size:111 final size:111
Alignment explanation
Indices: 51956--52440 Score: 677
Period size: 111 Copynumber: 4.3 Consensus size: 111
51946 TAGCGCCTAT
* * *
51956 AAAGTATCGATAC-TTTATAAAAATGTATCGATATTTTACAATATAACAAGTAAAAATATGACAA
1 AAAGTATCGATCCTTTTATAAAAATG-ATAGATACTTTACAATATAACAAGTAAAAATATGACAA
* * *
52020 AACCAATTTCATTATGAGAAAAACCGATAAAATTTACCTAATATGTTG
65 AACCAGTTTCATTATGACAAAAA-CGGTAAAATTTACCTAATATGTTG
* * * **
52068 AAAGTATCGATCCTTTTTATAAAAAGGATCA-ATACTTTACAATATAACATGTAAAAATACGGTA
1 AAAGTATCGATCC-TTTTATAAAAATGAT-AGATACTTTACAATATAACAAGTAAAAATATGACA
*
52132 AAACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTG
64 AAACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTAATATGTTG
* * *
52180 AAAGCATCGATCCTTTTATAAAAATAATAGATACTTTACAATATAACAGGTAAAAATATGACAAA
1 AAAGTATCGATCCTTTTATAAAAATGATAGATACTTTACAATATAACAAGTAAAAATATGACAAA
* * *
52245 ATCAGTTTCATTATGACAAAAACGGTAAAACTTACCTAATAAGTTG
66 ACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTAATATGTTG
52291 AAAGTATCGATCCTTTTATAAAAATGATAGATACTTTACAATATAACAAGTAAAAATATGACAAA
1 AAAGTATCGATCCTTTTATAAAAATGATAGATACTTTACAATATAACAAGTAAAAATATGACAAA
* *
52356 ACCAGTTTCATTATGACAAAACCGGTAAAATTTACCTGATATGTTG
66 ACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTAATATGTTG
** * * *
52402 AAAGTATAAATACTTTTTATAAAAAAGGATCGATACTTT
1 AAAGTATCGAT-CCTTTTAT-AAAAATGATAGATACTTT
52441 TTTAAAAGTT
Statistics
Matches: 331, Mismatches: 36, Indels: 11
0.88 0.10 0.03
Matches are distributed among these distances:
110 1 0.00
111 198 0.60
112 53 0.16
113 68 0.21
114 11 0.03
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.31
Consensus pattern (111 bp):
AAAGTATCGATCCTTTTATAAAAATGATAGATACTTTACAATATAACAAGTAAAAATATGACAAA
ACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTAATATGTTG
Found at i:52428 original size:23 final size:22
Alignment explanation
Indices: 52402--52447 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
52392 TGATATGTTG
*
52402 AAAGTATAAATACTTTTTATAAA
1 AAAGGATAAATACTTTTT-TAAA
**
52425 AAAGGATCGATACTTTTTTAAA
1 AAAGGATAAATACTTTTTTAAA
52447 A
1 A
52448 GTTATGTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.37
Consensus pattern (22 bp):
AAAGGATAAATACTTTTTTAAA
Found at i:53101 original size:112 final size:111
Alignment explanation
Indices: 52873--53245 Score: 532
Period size: 112 Copynumber: 3.3 Consensus size: 111
52863 TAGCGCCTAT
* *
52873 AAAGTATCGATAC-TTTACAAAAATGTATCGATATTTTACAATATAACAAGTAAAAATATGACAA
1 AAAGTATCGATCCTTTTATAAAAATG-ATCGATATTTTACAATATAACAAGTAAAAATATGACAA
* *
52937 AACCAGTTTCGTTATGACAAAAATGGTAAAATTTATCTGATATGTTG
65 AAACAGTTTCATTATGACAAAAATGGTAAAATTTATCTGATATGTTG
* *
52984 AAAGTATCGATCCTTTTATAAAAATGATAGATATTTTACAATATAACATGTAAAAATATGACAAA
1 AAAGTATCGATCCTTTTATAAAAATGATCGATATTTTACAATATAACAAGTAAAAATATGACAAA
* *
53049 AACAGTTTCATTATGACAAAAAAGGGTAAAATTTACCTGATATGTTG
66 AACAGTTTCATTATGAC-AAAAATGGTAAAATTTATCTGATATGTTG
* * * *
53096 AAAGTATCGATCATTTTATAAAAAAGATCGATATTTTACAATATAACAAGTATAAATATGACCAA
1 AAAGTATCGATCCTTTTATAAAAATGATCGATATTTTACAATATAACAAGTAAAAATATGACAAA
* * * * *
53161 ATCAGTTTCATTATGACAAAACTGATAAAATTTATTTAATATGTTG
66 AACAGTTTCATTATGACAAAAATGGTAAAATTTATCTGATATGTTG
* *
53207 AAAGTATAGATACTTTTTATAAAAATGATCGATACTTTT
1 AAAGTATCGAT-CCTTTTATAAAAATGATCGATA-TTTT
53246 TTGAAAGTTA
Statistics
Matches: 234, Mismatches: 24, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
111 97 0.41
112 133 0.57
113 4 0.02
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.34
Consensus pattern (111 bp):
AAAGTATCGATCCTTTTATAAAAATGATCGATATTTTACAATATAACAAGTAAAAATATGACAAA
AACAGTTTCATTATGACAAAAATGGTAAAATTTATCTGATATGTTG
Found at i:53239 original size:804 final size:804
Alignment explanation
Indices: 52107--53568 Score: 2469
Period size: 804 Copynumber: 1.8 Consensus size: 804
52097 CAATACTTTA
* **
52107 CAATATAACATGTAAAAATACGGTAAAACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTG
1 CAATATAACAAGTAAAAATACGACAAAACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTG
52172 ATATGTTGAAAGCATCGATCCTTTTATAAAAATAATAGATACTTTACAATATAACAGGTAAAAAT
66 ATATGTTGAAAGCATCGATCCTTTTATAAAAATAATAGATACTTTACAATATAACAGGTAAAAAT
*
52237 ATGACAAAATCAGTTTCATTATGACAAAAACGGTAAAACTTACCTAATAAGTTGAAAGTATCGAT
131 ATGACAAAAACAGTTTCATTATGACAAAAACGGTAAAACTTACCTAATAAGTTGAAAGTATCGAT
* *
52302 CCTTTTATAAAAATGATAGATACTTTACAATATAACAAGTAAAAATATGACAAAACCAGTTTCAT
196 CATTTTATAAAAAAGATAGATACTTTACAATATAACAAGTAAAAATATGACAAAACCAGTTTCAT
* *
52367 TATGACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTATAAATACTTTTTATAAAAAAGGAT
261 TATGACAAAACCGATAAAATTTACCTAATATGTTGAAAGTATAAATACTTTTTATAAAAAAGGAT
*
52432 CGATACTTTTTTAAAAGTTATGTAATTTATGTTTCAAAATTTTTTATTAGTGTTTCATGTTTTCC
326 CGATACTTTTTTAAAAGTTATGTAATTTATGTTTCAAAATTTTTTAATAGTGTTTCATGTTTTCC
*
52497 ACCTACAATATTAATTTAATAATTTTA-TTTACACAAAAAAATATTTGATTGTTTTGATATTTTA
391 ACCTACAATATTAATTTAATAATTTCATTTTA-ACAAAAAAATATTTGATTGTTTTGATATTTTA
52561 TAAAATATTATTTAGAATTTAAATTTAACAATTTTAACCAAAGACAATAATAAATATGTAATATC
455 TAAAATATTATTTAGAATTTAAATTTAACAATTTTAACCAAAGACAATAATAAATATGTAATATC
* *
52626 TATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACATAAAAAATAAATCATTAGGCGC
520 TATGTTTATTATTTTTAATTTAATAATAATATATACCGTAACATAAAAAATAAATCATTAGACGC
* *
52691 GTATAATTACTAAATTAATATCTTAAATCTCACTCAAAATATAACCTTAAATTAATGTTTTTCAC
585 GTATAATTACTAAATTAATATCTTAAAACTCACTCAAAATATAACCTTAAATTAATGTTTTCCAC
52756 AGTAAAATATCTACCTATTACATTAAACTACCTATTGGATATGTTGAAAGTATCGATTCCATTTA
650 AGTAAAATATCTACCTATTACATTAAACTACCTATTGGATATGTTGAAAGTATCGATTCCATTTA
52821 AATAAGTATCAAAACTTTTGGAATTTAAAAGAAAAACAATAATAGCGCCTATAAAGTATCGATAC
715 AATAAGTATCAAAACTTTTGGAATTTAAAAGAAAAACAATAATAGCGCCTATAAAGTATCGATAC
52886 TTTACAAAAATGTATCGATATTTTA
780 TTTACAAAAATGTATCGATATTTTA
* * * *
52911 CAATATAACAAGTAAAAATATGACAAAACCAGTTTCGTTATGACAAAAATGGTAAAATTTATCTG
1 CAATATAACAAGTAAAAATACGACAAAACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTG
* * * *
52976 ATATGTTGAAAGTATCGATCCTTTTATAAAAATGATAGATATTTTACAATATAACATGTAAAAAT
66 ATATGTTGAAAGCATCGATCCTTTTATAAAAATAATAGATACTTTACAATATAACAGGTAAAAAT
* * * *
53041 ATGACAAAAACAGTTTCATTATGACAAAAAAGGGTAAAATTTACCTGATATGTTGAAAGTATCGA
131 ATGACAAAAACAGTTTCATTATGAC-AAAAACGGTAAAACTTACCTAATAAGTTGAAAGTATCGA
* * * * *
53106 TCATTTTATAAAAAAGATCGATATTTTACAATATAACAAGTATAAATATGACCAAATCAGTTTCA
195 TCATTTTATAAAAAAGATAGATACTTTACAATATAACAAGTAAAAATATGACAAAACCAGTTTCA
* ** * *
53171 TTATGACAAAACTGATAAAATTTATTTAATATGTTGAAAGTATAGATACTTTTTAT-AAAAATGA
260 TTATGACAAAACCGATAAAATTTACCTAATATGTTGAAAGTATAAATACTTTTTATAAAAAAGGA
* * *
53235 TCGATACTTTTTTGAAAGTTATGTAATTTATGTTTCGAATTTTTTTAATAGTGTTTCATGTTTTC
325 TCGATACTTTTTTAAAAGTTATGTAATTTATGTTTCAAAATTTTTTAATAGTGTTTCATGTTTTC
* *
53300 CACCTATAATATTAATTTAATAATTTCATTTTAACAAAAAATTATTTGATTGTTTTGATATTTTA
390 CACCTACAATATTAATTTAATAATTTCATTTTAACAAAAAAATATTTGATTGTTTTGATATTTTA
* *
53365 TAAAATATTATTTAGATTTTAAATTTAACAATTTTAACCAAAGATAATAATAAATATGTAATATC
455 TAAAATATTATTTAGAATTTAAATTTAACAATTTTAACCAAAGACAATAATAAATATGTAATATC
* *
53430 TATGTTTATTATTTTTAATTTAATAATAATATATATCGTAACATAAAAAATAAATTATTAGACGC
520 TATGTTTATTATTTTTAATTTAATAATAATATATACCGTAACATAAAAAATAAATCATTAGACGC
*
53495 GTATAATTATTAAATTAATATCTTAAAACTCACTCAAAATATAACCTTAAATTAATGTTTTCCAC
585 GTATAATTACTAAATTAATATCTTAAAACTCACTCAAAATATAACCTTAAATTAATGTTTTCCAC
*
53560 AGTGAAATA
650 AGTAAAATA
53569 AGTATGGACA
Statistics
Matches: 609, Mismatches: 47, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
804 462 0.76
805 147 0.24
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.37
Consensus pattern (804 bp):
CAATATAACAAGTAAAAATACGACAAAACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTG
ATATGTTGAAAGCATCGATCCTTTTATAAAAATAATAGATACTTTACAATATAACAGGTAAAAAT
ATGACAAAAACAGTTTCATTATGACAAAAACGGTAAAACTTACCTAATAAGTTGAAAGTATCGAT
CATTTTATAAAAAAGATAGATACTTTACAATATAACAAGTAAAAATATGACAAAACCAGTTTCAT
TATGACAAAACCGATAAAATTTACCTAATATGTTGAAAGTATAAATACTTTTTATAAAAAAGGAT
CGATACTTTTTTAAAAGTTATGTAATTTATGTTTCAAAATTTTTTAATAGTGTTTCATGTTTTCC
ACCTACAATATTAATTTAATAATTTCATTTTAACAAAAAAATATTTGATTGTTTTGATATTTTAT
AAAATATTATTTAGAATTTAAATTTAACAATTTTAACCAAAGACAATAATAAATATGTAATATCT
ATGTTTATTATTTTTAATTTAATAATAATATATACCGTAACATAAAAAATAAATCATTAGACGCG
TATAATTACTAAATTAATATCTTAAAACTCACTCAAAATATAACCTTAAATTAATGTTTTCCACA
GTAAAATATCTACCTATTACATTAAACTACCTATTGGATATGTTGAAAGTATCGATTCCATTTAA
ATAAGTATCAAAACTTTTGGAATTTAAAAGAAAAACAATAATAGCGCCTATAAAGTATCGATACT
TTACAAAAATGTATCGATATTTTA
Found at i:53759 original size:11 final size:11
Alignment explanation
Indices: 53743--53767 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
53733 GATAATGCTA
53743 TATATTAATCG
1 TATATTAATCG
53754 TATATTAATCG
1 TATATTAATCG
53765 TAT
1 TAT
53768 TTCCTTAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (11 bp):
TATATTAATCG
Found at i:54100 original size:5 final size:5
Alignment explanation
Indices: 54090--54124 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
54080 CTTTCTATCT
*
54090 TTTTC TTTTC TTTTC TTTTC TTTTC AATTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC TTTT
54125 TGATTAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:58035 original size:2 final size:2
Alignment explanation
Indices: 58028--58058 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
58018 CTTATGGTTC
58028 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
58059 TTGCCTTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:64234 original size:270 final size:271
Alignment explanation
Indices: 63741--64254 Score: 879
Period size: 270 Copynumber: 1.9 Consensus size: 271
63731 TTACTAGATT
63741 CTTTAGGCAAGTTTTGGTTATGAATCTTGCCAAAGTCGGGCCTTTTGTTTCAGTTCCACCCCTTC
1 CTTTAGGCAAGTTTTGGTTATGAATCTTGCCAAAGTCGGGCCTTTTGTTTCAGTTCCACCCCTTC
* *
63806 CCCCTTCATAAATGTTTGGGGCCTTCTTTAATTTGCATCTTGATGTTAAACATAATTTTTCAAGA
66 CCCCTTCATAAATGTTAGGGGCCTTCTTTAATTTGCATCCTGATGTTAAACATAATTTTTCAAGA
* *
63871 TTTACGACCGATAATTCCACCGTAGAAGATGAAGGAAGGTATTTTACTTTTCTTCAAACACTATG
131 TTTACAACCGATAATTCCACCGTAGAAGATGAAGGAAGGTATTTTACATTTCTTCAAACACTATG
* *
63936 ATATTGAGAAAGAGAAGTTTCGGTAGTTTGTCTCATGTTGTCTATTTCCTTTTGCCTTTTGAAAC
196 ATATTGAGAAAGAAAAGTTTCAGTAGTTTGTCTCATGTTGTCTATTTCCTTTTGCCTTTTGAAAC
64001 AAAAGGCCCAA
261 AAAAGGCCCAA
***
64012 CTTT-GGCAAGTTTTGGTTATGAATCTTGCCAAAGTCGGGCCTTTTGTTTCAGTTCGGTCCCTTC
1 CTTTAGGCAAGTTTTGGTTATGAATCTTGCCAAAGTCGGGCCTTTTGTTTCAGTTCCACCCCTTC
*
64076 CCCCTTCATAAATGTTAGGGGTCTTCTTTAATTTGCATCCTGATGTTAAACATAATTTTTCAAGA
66 CCCCTTCATAAATGTTAGGGGCCTTCTTTAATTTGCATCCTGATGTTAAACATAATTTTTCAAGA
* * *
64141 TTTATAATCGATAATTCCACCGTAGAAGACT-AAGGAAGGTATTTTACATTTCTTCAAGCACTAT
131 TTTACAACCGATAATTCCACCGTAGAAGA-TGAAGGAAGGTATTTTACATTTCTTCAAACACTAT
*
64205 GATATTGAGAAAGAAAAGTTTTAGTAGTTTGTCTCATGTTGTCTATTTCC
195 GATATTGAGAAAGAAAAGTTTCAGTAGTTTGTCTCATGTTGTCTATTTCC
64255 CCTTTTCTTT
Statistics
Matches: 228, Mismatches: 14, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
270 223 0.98
271 5 0.02
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (271 bp):
CTTTAGGCAAGTTTTGGTTATGAATCTTGCCAAAGTCGGGCCTTTTGTTTCAGTTCCACCCCTTC
CCCCTTCATAAATGTTAGGGGCCTTCTTTAATTTGCATCCTGATGTTAAACATAATTTTTCAAGA
TTTACAACCGATAATTCCACCGTAGAAGATGAAGGAAGGTATTTTACATTTCTTCAAACACTATG
ATATTGAGAAAGAAAAGTTTCAGTAGTTTGTCTCATGTTGTCTATTTCCTTTTGCCTTTTGAAAC
AAAAGGCCCAA
Found at i:67245 original size:18 final size:17
Alignment explanation
Indices: 67213--67250 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
67203 TTCCAAAATG
67213 CCAAAATGGTATCGATA
1 CCAAAATGGTATCGATA
*
67230 CCAAAGTGGATATCGATA
1 CCAAAATGG-TATCGATA
67248 CCA
1 CCA
67251 TAAAAAGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (17 bp):
CCAAAATGGTATCGATA
Found at i:67857 original size:23 final size:23
Alignment explanation
Indices: 67827--67888 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
67817 GTCGAGGGTT
*
67827 CTATGTGGTCCTTCGGGACAAAC
1 CTATGTGGTCCTTCGGGACAAAA
* *
67850 CTATGTGGTCATTCGGGGCAAAA
1 CTATGTGGTCCTTCGGGACAAAA
67873 CTATGTGG-CACTTCGG
1 CTATGTGGTC-CTTCGG
67889 TGCAATTATG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 1 0.03
23 33 0.97
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.27
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGACAAAA
Found at i:73243 original size:18 final size:19
Alignment explanation
Indices: 73220--73259 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
73210 AAACTTTTAT
73220 AACATTT-AAATTATTCAA
1 AACATTTAAAATTATTCAA
73238 AACATTTACAAAATTATTCAA
1 AACATTT--AAAATTATTCAA
73259 A
1 A
73260 GCTTATACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
21 12 0.63
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (19 bp):
AACATTTAAAATTATTCAA
Found at i:73769 original size:31 final size:31
Alignment explanation
Indices: 73731--73886 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
73721 CCCGAAGGAC
* * *
73731 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
73762 CAGTCCATATGTCCCAAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
73793 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
73824 CAGTCCATATGTCTCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
73855 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
73886 C
1 C
73887 CCTCGACCCT
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
31 116 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:74892 original size:22 final size:21
Alignment explanation
Indices: 74867--74924 Score: 91
Period size: 20 Copynumber: 2.8 Consensus size: 21
74857 TTCGCTTGAG
74867 GGGTATCGATTCCCCATTGAAT
1 GGGTATCGATTCCCC-TTGAAT
*
74889 GGGTACCGATT-CCCTTGAAT
1 GGGTATCGATTCCCCTTGAAT
74909 GGGTATCGATTCCCCT
1 GGGTATCGATTCCCCT
74925 GTCCCAGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 16 0.48
21 7 0.21
22 10 0.30
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (21 bp):
GGGTATCGATTCCCCTTGAAT
Found at i:75847 original size:16 final size:16
Alignment explanation
Indices: 75808--75850 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
75798 AGCATCAGTT
*
75808 CTTATCACTCAAAATC
1 CTTATCAATCAAAATC
* *
75824 ATTAATCAATCAAATTC
1 CTT-ATCAATCAAAATC
75841 CTTATCAATC
1 CTTATCAATC
75851 TTTAATTACC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.35
Consensus pattern (16 bp):
CTTATCAATCAAAATC
Found at i:78625 original size:31 final size:31
Alignment explanation
Indices: 78587--78710 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
78577 CCCGAAAGAC
* * *
78587 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
78618 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
78649 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
78680 CAGTCCATATGTCCCGAAGAACATAGG-AAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
78710 C
1 C
78711 CCTCGACCCT
Statistics
Matches: 89, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
30 4 0.04
31 84 0.94
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:79720 original size:22 final size:20
Alignment explanation
Indices: 79695--79754 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 20
79685 TTCGCTTGAG
79695 GGGTATCGATTCCCCATTGAAT
1 GGGTA-CGATTCCCC-TTGAAT
79717 GGGTACTGATT-CCCTTGAAT
1 GGGTAC-GATTCCCCTTGAAT
79737 GGGTACCGATTCCCCTTG
1 GGGTA-CGATTCCCCTTG
79755 TCCAGAAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
20 15 0.43
21 11 0.31
22 9 0.26
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (20 bp):
GGGTACGATTCCCCTTGAAT
Found at i:82198 original size:101 final size:99
Alignment explanation
Indices: 82024--82213 Score: 301
Period size: 101 Copynumber: 1.9 Consensus size: 99
82014 TTTTTGTTTT
* * * * *
82024 ATACTTCAAGGGGAGTCATCTTATCACACTACCATCCACACTCTAAGTGAAAGGGCATACCTTCC
1 ATACTTCAAGGAGAGTCAGCTAATCACACAACCATCCACACTCTAAGTAAAAGGGCATACCTTCC
82089 ACCCCGAGCTAGTCAGGTAGAGTTTTTTTTAAGC
66 ACCCCGAGCTAGTCAGGTAGAGTTTTTTTTAAGC
82123 ATACTT-AAGGAGAGTCAGCTAATCACACAACCATCCCACACTCTAAGTAAAAAGGAGCATACCT
1 ATACTTCAAGGAGAGTCAGCTAATCACACAACCAT-CCACACTCTAAGT-AAAAGG-GCATACCT
82187 TCCACCCCGAGCTAGTCAGGTAGAGTT
63 TCCACCCCGAGCTAGTCAGGTAGAGTT
82214 ATCATGTGAC
Statistics
Matches: 83, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
98 24 0.29
99 19 0.23
100 5 0.06
101 35 0.42
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.24
Consensus pattern (99 bp):
ATACTTCAAGGAGAGTCAGCTAATCACACAACCATCCACACTCTAAGTAAAAGGGCATACCTTCC
ACCCCGAGCTAGTCAGGTAGAGTTTTTTTTAAGC
Found at i:83772 original size:2 final size:2
Alignment explanation
Indices: 83755--83788 Score: 50
Period size: 2 Copynumber: 16.0 Consensus size: 2
83745 GAATAAATGA
83755 AT AT GAT AT AT GAT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT -AT AT AT AT AT AT AT AT AT AT AT
83789 TCACAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 26 0.87
3 4 0.13
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (2 bp):
AT
Done.