Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001345.1 Hibiscus syriacus cultivar Beakdansim tig00002623_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: 74002
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1485 original size:25 final size:26
Alignment explanation
Indices: 1449--1507 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
1439 ATAAACCCTT
*
1449 AAAATTGTATAACTTCGTCTCTA-AC
1 AAAATTTTATAACTTCGTCTCTACAC
* * *
1474 ATAATTTTATAAGTTCGTTTCTACAC
1 AAAATTTTATAACTTCGTCTCTACAC
1500 AAAATTTT
1 AAAATTTT
1508 GCGTATATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 19 0.68
26 9 0.32
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.42
Consensus pattern (26 bp):
AAAATTTTATAACTTCGTCTCTACAC
Found at i:2954 original size:15 final size:15
Alignment explanation
Indices: 2934--2975 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2924 TTTAAGGACT
2934 AAATTAAAAAACATG
1 AAATTAAAAAACATG
*
2949 AAATT-ATAAAC-TG
1 AAATTAAAAAACATG
2962 AAATTAAACAAACA
1 AAATTAAA-AAACA
2976 GAGATCAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
13 7 0.32
14 6 0.27
15 9 0.41
ACGTcount: A:0.64, C:0.10, G:0.05, T:0.21
Consensus pattern (15 bp):
AAATTAAAAAACATG
Found at i:3101 original size:12 final size:12
Alignment explanation
Indices: 3084--3128 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
3074 TGGATATTAT
3084 TAATTTATGATA
1 TAATTTATGATA
*
3096 TAATTTATG-TT
1 TAATTTATGATA
3107 TGAAGTTTATGATA
1 T-AA-TTTATGATA
3121 TAATTTAT
1 TAATTTAT
3129 ATGATACATG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 2 0.07
12 16 0.57
13 8 0.29
14 2 0.07
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (12 bp):
TAATTTATGATA
Found at i:3208 original size:42 final size:42
Alignment explanation
Indices: 3129--3209 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
3119 TATAATTTAT
* * **
3129 ATGATACATGCATTAATAAATTATACATACATTTACATATAC
1 ATGATACATACATTAATAAATTATAAATACACATACATATAC
*
3171 ATGATACATACATTAAT-AATTATAAATTATACATACATA
1 ATGATACATACATTAATAAATTATAAA-TACACATACATA
3210 CGTACATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
41 8 0.24
42 25 0.76
ACGTcount: A:0.48, C:0.12, G:0.04, T:0.36
Consensus pattern (42 bp):
ATGATACATACATTAATAAATTATAAATACACATACATATAC
Found at i:3379 original size:19 final size:19
Alignment explanation
Indices: 3346--3395 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 19
3336 ATATATATAT
3346 ATTATATATTAAAATT-TTAA
1 ATTA-ATATTAAAATTATT-A
*
3366 ATTAATATTTAAATTATTA
1 ATTAATATTAAAATTATTA
3385 ATTAATTATTA
1 ATTAA-TATTA
3396 CATCATAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTAATATTAAAATTATTA
Found at i:3629 original size:27 final size:28
Alignment explanation
Indices: 3598--3659 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 28
3588 TAAATACATC
*
3598 ATTAATA-AAATTAATTTAATGATCATA
1 ATTAATATAAATTAATATAATGATCATA
** *
3625 ATTAA-ATTTATTAATATAATTATCATA
1 ATTAATATAAATTAATATAATGATCATA
3652 ATTAATAT
1 ATTAATAT
3660 GGAAAGTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 1 0.03
27 26 0.90
28 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (28 bp):
ATTAATATAAATTAATATAATGATCATA
Found at i:3643 original size:18 final size:18
Alignment explanation
Indices: 3598--3646 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
3588 TAAATACATC
*
3598 ATTAATAAAATT-AATTT
1 ATTAATATAATTAAATTT
* *
3615 AATGATCATAATTAAATTT
1 ATTAAT-ATAATTAAATTT
3634 ATTAATATAATTA
1 ATTAATATAATTA
3647 TCATAATTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 4 0.16
18 12 0.48
19 9 0.36
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAATATAATTAAATTT
Found at i:3687 original size:64 final size:63
Alignment explanation
Indices: 3603--3722 Score: 161
Period size: 64 Copynumber: 1.9 Consensus size: 63
3593 ACATCATTAA
* *
3603 TAAAATTAATTTAATGATCATAATTAAATTTATTAATATAAT-TATCATAATTAATATGGAAAG
1 TAAAATTAATCTAATAATCATAATTAAATTTATTAATATAATAT-TCATAATTAATATGGAAAG
* * * *
3666 TAAATATTAATCTAATAATCATAGTTAAGTTTATTAATCTAATATTCATACTTAATA
1 TAAA-ATTAATCTAATAATCATAATTAAATTTATTAATATAATATTCATAATTAATA
3723 ATTTGTTCTA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
63 4 0.08
64 44 0.90
65 1 0.02
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (63 bp):
TAAAATTAATCTAATAATCATAATTAAATTTATTAATATAATATTCATAATTAATATGGAAAG
Found at i:5045 original size:14 final size:13
Alignment explanation
Indices: 5024--5050 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5014 TTTTTTTTCT
5024 TTTGAAAAATTAC
1 TTTGAAAAATTAC
5037 TTTGAAAAATTAC
1 TTTGAAAAATTAC
5050 T
1 T
5051 CCTCCTTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (13 bp):
TTTGAAAAATTAC
Found at i:13363 original size:13 final size:13
Alignment explanation
Indices: 13345--13369 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13335 TCGAATATAA
13345 AATCTTAAAATTT
1 AATCTTAAAATTT
13358 AATCTTAAAATT
1 AATCTTAAAATT
13370 CATTAACACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
AATCTTAAAATTT
Found at i:16549 original size:2 final size:2
Alignment explanation
Indices: 16544--16575 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
16534 TGTTTGTTCT
16544 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
16576 AATACATTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19658 original size:755 final size:756
Alignment explanation
Indices: 18290--19806 Score: 2874
Period size: 755 Copynumber: 2.0 Consensus size: 756
18280 AAGAAATACA
18290 CATTTTAGCTTTTATCCCACATTGACAAGAAACATAACCTAAACACTTCAATATGCACATATAAG
1 CATTTTAGCTTTTATCCCACATTGACAAGAAACATAACCTAAACACTTCAATATGCACATATAAG
18355 CTAATTCCATTAAGCTCTTCAAAGCATGGAATTAATATGTATTAAATTACAATGTTAGACCCTAT
66 CTAATTCCATTAAGCTCTTCAAAGCATGGAATTAATATGTATTAAATTACAATGTTAGACCCTAT
* *
18420 AGTTTTATTTTTTTTTATTTTAAAATGCTAAGGCGCAGATGGTGATCTGCGCCTGTCCTTACGTG
131 AGTTTTA-TTGTTTTAATTTTAAAATGCTAAGGCGCAGATGGTGATCTGCGCCTGTCCTTACGTG
* *
18485 GCACCAGCTCGGATAAGGCGCGGATGACCATTCACGCCTTTCATGATGTGGCGCCAGTTCGGGCA
195 GCACCAGCTCGGATAAGACGCGGATGACCATTCACGCCTTTCATGATGTGGCGCCAGCTCGGGCA
*
18550 AAGGCGTGAATGACGATCCGCGCCTTGTTAGAAAGGGTGCTAGATCGGTAAAATTTGACAAAACG
260 AAGGCGTGAATGAAGATCCGCGCCTTGTTAGAAAGGGTGCTAGATCGGTAAAATTTGACAAAACG
18615 GTGTCTGATATGTAATTATTTCATGTCAGAGTGATTTTTGGGTAAAAATGCCAATATCAAGGCAA
325 GTGTCTGATATGTAATTATTTCATGTCAGAGTGATTTTTGGGTAAAAATGCCAATATCAAGGCAA
18680 TTTAATGGTTCAAATCAGACTAGATCGAGTCCAGGTTAACTCAGATTCGAGTTATTTTTAGGTTG
390 TTTAATGGTTCAAATCAGACTAGATCGAGTCCAGGTTAACTCAGATTCGAGTTATTTTTAGGTTG
18745 ATTTTAAATCAGATTCAGTTTGAGTTCGGATCGACTTAATTACAAGTCAGATCAATATTTGTTTA
455 ATTTTAAATCAGATTCAGTTTGAGTTCGGATCGACTTAATTACAAGTCAGATCAATATTTGTTTA
* *
18810 GGTTGAAATGGTTCGGGTTTGAATAAGTTAAATATCATGTTAATTTAGGTTCAGATGGACTTTGA
520 GGTTAAAATGGTTCGGGTTTGAATAAGTTAAATATCATGTTAATTTAGGTTCAGATGGACTTCGA
18875 GTCGAGTCCTGTTCAAATCGAGTCATATCATTGACGAATACAATTTAGGTTAGGTAATATCGGTT
585 GTCGAGTCCTGTTCAAATCGAGTCATATCATTGACGAATACAATTTAGGTTAGGTAATATCGGTT
18940 TCAGGTAAACTTCAAGTCGGGTCTTACTTAATACAAATAGACTTTTGGTTGGATCATTTTCGGGT
650 TCAGGTAAACTTCAAGTCGGGTCTTACTTAATACAAATAGACTTTTGGTTGGATCATTTTCGGGT
19005 GAATTATTTTCCACCTTTCACGAACGTTTAATGCCTTTGTAG
715 GAATTATTTTCCACCTTTCACGAACGTTTAATGCCTTTGTAG
19047 CATTTTAGCTTTTATCCCACATTGACAAGAAACATAACCTAAACACTTCAATATGCACATATAAG
1 CATTTTAGCTTTTATCCCACATTGACAAGAAACATAACCTAAACACTTCAATATGCACATATAAG
*
19112 CTAATTCCATTAAGCTCTTCAAATCATGGAATTAATATGTATTAAATTACAATGTTAGACCCTAT
66 CTAATTCCATTAAGCTCTTCAAAGCATGGAATTAATATGTATTAAATTACAATGTTAGACCCTAT
19177 AGTTTTA-TGTTTTAATTTTAAAATGCTAAGGCGCAGATGGTGATCTGCGCCTGTCCTTACGTGG
131 AGTTTTATTGTTTTAATTTTAAAATGCTAAGGCGCAGATGGTGATCTGCGCCTGTCCTTACGTGG
* *
19241 CACCAGCTCGGATAAGACGCGGATGACCATTCATGTCTTTCATGATGTGGCGCCAGCTCGGGCAA
196 CACCAGCTCGGATAAGACGCGGATGACCATTCACGCCTTTCATGATGTGGCGCCAGCTCGGGCAA
19306 AGGCGTGAATGAAGATCCGCGCCTTGTTAGAAAGGGTGCTAGATCGGTAAAATTTGACAAAACGG
261 AGGCGTGAATGAAGATCCGCGCCTTGTTAGAAAGGGTGCTAGATCGGTAAAATTTGACAAAACGG
*
19371 TGTCTGATATGTAATTATTTCATGTCAGAGTGATTTTTGGGTAAAAATGCCAATATGAAGGCAAT
326 TGTCTGATATGTAATTATTTCATGTCAGAGTGATTTTTGGGTAAAAATGCCAATATCAAGGCAAT
* * *
19436 TTAATGGTTCAAATTAGACTAGATCGAGTCTAGGTTGACTCAGATTCGAGTTATTTTTAGGTTGA
391 TTAATGGTTCAAATCAGACTAGATCGAGTCCAGGTTAACTCAGATTCGAGTTATTTTTAGGTTGA
19501 TTTTAAATCAGATTCAGTTTGAGTTCGGATCGACTTAATTACAAGTCAGATCAATATTTGTTTAG
456 TTTTAAATCAGATTCAGTTTGAGTTCGGATCGACTTAATTACAAGTCAGATCAATATTTGTTTAG
*
19566 GTTAAAATGGTTCGGGTTTGAATAAGTTAAATATCATGTTAATTTAGGTTCATATGGACTTCGAG
521 GTTAAAATGGTTCGGGTTTGAATAAGTTAAATATCATGTTAATTTAGGTTCAGATGGACTTCGAG
*
19631 TCGAGTCCTGTTCAAATCGAGTCATATCATTGACGAATACAATTTAGGTTAGGTAATATTGGTTT
586 TCGAGTCCTGTTCAAATCGAGTCATATCATTGACGAATACAATTTAGGTTAGGTAATATCGGTTT
19696 CAGGTAAACTTCAAGTCGGGTCTTACTTAATACAAATAGACTTTTGGTTGGATCATTTTCGGGTG
651 CAGGTAAACTTCAAGTCGGGTCTTACTTAATACAAATAGACTTTTGGTTGGATCATTTTCGGGTG
19761 AATTATTTTCCACCTTTCACGAACGTTTAATGCCTTTGTAG
716 AATTATTTTCCACCTTTCACGAACGTTTAATGCCTTTGTAG
19802 CATTT
1 CATTT
19807 CCATGACTTC
Statistics
Matches: 744, Mismatches: 16, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
755 608 0.82
757 136 0.18
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (756 bp):
CATTTTAGCTTTTATCCCACATTGACAAGAAACATAACCTAAACACTTCAATATGCACATATAAG
CTAATTCCATTAAGCTCTTCAAAGCATGGAATTAATATGTATTAAATTACAATGTTAGACCCTAT
AGTTTTATTGTTTTAATTTTAAAATGCTAAGGCGCAGATGGTGATCTGCGCCTGTCCTTACGTGG
CACCAGCTCGGATAAGACGCGGATGACCATTCACGCCTTTCATGATGTGGCGCCAGCTCGGGCAA
AGGCGTGAATGAAGATCCGCGCCTTGTTAGAAAGGGTGCTAGATCGGTAAAATTTGACAAAACGG
TGTCTGATATGTAATTATTTCATGTCAGAGTGATTTTTGGGTAAAAATGCCAATATCAAGGCAAT
TTAATGGTTCAAATCAGACTAGATCGAGTCCAGGTTAACTCAGATTCGAGTTATTTTTAGGTTGA
TTTTAAATCAGATTCAGTTTGAGTTCGGATCGACTTAATTACAAGTCAGATCAATATTTGTTTAG
GTTAAAATGGTTCGGGTTTGAATAAGTTAAATATCATGTTAATTTAGGTTCAGATGGACTTCGAG
TCGAGTCCTGTTCAAATCGAGTCATATCATTGACGAATACAATTTAGGTTAGGTAATATCGGTTT
CAGGTAAACTTCAAGTCGGGTCTTACTTAATACAAATAGACTTTTGGTTGGATCATTTTCGGGTG
AATTATTTTCCACCTTTCACGAACGTTTAATGCCTTTGTAG
Found at i:26432 original size:23 final size:21
Alignment explanation
Indices: 26380--26441 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
26370 TTTTGGTGCA
*
26380 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
26400 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
26421 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
26442 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:26449 original size:21 final size:21
Alignment explanation
Indices: 26423--26462 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
26413 CCCCCTTTGA
*
26423 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
26444 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
26463 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:28712 original size:16 final size:16
Alignment explanation
Indices: 28691--28726 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
28681 TTTTAAATGA
*
28691 TAAATGGGAGAAGTGT
1 TAAATGGGAGAAGTAT
28707 TAAATGGGAGAAGTAT
1 TAAATGGGAGAAGTAT
28723 TAAA
1 TAAA
28727 GTAAGGGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.31, T:0.25
Consensus pattern (16 bp):
TAAATGGGAGAAGTAT
Found at i:29262 original size:21 final size:20
Alignment explanation
Indices: 29215--29261 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
29205 TAGGGAACCA
29215 ATTCCCCATAGGGGGTACCG
1 ATTCCCCATAGGGGGTACCG
29235 ATTCCCCATAGGGGGTACCG
1 ATTCCCCATAGGGGGTACCG
29255 ATTCCCC
1 ATTCCCC
29262 CCACGCTCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.19, C:0.34, G:0.26, T:0.21
Consensus pattern (20 bp):
ATTCCCCATAGGGGGTACCG
Found at i:36196 original size:4 final size:4
Alignment explanation
Indices: 36180--36359 Score: 333
Period size: 4 Copynumber: 44.5 Consensus size: 4
36170 ATAATAAATT
*
36180 ATAC ATGC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
36228 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
36276 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
36324 ATAC ATAC ATAC ATAC ATAC ATAC ATGAAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC AT--AC ATAC AT
36360 GGTACATGTA
Statistics
Matches: 172, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
4 168 0.98
6 4 0.02
ACGTcount: A:0.49, C:0.24, G:0.01, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:37729 original size:13 final size:13
Alignment explanation
Indices: 37711--37735 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37701 TCATAACCCG
37711 ACCCGACCCGTTT
1 ACCCGACCCGTTT
37724 ACCCGACCCGTT
1 ACCCGACCCGTT
37736 GACCGTTGAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.48, G:0.16, T:0.20
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:42636 original size:13 final size:13
Alignment explanation
Indices: 42618--42647 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
42608 GGTCATAACC
42618 GACCCGACCCGTT
1 GACCCGACCCGTT
42631 GACCCGACCCGTT
1 GACCCGACCCGTT
42644 GACC
1 GACC
42648 GTTGACCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:45990 original size:18 final size:15
Alignment explanation
Indices: 45954--45982 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
45944 GAGCCTCGAT
45954 CCTCAGAGCCTTGCG
1 CCTCAGAGCCTTGCG
45969 CCTCAGAGCCTTGC
1 CCTCAGAGCCTTGC
45983 TGCGCCTCGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.41, G:0.24, T:0.21
Consensus pattern (15 bp):
CCTCAGAGCCTTGCG
Found at i:47724 original size:2 final size:2
Alignment explanation
Indices: 47717--47783 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
47707 GTAACATGTT
47717 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
47759 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
47784 TCGTACTAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:48797 original size:134 final size:133
Alignment explanation
Indices: 48374--48866 Score: 726
Period size: 131 Copynumber: 3.7 Consensus size: 133
48364 TTAATATTGA
* * * * * *
48374 AAATAGTAATATCTTTTCATTTCTG-TTGGAGTAATAAATGTCTGCTTAAAGGCATAAAATGTCA
1 AAATAGTGATATCTCTTCATTTC-GATTGGAGTAATAAATGACTGCTTTAAGGCATAAGAGGTCA
*
48438 TTTATTCTCGATTGGAAATAATTAGATATTAT-G-GTTTTCTCTCGAGTCAATATTGAATTTTAA
65 TTTATTCTCGATTGGAAATAATTAGATATTATCGTGTTTTCTCTCGAATCAATATTGAATTTTAA
*
48501 TACG
130 GACG
* *
48505 AAACAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCAT
1 AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATAAGAGGTCAT
* * *
48570 GTATTCTTGATTAGAAATAATTAGATATTA-C-TGTTTTCTCTCGAATCAATATTGAATTTTAAG
66 TTATTCTCGATTGGAAATAATTAGATATTATCGTGTTTTCTCTCGAATCAATATTGAATTTTAAG
*
48633 ATG
131 ACG
* * *
48636 AAATAGTGATATCTCTTCATTTCGATTGGAGTAGTAAATGAATGTTTTAAGGCATAAGAGGTCAT
1 AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATAAGAGGTCAT
* * *
48701 TTATTCTCGATTGGAAATAATTAGATATTATCGTTTTTTTTTCTTGAATCAATATTGAATTTTAA
66 TTATTCTCGATTGGAAATAATTAGATATTATCG-TGTTTTCTCTCGAATCAATATTGAATTTTAA
48766 GACG
130 GACG
* *
48770 AAATAGTGATATCTCTTCATTTCGATTGAAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCAT
1 AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATAAGAGGTCAT
*
48835 TTATTCTCAATTGGAAATAATTAGATATTATC
66 TTATTCTCGATTGGAAATAATTAGATATTATC
48867 ATAAATAGCC
Statistics
Matches: 324, Mismatches: 32, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
130 1 0.00
131 200 0.62
132 1 0.00
134 122 0.38
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.40
Consensus pattern (133 bp):
AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATAAGAGGTCAT
TTATTCTCGATTGGAAATAATTAGATATTATCGTGTTTTCTCTCGAATCAATATTGAATTTTAAG
ACG
Found at i:48854 original size:265 final size:262
Alignment explanation
Indices: 48374--48864 Score: 759
Period size: 265 Copynumber: 1.9 Consensus size: 262
48364 TTAATATTGA
* ** *
48374 AAATAGTAATATCTTTTCATTTCTGTTGGAGTAATAAATGTCTGCTTAAAGGCATAAAATGTCAT
1 AAATAGTAATATCTCTTCATTTCTGTTGGAGTAATAAATGAATGCTTAAAGGCATAAAAGGTCAT
* *
48439 TTATTCTCGATTGGAAATAATTAGATATTATGGTTTTCTCTCGAGTCAATATTGAATTTTAATAC
66 TTATTCTCGATTGGAAATAATTAGATATTATGGTTTTCTCTCGAATCAATATTGAATTTTAAGAC
*
48504 GAAACAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCA
131 GAAACAGTGATATCTCTTCATTTCGATTGAAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCA
**
48569 TGTATTCTTGATTAGAAATAATTAGATATTACTGTTTTCTCTCGAATCAATATTGAATTTTAAGA
196 TGTATTCTCAATTAGAAATAATTAGATATTACTGTTTTCTCTCGAATCAATATTGAATTTTAAGA
48634 TG
261 TG
* * * * *
48636 AAATAGTGATATCTCTTCATTTC-GATTGGAGTAGTAAATGAATGTTTTAAGGCATAAGAGGTCA
1 AAATAGTAATATCTCTTCATTTCTG-TTGGAGTAATAAATGAATGCTTAAAGGCATAAAAGGTCA
* * *
48700 TTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTTTTTTCTTGAATCAATATTGAATTTTA
65 TTTATTCTCGATTGGAAATAATTAGATATTAT-G--GTTTTCTCTCGAATCAATATTGAATTTTA
*
48765 AGACGAAATAGTGATATCTCTTCATTTCGATTGAAGTAATAAATGACTGCTTTAAGGCATGAGAG
127 AGACGAAACAGTGATATCTCTTCATTTCGATTGAAGTAATAAATGACTGCTTTAAGGCATGAGAG
* *
48830 GTCATTTATTCTCAATTGGAAATAATTAGATATTA
192 GTCATGTATTCTCAATTAGAAATAATTAGATATTA
48865 TCATAAATAG
Statistics
Matches: 205, Mismatches: 20, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
261 1 0.00
262 85 0.41
263 1 0.00
265 118 0.58
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (262 bp):
AAATAGTAATATCTCTTCATTTCTGTTGGAGTAATAAATGAATGCTTAAAGGCATAAAAGGTCAT
TTATTCTCGATTGGAAATAATTAGATATTATGGTTTTCTCTCGAATCAATATTGAATTTTAAGAC
GAAACAGTGATATCTCTTCATTTCGATTGAAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCA
TGTATTCTCAATTAGAAATAATTAGATATTACTGTTTTCTCTCGAATCAATATTGAATTTTAAGA
TG
Found at i:56312 original size:3 final size:3
Alignment explanation
Indices: 56304--56368 Score: 98
Period size: 3 Copynumber: 21.7 Consensus size: 3
56294 AAAAACCCAA
56304 AAT AAT AAT AAT AAT -AT AAT ATAT AA- AAT AAAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT -AAT AAT AAT AAT AAT
56349 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
56369 GCTTAATATA
Statistics
Matches: 58, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.07
3 48 0.83
4 6 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:56437 original size:21 final size:21
Alignment explanation
Indices: 56407--56446 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
56397 AAACTATATA
*
56407 ATATATTATATTTTCAAAATC
1 ATATAATATATTTTCAAAATC
56428 ATATAATATATTTTCAAAA
1 ATATAATATATTTTCAAAA
56447 CATTATGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (21 bp):
ATATAATATATTTTCAAAATC
Found at i:56489 original size:37 final size:36
Alignment explanation
Indices: 56448--56573 Score: 127
Period size: 37 Copynumber: 3.5 Consensus size: 36
56438 TTTTCAAAAC
56448 ATTAT-GTTTTCAAAAAATA-AGTTTTTAAAAATTACAT
1 ATTATAGTTTTC-AAAAATACA-TTTTTAAAAATTA-AT
*
56485 ATTATACGTTTTC-AAAATACATTTTCAAAAATTATAT
1 ATTATA-GTTTTCAAAAATACATTTTTAAAAATTA-AT
* * *
56522 ATTATACGTTTTCAAAAATATATTTTTAAAACTTATT
1 ATTATA-GTTTTCAAAAATACATTTTTAAAAATTAAT
56559 A-TATA-TTTTCAAAAA
1 ATTATAGTTTTCAAAAA
56574 CTATATGTTA
Statistics
Matches: 79, Mismatches: 6, Indels: 11
0.82 0.06 0.11
Matches are distributed among these distances:
34 10 0.13
36 4 0.05
37 40 0.51
38 19 0.24
39 6 0.08
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (36 bp):
ATTATAGTTTTCAAAAATACATTTTTAAAAATTAAT
Found at i:58278 original size:19 final size:19
Alignment explanation
Indices: 58227--58279 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
58217 TTCGAGAATG
* *
58227 AAAATCGCAACGCGAAATA
1 AAAATCGCAATGCGAAACA
*
58246 AAAATCGCAATGCGAAACC
1 AAAATCGCAATGCGAAACA
*
58265 AAAATCGCATTGCGA
1 AAAATCGCAATGCGA
58280 TTTTCATTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.47, C:0.23, G:0.17, T:0.13
Consensus pattern (19 bp):
AAAATCGCAATGCGAAACA
Found at i:58291 original size:19 final size:19
Alignment explanation
Indices: 58269--58381 Score: 92
Period size: 20 Copynumber: 6.1 Consensus size: 19
58259 GAAACCAAAA
*
58269 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
58288 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
58307 TCGTGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
58321 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
58340 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
58360 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
58380 TC
1 TC
58382 AACCAAAAGA
Statistics
Matches: 74, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
14 9 0.12
16 2 0.03
17 2 0.03
19 29 0.39
20 31 0.42
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:58333 original size:33 final size:34
Alignment explanation
Indices: 58291--58356 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 34
58281 TTTCATTTCG
*
58291 CGTTGCGATAGTCATTT-CGTGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTCT
58324 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
58357 ATTATCTCGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 17 0.55
34 14 0.45
ACGTcount: A:0.12, C:0.24, G:0.24, T:0.39
Consensus pattern (34 bp):
CGTTGCGATAGTCATTTCCGCGTTGCGATTCTCT
Found at i:58358 original size:20 final size:19
Alignment explanation
Indices: 58269--58381 Score: 92
Period size: 19 Copynumber: 6.1 Consensus size: 19
58259 GAAACCAAAA
* *
58269 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTCTCATT
**
58288 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTCTCATT
*
58307 TCGTGTTGCGATTCTC---
1 TCGCGTTGCGATTCTCATT
**
58323 T--CGTTGCGATAGTCATT
1 TCGCGTTGCGATTCTCATT
58340 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTCTCATT
* *
58360 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTCTCATT
58380 TC
1 TC
58382 AACCAAAAGA
Statistics
Matches: 74, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
14 10 0.14
16 1 0.01
17 1 0.01
19 31 0.42
20 30 0.41
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTCTCATT
Found at i:58507 original size:32 final size:28
Alignment explanation
Indices: 58436--58509 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 28
58426 AACTACTATT
58436 TATGTTTATTGTTTTTGGTATATCTTGA
1 TATGTTTATTGTTTTTGGTATATCTTGA
* *
58464 CA-GTGTA--GTTTTTGGTATATCTAACTTGA
1 TATGTTTATTGTTTTTGGTATA--T--CTTGA
58493 TATGTTTATTGTTTTTG
1 TATGTTTATTGTTTTTG
58510 TAGAAATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
25 12 0.34
27 5 0.14
28 1 0.03
29 6 0.17
30 4 0.11
32 7 0.20
ACGTcount: A:0.19, C:0.05, G:0.19, T:0.57
Consensus pattern (28 bp):
TATGTTTATTGTTTTTGGTATATCTTGA
Found at i:60234 original size:86 final size:84
Alignment explanation
Indices: 60068--60234 Score: 196
Period size: 86 Copynumber: 1.9 Consensus size: 84
60058 TAGATTGCTT
* * * *
60068 AGTAAATTTATTCGGTTGCTGCCAATGCTGCTAAACTGTTTATTAACACTGTTAGTGTTTGTCTT
1 AGTAAATTTATTCGGTTGCTGCCAATGCTGCTAAACTGTTTATTAACACTGTGAGAGTTAG-CTA
60133 TTTGTTTTGTCTTTTGGTTGA
65 TTTGTTTTG-CTTTTGGTTGA
* *
60154 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGA-AGTTAG
1 AGTAAATTTATTCGGTTGCTGCCAATGCTGCTAAAC--TGT-TT-ATTAACACTGTGAGAGTTAG
60218 -TATTTGTCTTTG-TTTTG
62 CTATTTGT-TTTGCTTTTG
60235 TCTTTTGGTT
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
86 40 0.57
87 6 0.09
88 7 0.10
89 6 0.09
90 11 0.16
ACGTcount: A:0.20, C:0.13, G:0.19, T:0.47
Consensus pattern (84 bp):
AGTAAATTTATTCGGTTGCTGCCAATGCTGCTAAACTGTTTATTAACACTGTGAGAGTTAGCTAT
TTGTTTTGCTTTTGGTTGA
Found at i:61955 original size:14 final size:14
Alignment explanation
Indices: 61936--61971 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
61926 ATTTTTTAAT
*
61936 TGATTTGTAAAAGG
1 TGATTTGTAAAACG
*
61950 TGATTTGTAAAACT
1 TGATTTGTAAAACG
61964 TGATTTGT
1 TGATTTGT
61972 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.03, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAACG
Found at i:62153 original size:19 final size:19
Alignment explanation
Indices: 62078--62144 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 19
62068 AAAAAGTACT
*
62078 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
62097 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
62111 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
62130 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
62145 TAAATTCGCG
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
14 10 0.24
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 25 0.61
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:62192 original size:33 final size:32
Alignment explanation
Indices: 62149--62260 Score: 145
Period size: 33 Copynumber: 3.4 Consensus size: 32
62139 CGAAATTAAA
* *
62149 TTCGCGTTGCGATTCCCTCGTTTCGATTTTCAT
1 TTCGCATTGCGATT-CCTCGTTGCGATTTTCAT
* *
62182 TTCGCATTGCGAAATT-CGCGTTGCGATTTTTAT
1 TTCGCATTGCG--ATTCCTCGTTGCGATTTTCAT
62215 TTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTCGCATTGCGATTC-CTCGTTGCGATTTTCAT
62248 TTCGCATTGCGAT
1 TTCGCATTGCGAT
62261 AGTAATTTCC
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
31 3 0.04
33 63 0.91
35 3 0.04
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (32 bp):
TTCGCATTGCGATTCCTCGTTGCGATTTTCAT
Found at i:62224 original size:19 final size:19
Alignment explanation
Indices: 62196--62260 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 19
62186 CATTGCGAAA
*
62196 TTCGCGTTGCGATTTTTAT
1 TTCGCATTGCGATTTTTAT
*
62215 TTCGCATTGCGA---TTCT
1 TTCGCATTGCGATTTTTAT
* *
62231 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTTAT
62248 TTCGCATTGCGAT
1 TTCGCATTGCGAT
62261 AGTAATTTCC
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
14 6 0.17
16 6 0.17
17 5 0.14
19 18 0.51
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (19 bp):
TTCGCATTGCGATTTTTAT
Found at i:64568 original size:12 final size:12
Alignment explanation
Indices: 64551--64587 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
64541 TCTTCAGGGA
64551 CTTTTTCTTCTT
1 CTTTTTCTTCTT
*
64563 CTTTTTCTTTTT
1 CTTTTTCTTCTT
64575 CTTTTTCTTCTT
1 CTTTTTCTTCTT
64587 C
1 C
64588 AGGATTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:64570 original size:6 final size:6
Alignment explanation
Indices: 64551--64583 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
64541 TCTTCAGGGA
*
64551 CTTTTT CTTCTT CTTTTT CTTTTT CTTTTT CTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTT
64584 CTTCAGGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (6 bp):
CTTTTT
Found at i:65627 original size:20 final size:21
Alignment explanation
Indices: 65602--65650 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
65592 TCCTAATTCT
*
65602 CAATGCGAA-TAAGTAAATCG
1 CAATGCGAATTAAGAAAATCG
**
65622 CAATGCGAATTTGGAAAATCG
1 CAATGCGAATTAAGAAAATCG
65643 CAATGCGA
1 CAATGCGA
65651 TACTGACTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.20
Consensus pattern (21 bp):
CAATGCGAATTAAGAAAATCG
Found at i:65672 original size:20 final size:20
Alignment explanation
Indices: 65639--65717 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
65629 AATTTGGAAA
* *
65639 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
65659 ATCGCAACGAGATAAT-ACAAA
1 ATCGCAACGAGATACTGAC--T
*
65680 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
* *
65700 TTCGCAACGAGATTCTGA
1 ATCGCAACGAGATACTGA
65718 AAAATCGCAA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.04
20 30 0.62
21 14 0.29
22 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:65727 original size:21 final size:21
Alignment explanation
Indices: 65659--65727 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
65649 GATACTGACT
**
65659 ATCGCAACGAGATAAT-ACAAA
1 ATCGCAACGAGATTCTGA-AAA
**
65680 ATCGCAACGAGATTCTG-ACT
1 ATCGCAACGAGATTCTGAAAA
*
65700 TTCGCAACGAGATTCTGAAAA
1 ATCGCAACGAGATTCTGAAAA
65721 ATCGCAA
1 ATCGCAA
65728 TCATATTCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
20 17 0.45
21 21 0.55
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGAGATTCTGAAAA
Found at i:66028 original size:20 final size:20
Alignment explanation
Indices: 65941--66028 Score: 79
Period size: 20 Copynumber: 4.4 Consensus size: 20
65931 CAACGGGGAA
65941 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
* *
65961 ATTGCAATGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
* ** ***
65981 ATCGTAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
66001 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
66021 ATCACAAC
1 ATCGCAAC
66029 TAGAAAATCG
Statistics
Matches: 51, Mismatches: 15, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
19 5 0.10
20 41 0.80
21 5 0.10
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:66079 original size:14 final size:16
Alignment explanation
Indices: 66059--66132 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
66049 TGAAAATCGC
66059 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
66074 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
66091 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
66110 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
66126 -TTGCGAT
1 ATTGCGAT
66133 AGTCAATTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:66096 original size:19 final size:19
Alignment explanation
Indices: 66055--66122 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
66045 GAAATGAAAA
66055 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
66071 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
66088 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
66107 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
66123 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:67755 original size:21 final size:21
Alignment explanation
Indices: 67731--67791 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
67721 AACGGTATGG
67731 GGGGACTCTTGAGGGA-GGATA
1 GGGGACTCTTGAGGGATGGA-A
* ** *
67752 GGGGCCTCTTGAACGATTGGAG
1 GGGGACTCTTGAGGGA-TGGAA
67774 GGGGACTCTTGAGGGATG
1 GGGGACTCTTGAGGGATG
67792 ACAGGTGAGT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
21 15 0.48
22 13 0.42
23 3 0.10
ACGTcount: A:0.20, C:0.13, G:0.46, T:0.21
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGGAA
Found at i:68220 original size:19 final size:18
Alignment explanation
Indices: 68156--68288 Score: 86
Period size: 20 Copynumber: 7.5 Consensus size: 18
68146 ACGAAACTTA
*
68156 AAATCGCAACGCGAAAATG
1 AAATCGCAATGCG-AAATG
* *
68175 ACTATCGCAACGCGGAAATGG
1 A-AATCGCAATGC-GAAAT-G
**
68196 CTATCGCAATGCGAAATG
1 AAATCGCAATGCGAAATG
*
68214 CAAATCGCAA--CGACA--
1 -AAATCGCAATGCGAAATG
68229 AAATCGCAATGCGAAATG
1 AAATCGCAATGCGAAATG
68247 AAAATCGCAA--CGACAA-G
1 -AAATCGCAATGCGA-AATG
68264 --ATCGCAATGCGAAATG
1 AAATCGCAATGCGAAATG
68280 AAATCGCAA
1 AAATCGCAA
68289 CGACAAAATC
Statistics
Matches: 92, Mismatches: 7, Indels: 31
0.71 0.05 0.24
Matches are distributed among these distances:
14 16 0.17
15 2 0.02
16 8 0.09
17 8 0.09
18 10 0.11
19 22 0.24
20 24 0.26
21 2 0.02
ACGTcount: A:0.43, C:0.23, G:0.21, T:0.14
Consensus pattern (18 bp):
AAATCGCAATGCGAAATG
Found at i:68234 original size:14 final size:14
Alignment explanation
Indices: 68215--68304 Score: 72
Period size: 14 Copynumber: 5.8 Consensus size: 14
68205 TGCGAAATGC
68215 AAATCGCAACGACA
1 AAATCGCAACGACA
*
68229 AAATCGCAATGCGAAATGA
1 AAATCGCAA--CG--A-CA
68248 AAATCGCAACGACA
1 AAATCGCAACGACA
* *
68262 AGATCGCAATGCGAAA
1 AAATCGCAA--CGACA
68278 TGAAATCGCAACGACA
1 --AAATCGCAACGACA
68294 AAATCGCAACG
1 AAATCGCAACG
68305 CGAAACACAA
Statistics
Matches: 61, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
14 29 0.48
15 1 0.02
16 10 0.16
17 2 0.03
18 9 0.15
19 10 0.16
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:68240 original size:33 final size:33
Alignment explanation
Indices: 68198--68320 Score: 194
Period size: 33 Copynumber: 3.8 Consensus size: 33
68188 GGAAATGGCT
68198 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
* *
68231 ATCGCAATGCGAAATGAAAATCGCAACGACAAG
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
68264 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
* **
68296 ATCGCAACGCGAAACACAAATCGCA
1 ATCGCAATGCGAAATGCAAATCGCA
68321 TTGCGATTTT
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
32 28 0.34
33 55 0.66
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGCAAATCGCAACGACAAA
Found at i:68317 original size:65 final size:66
Alignment explanation
Indices: 68198--68320 Score: 205
Period size: 65 Copynumber: 1.9 Consensus size: 66
68188 GGAAATGGCT
* *
68198 ATCGCAATGCGAAATGCAAATCGCAACGACAAAATCGCAATGCGAAATGAAAATCGCAACGACAA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
68263 G
66 G
68264 ATCGCAATGCGAAATG-AAATCGCAACGACAAAATCGCAACGCGAAA-CACAAATCGCA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAAATCGCAACGCGAAATCA-AAATCGCA
68321 TTGCGATTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
64 1 0.02
65 37 0.69
66 16 0.30
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (66 bp):
ATCGCAATGCGAAATGCAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
G
Found at i:68338 original size:19 final size:19
Alignment explanation
Indices: 68316--68379 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
68306 GAAACACAAA
68316 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
68335 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
68351 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
68368 TCGCATTGCGAT
1 TCGCATTGCGAT
68380 AGCCATTTCC
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 6 0.16
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 18 0.47
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:68398 original size:20 final size:19
Alignment explanation
Indices: 68364--68417 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
68354 TTGCGATTTT
*
68364 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
68383 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
68403 CATTTCGTGTTGCGA
1 CATTTCGCGTTGCGA
68418 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:68416 original size:19 final size:19
Alignment explanation
Indices: 68352--68417 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
68342 GCGATTTTGT
**
68352 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
68371 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
68391 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
68410 TGTTGCGA
1 CGTTGCGA
68418 AAGTAAACTA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 22 0.56
20 17 0.44
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:68925 original size:18 final size:18
Alignment explanation
Indices: 68899--68943 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
68889 GTCGATCAGA
*
68899 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
68917 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
68935 TGATGGCTC
1 TGATGGCTC
68944 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:70308 original size:20 final size:20
Alignment explanation
Indices: 70260--70318 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
70250 AATAGTTTCT
** *
70260 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
70280 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
70300 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
70319 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:70604 original size:21 final size:21
Alignment explanation
Indices: 70578--70620 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
70568 GATGGAGATA
70578 GACGGATTTCGTCGGAGATGG
1 GACGGATTTCGTCGGAGATGG
70599 GACGGATTTCGTCGGAGATGG
1 GACGGATTTCGTCGGAGATGG
70620 G
1 G
70621 TGAGAGAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.14, G:0.44, T:0.23
Consensus pattern (21 bp):
GACGGATTTCGTCGGAGATGG
Found at i:70829 original size:20 final size:20
Alignment explanation
Indices: 70804--70855 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
70794 TGCGATTATT
70804 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
*
70824 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGA
*
70844 ATCTCGTTGCGA
1 ATCGCGTTGCGA
70856 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:70889 original size:20 final size:20
Alignment explanation
Indices: 70864--70917 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
70854 GATTTTGTAT
70864 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
70884 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
70904 TATCGCATTGCGAT
1 TATCGCATTGCGAT
70918 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:70889 original size:61 final size:61
Alignment explanation
Indices: 70800--70920 Score: 170
Period size: 61 Copynumber: 2.0 Consensus size: 61
70790 GCATTGCGAT
* * * * *
70800 TATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTG
1 TATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTG
* * *
70861 TATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
70921 CCCAATTCGC
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 52 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (61 bp):
TATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTG
Found at i:70935 original size:21 final size:21
Alignment explanation
Indices: 70906--70960 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
70896 ATAGTCAGTA
*
70906 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
70927 TCGCGTTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
70948 TCGCGTTGCGATT
1 TCGCGTTGCGATT
70961 ACTTATTCGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.15, C:0.27, G:0.20, T:0.38
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCCAAT
Found at i:70936 original size:61 final size:61
Alignment explanation
Indices: 70803--70938 Score: 157
Period size: 61 Copynumber: 2.2 Consensus size: 61
70793 TTGCGATTAT
* * * * * ** *
70803 TATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAA
* * *
70864 TATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAA
70926 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
70939 TTTCCCAATT
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
61 60 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
TATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAA
Found at i:73558 original size:12 final size:12
Alignment explanation
Indices: 73527--73565 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
73517 ACCCACTACA
*
73527 CCCGCAATAGAG
1 CCCGCAATAGCG
73539 -CC-CAATAGCG
1 CCCGCAATAGCG
73549 CCCGCAATAGCG
1 CCCGCAATAGCG
73561 CCCGC
1 CCCGC
73566 GATGACCACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
10 7 0.29
11 4 0.17
12 13 0.54
ACGTcount: A:0.26, C:0.44, G:0.23, T:0.08
Consensus pattern (12 bp):
CCCGCAATAGCG
Done.