Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005090.1 Hibiscus syriacus cultivar Beakdansim tig00011446_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: 52024
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Found at i:97 original size:37 final size:38
Alignment explanation
Indices: 30--115 Score: 138
Period size: 37 Copynumber: 2.3 Consensus size: 38
20 CCAGAACGTG
30 ACGCTCCAATTCTTGTCTCTGATTTGTTTGGTAATAGTA
1 ACGCTCCAATTCTTG-CTCTGATTTGTTTGGTAATAGTA
* *
69 TCGCTCCAATTCTTG-TCTGATTTGTTTGGTAATGGTA
1 ACGCTCCAATTCTTGCTCTGATTTGTTTGGTAATAGTA
106 ACGCTCCAAT
1 ACGCTCCAAT
116 CTAGATATTG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
37 30 0.68
39 14 0.32
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.42
Consensus pattern (38 bp):
ACGCTCCAATTCTTGCTCTGATTTGTTTGGTAATAGTA
Found at i:8233 original size:24 final size:22
Alignment explanation
Indices: 8180--8243 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
8170 TCTACTAGTG
8180 TTCCAAATATATCGTCAGTGTT
1 TTCCAAATATATCGTCAGTGTT
*
8202 TTCCAAATATATCGTTAGTGTT
1 TTCCAAATATATCGTCAGTGTT
*
8224 TTCCTAAA-ATATAGT-AGTGT
1 TTCC-AAATATATCGTCAGTGT
8244 ATGTTTCCTC
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
21 5 0.13
22 31 0.79
23 3 0.08
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (22 bp):
TTCCAAATATATCGTCAGTGTT
Found at i:15525 original size:18 final size:19
Alignment explanation
Indices: 15502--15540 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
15492 TAATTAGTTT
15502 TTTCA-CCCACAAATTTTC
1 TTTCACCCCACAAATTTTC
15520 TTTCACCCCACAAATTTTC
1 TTTCACCCCACAAATTTTC
15539 TT
1 TT
15541 ACACAATACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.26, C:0.33, G:0.00, T:0.41
Consensus pattern (19 bp):
TTTCACCCCACAAATTTTC
Found at i:19786 original size:25 final size:25
Alignment explanation
Indices: 19754--19807 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
19744 ATTATTTAAC
*
19754 TAATTTAAATGGTTTCCTATAATTT
1 TAATTTAAATGGTTTCCTATAATTA
*
19779 TAATTTAAATGGTTTTCTATAATTA
1 TAATTTAAATGGTTTCCTATAATTA
19804 TAAT
1 TAAT
19808 ATGTATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.06, G:0.07, T:0.52
Consensus pattern (25 bp):
TAATTTAAATGGTTTCCTATAATTA
Found at i:22976 original size:35 final size:34
Alignment explanation
Indices: 22930--23042 Score: 145
Period size: 35 Copynumber: 3.2 Consensus size: 34
22920 CAAAACATTC
*
22930 TTCAATTTCATTCTAAACCCTAAATTCCAAAGTAA
1 TTCAATTTCATTCTAAACCC-AAATTCCAAAATAA
22965 TTCAATTTCATTCTAAACCCAAAATTCCAAAATAA
1 TTCAATTTCATTCTAAACCC-AAATTCCAAAATAA
* * * * *
23000 TTCAATTACATTTTAAAACGCAAATTCTAAAATAT
1 TTCAATTTCATTCT-AAACCCAAATTCCAAAATAA
23035 TTCAATTT
1 TTCAATTT
23043 AAGGAGGAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
35 64 0.93
36 5 0.07
ACGTcount: A:0.42, C:0.19, G:0.02, T:0.36
Consensus pattern (34 bp):
TTCAATTTCATTCTAAACCCAAATTCCAAAATAA
Found at i:24139 original size:35 final size:35
Alignment explanation
Indices: 24099--24175 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
24089 AAAAAAACAT
*
24099 AAATTGAAGTATTTTAGAATTTAGGTTTTAGAATG
1 AAATTGAAGTATTTTAGAATTTAGGGTTTAGAATG
* * *
24134 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAAGTATTTTAGAATTTAGGGTTTAGAATG
24169 AAATTGA
1 AAATTGA
24176 GGATTGTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.43
Consensus pattern (35 bp):
AAATTGAAGTATTTTAGAATTTAGGGTTTAGAATG
Found at i:29882 original size:15 final size:15
Alignment explanation
Indices: 29860--29908 Score: 82
Period size: 15 Copynumber: 3.3 Consensus size: 15
29850 AATTTTTTAT
29860 AATC-ATTGATTTTC
1 AATCTATTGATTTTC
29874 AATCTATTGATTTTC
1 AATCTATTGATTTTC
29889 AATCTATTGATTTTC
1 AATCTATTGATTTTC
29904 TAATC
1 -AATC
29909 CAAATTAGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.12
15 25 0.76
16 4 0.12
ACGTcount: A:0.29, C:0.14, G:0.06, T:0.51
Consensus pattern (15 bp):
AATCTATTGATTTTC
Found at i:33762 original size:14 final size:15
Alignment explanation
Indices: 33730--33762 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
33720 CTAGATCGCA
33730 TTTATTTTATTCGAG
1 TTTATTTTATTCGAG
*
33745 TTTATTTTTTTC-AG
1 TTTATTTTATTCGAG
33759 TTTA
1 TTTA
33763 CATTTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.18, C:0.06, G:0.09, T:0.67
Consensus pattern (15 bp):
TTTATTTTATTCGAG
Found at i:34395 original size:21 final size:20
Alignment explanation
Indices: 34328--34466 Score: 73
Period size: 21 Copynumber: 6.8 Consensus size: 20
34318 AAATGACCAA
***
34328 CAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
34348 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
34368 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
34389 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
34410 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
34430 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
34451 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
34467 ACACATAAAT
Statistics
Matches: 88, Mismatches: 26, Indels: 10
0.71 0.21 0.08
Matches are distributed among these distances:
19 1 0.01
20 41 0.47
21 46 0.52
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:34481 original size:40 final size:39
Alignment explanation
Indices: 34434--34627 Score: 199
Period size: 40 Copynumber: 4.8 Consensus size: 39
34424 GATTTTCCAG
* ** *
34434 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CATA
* * *
34474 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
* * *
34514 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
* ** *
34554 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT-A
* *
34595 AATCGCAACGAGAATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
34628 TATTTAAAGC
Statistics
Matches: 130, Mismatches: 21, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
39 1 0.01
40 98 0.75
41 31 0.24
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACCATA
Found at i:34517 original size:60 final size:60
Alignment explanation
Indices: 34434--34626 Score: 235
Period size: 60 Copynumber: 3.2 Consensus size: 60
34424 GATTTTCCAG
* ** *
34434 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
* * * *
34494 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATC-CGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACATAAATCGCAACGCGTATCCGTA
* ** * * *
34554 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGAGAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT-AAATCGCAACGCGTATCCGTA
34615 AATCGCAACGCG
1 AATCGCAACGCG
34627 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
59 1 0.01
60 79 0.71
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
Found at i:34599 original size:21 final size:20
Alignment explanation
Indices: 34434--34624 Score: 96
Period size: 20 Copynumber: 9.5 Consensus size: 20
34424 GATTTTCCAG
* *
34434 AATCGCAACGCGAATATGA-A
1 AATCGCAACGAGAATA-CATA
* *
34454 AATCGCAACGCGAACACATA
1 AATCGCAACGAGAATACATA
* * * *
34474 AATCGCAACGCGTATCCGTA
1 AATCGCAACGAGAATACATA
* * * *
34494 AATCGCAACGTGTATCCGTA
1 AATCGCAACGAGAATACATA
* * * *
34514 AATCGCAACGCGTATCCGTA
1 AATCGCAACGAGAATACATA
* * * * *
34534 AATCGCAATGCGTATCCGTA
1 AATCGCAACGAGAATACATA
* * * * *
34554 TATCGCAACGCGTATCCGTA
1 AATCGCAACGAGAATACATA
*
34574 AATCGCAACGATAATACATAA
1 AATCGCAACGAGAATACAT-A
* *
34595 AATCGCAACGAGAATCCGTA
1 AATCGCAACGAGAATACATA
34615 AATCGCAACG
1 AATCGCAACG
34625 CGATATTTAA
Statistics
Matches: 149, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
19 1 0.01
20 131 0.88
21 17 0.11
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGAGAATACATA
Found at i:35045 original size:33 final size:33
Alignment explanation
Indices: 35006--35076 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
34996 TTCACTTAGA
35006 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
35039 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
35072 TTTCA
1 TTTCA
35077 AGTTAGTATT
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:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:35182 original size:21 final size:20
Alignment explanation
Indices: 35156--35263 Score: 95
Period size: 21 Copynumber: 5.7 Consensus size: 20
35146 TGCAGAAGAG
35156 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
35177 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
35197 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
35218 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
35232 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
*
35251 TCGCAACGCGAAA
1 TCGCAACGAGAAA
35264 CCAAAATCGC
Statistics
Matches: 71, Mismatches: 9, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
14 11 0.15
16 2 0.03
17 2 0.03
19 12 0.17
20 18 0.25
21 26 0.37
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.11
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:35200 original size:20 final size:20
Alignment explanation
Indices: 35156--35232 Score: 100
Period size: 21 Copynumber: 3.8 Consensus size: 20
35146 TGCAGAAGAG
*
35156 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
35177 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
35197 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
35218 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
35233 CGCAACGCGA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
20 20 0.42
21 28 0.58
ACGTcount: A:0.45, C:0.17, G:0.25, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:35213 original size:41 final size:41
Alignment explanation
Indices: 35155--35232 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
35145 TTGCAGAAGA
*
35155 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
35196 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
35233 CGCAACGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:35254 original size:19 final size:19
Alignment explanation
Indices: 35168--35274 Score: 80
Period size: 19 Copynumber: 5.7 Consensus size: 19
35158 GCAACGAGAT
*
35168 AAATGAAAATCGCAACGAG
1 AAATGAAAATCGCAACGCG
*** *
35187 AGAATGACTGTCGCAACGAGAG
1 A-AATGAAAATCGCAAC--GCG
35209 AAATGAAAATCGCAA--CG
1 AAATGAAAATCGCAACGCG
*
35226 --A-GAGAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
35242 AAATGAAAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
**
35261 AAACCAAAATCGCA
1 AAATGAAAATCGCA
35275 TTGCGATTTT
Statistics
Matches: 69, Mismatches: 11, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 1 0.01
18 1 0.01
19 27 0.39
20 12 0.17
21 11 0.16
22 4 0.06
ACGTcount: A:0.47, C:0.21, G:0.22, T:0.10
Consensus pattern (19 bp):
AAATGAAAATCGCAACGCG
Found at i:35292 original size:19 final size:19
Alignment explanation
Indices: 35270--35334 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
35260 GAAACCAAAA
35270 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
35289 TCGCGTTGCGA--TTC---
1 TCGCATTGCGATTTTCATT
*
35303 TCTCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
35322 TCGCGTTGCGATT
1 TCGCATTGCGATT
35335 CTCTCGTTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
14 9 0.25
16 3 0.08
17 3 0.08
19 21 0.58
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:35315 original size:33 final size:33
Alignment explanation
Indices: 35273--35356 Score: 159
Period size: 33 Copynumber: 2.5 Consensus size: 33
35263 ACCAAAATCG
35273 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
35306 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
35339 CGTTGCGATTTTCATTTC
1 CATTGCGATTTTCATTTC
35357 TCTCGTTGCG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46
Consensus pattern (33 bp):
CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:35344 original size:14 final size:14
Alignment explanation
Indices: 35292--35348 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
35282 TTTCATTTCG
35292 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
35306 CATTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
35325 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
35339 CGTTGCGATT
1 CGTTGCGATT
35349 TTCATTTCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:35359 original size:21 final size:21
Alignment explanation
Indices: 35333--35397 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
35323 CGCGTTGCGA
35333 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
35354 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
35374 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
35395 TTC
1 TTC
35398 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:35394 original size:20 final size:20
Alignment explanation
Indices: 35332--35395 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
35322 TCGCGTTGCG
35332 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
***
35352 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
35373 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
35393 ATT
1 ATT
35396 TCAACCAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.12, C:0.25, G:0.16, T:0.47
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:37253 original size:93 final size:93
Alignment explanation
Indices: 37094--37748 Score: 1258
Period size: 93 Copynumber: 7.1 Consensus size: 93
37084 TAGATTGCTT
* *
37094 AGTAAATTTATTCGGTTGCTGCCATTTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
37159 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
37187 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
37252 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
37280 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
37345 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
37373 AGTAAATTTGTTTGGTTGCTGCCAATTTTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
37438 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
37466 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
37531 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
37559 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
37624 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
37652 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
37717 TTTATCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
37744 AGTAA
1 AGTAA
37749 TGCAATCCAT
Statistics
Matches: 555, Mismatches: 7, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 6 0.01
93 549 0.99
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.47
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:37818 original size:20 final size:20
Alignment explanation
Indices: 37793--37921 Score: 74
Period size: 19 Copynumber: 7.2 Consensus size: 20
37783 TAGTTTACTT
* *
37793 TCGCAACACAAAACTTAAAA
1 TCGCAACACGAAACTCAAAA
*
37813 TCGCAACGCGAAAC-CAAAA
1 TCGCAACACGAAACTCAAAA
* *
37832 TCGCAACGCGAAA-TGAAAA
1 TCGCAACACGAAACTCAAAA
*
37851 TCGC-A-AC-AAA---AGAA
1 TCGCAACACGAAACTCAAAA
*
37865 TCGCAACGCGAAAC-CAAAA
1 TCGCAACACGAAACTCAAAA
37884 TCGC-A-ACG--A--CAAAA
1 TCGCAACACGAAACTCAAAA
*
37898 TCGCAACGCGAAAC-CAAAA
1 TCGCAACACGAAACTCAAAA
37917 TCGCA
1 TCGCA
37922 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 10, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
14 16 0.18
15 3 0.03
16 6 0.07
17 6 0.07
18 3 0.03
19 42 0.48
20 12 0.14
ACGTcount: A:0.49, C:0.28, G:0.15, T:0.09
Consensus pattern (20 bp):
TCGCAACACGAAACTCAAAA
Found at i:37833 original size:19 final size:19
Alignment explanation
Indices: 37809--37921 Score: 129
Period size: 19 Copynumber: 6.5 Consensus size: 19
37799 CACAAAACTT
37809 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
**
37828 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAACC
37847 AAAATCGCAA--C-AAA--
1 AAAATCGCAACGCGAAACC
*
37861 AGAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
37880 AAAATCGCAA--CG--A-C
1 AAAATCGCAACGCGAAACC
37894 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
37913 AAAATCGCA
1 AAAATCGCA
37922 TTGCGATTTT
Statistics
Matches: 80, Mismatches: 4, Indels: 20
0.77 0.04 0.19
Matches are distributed among these distances:
14 20 0.25
15 1 0.01
16 6 0.08
17 6 0.08
18 1 0.01
19 46 0.57
ACGTcount: A:0.50, C:0.27, G:0.16, T:0.07
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACC
Found at i:37867 original size:33 final size:33
Alignment explanation
Indices: 37828--37921 Score: 145
Period size: 33 Copynumber: 2.8 Consensus size: 33
37818 ACGCGAAACC
**
37828 AAAATCGCAACGCGAAATGAAAATCGCAAC-AA
1 AAAATCGCAACGCGAAACCAAAATCGCAACGAA
*
37860 AAGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 AA-AATCGCAACGCGAAACCAAAATCGCAACGAA
37894 AAAATCGCAACGCGAAACCAAAATCGCA
1 AAAATCGCAACGCGAAACCAAAATCGCA
37922 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 2 0.04
33 52 0.91
34 3 0.05
ACGTcount: A:0.50, C:0.27, G:0.16, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGCGAAACCAAAATCGCAACGAA
Found at i:37898 original size:14 final size:14
Alignment explanation
Indices: 37879--37905 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
37869 AACGCGAAAC
37879 CAAAATCGCAACGA
1 CAAAATCGCAACGA
37893 CAAAATCGCAACG
1 CAAAATCGCAACG
37906 CGAAACCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.30, G:0.15, T:0.07
Consensus pattern (14 bp):
CAAAATCGCAACGA
Found at i:37919 original size:52 final size:51
Alignment explanation
Indices: 37809--37921 Score: 138
Period size: 52 Copynumber: 2.2 Consensus size: 51
37799 CACAAAACTT
* * *
37809 AAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACAA
1 AAAATCGCAACGCGAAACCAAAATCGCAACGCAAAATGAAAAGCGAAACAA
* * *
37860 AAGAATCGCAACGCGAAACCAAAATCGCAACGACAAAATCGCAACGCGAAAC-C
1 AA-AATCGCAACGCGAAACCAAAATCGCAACG-CAAAAT-GAAAAGCGAAACAA
37913 AAAATCGCA
1 AAAATCGCA
37922 TTGCGATTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
51 2 0.04
52 36 0.68
53 7 0.13
54 8 0.15
ACGTcount: A:0.50, C:0.27, G:0.16, T:0.07
Consensus pattern (51 bp):
AAAATCGCAACGCGAAACCAAAATCGCAACGCAAAATGAAAAGCGAAACAA
Found at i:37939 original size:19 final size:19
Alignment explanation
Indices: 37917--38089 Score: 168
Period size: 19 Copynumber: 9.6 Consensus size: 19
37907 GAAACCAAAA
*
37917 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
37936 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
37952 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
37969 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
37985 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
38002 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
38021 TCGCGTTGCGATTTTTGTT
1 TCGCGTTGCGATTTTCATT
* *
38040 TCTCGTTGCGATTATCATT
1 TCGCGTTGCGATTTTCATT
*
38059 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
38079 TCGTGTTGCGA
1 TCGCGTTGCGA
38090 AAGTAAACTA
Statistics
Matches: 127, Mismatches: 16, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
14 15 0.12
16 11 0.09
17 11 0.09
19 78 0.61
20 12 0.09
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:37958 original size:14 final size:14
Alignment explanation
Indices: 37939--37995 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
37929 TTTCATTTCG
37939 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
37953 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
37970 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
37986 CGTTGCGATT
1 CGTTGCGATT
37996 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:38047 original size:38 final size:38
Alignment explanation
Indices: 37917--38089 Score: 168
Period size: 33 Copynumber: 4.8 Consensus size: 38
37907 GAAACCAAAA
*
37917 TCGCATTGCGATTTTCATTTCGCGTTGCGA-T-TC-TT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* *
37952 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* **
37985 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
** *
38021 TCGCGTTGCGATTTTTGTTTCTCGTTGCGATTATCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* *
38059 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
38090 AAGTAAACTA
Statistics
Matches: 116, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
33 56 0.48
34 1 0.01
35 2 0.02
36 2 0.02
38 44 0.38
39 11 0.09
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
Found at i:40033 original size:14 final size:14
Alignment explanation
Indices: 40014--40049 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
40004 ATTGTTTAAT
40014 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
40028 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
40042 TGATTTGT
1 TGATTTGT
40050 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:40164 original size:19 final size:19
Alignment explanation
Indices: 40140--40260 Score: 145
Period size: 19 Copynumber: 6.8 Consensus size: 19
40130 GCATTATGTT
40140 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
40159 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
*
40176 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC
40192 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
*
40209 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC
40225 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
40244 GGAAATGAAAATCGCAA
1 -GAAATGAAAATCGCAA
40261 CGAGAGAATC
Statistics
Matches: 87, Mismatches: 4, Indels: 21
0.78 0.04 0.19
Matches are distributed among these distances:
14 20 0.23
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 39 0.45
20 16 0.18
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:40186 original size:14 final size:14
Alignment explanation
Indices: 40167--40221 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
40157 GCGAAATGAA
40167 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
40181 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
40200 AATCGCAACGAGAG
1 AATCGCAACGAGAG
40214 AATCGCAA
1 AATCGCAA
40222 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:40190 original size:33 final size:33
Alignment explanation
Indices: 40148--40240 Score: 186
Period size: 33 Copynumber: 2.8 Consensus size: 33
40138 TTGAAATGAA
40148 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
40181 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
40214 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
40241 TGCGGAAATG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:40332 original size:14 final size:14
Alignment explanation
Indices: 40313--40367 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
40303 CATTTCCGCA
40313 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
40327 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
40344 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
40360 TTGCGATT
1 TTGCGATT
40368 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:40338 original size:53 final size:53
Alignment explanation
Indices: 40327--40492 Score: 291
Period size: 53 Copynumber: 3.2 Consensus size: 53
40317 GATTCTCTCG
40327 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
40379 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
* *
40432 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCCGCATTGCGATTCTC-TCGTTGCGATTTTCATTTCGCA
40485 TTGCGATT
1 TTGCGATT
40493 CTCTCGTTGC
Statistics
Matches: 110, Mismatches: 2, Indels: 3
0.96 0.02 0.03
Matches are distributed among these distances:
52 15 0.14
53 94 0.85
54 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (53 bp):
TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:40345 original size:86 final size:86
Alignment explanation
Indices: 40255--40431 Score: 273
Period size: 86 Copynumber: 2.1 Consensus size: 86
40245 GAAATGAAAA
40255 TCGCAACGAGAGAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGAT
1 TCGCAACGAGAGAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGAT
40320 TCTCTCGTTGCGATTTTCATT
66 TCTCTCGTTGCGATTTTCATT
** * *** * **
40341 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGAT
1 TCGCAACGAGAGAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGAT
40406 TCTCTCGTTGCGATTTTCATT
66 TCTCTCGTTGCGATTTTCATT
40427 TCGCA
1 TCGCA
40432 TTGCGATTTT
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
86 82 1.00
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.41
Consensus pattern (86 bp):
TCGCAACGAGAGAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGAT
TCTCTCGTTGCGATTTTCATT
Found at i:40432 original size:86 final size:90
Alignment explanation
Indices: 40275--40506 Score: 358
Period size: 86 Copynumber: 2.7 Consensus size: 90
40265 AGAATCGCAA
40275 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
40340 TTCGCATTGCGA-TTC-TCT-CG-T
66 TTCGCATTGCGATTTCATCTCCGAT
40361 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
*
40426 TTCGCATTGCGATTTTCATTTCCGCAT
66 TTCGCATTGCGA-TTTCATCTCCG-AT
*
40453 TGCGATTTTCA--T-G--TTGGGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
40507 GTAATTTCCG
Statistics
Matches: 138, Mismatches: 2, Indels: 12
0.91 0.01 0.08
Matches are distributed among these distances:
86 103 0.75
87 14 0.10
88 3 0.02
89 3 0.02
90 3 0.02
92 12 0.09
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (90 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCGCATTGCGATTTCATCTCCGAT
Found at i:40514 original size:33 final size:33
Alignment explanation
Indices: 40293--40506 Score: 220
Period size: 33 Copynumber: 6.2 Consensus size: 33
40283 TCATTTCGCA
40293 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
40327 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
40360 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG
* * * * *
40397 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
*
40432 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
40466 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
40499 TTGCGATT
1 TTGCGATT
40507 GTAATTTCCG
Statistics
Matches: 150, Mismatches: 15, Indels: 31
0.77 0.08 0.16
Matches are distributed among these distances:
31 4 0.03
32 7 0.05
33 77 0.51
34 31 0.21
35 4 0.03
36 3 0.02
37 2 0.01
38 2 0.01
39 8 0.05
40 3 0.02
41 9 0.06
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:40521 original size:53 final size:53
Alignment explanation
Indices: 40327--40525 Score: 196
Period size: 53 Copynumber: 3.8 Consensus size: 53
40317 GATTCTCTCG
* *
40327 TTGCGATTTTCA-TTTCGCATTGCGA-TTCTC-TCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCAGTTCCGCATTGCAATTTC-CAT-GTTGCGATTTTCATTTCGCA
* *
40379 TTGCGATTTTCATTTCCGCATTGCGA-TTCTC-TCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCAGTTCCGCATTGCAATTTC-CAT-GTTGCGATTTTCATTTCGCA
* * * *
40432 TTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCA
1 TTGCGATTTTCAGTTCCGCATTGCAATTTCCATGTTGCGATTTTCATTTCGCA
* * *
40485 TTGCGATTCTCTC-GTTGCG-ATTGTAATTTCCGTGTTGCGAT
1 TTGCGATT-T-TCAGTTCCGCATTGCAATTTCCATGTTGCGAT
40526 AGTCAAATGC
Statistics
Matches: 132, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
52 12 0.09
53 110 0.83
54 8 0.06
55 2 0.02
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (53 bp):
TTGCGATTTTCAGTTCCGCATTGCAATTTCCATGTTGCGATTTTCATTTCGCA
Found at i:42805 original size:12 final size:12
Alignment explanation
Indices: 42788--42812 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42778 TCTTCGGGGA
42788 CTTTTTCTTCTT
1 CTTTTTCTTCTT
42800 CTTTTTCTTCTT
1 CTTTTTCTTCTT
42812 C
1 C
42813 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:43020 original size:24 final size:24
Alignment explanation
Indices: 42986--43032 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
42976 CTGAAACATC
42986 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
43010 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
43033 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:43749 original size:20 final size:20
Alignment explanation
Indices: 43721--43949 Score: 253
Period size: 20 Copynumber: 11.4 Consensus size: 20
43711 AAATTTCAGT
* * *
43721 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
43741 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
43761 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
43781 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
43801 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
43821 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
43841 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
43861 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
43881 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
43901 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
43921 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
43941 GTTGCGATT
1 GTTGCGATT
43950 CTGGAAAATC
Statistics
Matches: 185, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
20 184 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:44541 original size:23 final size:24
Alignment explanation
Indices: 44515--44569 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
44505 AACAAGTTAG
*
44515 AAAATATTTATA-TATTTTCTTTA
1 AAAATATTTAAATTATTTTCTTTA
*
44538 AAAA-ATTTAAATTATTTTTTTTA
1 AAAATATTTAAATTATTTTCTTTA
* *
44561 TATATATTT
1 AAAATATTT
44570 TTTTACAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 6 0.23
23 16 0.62
24 4 0.15
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (24 bp):
AAAATATTTAAATTATTTTCTTTA
Done.