Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009574.1 Hibiscus syriacus cultivar Beakdansim tig00116939_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: 2686660
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 14
Found at i:2615200 original size:30 final size:30
Alignment explanation
Indices: 2615166--2615235 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
2615156 GTTATATGAG
*
2615166 CTATGTGATAAAGGTATGTAAATGA-TATGC
1 CTATGTGATAAAGGTATGAAAAT-ACTATGC
*
2615196 CTATGTGATAAAGGTATGAAAATACTATGT
1 CTATGTGATAAAGGTATGAAAATACTATGC
*
2615226 CTACGTGATA
1 CTATGTGATA
2615236 TGAACTACGG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 1 0.03
30 35 0.97
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (30 bp):
CTATGTGATAAAGGTATGAAAATACTATGC
Found at i:2615583 original size:149 final size:149
Alignment explanation
Indices: 2615313--2615614 Score: 577
Period size: 149 Copynumber: 2.0 Consensus size: 149
2615303 GAGTAGAGGG
2615313 TCTATTCGGTTCTTTAGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1 TCTATTCGGTTCTTTAGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
* * *
2615378 ATTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTACGTGGTCCTTATGGACATTATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTACGTGGTCCTTATGGACATCATTA
2615443 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
2615462 TCTATTCGGTTCTTTAGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1 TCTATTCGGTTCTTTAGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
2615527 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTACGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTACGTGGTCCTTATGGACATCATTA
2615592 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
2615611 TCTA
1 TCTA
2615615 CGGGGCACTT
Statistics
Matches: 150, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 150 1.00
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (149 bp):
TCTATTCGGTTCTTTAGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTACGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:2615639 original size:23 final size:23
Alignment explanation
Indices: 2615595--2615639 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2615585 ATCATTATAT
*
2615595 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
2615618 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
2615640 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:2621696 original size:21 final size:21
Alignment explanation
Indices: 2621670--2621712 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2621660 TTTCTGGGTT
* *
2621670 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
2621691 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
2621712 A
1 A
2621713 CGAACATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:2621772 original size:66 final size:68
Alignment explanation
Indices: 2621692--2621842 Score: 216
Period size: 67 Copynumber: 2.2 Consensus size: 68
2621682 ACCCATTCAA
* *
2621692 GGGGAACCGATACCCCTTCAACGAACATG-ATTTCCAGAATGCTAGAGGGGAATCGATACCCCC-
1 GGGGAACCGATACCCCCTCAACGAACATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
2621755 AGG
66 AGG
* * * * *
2621758 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGAATGCTTGTGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAACATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
2621823 AGG
66 AGG
*
2621826 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
2621843 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
66 25 0.33
67 31 0.41
68 19 0.25
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAACATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
AGG
Found at i:2622182 original size:34 final size:29
Alignment explanation
Indices: 2622143--2622214 Score: 126
Period size: 29 Copynumber: 2.5 Consensus size: 29
2622133 CATATTATGA
*
2622143 TACATGACATGAATTTATATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
2622172 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
2622201 TACATGACATGAAT
1 TACATGACATGAAT
2622215 ATGCAGAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:2622270 original size:30 final size:30
Alignment explanation
Indices: 2622236--2622305 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
2622226 GTTATATGAG
*
2622236 CTATGTGATAAAGGTATGTAAATGA-TATGC
1 CTATGTGATAAAGGTATGGAAAT-ACTATGC
*
2622266 CTATGTGATAAAGGTATGGAAATACTATGT
1 CTATGTGATAAAGGTATGGAAATACTATGC
*
2622296 CTACGTGATA
1 CTATGTGATA
2622306 TGAACTACGG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 1 0.03
30 35 0.97
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.33
Consensus pattern (30 bp):
CTATGTGATAAAGGTATGGAAATACTATGC
Found at i:2622662 original size:149 final size:149
Alignment explanation
Indices: 2622383--2622684 Score: 577
Period size: 149 Copynumber: 2.0 Consensus size: 149
2622373 GAGTAGAGGG
2622383 TCTATTCGGTTCTTTAGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1 TCTATTCGGTTCTTTAGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
* * *
2622448 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTACGTGGTCCTTATGGGCATTATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTACGTGGTCCTTATGGACATCATTA
2622513 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
2622532 TCTATTCGGTTCTTTAGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1 TCTATTCGGTTCTTTAGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
2622597 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTACGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTACGTGGTCCTTATGGACATCATTA
2622662 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
2622681 TCTA
1 TCTA
2622685 CGGGGCACTT
Statistics
Matches: 150, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 150 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (149 bp):
TCTATTCGGTTCTTTAGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTACGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:2622709 original size:23 final size:23
Alignment explanation
Indices: 2622665--2622709 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2622655 ATCATTATAT
*
2622665 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
2622688 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
2622710 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:2625368 original size:34 final size:34
Alignment explanation
Indices: 2625324--2625391 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
2625314 ATTGTTTTTC
* * *
2625324 CTTTTCAGCAAGTGAGATTTAAATTTTGATAATT
1 CTTTTCAGCAAATGAGATTTAAACTTCGATAATT
* *
2625358 CTTTTTAGCAAATGGGATTTAAACTTCGATAATT
1 CTTTTCAGCAAATGAGATTTAAACTTCGATAATT
2625392 TTACGAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.43
Consensus pattern (34 bp):
CTTTTCAGCAAATGAGATTTAAACTTCGATAATT
Found at i:2626462 original size:21 final size:20
Alignment explanation
Indices: 2626436--2626474 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2626426 ACGTGGTACT
2626436 TTAAAAAAATATTTTTTAATC
1 TTAAAAAAA-ATTTTTTAATC
*
2626457 TTAAAAAAAGTTTTTTAA
1 TTAAAAAAAATTTTTTAA
2626475 AATAAAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (20 bp):
TTAAAAAAAATTTTTTAATC
Found at i:2631525 original size:21 final size:21
Alignment explanation
Indices: 2631494--2631549 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
2631484 ATAGAATATG
2631494 TATACTTATTAAAAAT-TATTTA
1 TATA-TTATTAAAAATAT-TTTA
* *
2631516 TTTATTATTAATAATATTTTA
1 TATATTATTAAAAATATTTTA
*
2631537 TATATTATCAAAA
1 TATATTATTAAAA
2631550 TTTAAGTTGA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (21 bp):
TATATTATTAAAAATATTTTA
Found at i:2634928 original size:61 final size:61
Alignment explanation
Indices: 2634853--2634972 Score: 179
Period size: 61 Copynumber: 2.0 Consensus size: 61
2634843 ATCTCTTACA
* * * *
2634853 ATTTGTTCTTTATCCAATCAGGTGATTGACAAATGTTACCATTTAATTAGCGATTAAATTT
1 ATTTGTTCTTTATCCAATCAGATGATTGACAAATGCTACCATCTAATTAACGATTAAATTT
*
2634914 ATTTGTT-TTATATCCAATCAGATGATTGACAGATGCTACCATCTAATTAACGATTAAAT
1 ATTTGTTCTT-TATCCAATCAGATGATTGACAAATGCTACCATCTAATTAACGATTAAAT
2634973 AAATTTAATT
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
60 2 0.04
61 51 0.96
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (61 bp):
ATTTGTTCTTTATCCAATCAGATGATTGACAAATGCTACCATCTAATTAACGATTAAATTT
Found at i:2635333 original size:29 final size:28
Alignment explanation
Indices: 2635290--2635415 Score: 92
Period size: 29 Copynumber: 4.3 Consensus size: 28
2635280 TTGAGCCACT
* *
2635290 TGACTATTAAGAGTTATAAAATGGTCACC
1 TGACTATTAAAAGTTACAAAATGGTC-CC
* *
2635319 TGACTATTAAAAGTTACAAAATGATCCT
1 TGACTATTAAAAGTTACAAAATGGTCCC
* ****
2635347 TCGACTA-TAAGGAGTTACTTTGTTGAGTCCC
1 T-GACTATTAA-AAGTTAC-AAAATG-GTCCC
*
2635378 TTAACTATTAAAAGTTACAAAATGGTCACC
1 -TGACTATTAAAAGTTACAAAATGGTC-CC
2635408 TGACTATT
1 TGACTATT
2635416 CATTATATTC
Statistics
Matches: 72, Mismatches: 18, Indels: 14
0.69 0.17 0.13
Matches are distributed among these distances:
28 5 0.07
29 44 0.61
30 6 0.08
31 13 0.18
32 4 0.06
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (28 bp):
TGACTATTAAAAGTTACAAAATGGTCCC
Found at i:2643482 original size:2 final size:2
Alignment explanation
Indices: 2643475--2643503 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2643465 CTGCAACATG
2643475 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2643504 GATAGATAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2644007 original size:12 final size:12
Alignment explanation
Indices: 2643990--2644016 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2643980 TAAAACACAT
2643990 GGGCTGCTAAGG
1 GGGCTGCTAAGG
2644002 GGGCTGCTAAGG
1 GGGCTGCTAAGG
2644014 GGG
1 GGG
2644017 GGGCTGCTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.15, G:0.56, T:0.15
Consensus pattern (12 bp):
GGGCTGCTAAGG
Found at i:2645222 original size:15 final size:16
Alignment explanation
Indices: 2645202--2645233 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2645192 TGGCAGATCC
2645202 AAATCCAG-ACGGGAA
1 AAATCCAGAACGGGAA
2645217 AAATCCAGAACGGGAA
1 AAATCCAGAACGGGAA
2645233 A
1 A
2645234 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.50, C:0.19, G:0.25, T:0.06
Consensus pattern (16 bp):
AAATCCAGAACGGGAA
Found at i:2648508 original size:12 final size:12
Alignment explanation
Indices: 2648491--2648517 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2648481 TAAAACACAT
2648491 GGGCTGCTAAGG
1 GGGCTGCTAAGG
2648503 GGGCTGCTAAGG
1 GGGCTGCTAAGG
2648515 GGG
1 GGG
2648518 GGGGGGGCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.15, G:0.56, T:0.15
Consensus pattern (12 bp):
GGGCTGCTAAGG
Found at i:2649882 original size:20 final size:20
Alignment explanation
Indices: 2649859--2649896 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2649849 TTTAATTACT
2649859 AAATGT-TTAATTTATCTAAC
1 AAATGTATTAATTT-TCTAAC
*
2649879 AAATTTATTAATTTTCTA
1 AAATGTATTAATTTTCTA
2649897 GAAAGGTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.50
Consensus pattern (20 bp):
AAATGTATTAATTTTCTAAC
Found at i:2650804 original size:14 final size:14
Alignment explanation
Indices: 2650782--2650829 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
2650772 TCGATTATAT
*
2650782 ATTTGTTTATGTTC
1 ATTTATTTATGTTC
2650796 ATTTATTTATGTTC
1 ATTTATTTATGTTC
*
2650810 ATTTATGTT-CGTTC
1 ATTTAT-TTATGTTC
2650824 ATTTAT
1 ATTTAT
2650830 GTTTGAACAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 29 0.94
15 2 0.06
ACGTcount: A:0.19, C:0.08, G:0.10, T:0.62
Consensus pattern (14 bp):
ATTTATTTATGTTC
Found at i:2650817 original size:24 final size:24
Alignment explanation
Indices: 2650787--2650832 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2650777 TATATATTTG
*
2650787 TTTATGTTCATTTATTTATGTTCA
1 TTTATGTTCATTCATTTATGTTCA
*
2650811 TTTATGTTCGTTCATTTATGTT
1 TTTATGTTCATTCATTTATGTT
2650833 TGAACAGAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.17, C:0.09, G:0.11, T:0.63
Consensus pattern (24 bp):
TTTATGTTCATTCATTTATGTTCA
Found at i:2651133 original size:10 final size:10
Alignment explanation
Indices: 2651097--2651197 Score: 66
Period size: 10 Copynumber: 10.1 Consensus size: 10
2651087 GTGTTTGTGT
2651097 TGTTCGTTTA
1 TGTTCGTTTA
* *
2651107 TATTAGTTTA
1 TGTTCGTTTA
2651117 TTGTGTTCGTTTA
1 ---TGTTCGTTTA
2651130 TGTTCGTTTA
1 TGTTCGTTTA
* *
2651140 TTTTCATTTA
1 TGTTCGTTTA
*
2651150 TGTTCATTTA
1 TGTTCGTTTA
2651160 T-TAT-G-TT-
1 TGT-TCGTTTA
* *
2651167 CGTTCGTTTG
1 TGTTCGTTTA
2651177 TGTTCGTTTA
1 TGTTCGTTTA
*
2651187 TGTTCTTTTA
1 TGTTCGTTTA
2651197 T
1 T
2651198 CATTTAAATG
Statistics
Matches: 71, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
7 1 0.01
8 4 0.06
9 3 0.04
10 55 0.77
13 8 0.11
ACGTcount: A:0.13, C:0.09, G:0.16, T:0.62
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:2651138 original size:23 final size:22
Alignment explanation
Indices: 2651096--2651170 Score: 82
Period size: 23 Copynumber: 3.4 Consensus size: 22
2651086 TGTGTTTGTG
* *
2651096 TTGTTCGTTTATATTAGTTTAT
1 TTGTTCGTTTATGTTCGTTTAT
2651118 TGTGTTCGTTTATGTTCGTTTA-
1 T-TGTTCGTTTATGTTCGTTTAT
* *
2651140 TT-TTCATTTATGTTCATTTAT
1 TTGTTCGTTTATGTTCGTTTAT
2651161 TATGTTCGTT
1 T-TGTTCGTT
2651171 CGTTTGTGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
20 16 0.36
21 2 0.05
22 3 0.07
23 23 0.52
ACGTcount: A:0.15, C:0.08, G:0.15, T:0.63
Consensus pattern (22 bp):
TTGTTCGTTTATGTTCGTTTAT
Found at i:2653619 original size:18 final size:18
Alignment explanation
Indices: 2653577--2653619 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
2653567 GTAAATAAGA
2653577 TGGGAAATTTATGGAAAG
1 TGGGAAATTTATGGAAAG
* * *
2653595 TGAGAAATTTGTGGAAGG
1 TGGGAAATTTATGGAAAG
2653613 TGGGAAA
1 TGGGAAA
2653620 GAAACCAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.26
Consensus pattern (18 bp):
TGGGAAATTTATGGAAAG
Found at i:2654030 original size:29 final size:29
Alignment explanation
Indices: 2653995--2654076 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
2653985 AAACTAAATT
*
2653995 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
2654024 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
2654053 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
2654077 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:2658768 original size:29 final size:29
Alignment explanation
Indices: 2658733--2658814 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
2658723 AAACTAAATT
*
2658733 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
2658762 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
2658791 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
2658815 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:2665931 original size:46 final size:43
Alignment explanation
Indices: 2665841--2665931 Score: 96
Period size: 46 Copynumber: 2.0 Consensus size: 43
2665831 CATGAAAGTT
* *
2665841 TTATTATATTTTTTTTAAAAAAATCAACACATAAATGTTAATA
1 TTATTATATTTTTTTTAAAAAAATCAAAACATAAATATTAATA
*
2665884 TTATTAATATTTTAATTTTAAAAAAAT-AAAATCTTAATATATT-ATA
1 TTATT-ATATTTT--TTTTAAAAAAATCAAAA-CATAA-ATATTAATA
2665930 TT
1 TT
2665932 TTCAAGTTGC
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
43 5 0.12
44 7 0.17
45 3 0.08
46 21 0.52
47 4 0.10
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (43 bp):
TTATTATATTTTTTTTAAAAAAATCAAAACATAAATATTAATA
Found at i:2672952 original size:91 final size:91
Alignment explanation
Indices: 2672797--2672976 Score: 292
Period size: 91 Copynumber: 2.0 Consensus size: 91
2672787 TACCTGCAAG
* * *
2672797 AGCAGCACAGCATACCTTAATGACAGAATTAGGGGTAAAAGAAGATGAGAAACAAGGCTTCAAGT
1 AGCAGCACACCATACCTTAAAGACAGAACTAGGGGTAAAAGAAGATGAGAAACAAGGCTTCAAGT
2672862 GATATGTTCTGGTAAACTTGCAGATA
66 GATATGTTCTGGTAAACTTGCAGATA
*
2672888 AGCAGCACACCATACCTTAAAGACAGAACTA-GGGTCAAAA-AGAGATGAGAAACAAGGTTTCAA
1 AGCAGCACACCATACCTTAAAGACAGAACTAGGGGT-AAAAGA-AGATGAGAAACAAGGCTTCAA
2672951 GTGATATGTTCTGGTAAACTTGCAGA
64 GTGATATGTTCTGGTAAACTTGCAGA
2672977 CAATTTGGTA
Statistics
Matches: 83, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
90 5 0.06
91 78 0.94
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (91 bp):
AGCAGCACACCATACCTTAAAGACAGAACTAGGGGTAAAAGAAGATGAGAAACAAGGCTTCAAGT
GATATGTTCTGGTAAACTTGCAGATA
Found at i:2675500 original size:63 final size:62
Alignment explanation
Indices: 2675391--2675514 Score: 187
Period size: 63 Copynumber: 2.0 Consensus size: 62
2675381 AACCTTGACA
* *
2675391 ACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
* *
2675453 ACTGTCCATATGTCTCGAA-AGACATAGGTAAAACTGTCCATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATAGGTCCCGAAGA-ACATAGGT-AAACTGTCCATATGTTCCGTAGAACATAGGTA
2675515 AACCCTCGAC
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
61 1 0.02
62 24 0.43
63 31 0.55
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.27
Consensus pattern (62 bp):
ACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
Found at i:2675510 original size:32 final size:31
Alignment explanation
Indices: 2675390--2675517 Score: 152
Period size: 31 Copynumber: 4.1 Consensus size: 31
2675380 GAACCTTGAC
* * * *
2675390 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
*
2675421 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
* *
2675452 TACTGTCCATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGT-A
2675484 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
2675515 AAC
1 AAC
2675518 CCTCGACTCT
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
30 4 0.05
31 51 0.62
32 23 0.28
33 4 0.05
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTA
Found at i:2680354 original size:22 final size:23
Alignment explanation
Indices: 2680326--2680379 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
2680316 CTATTCTTTC
2680326 GCTTCAATTGAG-AAAATTTTAG
1 GCTTCAATTGAGCAAAATTTTAG
*
2680348 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGC-AAAATTTTAG
*
2680372 GTTTCAAT
1 GCTTCAAT
2680380 CGAACTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 12 0.43
24 16 0.57
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (23 bp):
GCTTCAATTGAGCAAAATTTTAG
Found at i:2684371 original size:20 final size:21
Alignment explanation
Indices: 2684346--2684397 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2684336 TTTTCCCAAT
*
2684346 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
2684366 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
2684387 TCGCAATGCGA
1 TCGCAATGCGA
2684398 TAATACAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:2684456 original size:20 final size:20
Alignment explanation
Indices: 2684408--2684460 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
2684398 TAATACAAAA
* *
2684408 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
2684428 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
*
2684448 TCGCTACGCGATT
1 TCGCAACGCGATT
2684461 TACATAGCGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:2685022 original size:18 final size:18
Alignment explanation
Indices: 2684999--2685038 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2684989 ACGAGATAAT
*
2684999 CGCAACGCGAAATAAAAA
1 CGCAACGCGAAACAAAAA
*
2685017 CGCAACGCGAAACAAAAT
1 CGCAACGCGAAACAAAAA
2685035 CGCA
1 CGCA
2685039 TTGCGATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.28, G:0.17, T:0.05
Consensus pattern (18 bp):
CGCAACGCGAAACAAAAA
Found at i:2685080 original size:20 final size:19
Alignment explanation
Indices: 2685034--2685199 Score: 127
Period size: 20 Copynumber: 9.1 Consensus size: 19
2685024 CGAAACAAAA
*
2685034 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
2685053 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
2685072 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
2685092 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
2685108 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
2685125 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
2685139 TCTCGTTACGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
2685158 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
2685178 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
2685198 TC
1 TC
2685200 AACCAAAAGA
Statistics
Matches: 117, Mismatches: 17, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
14 19 0.16
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 41 0.35
20 48 0.41
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2685115 original size:39 final size:39
Alignment explanation
Indices: 2685039--2685115 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
2685029 CAAAATCGCA
* **
2685039 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
2685078 TTGCGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
2685116 ATAGTCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 32 0.94
40 2 0.06
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.45
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
Found at i:2685169 original size:34 final size:33
Alignment explanation
Indices: 2685087--2685174 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
2685077 GTTGCGATTT
* * *
2685087 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCACGATAG
*
2685120 TCATTTCGCGTTGCGATTCTCTCGTTACGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCACGATAG
2685153 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
2685175 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 35 0.70
34 15 0.30
ACGTcount: A:0.12, C:0.25, G:0.24, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCACGATAG
Done.