Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006499.1 Hibiscus syriacus cultivar Beakdansim tig00015812_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: 107163
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Found at i:5722 original size:156 final size:157
Alignment explanation
Indices: 5378--5744 Score: 447
Period size: 156 Copynumber: 2.3 Consensus size: 157
5368 AAGTCTATTT
* *
5378 TTTTTTACCAAATTTGAATTACATACCCATAAATCATCGTAGAATACATATGTACTTTCAATTCC
1 TTTTTTACCAAATTTGAA-TACATGCTCATAAATCATCGTAGAATACATATGTACTTTCAATTCC
* * * *
5443 TCTTTTTTGTAACAATTTTTTTATTTTTCAATTTAGTCCCTTGATTTTTCATATTTTTCTTATTT
65 TCTTTTTTGTAACAATATTTTTATTTTTCAATTTAATCCCTTAATTTTTCATATTTTTATTATTT
*
5508 ATAAAATTCATCATTTATTTTAAGTTCA
130 ATAAAATTCATCATTTATTGTAAGTTCA
* * * * *
5536 TCTCTTACTAAATTTGAATCACATGTTCATAAATCATTGTAGAATACATATGTACTTTCAA-T-C
1 TTTTTTACCAAATTTGAAT-ACATGCTCATAAATCATCGTAGAATACATATGTACTTTCAATTCC
*
5599 TC-TTTTTGATAATAATATTTTTATTTTTCAATTTAATCCCTTAATTTTTCATATTTTTATTATT
65 TCTTTTTTG-TAACAATATTTTTATTTTTCAATTTAATCCCTTAATTTTTCATATTTTTATTATT
* * * **
5663 TTTTAAATTCATTA-TTATTGTAAGTTTG
129 TATAAAATTCATCATTTATTGTAAGTTCA
* * * *
5691 TTTTTTAACCAAATTTGAACTACTTGCTCATATACCA-CAATAGAATACATATGT
1 TTTTTT-ACCAAATTTGAA-TACATGCTCATAAATCATC-GTAGAATACATATGT
5745 GTTTCTTGTT
Statistics
Matches: 177, Mismatches: 27, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
155 21 0.12
156 101 0.57
157 3 0.02
158 52 0.29
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.49
Consensus pattern (157 bp):
TTTTTTACCAAATTTGAATACATGCTCATAAATCATCGTAGAATACATATGTACTTTCAATTCCT
CTTTTTTGTAACAATATTTTTATTTTTCAATTTAATCCCTTAATTTTTCATATTTTTATTATTTA
TAAAATTCATCATTTATTGTAAGTTCA
Found at i:10792 original size:20 final size:21
Alignment explanation
Indices: 10767--10825 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 21
10757 GGACGAAGGG
10767 ATTATTTTAATTTTTT-TAAA-
1 ATTATTTT-ATTTTTTATAAAT
10787 ATTATTTTTATTTTTTAATAAAT
1 ATTA-TTTTATTTTTT-ATAAAT
10810 ATT-TTTTATTTTTTAT
1 ATTATTTTATTTTTTAT
10826 TTTTTAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
20 13 0.37
21 15 0.43
22 4 0.11
23 3 0.09
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
ATTATTTTATTTTTTATAAAT
Found at i:10801 original size:21 final size:21
Alignment explanation
Indices: 10767--10823 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
10757 GGACGAAGGG
*
10767 ATTATTTTAATTTTTTTAA-A
1 ATTATTTTTATTTTTTTAATA
10787 ATTATTTTTA-TTTTTTAATA
1 ATTATTTTTATTTTTTTAATA
*
10807 AATATTTTTTATTTTTT
1 ATTA-TTTTTATTTTTT
10824 ATTTTTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 8 0.25
20 13 0.41
21 6 0.19
22 5 0.16
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
ATTATTTTTATTTTTTTAATA
Found at i:11907 original size:2 final size:2
Alignment explanation
Indices: 11900--11924 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11890 AAATATTATT
11900 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 T
11925 TGGGGTTAAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14230 original size:2 final size:2
Alignment explanation
Indices: 14223--14248 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14213 ATTTCTGACT
14223 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
14249 CACACACATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18363 original size:30 final size:30
Alignment explanation
Indices: 18312--18390 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
18302 ACATCGTTCC
* **
18312 CCATTCTTACATCTATATGGGATAAACTCT
1 CCATTCTGACATCTGCATGGGATAAACTCT
* * *
18342 -CATTTCTGATATTTGCATGGGATAAATTCT
1 CCA-TTCTGACATCTGCATGGGATAAACTCT
18372 CCATTCTGACATCTGCATG
1 CCATTCTGACATCTGCATG
18391 AGATTAGATC
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
29 2 0.05
30 35 0.90
31 2 0.05
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.38
Consensus pattern (30 bp):
CCATTCTGACATCTGCATGGGATAAACTCT
Found at i:19718 original size:24 final size:24
Alignment explanation
Indices: 19684--19730 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
19674 CAAAATAAAG
19684 AAATTAAAACCCCACAACAATTAA
1 AAATTAAAACCCCACAACAATTAA
*
19708 AAATTACAACCCCACAACAATTA
1 AAATTAAAACCCCACAACAATTA
19731 CAATCAGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.55, C:0.28, G:0.00, T:0.17
Consensus pattern (24 bp):
AAATTAAAACCCCACAACAATTAA
Found at i:26328 original size:2 final size:2
Alignment explanation
Indices: 26323--26347 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
26313 TTAATCATTA
26323 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
26348 ACGATATAAT
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:27581 original size:16 final size:17
Alignment explanation
Indices: 27549--27585 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
27539 TCCCTAAAAT
27549 TTTTAATTTTTCATATA
1 TTTTAATTTTTCATATA
27566 TTTTAATTTTTC-TATA
1 TTTTAATTTTTCATATA
27582 TTTT
1 TTTT
27586 TTATTACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTAATTTTTCATATA
Found at i:32045 original size:49 final size:49
Alignment explanation
Indices: 31921--32212 Score: 279
Period size: 49 Copynumber: 5.8 Consensus size: 49
31911 AGTGACATCT
* * * * *
31921 TTTATGC-TAAAATGCACCGTTATACATTTAAC-TGTCATTAGTGACACC
1 TTTATGCAAAAAATGCACCTTTATGCATTTAACTTG-CATTAGTGGCACA
* * * * *
31969 TTTCTAC-CAAAATGCA-CTGATATGCATTTAACTCGCATTAGTGGCACA
1 TTTATGCAAAAAATGCACCT-TTATGCATTTAACTTGCATTAGTGGCACA
32017 TTTATGCAAAAAATGCACCTTTATGCATTTAACTTGCATTAGTGGCACA
1 TTTATGCAAAAAATGCACCTTTATGCATTTAACTTGCATTAGTGGCACA
* *
32066 TTTATGCAAAAAATGCACCATTATGCATTTAACTTGCATTAGTGACATCTTTCAA
1 TTTATGCAAAAAATGCACCTTTATGCATTTAACTTGCATTAGTGGCA-----C-A
* * *
32121 TCTTTCTGTCAAAAAA-GCACATTTATGCATTTAACTTGCATTAGTGGTACA
1 --TTTATG-CAAAAAATGCACCTTTATGCATTTAACTTGCATTAGTGGCACA
* * * *
32172 TTTCTGCAAAAAACGCACCATTATGCATTTAACTTTCATTA
1 TTTATGCAAAAAATGCACCTTTATGCATTTAACTTGCATTA
32213 TAGAGCAGTT
Statistics
Matches: 206, Mismatches: 24, Indels: 27
0.80 0.09 0.11
Matches are distributed among these distances:
47 1 0.00
48 47 0.23
49 111 0.54
50 2 0.01
51 1 0.00
52 1 0.00
54 1 0.00
55 1 0.00
57 34 0.17
58 7 0.03
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (49 bp):
TTTATGCAAAAAATGCACCTTTATGCATTTAACTTGCATTAGTGGCACA
Found at i:35328 original size:62 final size:62
Alignment explanation
Indices: 35220--35343 Score: 205
Period size: 62 Copynumber: 2.0 Consensus size: 62
35210 ACAACTAAGA
35220 AAACTTCTGAACAAATACTACATTGTAATCATCCACTCTATTTATTCATAATTTTTCTTAAT
1 AAACTTCTGAACAAATACTACATTGTAATCATCCACTCTATTTATTCATAATTTTTCTTAAT
* **
35282 AAACTTCT-AACAAATACTACCTTGTAATCATTCTGCTCTATTTATTCATAATTTTTCTTAAT
1 AAACTTCTGAACAAATACTACATTGTAATCA-TCCACTCTATTTATTCATAATTTTTCTTAAT
35344 TATTGATAAC
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
61 21 0.36
62 37 0.64
ACGTcount: A:0.34, C:0.19, G:0.03, T:0.44
Consensus pattern (62 bp):
AAACTTCTGAACAAATACTACATTGTAATCATCCACTCTATTTATTCATAATTTTTCTTAAT
Found at i:37051 original size:2 final size:2
Alignment explanation
Indices: 37046--37089 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
37036 TGCGCGTGTG
37046 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37088 TA
1 TA
37090 AAAAAAAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40281 original size:23 final size:23
Alignment explanation
Indices: 40237--40281 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
40227 TATTGATTAA
* * *
40237 CGCTAAACGAATGTGTTGACGAG
1 CGCTAAACAAATATGTTCACGAG
*
40260 CGCTAAACAAATATTTTCACGA
1 CGCTAAACAAATATGTTCACGA
40282 ACACTAAATG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (23 bp):
CGCTAAACAAATATGTTCACGAG
Found at i:41499 original size:60 final size:60
Alignment explanation
Indices: 41402--41524 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 60
41392 ATGAATTTAC
* * *
41402 GGATGAAATTGGAGGCTTTAAAAGTTTAGGGACCAATTTAGAATAAGAGCCATAGTTTGG
1 GGATGAAATTGGAAGATTCAAAAGTTTAGGGACCAATTTAGAATAAGAGCCATAGTTTGG
* * * ** *
41462 GGATGAAATTGGAATATTCAAAAGTTTAGGGATCAATTTAGAATGAGATTCATATTTTGG
1 GGATGAAATTGGAAGATTCAAAAGTTTAGGGACCAATTTAGAATAAGAGCCATAGTTTGG
41522 GGA
1 GGA
41525 CATATGATGC
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.36, C:0.07, G:0.27, T:0.31
Consensus pattern (60 bp):
GGATGAAATTGGAAGATTCAAAAGTTTAGGGACCAATTTAGAATAAGAGCCATAGTTTGG
Found at i:41505 original size:29 final size:31
Alignment explanation
Indices: 41421--41505 Score: 75
Period size: 29 Copynumber: 2.8 Consensus size: 31
41411 TGGAGGCTTT
*
41421 AAAAGTTTAGGGACCAATTTAGAATAAGAGC
1 AAAAGTTTAGGGATCAATTTAGAATAAGAGC
* * * * * * **
41452 CATAGTTTGGGGATGAAATTGGAAT-A-TTC
1 AAAAGTTTAGGGATCAATTTAGAATAAGAGC
41481 AAAAGTTTAGGGATCAATTTAGAAT
1 AAAAGTTTAGGGATCAATTTAGAAT
41506 GAGATTCATA
Statistics
Matches: 39, Mismatches: 15, Indels: 2
0.70 0.27 0.04
Matches are distributed among these distances:
29 20 0.51
30 1 0.03
31 18 0.46
ACGTcount: A:0.40, C:0.07, G:0.24, T:0.29
Consensus pattern (31 bp):
AAAAGTTTAGGGATCAATTTAGAATAAGAGC
Found at i:42445 original size:14 final size:12
Alignment explanation
Indices: 42408--42433 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42398 GTGATTCTTC
42408 CGTATTCGAATA
1 CGTATTCGAATA
42420 CGTATTCGAATA
1 CGTATTCGAATA
42432 CG
1 CG
42434 ATCTTTCGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (12 bp):
CGTATTCGAATA
Found at i:46616 original size:60 final size:59
Alignment explanation
Indices: 46537--46687 Score: 184
Period size: 60 Copynumber: 2.6 Consensus size: 59
46527 GAACATATGA
* * *
46537 ATAGTCGGATGATCATTTTATAACTTTTAATAGTCAAGGGACTCAACAAAGTAATC-TCCC
1 ATAGTCGG-TGACCATTTTATAACTTTTAATAGTCAAGGGACTCAACAAAATAA-CATACC
* ** *
46597 ATAGTCCGGTGACCATTTTATAATTTTTAATAGTCGTGGGACTCAACAAAATAACATACT
1 ATAGT-CGGTGACCATTTTATAACTTTTAATAGTCAAGGGACTCAACAAAATAACATACC
46657 ATAGTC---GACCATTTTATAACTTTTAATAGTC
1 ATAGTCGGTGACCATTTTATAACTTTTAATAGTC
46688 GGAGACTCAA
Statistics
Matches: 81, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
56 24 0.30
59 2 0.02
60 52 0.64
61 3 0.04
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (59 bp):
ATAGTCGGTGACCATTTTATAACTTTTAATAGTCAAGGGACTCAACAAAATAACATACC
Found at i:47443 original size:31 final size:32
Alignment explanation
Indices: 47409--47539 Score: 153
Period size: 31 Copynumber: 4.2 Consensus size: 32
47399 AAACATTATA
* *
47409 TACTAAAACAGATC-AAAACTGATAATTTAAA
1 TACTAAAACAGAACAAAAACTGATAATTTAAG
* * *
47440 TACTAAAACA-AACCAAAATTGATAGTTTAAG
1 TACTAAAACAGAACAAAAACTGATAATTTAAG
* *
47471 TAATAAAAC-GAACAAAAATTGATAATTTAAG
1 TACTAAAACAGAACAAAAACTGATAATTTAAG
* *
47502 TACTAAAACA-AACTAAAACTGATAGTTTAAG
1 TACTAAAACAGAACAAAAACTGATAATTTAAG
47533 TACTAAA
1 TACTAAA
47540 TACATAATTT
Statistics
Matches: 86, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
30 2 0.02
31 84 0.98
ACGTcount: A:0.54, C:0.11, G:0.08, T:0.26
Consensus pattern (32 bp):
TACTAAAACAGAACAAAAACTGATAATTTAAG
Found at i:47494 original size:62 final size:62
Alignment explanation
Indices: 47423--47539 Score: 189
Period size: 62 Copynumber: 1.9 Consensus size: 62
47413 AAAACAGATC
*
47423 AAAACTGATAATTTAAATACTAAAACAAACCAAAATTGATAGTTTAAGTAATAAAACGAACA
1 AAAACTGATAATTTAAATACTAAAACAAACCAAAACTGATAGTTTAAGTAATAAAACGAACA
* * * *
47485 AAAATTGATAATTTAAGTACTAAAACAAACTAAAACTGATAGTTTAAGTACTAAA
1 AAAACTGATAATTTAAATACTAAAACAAACCAAAACTGATAGTTTAAGTAATAAA
47540 TACATAATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 50 1.00
ACGTcount: A:0.55, C:0.10, G:0.09, T:0.26
Consensus pattern (62 bp):
AAAACTGATAATTTAAATACTAAAACAAACCAAAACTGATAGTTTAAGTAATAAAACGAACA
Found at i:48260 original size:31 final size:31
Alignment explanation
Indices: 48217--48282 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
48207 GGAACCGATC
48217 ATACCAAAATAAAGGAATGTGTGCATGGAAT
1 ATACCAAAATAAAGGAATGTGTGCATGGAAT
* *
48248 ATACTAAAATAAAGGAGTGTGTGCATGGAAT
1 ATACCAAAATAAAGGAATGTGTGCATGGAAT
48279 -TACC
1 ATACC
48283 GGCGACGGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 3 0.09
31 29 0.91
ACGTcount: A:0.42, C:0.11, G:0.23, T:0.24
Consensus pattern (31 bp):
ATACCAAAATAAAGGAATGTGTGCATGGAAT
Found at i:50669 original size:29 final size:29
Alignment explanation
Indices: 50637--50705 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
50627 TTTAAGTAAT
50637 TAAAGTATTTCTTTGTCAAAATAAGTACC
1 TAAAGTATTTCTTTGTCAAAATAAGTACC
* * * **
50666 TAAAATTATTTTTTTGTTAAAATAAGTATT
1 T-AAAGTATTTCTTTGTCAAAATAAGTACC
50696 TAAAGTATTT
1 TAAAGTATTT
50706 AAATTTTTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 9 0.27
30 24 0.73
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.46
Consensus pattern (29 bp):
TAAAGTATTTCTTTGTCAAAATAAGTACC
Found at i:55609 original size:32 final size:33
Alignment explanation
Indices: 55547--55609 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
55537 AAGAAGAGAC
* *
55547 GAAAAAGGGGTAAATTACACCATGAGTCATTAG
1 GAAAAAGGGGTAAATTACACCATCAATCATTAG
55580 GAAAAA-GGGTAAATTACACCATCAATCATT
1 GAAAAAGGGGTAAATTACACCATCAATCATT
55610 TAACTTTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 22 0.79
33 6 0.21
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.22
Consensus pattern (33 bp):
GAAAAAGGGGTAAATTACACCATCAATCATTAG
Found at i:60596 original size:20 final size:20
Alignment explanation
Indices: 60571--60611 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
60561 GGGCGCGGCT
60571 TATCATAATAGCATCCGTCA
1 TATCATAATAGCATCCGTCA
60591 TATCATAATAGCATCCGTCA
1 TATCATAATAGCATCCGTCA
60611 T
1 T
60612 GTCTGCAACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.32
Consensus pattern (20 bp):
TATCATAATAGCATCCGTCA
Found at i:62189 original size:11 final size:11
Alignment explanation
Indices: 62175--62246 Score: 60
Period size: 11 Copynumber: 6.7 Consensus size: 11
62165 AATTTCAATA
62175 AATTTAATAAT
1 AATTTAATAAT
* *
62186 AATTTTATAAC
1 AATTTAATAAT
*
62197 AATTCAATAAT
1 AATTTAATAAT
*
62208 -ATTTAATGAT
1 AATTTAATAAT
62218 CAATTT-ATAAT
1 -AATTTAATAAT
* *
62229 AGTTTGATAA-
1 AATTTAATAAT
62239 AATTTAAT
1 AATTTAAT
62247 GATCATTTTG
Statistics
Matches: 47, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
10 18 0.38
11 25 0.53
12 4 0.09
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (11 bp):
AATTTAATAAT
Found at i:62225 original size:32 final size:31
Alignment explanation
Indices: 62172--62311 Score: 122
Period size: 32 Copynumber: 4.4 Consensus size: 31
62162 TAAAATTTCA
* *
62172 ATAAATTTAATAAT-AATTTTATAACAATTCA
1 ATAAATTTAATGATCAA-TTTATAACAATTCG
* * *
62203 ATAATATTTAATGATCAATTTATAATAGTTTG
1 ATAA-ATTTAATGATCAATTTATAACAATTCG
* * *
62235 ATAAAATTTAATGATCATTTTGTAATAATTCG
1 AT-AAATTTAATGATCAATTTATAACAATTCG
* * *
62267 ATAAAATCTAATCATC-ATCTTATAACAGTTCG
1 AT-AAATTTAATGATCAAT-TTATAACAATTCG
62299 ATAAATTTAATGA
1 ATAAATTTAATGA
62312 CTATTTTATA
Statistics
Matches: 88, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
31 14 0.16
32 70 0.80
33 4 0.05
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.41
Consensus pattern (31 bp):
ATAAATTTAATGATCAATTTATAACAATTCG
Found at i:62290 original size:64 final size:63
Alignment explanation
Indices: 62172--62323 Score: 173
Period size: 64 Copynumber: 2.4 Consensus size: 63
62162 TAAAATTTCA
* * * * * *
62172 ATAAATTTAATAATAATTTTATAACAATTCAATAATATTTAATGATCAATTTATAATAGTTTG
1 ATAAATTTAATGATAATTTTATAACAATTCAATAAAATCTAATCATCAATTTATAACAGTTCG
* * * *
62235 ATAAAATTTAATGATCATTTTGTAATAATTCGATAAAATCTAATCATC-ATCTTATAACAGTTCG
1 AT-AAATTTAATGATAATTTTATAACAATTCAATAAAATCTAATCATCAAT-TTATAACAGTTCG
62299 ATAAATTTAATGACT-ATTTTATAAC
1 ATAAATTTAATGA-TAATTTTATAAC
62324 TTTTGAAAGT
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
63 23 0.31
64 51 0.69
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.42
Consensus pattern (63 bp):
ATAAATTTAATGATAATTTTATAACAATTCAATAAAATCTAATCATCAATTTATAACAGTTCG
Found at i:63173 original size:3 final size:3
Alignment explanation
Indices: 63165--63190 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
63155 AAGGGTCAAC
63165 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
63191 TTAAATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:64766 original size:23 final size:22
Alignment explanation
Indices: 64740--64813 Score: 64
Period size: 23 Copynumber: 3.4 Consensus size: 22
64730 AAAATAAAAT
*
64740 TATTATAAATTATATTAATTATT
1 TATTA-AAATTATATTAATTATA
* **
64763 TATTAAAA-TA-A-GAACCATA
1 TATTAAAATTATATTAATTATA
*
64782 TATTATTAATTATATTAATTATA
1 TATTA-AAATTATATTAATTATA
64805 TATTAAAAT
1 TATTAAAAT
64814 AATAATATTA
Statistics
Matches: 38, Mismatches: 9, Indels: 9
0.68 0.16 0.16
Matches are distributed among these distances:
19 9 0.24
20 3 0.08
21 4 0.11
22 7 0.18
23 15 0.39
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (22 bp):
TATTAAAATTATATTAATTATA
Found at i:64769 original size:37 final size:37
Alignment explanation
Indices: 64728--64824 Score: 115
Period size: 42 Copynumber: 2.5 Consensus size: 37
64718 TTATATTTCT
*
64728 TTAAAATAAAATTATTATAAATTATATTAATTATTTA
1 TTAAAATAAAATTATTATAAATTATATTAATTATATA
*
64765 TTAAAATAAGAACCATATATTATTAATTATATTAATTATATA
1 TTAAAAT-A-AA--AT-TATTATAAATTATATTAATTATATA
64807 TTAAAATAATAA-TATTAT
1 TTAAAATAA-AATTATTAT
64825 TAAAACATTA
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
37 13 0.25
38 1 0.02
39 3 0.06
40 1 0.02
41 4 0.08
42 30 0.58
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (37 bp):
TTAAAATAAAATTATTATAAATTATATTAATTATATA
Found at i:64816 original size:16 final size:17
Alignment explanation
Indices: 64781--64829 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
64771 TAAGAACCAT
* *
64781 ATATTATTAATTATATTA
1 ATATTATTAA-AATAATA
64799 ATTATATATTAAAATAATA
1 A-TAT-TATTAAAATAATA
64818 ATATTATTAAAA
1 ATATTATTAAAA
64830 CATTAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 8 0.30
18 4 0.15
19 9 0.33
20 6 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATTATTAAAATAATA
Found at i:64854 original size:8 final size:8
Alignment explanation
Indices: 64804--64855 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
64794 TATTAATTAT
64804 ATATTAAA
1 ATATTAAA
*
64812 ATAATAATA
1 ATATTAA-A
*
64821 TTATTAAA
1 ATATTAAA
*
64829 ACATTAAA
1 ATATTAAA
*
64837 A-ATTATA
1 ATATTAAA
64844 ATATTAAA
1 ATATTAAA
64852 ATAT
1 ATAT
64856 GAATATTATA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
7 6 0.17
8 23 0.66
9 6 0.17
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATTAAA
Found at i:64987 original size:25 final size:25
Alignment explanation
Indices: 64959--65015 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
64949 TTGTATTACT
64959 AATT-TATTATATATTATTAAAATAA
1 AATTATATTATATA-TATTAAAATAA
* *
64984 AATTATATTATATATATTATAATAT
1 AATTATATTATATATATTAAAATAA
65009 AATTATA
1 AATTATA
65016 ACAATATAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 20 0.69
26 9 0.31
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
AATTATATTATATATATTAAAATAA
Found at i:65396 original size:19 final size:18
Alignment explanation
Indices: 65352--65402 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
65342 AAAAATAAAA
65352 AAATATT-TTAAAATTAT
1 AAATATTATTAAAATTAT
65369 AAATAATTATTAAAATTATT
1 AAAT-ATTATTAAAATTA-T
*
65389 CAATATTA-TAAAAT
1 AAATATTATTAAAAT
65403 AATTATTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 4 0.13
18 9 0.30
19 13 0.43
20 4 0.13
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATATTATTAAAATTAT
Found at i:65423 original size:30 final size:29
Alignment explanation
Indices: 65364--65423 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
65354 ATATTTTAAA
** *
65364 ATTATAAATAATTATTAAAATTATTCAAT
1 ATTATAAATAATTATTAAAAAAATACAAT
65393 ATTATAAAATAATTATTAAAAAAATACAAT
1 ATTAT-AAATAATTATTAAAAAAATACAAT
65423 A
1 A
65424 AATATAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 5 0.19
30 22 0.81
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (29 bp):
ATTATAAATAATTATTAAAAAAATACAAT
Found at i:67836 original size:31 final size:32
Alignment explanation
Indices: 67763--67846 Score: 125
Period size: 31 Copynumber: 2.7 Consensus size: 32
67753 GAAATTTAGT
* *
67763 TACTAGAATGAAACAAAAAGTTAACGGTATGG
1 TACTAAAATGAAACAAAAAGTTAACGGTAGGG
*
67795 TACTAAAATGAAACAAAAAGTTAAC-GTCGGG
1 TACTAAAATGAAACAAAAAGTTAACGGTAGGG
*
67826 TATTAAAATGAAACAAAAAGT
1 TACTAAAATGAAACAAAAAGT
67847 AAACATCAGG
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
31 24 0.50
32 24 0.50
ACGTcount: A:0.51, C:0.10, G:0.18, T:0.21
Consensus pattern (32 bp):
TACTAAAATGAAACAAAAAGTTAACGGTAGGG
Found at i:67859 original size:31 final size:31
Alignment explanation
Indices: 67769--67859 Score: 121
Period size: 31 Copynumber: 2.9 Consensus size: 31
67759 TAGTTACTAG
*
67769 AATGAAACAAAAAGTTAACGGT-ATGGTACTAA
1 AATGAAACAAAAAGTTAAC-GTCA-GGTATTAA
*
67801 AATGAAACAAAAAGTTAACGTCGGGTATTAA
1 AATGAAACAAAAAGTTAACGTCAGGTATTAA
* *
67832 AATGAAACAAAAAGTAAACATCAGGTAT
1 AATGAAACAAAAAGTTAACGTCAGGTAT
67860 GATTTTGAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
31 34 0.64
32 19 0.36
ACGTcount: A:0.52, C:0.10, G:0.18, T:0.21
Consensus pattern (31 bp):
AATGAAACAAAAAGTTAACGTCAGGTATTAA
Found at i:77069 original size:533 final size:533
Alignment explanation
Indices: 76063--77132 Score: 2131
Period size: 533 Copynumber: 2.0 Consensus size: 533
76053 AGATTGTAAC
76063 ATGGTTGCAAAAAAAAATATTATTTGTTTTTGTTATAGGGGGTTTCACGGGCATCTGTTTTCTCC
1 ATGGTTGCAAAAAAAAATATTATTTGTTTTTGTTATAGGGGGTTTCACGGGCATCTGTTTTCTCC
76128 ATATTCCACATGTGTTATTGGATGTCTTAATCTTCTTTTATATGGTAATGGTGCTTTGCTTATGA
66 ATATTCCACATGTGTTATTGGATGTCTTAATCTTCTTTTATATGGTAATGGTGCTTTGCTTATGA
76193 TTTCTTCTCATTTAACTTGTTTTCTTGGTATTTTTATTCGTCAGTCTAATTTTTATTTTCAGTGA
131 TTTCTTCTCATTTAACTTGTTTTCTTGGTATTTTTATTCGTCAGTCTAATTTTTATTTTCAGTGA
76258 ATTAAAATACCATTGTGAGTTTAAAAAGTCCCAACTCCCTTTACTGATATGTGCTTTATTGAATT
196 ATTAAAATACCATTGTGAGTTTAAAAAGTCCCAACTCCCTTTACTGATATGTGCTTTATTGAATT
76323 TTCTACTGCATTAGCTGCTGTTTAGTTATTTGAGTTTCGCCTTCCATATTTGATCACTTTTTAAC
261 TTCTACTGCATTAGCTGCTGTTTAGTTATTTGAGTTTCGCCTTCCATATTTGATCACTTTTTAAC
76388 TATAATATTACTTTAAAATGCAGTTAGAATGGTACTTGGGACATAAGTTATGATTTTGGAGTAGT
326 TATAATATTACTTTAAAATGCAGTTAGAATGGTACTTGGGACATAAGTTATGATTTTGGAGTAGT
76453 TGTGGAATTTACAAGTTCTAATTTCTGCTTACATTTGATTAAGAAACTTGGTGTTTCAATAGAGT
391 TGTGGAATTTACAAGTTCTAATTTCTGCTTACATTTGATTAAGAAACTTGGTGTTTCAATAGAGT
76518 ACTTGATGCCTTACATATATCAGTAATTACGTTTACATTTTTATGATAAAACGGGTAGGAGTTTC
456 ACTTGATGCCTTACATATATCAGTAATTACGTTTACATTTTTATGATAAAACGGGTAGGAGTTTC
76583 TGTTTCATAACTG
521 TGTTTCATAACTG
76596 ATGGTTGCAAAAAAAAATATTATTTGTTTTTGTTATAGGGGGTTTCACGGGCATCTGTTTTCTCC
1 ATGGTTGCAAAAAAAAATATTATTTGTTTTTGTTATAGGGGGTTTCACGGGCATCTGTTTTCTCC
76661 ATATTCCACATGTGTTATTGGATGTCTTAATCTTCTTTTATATGGTAATGGTGCTTTGCTTATGA
66 ATATTCCACATGTGTTATTGGATGTCTTAATCTTCTTTTATATGGTAATGGTGCTTTGCTTATGA
76726 TTTCTTCTCATTTAACTTGTTTTCTTGGTATTTTTATTCGTCAGTCTAATTTTTATTTTCAGTGA
131 TTTCTTCTCATTTAACTTGTTTTCTTGGTATTTTTATTCGTCAGTCTAATTTTTATTTTCAGTGA
76791 ATTAAAATACCATTGTGAGTTTAAAAAGTCCCAACTCCCTTTACTGATATGTGCTTTATTGAATT
196 ATTAAAATACCATTGTGAGTTTAAAAAGTCCCAACTCCCTTTACTGATATGTGCTTTATTGAATT
76856 TTCTACTGCATTAGCTGCTGTTTAGTTATTTGAGTTTCGCCTTCCATATTTGATCACTTTTTAAC
261 TTCTACTGCATTAGCTGCTGTTTAGTTATTTGAGTTTCGCCTTCCATATTTGATCACTTTTTAAC
76921 TATAATATTACTTTAAAATGCAGTTAGAATGGTACTTGGGACATAAGTTATGATTTTGGAGTAGT
326 TATAATATTACTTTAAAATGCAGTTAGAATGGTACTTGGGACATAAGTTATGATTTTGGAGTAGT
76986 TGTGGAATTTACAAGTTCTAATTTCTGCTTACATTTGATTAAGAAACTTGGTGTTTCAATAGAGT
391 TGTGGAATTTACAAGTTCTAATTTCTGCTTACATTTGATTAAGAAACTTGGTGTTTCAATAGAGT
77051 ACTTGATGCCTTACATATATCAGTAATTACGTTTACATTTTTATGATAAAACGGGTAGGAGTTTC
456 ACTTGATGCCTTACATATATCAGTAATTACGTTTACATTTTTATGATAAAACGGGTAGGAGTTTC
*
77116 TGTTTCATATCTG
521 TGTTTCATAACTG
77129 ATGG
1 ATGG
77133 ATTTTAGAAG
Statistics
Matches: 536, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
533 536 1.00
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.44
Consensus pattern (533 bp):
ATGGTTGCAAAAAAAAATATTATTTGTTTTTGTTATAGGGGGTTTCACGGGCATCTGTTTTCTCC
ATATTCCACATGTGTTATTGGATGTCTTAATCTTCTTTTATATGGTAATGGTGCTTTGCTTATGA
TTTCTTCTCATTTAACTTGTTTTCTTGGTATTTTTATTCGTCAGTCTAATTTTTATTTTCAGTGA
ATTAAAATACCATTGTGAGTTTAAAAAGTCCCAACTCCCTTTACTGATATGTGCTTTATTGAATT
TTCTACTGCATTAGCTGCTGTTTAGTTATTTGAGTTTCGCCTTCCATATTTGATCACTTTTTAAC
TATAATATTACTTTAAAATGCAGTTAGAATGGTACTTGGGACATAAGTTATGATTTTGGAGTAGT
TGTGGAATTTACAAGTTCTAATTTCTGCTTACATTTGATTAAGAAACTTGGTGTTTCAATAGAGT
ACTTGATGCCTTACATATATCAGTAATTACGTTTACATTTTTATGATAAAACGGGTAGGAGTTTC
TGTTTCATAACTG
Found at i:78875 original size:297 final size:297
Alignment explanation
Indices: 78340--78938 Score: 1135
Period size: 297 Copynumber: 2.0 Consensus size: 297
78330 AACAGTGGGG
78340 TATGTATGAATGAACATGTATTCTGCTCCGGGATATCTTATTTCTTTCATTATGAATGACTTAAG
1 TATGTATGAATGAACATGTATTCTGCTCCGGGATATCTTATTTCTTTCATTATGAATGACTTAAG
*
78405 GTGTTTCTTTGTAATTCTGTTGCAGAGACTGCTGATAGGCTTTTTGTGAGATAAATGTTTCTTTA
66 GCGTTTCTTTGTAATTCTGTTGCAGAGACTGCTGATAGGCTTTTTGTGAGATAAATGTTTCTTTA
*
78470 CCTCCCAATGTTGTCTATAAAAAGGTCCATCTACGGCGTAGTTAAAGTAAAAAGGAGAAAGAATG
131 CCTCCAAATGTTGTCTATAAAAAGGTCCATCTACGGCGTAGTTAAAGTAAAAAGGAGAAAGAATG
78535 TACTCAGGGTTGGACCCTGACTGATGAACCACTCAAAAAACTCTGCCAAAAAACCATGCAAGTAA
196 TACTCAGGGTTGGACCCTGACTGATGAACCACTCAAAAAACTCTGCCAAAAAACCATGCAAGTAA
78600 GAACCAATTACTCTTTTCTTGTATACCATTTGTCACA
261 GAACCAATTACTCTTTTCTTGTATACCATTTGTCACA
78637 TATGTATGAATGAACATGTATTCTGCTCCGGGATATCTTATTTCTTTCATTATGAATGACTTAAG
1 TATGTATGAATGAACATGTATTCTGCTCCGGGATATCTTATTTCTTTCATTATGAATGACTTAAG
* *
78702 GCGTTTCTTTGTAATTCTGTTGCAGGGACTGCTGATAGGTTTTTTGTGAGATAAATGTTTCTTTA
66 GCGTTTCTTTGTAATTCTGTTGCAGAGACTGCTGATAGGCTTTTTGTGAGATAAATGTTTCTTTA
78767 CCTCCAAATGTTGTCTATAAAAAGGTCCATCTACGGCGTAGTTAAAGTAAAAAGGAGAAAGAATG
131 CCTCCAAATGTTGTCTATAAAAAGGTCCATCTACGGCGTAGTTAAAGTAAAAAGGAGAAAGAATG
* * *
78832 TACTCATGGTTGGACCCTGACTGATGAACCACTCGACAAACTCTGCCAAAAAACCATGCAAGTAA
196 TACTCAGGGTTGGACCCTGACTGATGAACCACTCAAAAAACTCTGCCAAAAAACCATGCAAGTAA
78897 GAACCAATTACTCTTTTCTTGTATACCATTTGTCACA
261 GAACCAATTACTCTTTTCTTGTATACCATTTGTCACA
78934 TATGT
1 TATGT
78939 CACTGGATTT
Statistics
Matches: 295, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
297 295 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (297 bp):
TATGTATGAATGAACATGTATTCTGCTCCGGGATATCTTATTTCTTTCATTATGAATGACTTAAG
GCGTTTCTTTGTAATTCTGTTGCAGAGACTGCTGATAGGCTTTTTGTGAGATAAATGTTTCTTTA
CCTCCAAATGTTGTCTATAAAAAGGTCCATCTACGGCGTAGTTAAAGTAAAAAGGAGAAAGAATG
TACTCAGGGTTGGACCCTGACTGATGAACCACTCAAAAAACTCTGCCAAAAAACCATGCAAGTAA
GAACCAATTACTCTTTTCTTGTATACCATTTGTCACA
Found at i:79676 original size:172 final size:172
Alignment explanation
Indices: 79390--79734 Score: 681
Period size: 172 Copynumber: 2.0 Consensus size: 172
79380 GCAAAGACAG
*
79390 TTTGAGTTTTCATGTAAGGAAACCTCCTTTACATATCAAGTATTGAACAACTTTGTGGGAAAATG
1 TTTGAGTTTTCATGTAAAGAAACCTCCTTTACATATCAAGTATTGAACAACTTTGTGGGAAAATG
79455 TCCACATAAGTTGAGTCATTCACTGTTACTTTCTAGACCACAATATTTTCTTTGAACTAATTTCC
66 TCCACATAAGTTGAGTCATTCACTGTTACTTTCTAGACCACAATATTTTCTTTGAACTAATTTCC
79520 TAATTTACCTTCTGAGGACAATGCATGGCATGCGGACCACAT
131 TAATTTACCTTCTGAGGACAATGCATGGCATGCGGACCACAT
79562 TTTGAGTTTTCATGTAAAGAAACCTCCTTTACATATCAAGTATTGAACAACTTTGTGGGAAAATG
1 TTTGAGTTTTCATGTAAAGAAACCTCCTTTACATATCAAGTATTGAACAACTTTGTGGGAAAATG
79627 TCCACATAAGTTGAGTCATTCACTGTTACTTTCTAGACCACAATATTTTCTTTGAACTAATTTCC
66 TCCACATAAGTTGAGTCATTCACTGTTACTTTCTAGACCACAATATTTTCTTTGAACTAATTTCC
79692 TAATTTACCTTCTGAGGACAATGCATGGCATGCGGACCACAT
131 TAATTTACCTTCTGAGGACAATGCATGGCATGCGGACCACAT
79734 T
1 T
79735 GTCCCTATTT
Statistics
Matches: 172, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
172 172 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (172 bp):
TTTGAGTTTTCATGTAAAGAAACCTCCTTTACATATCAAGTATTGAACAACTTTGTGGGAAAATG
TCCACATAAGTTGAGTCATTCACTGTTACTTTCTAGACCACAATATTTTCTTTGAACTAATTTCC
TAATTTACCTTCTGAGGACAATGCATGGCATGCGGACCACAT
Found at i:80850 original size:235 final size:234
Alignment explanation
Indices: 80437--80911 Score: 916
Period size: 235 Copynumber: 2.0 Consensus size: 234
80427 TTGAATCATC
80437 ATTTTTTCCAGTGTGAAAGCTATCATCTCTAAATATTTGACCTTTTCATGTGCTCTAGTTGCAGA
1 ATTTTTTCCAGTGTGAAAGCTATCATCTCTAAATATTTGACCTTTTCATGTGCTCTAGTTGCAGA
80502 TTGCTGCAGGACTAAGCAAAAGGCAGTTAGCAAGGGACCAATTGAACTTGATTCTGAATTAACGA
66 TTGCTGCAGGACTAAGCAAAAGGCAGTTAGCAAGGGACCAATTGAACTTGATTCTGAATTAACGA
80567 AACTGAAATGTGAGTTGTTACTGTTATTTTTTTCATATTTTTAATGATTTGCATAAAATTTTAGA
131 AACTGAAATGTGAGTTGTTACTGTTATTTTTTTCATATTTTTAATGATTTGCATAAAATTTTAGA
80632 ATGTTATTGACTTGAGTTGGTTTATGGGTGCCTTTCCAA
196 ATGTTATTGACTTGAGTTGGTTTATGGGTGCCTTTCCAA
80671 ATATTTTTCCAGTGTGAAAGCTATCATCTCTAAATATTTGACCTTTTCATGTGCTCTAGTTGCAG
1 AT-TTTTTCCAGTGTGAAAGCTATCATCTCTAAATATTTGACCTTTTCATGTGCTCTAGTTGCAG
80736 ATTGCTGCAGGACTAAGCAAAAGGCAGTTAGCAAGGGACCAATTGAACTTGATTCTGAATTAAC-
65 ATTGCTGCAGGACTAAGCAAAAGGCAGTTAGCAAGGGACCAATTGAACTTGATTCTGAATTAACG
*
80800 AGAACTGCAATGTGAGTTGTTACTGTTATTTTTTTCATATTTTTAATGATTTGCATAAAATTTTA
130 A-AACTGAAATGTGAGTTGTTACTGTTATTTTTTTCATATTTTTAATGATTTGCATAAAATTTTA
80865 GAATGTTATTGACTTGAGTTGGTTTATGGGTGCCTTTCCAA
194 GAATGTTATTGACTTGAGTTGGTTTATGGGTGCCTTTCCAA
80906 ATTTTT
1 ATTTTT
80912 CATGCCTTTT
Statistics
Matches: 238, Mismatches: 1, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
234 7 0.03
235 231 0.97
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (234 bp):
ATTTTTTCCAGTGTGAAAGCTATCATCTCTAAATATTTGACCTTTTCATGTGCTCTAGTTGCAGA
TTGCTGCAGGACTAAGCAAAAGGCAGTTAGCAAGGGACCAATTGAACTTGATTCTGAATTAACGA
AACTGAAATGTGAGTTGTTACTGTTATTTTTTTCATATTTTTAATGATTTGCATAAAATTTTAGA
ATGTTATTGACTTGAGTTGGTTTATGGGTGCCTTTCCAA
Found at i:89318 original size:303 final size:297
Alignment explanation
Indices: 88887--89615 Score: 1031
Period size: 303 Copynumber: 2.4 Consensus size: 297
88877 TTTCCATATT
88887 TTTCATGCCTTTTCATGGTTTAGGTCTTTAGTCCCGTATCTATGGTTCATTGTATTAGATAT-AA
1 TTTCATGCCTTTTCATGGTTTAGGTCTTTAGTCCCGTATCTATGGTTCATTGTATTAGATATAAA
* *
88951 ---CGAATCATCATCTTCTCCAGTGTGAAAGCTATCATCTCTAAATATCTGACCTTTTCATGTGC
66 TGTTGAATCATCATCTTCTCCAGTGTGAAAGCTATCATCTCTAAATATTTGACCTTTTCATGTGC
** *
89013 TCTAGTTGCAGATTGCTGCAGGACTAAGCAAAAGGCAGTTAGTAAGGGACCAATTGAACTTGATT
131 TCTAGTTGCAGATTGCTGCAGGACTAAGCAAAAGGCAGTTAACAAAGGACCAATTGAACTTGATT
* *
89078 CTTAATTAACAGAACTGCAATGTGAGTTGTTACTGTTATTTTTTTTCTTCATATTTTTAATGATT
196 ATGAATTAACAGAACTGCAATGTGAGTTGTTACTGTTA-----TTT-TTCATATTTTTAATGATT
89143 TGCATAAAATTTTAGAATGTTATTGACTTGAGTTGGTTTAT-G-G-
255 TGCAT-AAA--TTAGAATGTTATTGACTTGAGTTGGTTTATGGTGC
* *
89186 TTTCATGCCTTTTAATGGTTTTGGTCTTTAGTCCCGTATCTATGGTTCATTGTATTAGATATAAA
1 TTTCATGCCTTTTCATGGTTTAGGTCTTTAGTCCCGTATCTATGGTTCATTGTATTAGATATAAA
*
89251 TGTTGAATCATCATCTTCTCCAGTGTGAAAGCTATCATCTATAAATATTTGACCTTTTCATGTGC
66 TGTTGAATCATCATCTTCTCCAGTGTGAAAGCTATCATCTCTAAATATTTGACCTTTTCATGTGC
* *
89316 TCTAGTTGCAGATTGCTGCAGGACTAAGCGAAAGGCAGTTAACAAAGGACCAATTGAACTTGTTT
131 TCTAGTTGCAGATTGCTGCAGGACTAAGCAAAAGGCAGTTAACAAAGGACCAATTGAACTTGATT
*
89381 ATGAATTAACAGAACTGCAATGTGGGTTGTTACTGTTATTTTTCATATTTTTAATGATTTGCATA
196 ATGAATTAACAGAACTGCAATGTGAGTTGTTACTGTTATTTTTCATATTTTTAATGATTTGCATA
*
89446 AATTAGAATGTTATTGACTTTAGTTGGTTTATGGGTTCATGCC
261 AATTAGAATGTTATTGACTTGAGTTGGTTTAT-GG----TG-C
89489 TTTCCATAATTTTAATGCCTTTTCATGGTTTAGGTCTTTAGTCCCGTATCTATGGTTCATTGTAT
1 TTT-C---------ATGCCTTTTCATGGTTTAGGTCTTTAGTCCCGTATCTATGGTTCATTGTAT
* **
89554 TAGATATAAATGTTGAATCATCATTTTCTCCAGTGTGAAAGCTATTTTCTCTAAATATTTGA
56 TAGATATAAATGTTGAATCATCATCTTCTCCAGTGTGAAAGCTATCATCTCTAAATATTTGA
89616 TCTTCGAGCC
Statistics
Matches: 387, Mismatches: 20, Indels: 32
0.88 0.05 0.07
Matches are distributed among these distances:
294 29 0.07
296 4 0.01
297 23 0.06
298 3 0.01
299 60 0.16
300 2 0.01
301 1 0.00
303 157 0.41
304 1 0.00
313 107 0.28
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (297 bp):
TTTCATGCCTTTTCATGGTTTAGGTCTTTAGTCCCGTATCTATGGTTCATTGTATTAGATATAAA
TGTTGAATCATCATCTTCTCCAGTGTGAAAGCTATCATCTCTAAATATTTGACCTTTTCATGTGC
TCTAGTTGCAGATTGCTGCAGGACTAAGCAAAAGGCAGTTAACAAAGGACCAATTGAACTTGATT
ATGAATTAACAGAACTGCAATGTGAGTTGTTACTGTTATTTTTCATATTTTTAATGATTTGCATA
AATTAGAATGTTATTGACTTGAGTTGGTTTATGGTGC
Found at i:92197 original size:11 final size:11
Alignment explanation
Indices: 92173--92217 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
92163 TTGGTGCTGG
92173 AAACAAGATAA
1 AAACAAGATAA
* *
92184 AAATAAGATTA
1 AAACAAGATAA
92195 AAACAAGATAA
1 AAACAAGATAA
92206 AGAA-AAGATAA
1 A-AACAAGATAA
92217 A
1 A
92218 TGATTGCAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:92201 original size:22 final size:22
Alignment explanation
Indices: 92173--92214 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
92163 TTGGTGCTGG
92173 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
92195 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
92215 AAATGATTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:96921 original size:30 final size:30
Alignment explanation
Indices: 96885--96945 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
96875 CGGATTTTCA
96885 AAAAAATGACTAG-AAATATTATTAGGCGCT
1 AAAAAATGAC-AGAAAATATTATTAGGCGCT
*
96915 AAAAAATGACCGAAAATATTATTAGGCGCT
1 AAAAAATGACAGAAAATATTATTAGGCGCT
96945 A
1 A
96946 CTAGTTTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 1 0.03
30 28 0.97
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (30 bp):
AAAAAATGACAGAAAATATTATTAGGCGCT
Found at i:99239 original size:20 final size:20
Alignment explanation
Indices: 99203--99241 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
99193 AAGCTCTCTC
**
99203 CTATACCTCTCTTAAAGACA
1 CTATACCTCTCCCAAAGACA
99223 CTATACCTCTCCCAAAGAC
1 CTATACCTCTCCCAAAGAC
99242 CACCCTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.36, G:0.05, T:0.26
Consensus pattern (20 bp):
CTATACCTCTCCCAAAGACA
Found at i:102258 original size:2 final size:2
Alignment explanation
Indices: 102253--102335 Score: 138
Period size: 2 Copynumber: 43.5 Consensus size: 2
102243 TTTTATTATT
102253 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
102293 TA TA TA TA T- TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
102333 TA T
1 TA T
102336 GAAGGGGTAT
Statistics
Matches: 77, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
1 4 0.05
2 73 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:103492 original size:27 final size:27
Alignment explanation
Indices: 103431--103496 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
103421 GAAACATTAT
* *
103431 TATTTCTACCGGTTTTATTATTATTGGG
1 TATTT-TACCGGTTTCATTATTATTGGA
* * *
103459 CACTTTACCGGTTTCGTTATTATTGGA
1 TATTTTACCGGTTTCATTATTATTGGA
103486 TATTTTACCGG
1 TATTTTACCGG
103497 ATATTTTGTT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
27 28 0.90
28 3 0.10
ACGTcount: A:0.18, C:0.15, G:0.18, T:0.48
Consensus pattern (27 bp):
TATTTTACCGGTTTCATTATTATTGGA
Found at i:105914 original size:20 final size:20
Alignment explanation
Indices: 105889--105935 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
105879 AGTCATTTCG
105889 GTATCGATACTGAAGAGTGA
1 GTATCGATACTGAAGAGTGA
*
105909 GTATCGATACTGAAGAGTGG
1 GTATCGATACTGAAGAGTGA
105929 GTATCGA
1 GTATCGA
105936 CTGTAAGGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.32, C:0.11, G:0.32, T:0.26
Consensus pattern (20 bp):
GTATCGATACTGAAGAGTGA
Done.