Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006909.1 Hibiscus syriacus cultivar Beakdansim tig00017674_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: 91657
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:477 original size:21 final size:21
Alignment explanation
Indices: 426--478 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
416 ATTATGATTA
* *
426 TCGCAATGCAATTTTCCAATT
1 TCGCAGTGCGATTTTCCAATT
447 TCGC-GTTGCGATTTTCCCAA-T
1 TCGCAG-TGCGATTTT-CCAATT
468 TCGCAGTGCGA
1 TCGCAGTGCGA
479 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 22 0.81
22 5 0.19
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAGTGCGATTTTCCAATT
Found at i:511 original size:21 final size:21
Alignment explanation
Indices: 485--582 Score: 142
Period size: 21 Copynumber: 4.7 Consensus size: 21
475 GCGAATAAGT
485 AAATCGCAATGCGAATTTGGA
1 AAATCGCAATGCGAATTTGGA
* * *
506 AAATCGTAATGAGAATTTGAA
1 AAATCGCAATGCGAATTTGGA
527 AAATCGCAATGCGAATTTGGA
1 AAATCGCAATGCGAATTTGGA
* *
548 AAATCGTAATGCAAATTTGGA
1 AAATCGCAATGCGAATTTGGA
*
569 AAATCGCAACGCGA
1 AAATCGCAATGCGA
583 TACTGACTAT
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 66 1.00
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.23
Consensus pattern (21 bp):
AAATCGCAATGCGAATTTGGA
Found at i:532 original size:42 final size:42
Alignment explanation
Indices: 485--582 Score: 162
Period size: 42 Copynumber: 2.3 Consensus size: 42
475 GCGAATAAGT
485 AAATCGCAATGCGAATTTGGAAAATCGTAATG-AGAATTTGAA
1 AAATCGCAATGCGAATTTGGAAAATCGTAATGCA-AATTTGAA
*
527 AAATCGCAATGCGAATTTGGAAAATCGTAATGCAAATTTGGA
1 AAATCGCAATGCGAATTTGGAAAATCGTAATGCAAATTTGAA
*
569 AAATCGCAACGCGA
1 AAATCGCAATGCGA
583 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
42 52 0.98
43 1 0.02
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.23
Consensus pattern (42 bp):
AAATCGCAATGCGAATTTGGAAAATCGTAATGCAAATTTGAA
Found at i:596 original size:20 final size:20
Alignment explanation
Indices: 571--685 Score: 124
Period size: 20 Copynumber: 5.7 Consensus size: 20
561 AATTTGGAAA
571 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * *
591 ATCGCAACACGCTAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
612 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
632 TTCGCAACGCGATACTTACT
1 ATCGCAACGCGATACTGACT
*
652 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
672 TTCGCAACGAGATA
1 ATCGCAACGCGATA
686 ATACATAATC
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.79
21 13 0.16
22 2 0.03
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:668 original size:40 final size:40
Alignment explanation
Indices: 569--705 Score: 168
Period size: 41 Copynumber: 3.4 Consensus size: 40
559 CAAATTTGGA
* * *
569 AAATCGCAACGCGATACTGACTATCGCAACACGCTAATAC
1 AAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
*
609 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATACTTAC
1 -AAATCGCAACGCGATACTGACTTTCGCAACGCGATA-ATAC
** *
651 -TTTCGCAACGCGATACTGACTTTCGCAACGAGATAATAC
1 AAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
*
690 ATAATCGCAATGCGAT
1 A-AATCGCAACGCGAT
706 TTTCAAAGCG
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
39 3 0.04
40 32 0.39
41 44 0.54
42 3 0.04
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (40 bp):
AAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:1219 original size:20 final size:20
Alignment explanation
Indices: 1172--1228 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
1162 TATTCTCTCA
* **
1172 TTGCGATAGTCAAATTCGCG
1 TTGCGATTGTCATTTTCGCG
*
1192 TTGCGATTGTCATTTTCGTG
1 TTGCGATTGTCATTTTCGCG
*
1212 TTGCGATTTTCATTTTC
1 TTGCGATTGTCATTTTC
1229 AGAAACTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.16, C:0.18, G:0.21, T:0.46
Consensus pattern (20 bp):
TTGCGATTGTCATTTTCGCG
Found at i:1418 original size:25 final size:24
Alignment explanation
Indices: 1364--1418 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1354 TGTTTTTTAT
* *
1364 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1388 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1414 TGTTT
1 TGTTT
1419 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:2560 original size:18 final size:18
Alignment explanation
Indices: 2539--2586 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
2529 TCCACTTCGG
*
2539 GAGCCAACACCTCACCCA
1 GAGCCATCACCTCACCCA
*
2557 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
2575 GAGCCATCACCT
1 GAGCCATCACCT
2587 GATCGACCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.29, C:0.46, G:0.12, T:0.12
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2973 original size:18 final size:18
Alignment explanation
Indices: 2950--2999 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
2940 TTTACTCGTA
2950 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
2968 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
2986 ATTTCACTTAGATT
1 ATTTCACTTAGATT
3000 GCTTAATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:3161 original size:20 final size:20
Alignment explanation
Indices: 3136--3181 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
3126 TAGTTTACTT
3136 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
** * *
3156 TCGCAATGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
3176 TCGCAA
1 TCGCAA
3182 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:3190 original size:19 final size:20
Alignment explanation
Indices: 3147--3191 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
3137 CGCAACACGA
3147 AAATGACTATCGCAATGCGG
1 AAATGACTATCGCAATGCGG
*
3167 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAATGCGG
3186 AAATGA
1 AAATGA
3192 AAATCGCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (20 bp):
AAATGACTATCGCAATGCGG
Found at i:3197 original size:19 final size:19
Alignment explanation
Indices: 3155--3271 Score: 101
Period size: 19 Copynumber: 6.6 Consensus size: 19
3145 GAAAATGACT
***
3155 ATCGCAATGCGGAAATGGCT
1 ATCGCAATGC-GAAATGAAA
3175 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3194 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
3208 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3227 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
3241 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3260 ATCGCAATGCGA
1 ATCGCAATGCGA
3272 TTTGTGTTTC
Statistics
Matches: 79, Mismatches: 8, Indels: 21
0.73 0.07 0.19
Matches are distributed among these distances:
14 20 0.25
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 37 0.47
20 10 0.13
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3210 original size:14 final size:14
Alignment explanation
Indices: 3191--3249 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
3181 ATGCGAAATG
3191 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
3205 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
3224 AAAATCGCAACGAC
1 AAAATCGCAACGAC
3238 AAAATCGCAACG
1 AAAATCGCAACG
3250 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:3217 original size:33 final size:33
Alignment explanation
Indices: 3175--3266 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
3165 GGAAATGGCT
3175 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
3208 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
3241 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
3267 TGCGATTTGT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:3283 original size:19 final size:19
Alignment explanation
Indices: 3278--3402 Score: 89
Period size: 20 Copynumber: 6.7 Consensus size: 19
3268 GCGATTTGTG
*
3278 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
3297 TTTCGCATTGCGA-TTT--
1 TTTCGCATTGCGATTTTCA
3313 TTTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
***
3330 TTTCGCATTGCGATAGCCA
1 TTTCGCATTGCGATTTTCA
* ***
3349 TTTTCGCGTTGCGATAGCCA
1 -TTTCGCATTGCGATTTTCA
**
3369 TTTCCGCATTGCGATAGTCA
1 TTT-CGCATTGCGATTTTCA
*
3389 TTTTCGCGTTGCGA
1 -TTTCGCATTGCGA
3403 AAGTAAGTTT
Statistics
Matches: 90, Mismatches: 8, Indels: 15
0.80 0.07 0.13
Matches are distributed among these distances:
14 6 0.07
15 3 0.03
16 5 0.06
17 5 0.06
18 3 0.03
19 24 0.27
20 41 0.46
21 3 0.03
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.42
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:3355 original size:20 final size:20
Alignment explanation
Indices: 3330--3402 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
3320 GCGATTTTCA
3330 TTTCGCATTGCGATAGCCAT
1 TTTCGCATTGCGATAGCCAT
*
3350 TTTCGCGTTGCGATAGCCAT
1 TTTCGCATTGCGATAGCCAT
* *
3370 TTCCGCATTGCGATAGTCAT
1 TTTCGCATTGCGATAGCCAT
*
3390 TTTCGCGTTGCGA
1 TTTCGCATTGCGA
3403 AAGTAAGTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (20 bp):
TTTCGCATTGCGATAGCCAT
Found at i:3413 original size:20 final size:19
Alignment explanation
Indices: 3350--3428 Score: 68
Period size: 20 Copynumber: 4.0 Consensus size: 19
3340 CGATAGCCAT
* **
3350 TTTCGCGTTGCGATAGCCA
1 TTTCGCGTTGCGAAAGTAA
* * *
3369 TTTCCGCATTGCGATAGTCAT
1 TTT-CGCGTTGCGAAAGT-AA
3390 TTTCGCGTTGCGAAAGTAA
1 TTTCGCGTTGCGAAAGTAA
*
3409 GTTTCGTGTTGCGAAAGTAA
1 -TTTCGCGTTGCGAAAGTAA
3429 ACTATTCTTC
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
19 4 0.08
20 42 0.86
21 3 0.06
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (19 bp):
TTTCGCGTTGCGAAAGTAA
Found at i:3803 original size:21 final size:20
Alignment explanation
Indices: 3777--3845 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
3767 CTGTCATCCC
3777 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
3798 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
* *
3819 TCAAGAGTCCCCCCCACCGT
1 TCAAGAGTCCCCTCCATCGT
3839 TCAAGAG
1 TCAAGAG
3846 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
20 10 0.27
21 26 0.70
22 1 0.03
ACGTcount: A:0.25, C:0.41, G:0.16, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:3857 original size:41 final size:42
Alignment explanation
Indices: 3767--3857 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 42
3757 CCCGACTCAC
* *
3767 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
* *
3809 CTATCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
3850 CTGTCATC
1 CTGTCATC
3858 GTTGAAGAGG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 23 0.52
42 21 0.48
ACGTcount: A:0.22, C:0.42, G:0.15, T:0.21
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
Found at i:5449 original size:19 final size:19
Alignment explanation
Indices: 5425--5470 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
5415 GCAACGAGAG
*
5425 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATAAA
5444 AATCGCAATGCGAAATAAA
1 AATCGCAATGCGAAATAAA
5463 AATCGCAA
1 AATCGCAA
5471 CGTTCAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATAAA
Found at i:5700 original size:20 final size:20
Alignment explanation
Indices: 5639--5708 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
5629 TTCAGAATCT
* *
5639 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGATAGTCAGTATCG
* *
5659 CGTTGCGATTTTGT-ATTATCG
1 CGTTGCGA--TAGTCAGTATCG
5680 CGTTGCGATAGTCAGTATCG
1 CGTTGCGATAGTCAGTATCG
*
5700 CATTGCGAT
1 CGTTGCGAT
5709 TTTCCAAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
19 3 0.08
20 22 0.55
21 13 0.32
22 2 0.05
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAGTATCG
Found at i:5790 original size:21 final size:22
Alignment explanation
Indices: 5738--5790 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
5728 ATTTACTTAT
*
5738 TCGCATTGTG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
** *
5759 TCGCAACGCGAAATT-GTAAAA
1 TCGCATTGCGAAATTGGGAAAA
5780 TCGCATTGCGA
1 TCGCATTGCGA
5791 TAGTCATAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:7500 original size:60 final size:60
Alignment explanation
Indices: 7436--7562 Score: 141
Period size: 60 Copynumber: 2.1 Consensus size: 60
7426 TCTCACCCTT
* * * * *
7436 AAACTATGATA-ACAATTCTAAATTAGTCCTCAAA-TTTTTGAACATTTCAATTTCATCCCC
1 AAACTATGACATAC-ATTCTAAATTACTCCCCAAACTGTTTGAACATTCCAATTTCAT-CCC
* * **
7496 AAACTATGACATTCATTCTAAATTACTCCCCAAACTGTTTGAATATTCCAATTTTGTCCC
1 AAACTATGACATACATTCTAAATTACTCCCCAAACTGTTTGAACATTCCAATTTCATCCC
7556 AAACTAT
1 AAACTAT
7563 ACACATATAT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
60 38 0.68
61 18 0.32
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.36
Consensus pattern (60 bp):
AAACTATGACATACATTCTAAATTACTCCCCAAACTGTTTGAACATTCCAATTTCATCCC
Found at i:21894 original size:8 final size:8
Alignment explanation
Indices: 21881--21907 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
21871 GATTCTCCCG
21881 TATGTATA
1 TATGTATA
21889 TATGTATA
1 TATGTATA
21897 TATGTATA
1 TATGTATA
21905 TAT
1 TAT
21908 CTTCTTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (8 bp):
TATGTATA
Found at i:26453 original size:101 final size:102
Alignment explanation
Indices: 26269--26472 Score: 401
Period size: 101 Copynumber: 2.0 Consensus size: 102
26259 CGAAGAAGAA
26269 AGTGCATTAAATTTCATAATTGCATACATCGTAGGCATGAATAGGATCATGACATTGCATGATTA
1 AGTGCATTAAATTTCATAATTGCATACATCGTAGGCATGAATAGGATCATGACATTGCATGATTA
26334 TTTTAAATGTTTGCAGATTTCCCAACAATCGTTGAAG
66 TTTTAAATGTTTGCAGATTTCCCAACAATCGTTGAAG
26371 AGTGCATT-AATTTCATAATTGCATACATCGTAGGCATGAATAGGATCATGACATTGCATGATTA
1 AGTGCATTAAATTTCATAATTGCATACATCGTAGGCATGAATAGGATCATGACATTGCATGATTA
26435 TTTTAAATGTTTGCAGATTTCCCAACAATCGTTGAAG
66 TTTTAAATGTTTGCAGATTTCCCAACAATCGTTGAAG
26472 A
1 A
26473 TCGTTCGAAT
Statistics
Matches: 102, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
101 94 0.92
102 8 0.08
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (102 bp):
AGTGCATTAAATTTCATAATTGCATACATCGTAGGCATGAATAGGATCATGACATTGCATGATTA
TTTTAAATGTTTGCAGATTTCCCAACAATCGTTGAAG
Found at i:26655 original size:54 final size:52
Alignment explanation
Indices: 26523--27145 Score: 437
Period size: 51 Copynumber: 11.9 Consensus size: 52
26513 CACGATTGTT
* * * * * * * *
26523 GAAGATATTCGAGTTCTATTCTCCTTAAAGGAAGAAGGAGCAAACCAGTTTGAA
1 GAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCG--TGAA
* * * *
26577 G-AGATG-TCTAAGTTCCATACTCCCTAGAGAAAGAGAGAGTGAACCCGTAAGAA
1 GAAGATGTTC-GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGT--GAA
* * * **
26630 GAAGATTTTTGAGTTCTATACTCCCT-GAAGAAAAAGGGAGCGAACCC-TGTC
1 GAAGATGTTCGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTGAA
* * *
26681 GAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAGGGAGCGAACCCGTG-T
1 GAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGAA
* * * * * * * * *
26732 GAAGATATCCGAGTTCCATACTCCTTAAAGGAAGAAGGAGCAAACCAGTTTGAA
1 GAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCG--TGAA
* * * *
26786 G-AGATG-TCTAAGTTCCATACTCCCTAGAGAAAGAGAGAGTGAACCCGTAAGAA
1 GAAGATGTTC-GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGT--GAA
* * * **
26839 GAAGATTTTTGAGTTCTATACTCCCT-GAAGAAAAAGGGAGCGAACCC-TGTC
1 GAAGATGTTCGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTGAA
* * *
26890 GAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAGGGAGCGAACCCGTG-T
1 GAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGAA
* * * * * **
26941 GAAGATATCCGAGTTCCATACTCCTTA-ATGAAAGAAGGAGCGAACCCGT-TT
1 GAAGATGTTCGAGTTCTATACTCCCTAGA-GAAAGAGGGAGCGAACCCGTGAA
* ** * * *
26992 GAAGATGTTCGAGTTCTGTACTCTTTAAAGAGAGAAGGAGCGAACCCGTAAGAA
1 GAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGT--GAA
* * * *
27046 GAAGATTTTTGAGTTCTATACTCCCT-GAAGAAAGAGGGAGAGAACCCGTCTGCA
1 GAAGATGTTCGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCG--TGAA
* *
27100 GAAGATTTTCAAGTTCTATACTCCCT-GAAGAAAGAGGGAGCGAACC
1 GAAGATGTTCGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACC
27146 TGCTGTCTGA
Statistics
Matches: 455, Mismatches: 86, Indels: 56
0.76 0.14 0.09
Matches are distributed among these distances:
50 1 0.00
51 212 0.47
52 8 0.02
53 78 0.17
54 153 0.34
55 2 0.00
56 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (52 bp):
GAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGAA
Found at i:26843 original size:158 final size:154
Alignment explanation
Indices: 26641--27040 Score: 427
Period size: 158 Copynumber: 2.6 Consensus size: 154
26631 AAGATTTTTG
* *
26641 AGTTCTATACTCCCTGAA-GAAA-AAGGGAGCGAACCCTGT-CGAAGATGTTCGAGTTCTATACT
1 AGTTCCATACTCCCT-AATGAAAGAA-GGAGCGAACCC-GTAAGAAGATGTTCGAGTTCTATACT
*
26703 CCTTAAAGAAAGAGGGAGCGAACCCGTGT-GAAGATATCCGAGTTCCATACTCCTTAAAGGAAGA
63 CCTTAAAGAAAGAGGGAGCGAACCCGTGTCGAAGATATCCGAGTTCCATACTCCTTAAAGAAAGA
* * *
26767 AGGAGCAAACCAGTTTGAAGAGATGTCTA
128 AGGAGCAAACCAGTGTG-A-AGATATCCA
* * *
26796 AGTTCCATACTCCCTAGA-GAAAG-AGAGAGTGAACCCGTAAGAAGAAGATTTTTGAGTTCTATA
1 AGTTCCATACTCCCTA-ATGAAAGAAG-GAGCGAACCCGT---AAGAAGATGTTCGAGTTCTATA
* * * * * *
26859 CTCCCTGAAGAAAAAGGGAGCGAACCC-TGTCGAAGATGTTCGAGTTCTATACTCCTTAAAGAAA
61 CTCCTTAAAGAAAGAGGGAGCGAACCCGTGTCGAAGATATCCGAGTTCCATACTCCTTAAAGAAA
* * * *
26923 GAGGGAGCGAACCCGTGTGAAGATATCCG
126 GAAGGAGCAAACCAGTGTGAAGATATCCA
* ** * *
26952 AGTTCCATACTCCTTAATGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTGTACTCTT
1 AGTTCCATACTCCCTAATGAAAGAAGGAGCGAACCCGTAAGAAGATGTTCGAGTTCTATACTCCT
* *
27017 TAAAGAGAGAAGGAGCGAACCCGT
66 TAAAGAAAGAGGGAGCGAACCCGT
27041 AAGAAGAAGA
Statistics
Matches: 202, Mismatches: 32, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
153 38 0.19
154 5 0.02
155 30 0.15
156 37 0.18
157 6 0.03
158 86 0.43
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.23
Consensus pattern (154 bp):
AGTTCCATACTCCCTAATGAAAGAAGGAGCGAACCCGTAAGAAGATGTTCGAGTTCTATACTCCT
TAAAGAAAGAGGGAGCGAACCCGTGTCGAAGATATCCGAGTTCCATACTCCTTAAAGAAAGAAGG
AGCAAACCAGTGTGAAGATATCCA
Found at i:26882 original size:209 final size:209
Alignment explanation
Indices: 26522--27145 Score: 977
Period size: 209 Copynumber: 3.0 Consensus size: 209
26512 ACACGATTGT
* * *
26522 TGAAGATATTCGAGTTCTATTCTCCTTAAAGGAAGAAGGAGCAAACCAGTTTGAAGAGATGTCTA
1 TGAAGATATCCGAGTTCCATACTCCTTAAAGGAAGAAGGAGCAAACCAGTTTGAAGAGATGTCTA
26587 AGTTCCATACTCCCTAGAGAAAGAGAGAGTGAACCCGTAAGAAGAAGATTTTTGAGTTCTATACT
66 AGTTCCATACTCCCTAGAGAAAGAGAGAGTGAACCCGTAAGAAGAAGATTTTTGAGTTCTATACT
26652 CCCTGAAGAAAAAGGGAGCGAACCCTGTCGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAG
131 CCCTGAAGAAAAAGGGAGCGAACCCTGTCGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAG
26717 GGAGCGAACCCGTG
196 GGAGCGAACCCGTG
26731 TGAAGATATCCGAGTTCCATACTCCTTAAAGGAAGAAGGAGCAAACCAGTTTGAAGAGATGTCTA
1 TGAAGATATCCGAGTTCCATACTCCTTAAAGGAAGAAGGAGCAAACCAGTTTGAAGAGATGTCTA
26796 AGTTCCATACTCCCTAGAGAAAGAGAGAGTGAACCCGTAAGAAGAAGATTTTTGAGTTCTATACT
66 AGTTCCATACTCCCTAGAGAAAGAGAGAGTGAACCCGTAAGAAGAAGATTTTTGAGTTCTATACT
26861 CCCTGAAGAAAAAGGGAGCGAACCCTGTCGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAG
131 CCCTGAAGAAAAAGGGAGCGAACCCTGTCGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAG
26926 GGAGCGAACCCGTG
196 GGAGCGAACCCGTG
* * * *
26940 TGAAGATATCCGAGTTCCATACTCCTTAATGAAAGAAGGAGCGAACCCGTTTG-A-AGATGT-TC
1 TGAAGATATCCGAGTTCCATACTCCTTAAAGGAAGAAGGAGCAAACCAGTTTGAAGAGATGTCT-
* ** ** * * *
27002 GAGTTCTGTACTCTTTAAAGAGAGA-AGGAGCGAACCCGTAAGAAGAAGATTTTTGAGTTCTATA
65 AAGTTCCATACTCCCTAGAGAAAGAGA-GAGTGAACCCGTAAGAAGAAGATTTTTGAGTTCTATA
* * * * * * *
27066 CTCCCTGAAGAAAGAGGGAGAGAACCCGTCTGCAGAAGATTTTCAAGTTCTATACTCCCTGAAGA
129 CTCCCTGAAGAAAAAGGGAGCGAACCC-TGT-C-GAAGATGTTCGAGTTCTATACTCCTTAAAGA
27131 AAGAGGGAGCGAACC
191 AAGAGGGAGCGAACC
27146 TGCTGTCTGA
Statistics
Matches: 388, Mismatches: 22, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
206 2 0.01
207 85 0.22
208 3 0.01
209 256 0.66
210 42 0.11
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (209 bp):
TGAAGATATCCGAGTTCCATACTCCTTAAAGGAAGAAGGAGCAAACCAGTTTGAAGAGATGTCTA
AGTTCCATACTCCCTAGAGAAAGAGAGAGTGAACCCGTAAGAAGAAGATTTTTGAGTTCTATACT
CCCTGAAGAAAAAGGGAGCGAACCCTGTCGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAG
GGAGCGAACCCGTG
Found at i:26983 original size:260 final size:263
Alignment explanation
Indices: 26630--27159 Score: 694
Period size: 260 Copynumber: 2.0 Consensus size: 263
26620 CCCGTAAGAA
* * * * *
26630 GAAGATTTTTGAGTTCTATACTCCCTGAAGAAAAAGGGAGCGAACCCTGTCGAAGATGTTCGAGT
1 GAAGATGTTCGAGTTCTATACTCCCTAAAGAAAAAGGGAGCGAACCCTGTCGAAGATATCCGAGT
* *
26695 TCTATACTCCTTAAAGAAAGAGGGAGCGAACCCGTGTGAAGATATCCGAGTTCCATACTCCTTAA
66 TCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTGTGAAGATATCCGAGTTCCATACTCCTTAA
**
26760 AG-GAAGAAGGAGCAAACCAGTTTGAAG-AGATGTCTAAGTTCCATACTCCCT-AGAGAAAGAGA
131 AGAG-AGAAGGAGCAAACCAGTAAGAAGAAGATGTCTAAGTTCCATACTCCCTGA-AGAAAGAGA
* **
26822 GAGTGAACCCGTAAGAAGAAGATTTTTGAGTTCTATACTCCCTGAAGAAAAAGGGAGCGAACC-C
194 GAGAGAACCCGTAAGAAGAAGATTTTCAAGTTCTATACTCCCTGAAGAAAAAGGGAGCGAACCGC
26886 TGTC-
259 TGTCT
* *
26890 GAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAGGGAGCGAACCCGTGT-GAAGATATCCGAG
1 GAAGATGTTCGAGTTCTATACTCCCTAAAGAAAAAGGGAGCGAACCC-TGTCGAAGATATCCGAG
* * * * ** *
26954 TTCCATACTCCTTAATGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTGTACTCTTTA
65 TTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTGTGAAGATATCCGAGTTCCATACTCCTTA
* * * * * * *
27019 AAGAGAGAAGGAGCGAACCCGTAAGAAGAAGATTTTTGAGTTCTATACTCCCTGAAGAAAGAGGG
130 AAGAGAGAAGGAGCAAACCAGTAAGAAGAAGATGTCTAAGTTCCATACTCCCTGAAGAAAGAGAG
** * *
27084 AGAGAACCCGTCTGCAGAAGATTTTCAAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCTGC
195 AGAGAACCCGTAAGAAGAAGATTTTCAAGTTCTATACTCCCTGAAGAAAAAGGGAGCGAACC-GC
27149 TGTCT
259 TGTCT
27154 GAAGAT
1 GAAGAT
27160 TTTTCAAGTC
Statistics
Matches: 231, Mismatches: 32, Indels: 10
0.85 0.12 0.04
Matches are distributed among these distances:
260 131 0.57
261 88 0.38
262 1 0.00
263 5 0.02
264 6 0.03
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.23
Consensus pattern (263 bp):
GAAGATGTTCGAGTTCTATACTCCCTAAAGAAAAAGGGAGCGAACCCTGTCGAAGATATCCGAGT
TCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTGTGAAGATATCCGAGTTCCATACTCCTTAA
AGAGAGAAGGAGCAAACCAGTAAGAAGAAGATGTCTAAGTTCCATACTCCCTGAAGAAAGAGAGA
GAGAACCCGTAAGAAGAAGATTTTCAAGTTCTATACTCCCTGAAGAAAAAGGGAGCGAACCGCTG
TCT
Found at i:31108 original size:39 final size:40
Alignment explanation
Indices: 31047--31124 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 40
31037 GGGTCGAATT
*
31047 TTTTTTTAAAAAATTCTGGTTCGGGTCGGGTCGGGTCGGA
1 TTTTTTTAAAAAATACTGGTTCGGGTCGGGTCGGGTCGGA
**
31087 TTTTTTTAAAATGTACT-GTTCGGGTCGGGTCGGGTCGG
1 TTTTTTTAAAAAATACTGGTTCGGGTCGGGTCGGGTCGG
31125 GTTTAGGGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 21 0.60
40 14 0.40
ACGTcount: A:0.15, C:0.13, G:0.33, T:0.38
Consensus pattern (40 bp):
TTTTTTTAAAAAATACTGGTTCGGGTCGGGTCGGGTCGGA
Found at i:33184 original size:22 final size:22
Alignment explanation
Indices: 33156--33204 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
33146 CTACTTGTTG
*
33156 TTATAGATAATAATTTAGA-ATA
1 TTATAGATAATAATCTA-ATATA
33178 TTATAGATAATAATCTAATATA
1 TTATAGATAATAATCTAATATA
33200 TTATA
1 TTATA
33205 ATATATAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (22 bp):
TTATAGATAATAATCTAATATA
Found at i:36450 original size:21 final size:21
Alignment explanation
Indices: 36426--36467 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
36416 AGTAGAAGAT
* *
36426 GAGGAAGGATTACCTTCGTAA
1 GAGGAAGAAGTACCTTCGTAA
*
36447 GAGGATGAAGTACCTTCGTAA
1 GAGGAAGAAGTACCTTCGTAA
36468 TGTTCTCTGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (21 bp):
GAGGAAGAAGTACCTTCGTAA
Found at i:40476 original size:3 final size:3
Alignment explanation
Indices: 40468--40525 Score: 73
Period size: 3 Copynumber: 19.3 Consensus size: 3
40458 CTTTTTTGTA
** *
40468 TAT TAT TAT TAT CGT TAT TTT TAT TAT TAT TAT TAT TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
40514 TAT TA- TAT TAT T
1 TAT TAT TAT TAT T
40526 TTTTACATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 2 0.04
3 42 0.89
4 3 0.06
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:40536 original size:19 final size:19
Alignment explanation
Indices: 40482--40536 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 19
40472 ATTATTATCG
* *
40482 TTATTTTTA-TTATTATTA
1 TTATTATTATTTAATATTA
*
40500 TTATTATTATTTATTATTA
1 TTATTATTATTTAATATTA
*
40519 -TATTATTTTTTACATATT
1 TTATTATTATTTA-ATATT
40537 TTGCAGGCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 19 0.59
19 13 0.41
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (19 bp):
TTATTATTATTTAATATTA
Found at i:40536 original size:22 final size:22
Alignment explanation
Indices: 40467--40536 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 22
40457 TCTTTTTTGT
** *
40467 ATATTATTATTATCGTTATT-T
1 ATATTATTATTATTATTATTAC
* *
40488 TTATTATTATTATTATTATTAT
1 ATATTATTATTATTATTATTAC
* *
40510 TTATTATTA-TATTATTTTTTAC
1 ATATTATTATTATTA-TTATTAC
40532 ATATT
1 ATATT
40537 TTGCAGGCCA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
21 22 0.54
22 19 0.46
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (22 bp):
ATATTATTATTATTATTATTAC
Found at i:40576 original size:11 final size:11
Alignment explanation
Indices: 40560--40591 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
40550 CCCAATACAA
40560 CAAGGCCCAAC
1 CAAGGCCCAAC
40571 CAAGGCCCAAC
1 CAAGGCCCAAC
40582 CAAGGCCCAA
1 CAAGGCCCAA
40592 GCATGAGCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.38, C:0.44, G:0.19, T:0.00
Consensus pattern (11 bp):
CAAGGCCCAAC
Found at i:47106 original size:22 final size:22
Alignment explanation
Indices: 47080--47202 Score: 84
Period size: 23 Copynumber: 5.2 Consensus size: 22
47070 AGATCCAATC
47080 AAAAACAAAGAAAAATCAAAGA
1 AAAAACAAAGAAAAATCAAAGA
*
47102 GAAAAGAGCAAAGAAAAAAACAAAGA
1 -AAAA-A-CAAAG-AAAAATCAAAGA
* * * * *
47128 GCAGAGAGAAAAAAAAATCAAAGC
1 --AAAAACAAAGAAAAATCAAAGA
* *
47152 AAAAAGAAAAAAAAATCAAAGCA
1 AAAAACAAAGAAAAATCAAAG-A
* *
47175 AAAATCAAAGAAAAAGCAAAGA
1 AAAAACAAAGAAAAATCAAAGA
47197 ACAAAA
1 A-AAAA
47203 AGAGGACAAA
Statistics
Matches: 78, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
22 21 0.27
23 24 0.31
24 11 0.14
25 8 0.10
26 12 0.15
27 2 0.03
ACGTcount: A:0.73, C:0.10, G:0.14, T:0.03
Consensus pattern (22 bp):
AAAAACAAAGAAAAATCAAAGA
Found at i:47116 original size:12 final size:11
Alignment explanation
Indices: 47080--47197 Score: 62
Period size: 12 Copynumber: 10.2 Consensus size: 11
47070 AGATCCAATC
47080 AAAAA-CAAAG
1 AAAAAGCAAAG
*
47090 AAAAATCAAAGAG
1 AAAAAGC-AA-AG
47103 AAAAGAGCAAAG
1 AAAA-AGCAAAG
*
47115 AAAAAAACAAAG
1 -AAAAAGCAAAG
* *
47127 AGCAGAGAG-AAAA
1 A--A-AAAGCAAAG
*
47140 AAAAATCAAAG
1 AAAAAGCAAAG
*
47151 CAAAAAG-AAAA
1 -AAAAAGCAAAG
*
47162 AAAAATCAAAG
1 AAAAAGCAAAG
*
47173 CAAAAATCAAAG
1 -AAAAAGCAAAG
47185 AAAAAGCAAAG
1 AAAAAGCAAAG
47196 AA
1 AA
47198 CAAAAAGAGG
Statistics
Matches: 83, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
10 12 0.14
11 24 0.29
12 26 0.31
13 17 0.20
14 4 0.05
ACGTcount: A:0.73, C:0.09, G:0.14, T:0.03
Consensus pattern (11 bp):
AAAAAGCAAAG
Found at i:47128 original size:19 final size:21
Alignment explanation
Indices: 47104--47142 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
47094 ATCAAAGAGA
47104 AAAGAGCA-A-AGAAAAAAAC
1 AAAGAGCAGAGAGAAAAAAAC
47123 AAAGAGCAGAGAGAAAAAAA
1 AAAGAGCAGAGAGAAAAAAA
47143 AATCAAAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 1 0.06
21 9 0.50
ACGTcount: A:0.72, C:0.08, G:0.21, T:0.00
Consensus pattern (21 bp):
AAAGAGCAGAGAGAAAAAAAC
Found at i:48843 original size:36 final size:35
Alignment explanation
Indices: 48788--48930 Score: 173
Period size: 36 Copynumber: 4.0 Consensus size: 35
48778 TTTTGAGAAT
48788 TTTAAAACAAATTTTTGTCTCGCTTGAGACAATTTC
1 TTTAAAACAAA-TTTTGTCTCGCTTGAGACAATTTC
* *
48824 TTTCAAAGCAAATTTTGTCTCGCTTGAGACAGCTTTC
1 TTT-AAAACAAATTTTGTCTCGCTTGAGACA-ATTTC
* * *
48861 -TAAAAACAAATTTTGTCTCGTTTGAGACAAATTC
1 TTTAAAACAAATTTTGTCTCGCTTGAGACAATTTC
* *
48895 TCTTAAAACAAACTTCGTCTCGCTTGAGAC-ATTTC
1 T-TTAAAACAAATTTTGTCTCGCTTGAGACAATTTC
48930 T
1 T
48931 CCTTTGAGAT
Statistics
Matches: 91, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
34 3 0.03
35 30 0.33
36 47 0.52
37 11 0.12
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.38
Consensus pattern (35 bp):
TTTAAAACAAATTTTGTCTCGCTTGAGACAATTTC
Found at i:48877 original size:71 final size:72
Alignment explanation
Indices: 48791--48925 Score: 202
Period size: 71 Copynumber: 1.9 Consensus size: 72
48781 TGAGAATTTT
* * * *
48791 AAAACAAATTTTTGTCTCGCTTGAGACAATTTCT-TTCAAAGCAAATTTTGTCTCGCTTGAGACA
1 AAAACAAATTTTTGTCTCGCTTGAGACAAATTCTCTT-AAAACAAACTTCGTCTCGCTTGAGACA
48855 GCTTTCTA
65 GCTTTCTA
*
48863 AAAACAAA-TTTTGTCTCGTTTGAGACAAATTCTCTTAAAACAAACTTCGTCTCGCTTGAGACA
1 AAAACAAATTTTTGTCTCGCTTGAGACAAATTCTCTTAAAACAAACTTCGTCTCGCTTGAGACA
48926 TTTCTCCTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
71 47 0.82
72 10 0.18
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (72 bp):
AAAACAAATTTTTGTCTCGCTTGAGACAAATTCTCTTAAAACAAACTTCGTCTCGCTTGAGACAG
CTTTCTA
Found at i:49011 original size:106 final size:103
Alignment explanation
Indices: 48892--49140 Score: 299
Period size: 106 Copynumber: 2.4 Consensus size: 103
48882 TTGAGACAAA
* *
48892 TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACATTTCTCCTTTGAGATACAAAATTTTGAATTT
1 TTCTTTTAAAACAAACTTCGTCTCGCTTGAGACATTTCTCCTTTGAGAT-CAAAATTTCGAATTT
*
48957 GATTCAC-TTAAAACAAAATTAATCTCACCTT-AGATTGTTGT
65 GATTCACATT-AAACAAAATTAATCTCA-CTTGAGATCG-T-T
* * *
48998 TTCTTTTAAAACAAATTTCGTCTCGCTTGAGACCTTT-TCCCTTTGAGATCCAAATTTCGAATTT
1 TTCTTTTAAAACAAACTTCGTCTCGCTTGAGACATTTCT-CCTTTGAGATCAAAATTTCGAATTT
* * *
49062 GTTTCACATTAAACAAAGTTGATCTCACTTGAGATCGTT
65 GATTCACATTAAACAAAATTAATCTCACTTGAGATCGTT
** *
49101 TTC-TCAAAAACAAACTTTGTCTCGCTTGAGACAATTTCTC
1 TTCTTTTAAAACAAACTTCGTCTCGCTTGAGAC-ATTTCTC
49141 TAAAAACAAA
Statistics
Matches: 124, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
102 25 0.20
103 8 0.06
104 5 0.04
105 40 0.32
106 46 0.37
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (103 bp):
TTCTTTTAAAACAAACTTCGTCTCGCTTGAGACATTTCTCCTTTGAGATCAAAATTTCGAATTTG
ATTCACATTAAACAAAATTAATCTCACTTGAGATCGTT
Found at i:49129 original size:36 final size:36
Alignment explanation
Indices: 49084--49203 Score: 122
Period size: 36 Copynumber: 3.4 Consensus size: 36
49074 ACAAAGTTGA
**
49084 TCTCACTTGAGATCGTTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAGA-CAATTTCTCTAAAAACAAACTTTG
*
49120 TCTCGCTTGAGACAATTTCTCTAAAAACAAACTTTG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
* * * *
49156 TCTCATTTGAGACTATATCT-T-AAAGCAAA-TTTCG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTT-G
*
49190 TCTCGCTTGAGACA
1 TCTCACTTGAGACA
49204 TCATTTTCTC
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
33 3 0.04
34 19 0.27
35 8 0.11
36 41 0.58
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (36 bp):
TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
Found at i:49493 original size:29 final size:29
Alignment explanation
Indices: 49455--49531 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 29
49445 ACAGTGTCTC
*
49455 TTGAGATAAAAATCTTGGAGTTTGTTCCTT
1 TTGA-ATAAAAATCTTTGAGTTTGTTCCTT
*
49485 TTGAATAAAAATCTTTGAG-TTGTTTCTT
1 TTGAATAAAAATCTTTGAGTTTGTTCCTT
*
49513 TTGAA-AAATATCTTTGAGT
1 TTGAATAAAAATCTTTGAGT
49532 CTATTTATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 12 0.28
28 13 0.30
29 14 0.33
30 4 0.09
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (29 bp):
TTGAATAAAAATCTTTGAGTTTGTTCCTT
Found at i:49542 original size:28 final size:27
Alignment explanation
Indices: 49483--49546 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 27
49473 AGTTTGTTCC
* *
49483 TTTTGAATAAAAATCTTTGAGTTGTTTC
1 TTTTGAA-AAAAATCTTTGAGTTATTTA
*
49511 TTTTGAAAAATATCTTTGAGTCTATTTA
1 TTTTGAAAAAAATCTTTGAGT-TATTTA
49539 TTTTGAAA
1 TTTTGAAA
49547 CAAAGTTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 13 0.41
28 19 0.59
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.50
Consensus pattern (27 bp):
TTTTGAAAAAAATCTTTGAGTTATTTA
Found at i:49620 original size:52 final size:53
Alignment explanation
Indices: 49542--49645 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 53
49532 CTATTTATTT
49542 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAATCTTTGAGTC
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
*
49594 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTGAAAAAAATCTTTGAG
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAAATCTTTGAG
49646 ATTGTTTCTT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 36 0.73
54 13 0.27
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (53 bp):
TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
Found at i:49645 original size:26 final size:28
Alignment explanation
Indices: 49615--49673 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 28
49605 TTTGTCTCTC
49615 TTGAGA-CAATT-TTGTGAAAAAAATCT
1 TTGAGATCAATTCTTGTGAAAAAAATCT
*** *
49641 TTGAGATTGTTTCTTTTGAAAAAAATCT
1 TTGAGATCAATTCTTGTGAAAAAAATCT
49669 TTGAG
1 TTGAG
49674 TTGGTTTCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 6 0.22
27 2 0.07
28 19 0.70
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.41
Consensus pattern (28 bp):
TTGAGATCAATTCTTGTGAAAAAAATCT
Found at i:49689 original size:27 final size:28
Alignment explanation
Indices: 49629--49695 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
49619 GACAATTTTG
49629 TGAAAAAAATCTTTGAGATTGTTTCTTT
1 TGAAAAAAATCTTTGAGATTGTTTCTTT
49657 TGAAAAAAATCTTTGAG-TTGGTTTCTTT
1 TGAAAAAAATCTTTGAGATT-GTTTCTTT
*
49685 TAAAACAAAAT
1 TGAAA-AAAAT
49696 TTTATCTCTT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
27 2 0.06
28 29 0.81
29 5 0.14
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.42
Consensus pattern (28 bp):
TGAAAAAAATCTTTGAGATTGTTTCTTT
Found at i:49786 original size:62 final size:63
Alignment explanation
Indices: 49651--49787 Score: 188
Period size: 63 Copynumber: 2.2 Consensus size: 63
49641 TTGAGATTGT
* * *
49651 TTCTTTTGAAAAAAATCTTTGAGTTGGTTTCTTTTAAAACAAAATTTTATCTCTTAACGACAAT
1 TTCTTTTG-AAAAAATCTTTGAGTTGGTTTCTTTGAAAACAAAATTTTATCTCTCAACGACAAC
* * *
49715 TTCTTTTGAAAAAATCTTTGAGTCT-GTTTCTTTGGAAACAAAATTTTGTCTCTCGA-GACAAC
1 TTCTTTTGAAAAAATCTTTGAGT-TGGTTTCTTTGAAAACAAAATTTTATCTCTCAACGACAAC
49777 TTCTTTTGAAA
1 TTCTTTTGAAA
49788 CCACCCACAT
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
62 16 0.24
63 41 0.62
64 9 0.14
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (63 bp):
TTCTTTTGAAAAAATCTTTGAGTTGGTTTCTTTGAAAACAAAATTTTATCTCTCAACGACAAC
Found at i:49877 original size:31 final size:31
Alignment explanation
Indices: 49842--49917 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
49832 CCTTGAGGCA
49842 GTTTCTCTAT-AAATATAAA-ATCTTTGAGTTT
1 GTTTCTCT-TGAAATA-AAACATCTTTGAGTTT
*
49873 GTTTCTCTTGAAATAAAACCATCTTTGAG-TC
1 GTTTCTCTTGAAATAAAA-CATCTTTGAGTTT
*
49904 GTTTCCCTTGAAAT
1 GTTTCTCTTGAAAT
49918 GAATTTTCAC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
30 4 0.10
31 27 0.68
32 9 0.22
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (31 bp):
GTTTCTCTTGAAATAAAACATCTTTGAGTTT
Found at i:50102 original size:62 final size:64
Alignment explanation
Indices: 50022--50140 Score: 165
Period size: 63 Copynumber: 1.9 Consensus size: 64
50012 CTTTTAAAAC
**
50022 AAACATCTTTGAGATCATTTCCCTTT-AAA-TGAATTTTGTCTCAT-TTGAGACAGTTTTCCTTT
1 AAACATCTTTGAGATCATTT-CCTTTGAAACAAAATTTTGTCTCATATTGAGACAGTTTTCCTTT
*
50084 AAACAATCTTTGAG-TCATTTCCTTTGAAACAAAATTTTGTCTCTTATTGAGACAGTT
1 AAAC-ATCTTTGAGATCATTTCCTTTGAAACAAAATTTTGTCTCATATTGAGACAGTT
50141 GCTTTTGAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
61 5 0.10
62 13 0.26
63 21 0.42
64 11 0.22
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.43
Consensus pattern (64 bp):
AAACATCTTTGAGATCATTTCCTTTGAAACAAAATTTTGTCTCATATTGAGACAGTTTTCCTTT
Found at i:50287 original size:46 final size:45
Alignment explanation
Indices: 50219--50681 Score: 264
Period size: 46 Copynumber: 10.7 Consensus size: 45
50209 ACCATAACTT
* * *
50219 TTAGATGGCCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACC
1 TTAGATGGCCAGAAC-TCCTCATCACGTAGGAGCCGTGTCATCACC
* *
50264 TTTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTC-CC
1 -TTAGATGGCCAGAACTCCTCATCACGTAGGAGCCGTGTCA-TCACC
* * *
50310 -CAGA---CCAGATCTCCTCATCACGTAGGAGCCGTGCCA--ACC
1 TTAGATGGCCAGAACTCCTCATCACGTAGGAGCCGTGTCATCACC
* ** * * *
50349 ATAGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACC
1 TTAGATGGCCAGAAC-TCCTCATCACGTAGGAGCCGTGTCATCACC
* *
50394 TTTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTC-CC
1 -TTAGATGGCCAGAACTCCTCATCACGTAGGAGCCGTGTCA-TCACC
* * *
50440 -CAGA---CCAGATCTCCTCATCACGTAGGAGCCGTGCCA--ACC
1 TTAGATGGCCAGAACTCCTCATCACGTAGGAGCCGTGTCATCACC
* ** * * *
50479 ATAGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACC
1 TTAGATGGCCAGAAC-TCCTCATCACGTAGGAGCCGTGTCATCACC
* * *
50524 TTTAGATGGCCAGAACTCTTCATCACGTATGATCCGTGTCATTC-CC
1 -TTAGATGGCCAGAACTCCTCATCACGTAGGAGCCGTGTCA-TCACC
* * * *
50570 -CAGA---CCAGATCTCCTCATCACGTATGAGCAGTGTCA--ACC
1 TTAGATGGCCAGAACTCCTCATCACGTAGGAGCCGTGTCATCACC
* * ** * *
50609 CTCGA---CCAGATTTCCTCATCACGTAGGAACCATGTCA-C-CC
1 TTAGATGGCCAGAACTCCTCATCACGTAGGAGCCGTGTCATCACC
* * * *
50649 TTAGATGACCCGAACTCTTCATCACGTATGAGC
1 TTAGATGGCCAGAACTCCTCATCACGTAGGAGC
50682 AGTGGCGTCC
Statistics
Matches: 326, Mismatches: 61, Indels: 63
0.72 0.14 0.14
Matches are distributed among these distances:
39 6 0.02
40 40 0.12
41 84 0.26
42 2 0.01
43 71 0.22
44 9 0.03
45 6 0.02
46 99 0.30
47 9 0.03
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (45 bp):
TTAGATGGCCAGAACTCCTCATCACGTAGGAGCCGTGTCATCACC
Found at i:50330 original size:41 final size:40
Alignment explanation
Indices: 50273--50645 Score: 221
Period size: 41 Copynumber: 8.8 Consensus size: 40
50263 CTTTAGATGG
* * *
50273 CCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCAGA
1 CCAGATCTCCTCATCACGTAGGAGCCGTGTCA-TCCCCAGA
* * **
50314 CCAGATCTCCTCATCACGTAGGAGCCGTGCCAACCATAGATAA
1 CCAGATCTCCTCATCACGTAGGAGCCGTGTCATCCCCAG---A
* * * *
50357 CCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGA
1 CCAGATC-TCCTCATCACGTAGGAGCCGTGTCATC-CC--CAGA
* * *
50400 TGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCAGA
1 ---CCAGATCTCCTCATCACGTAGGAGCCGTGTCA-TCCCCAGA
* * **
50444 CCAGATCTCCTCATCACGTAGGAGCCGTGCCAACCATAGATAA
1 CCAGATCTCCTCATCACGTAGGAGCCGTGTCATCCCCAG---A
* * * *
50487 CCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGA
1 CCAGATC-TCCTCATCACGTAGGAGCCGTGTCATC-CC--CAGA
* * * *
50530 TGGCCAGAACTCTTCATCACGTATGATCCGTGTCATTCCCCAGA
1 ---CCAGATCTCCTCATCACGTAGGAGCCGTGTCA-TCCCCAGA
* * *
50574 CCAGATCTCCTCATCACGTATGAGCAGTGTCAACCCTC-GA
1 CCAGATCTCCTCATCACGTAGGAGCCGTGTCATCCC-CAGA
* * *
50614 CCAGATTTCCTCATCACGTAGGAACCATGTCA
1 CCAGATCTCCTCATCACGTAGGAGCCGTGTCA
50646 CCCTTAGATG
Statistics
Matches: 259, Mismatches: 48, Indels: 51
0.72 0.13 0.14
Matches are distributed among these distances:
40 40 0.15
41 85 0.33
42 2 0.01
43 58 0.22
44 8 0.03
46 60 0.23
47 6 0.02
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.24
Consensus pattern (40 bp):
CCAGATCTCCTCATCACGTAGGAGCCGTGTCATCCCCAGA
Found at i:50374 original size:43 final size:44
Alignment explanation
Indices: 50234--50515 Score: 179
Period size: 41 Copynumber: 6.5 Consensus size: 44
50224 TGGCCAGCCG
* ** * ** *
50234 TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
1 TCCTCATCACGTAGGAGCCGTGCCAT-ACC-ATAGATAACCAGACC
* * * * ** *
50280 TCTTCATCACGTATGAGCCGTGTCATTCCCCAG---ACCAGATC
1 TCCTCATCACGTAGGAGCCGTGCCATACCATAGATAACCAGACC
50321 TCCTCATCACGTAGGAGCCGTGCCA-ACCATAGATAACCAG-CC
1 TCCTCATCACGTAGGAGCCGTGCCATACCATAGATAACCAGACC
* ** * ** *
50363 GTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
1 -TCCTCATCACGTAGGAGCCGTGCCAT-ACC-ATAGATAACCAGACC
* * * * ** *
50410 TCTTCATCACGTATGAGCCGTGTCATTCCCCAG---ACCAGATC
1 TCCTCATCACGTAGGAGCCGTGCCATACCATAGATAACCAGACC
50451 TCCTCATCACGTAGGAGCCGTGCCA-ACCATAGATAACCAG-CC
1 TCCTCATCACGTAGGAGCCGTGCCATACCATAGATAACCAGACC
*
50493 GTCCTCATCACGTAGGAACCGTG
1 -TCCTCATCACGTAGGAGCCGTG
50516 TTATCACCTT
Statistics
Matches: 184, Mismatches: 40, Indels: 27
0.73 0.16 0.11
Matches are distributed among these distances:
40 8 0.04
41 56 0.30
42 2 0.01
43 53 0.29
44 4 0.02
45 7 0.04
46 53 0.29
47 1 0.01
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (44 bp):
TCCTCATCACGTAGGAGCCGTGCCATACCATAGATAACCAGACC
Found at i:50453 original size:130 final size:130
Alignment explanation
Indices: 50227--50681 Score: 751
Period size: 130 Copynumber: 3.5 Consensus size: 130
50217 TTTTAGATGG
50227 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
50292 ATGAGCCGTGTCATTCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGCCAACCATAGATAA
66 ATGAGCCGTGTCATTCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGCCAACCATAGATAA
50357 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
50422 ATGAGCCGTGTCATTCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGCCAACCATAGATAA
66 ATGAGCCGTGTCATTCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGCCAACCATAGATAA
50487 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
* * * * * *
50552 ATGATCCGTGTCATTCCCCAGACCAGATCTCCTCATCACGTATGAGCAGTGTCAACCCTCG---A
66 ATGAGCCGTGTCATTCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGCCAACCATAGATAA
*** * * * *
50614 CCAGATTTCCTCATCACGTAGGAACCATG---TCACCCTTAGATGACCCGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
50676 ATGAGC
66 ATGAGC
50682 AGTGGCGTCC
Statistics
Matches: 311, Mismatches: 14, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
124 35 0.11
127 26 0.08
130 250 0.80
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.24
Consensus pattern (130 bp):
CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
ATGAGCCGTGTCATTCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGCCAACCATAGATAA
Found at i:50645 original size:40 final size:39
Alignment explanation
Indices: 50533--50649 Score: 105
Period size: 40 Copynumber: 2.9 Consensus size: 39
50523 CTTTAGATGG
* * *
50533 CCAGAACTCTTCATCACGTATGATCC-GTGTCATTCCC-CAGA
1 CCAGATCTCCTCATCACGTAGGA-CCAGTGTCA--CCCTC-GA
* *
50574 CCAGATCTCCTCATCACGTATGAGCAGTGTCAACCCTCGA
1 CCAGATCTCCTCATCACGTAGGACCAGTGTC-ACCCTCGA
*
50614 CCAGATTTCCTCATCACGTAGGAACCA-TGTCACCCT
1 CCAGATCTCCTCATCACGTAGG-ACCAGTGTCACCCT
50650 TAGATGACCC
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
39 5 0.08
40 30 0.45
41 30 0.45
42 1 0.02
ACGTcount: A:0.25, C:0.35, G:0.15, T:0.25
Consensus pattern (39 bp):
CCAGATCTCCTCATCACGTAGGACCAGTGTCACCCTCGA
Found at i:50851 original size:3 final size:3
Alignment explanation
Indices: 50843--50900 Score: 73
Period size: 3 Copynumber: 19.3 Consensus size: 3
50833 CTTTTTTGTA
** *
50843 TAT TAT TAT TAT CGT TAT TTT TAT TAT TAT TAT TAT TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
50889 TAT TA- TAT TAT T
1 TAT TAT TAT TAT T
50901 TTTTTACATA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 2 0.04
3 42 0.89
4 3 0.06
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:50952 original size:11 final size:11
Alignment explanation
Indices: 50936--50967 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
50926 CCCAATACAA
50936 CAAGGCCCAAC
1 CAAGGCCCAAC
50947 CAAGGCCCAAC
1 CAAGGCCCAAC
50958 CAAGGCCCAA
1 CAAGGCCCAA
50968 GCATGAGCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.38, C:0.44, G:0.19, T:0.00
Consensus pattern (11 bp):
CAAGGCCCAAC
Found at i:57145 original size:6 final size:6
Alignment explanation
Indices: 57134--57158 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
57124 ACCAACTAAC
57134 CCCAAA CCCAAA CCCAAA CCCAAA C
1 CCCAAA CCCAAA CCCAAA CCCAAA C
57159 AAACTCTACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (6 bp):
CCCAAA
Found at i:58441 original size:2 final size:2
Alignment explanation
Indices: 58436--58470 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
58426 TTTTTTTTAA
58436 AT AT AT 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 AT AT AT A
58471 GAGAAAATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:60314 original size:13 final size:13
Alignment explanation
Indices: 60298--60355 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 13
60288 TAATATGATT
60298 TATTAAATAAAAA
1 TATTAAATAAAAA
60311 TATTAAAATAAAAA
1 TATT-AAATAAAAA
60325 TATTAGAATAAATAAA
1 TATTA-AAT-AA-AAA
*
60341 TATTTAATATAAAA
1 TATTAAATA-AAAA
60355 T
1 T
60356 TAAGAAAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
13 5 0.13
14 21 0.54
15 6 0.15
16 7 0.18
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (13 bp):
TATTAAATAAAAA
Found at i:61177 original size:30 final size:30
Alignment explanation
Indices: 61132--61270 Score: 206
Period size: 30 Copynumber: 4.5 Consensus size: 30
61122 TTGTGTTTGA
* *
61132 TTTATAATCTATTAAATATAATAAATATTATT
1 TTTATAA--TATTAAATCTATTAAATATTATT
61164 TTTATAATATTAAATCTATTAAATATTATT
1 TTTATAATATTAAATCTATTAAATATTATT
61194 TTTATAATATTAAATCTATTAAATATTATT
1 TTTATAATATTAAATCTATTAAATATTATT
61224 TTTATAATATTAAATCTATTAAATATTATAT
1 TTTATAATATTAAATCTATTAAATATTAT-T
* *
61255 TAATATTATATTAAAT
1 T-TTATAATATTAAAT
61271 ATAAAGTTAT
Statistics
Matches: 101, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
30 80 0.79
31 2 0.02
32 19 0.19
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (30 bp):
TTTATAATATTAAATCTATTAAATATTATT
Found at i:64187 original size:16 final size:17
Alignment explanation
Indices: 64166--64203 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
64156 AGTAAAAATG
*
64166 GAATTTTTAATT-AATT
1 GAATTTTAAATTCAATT
64182 GAATTTTAAATTCAATT
1 GAATTTTAAATTCAATT
*
64199 AAATT
1 GAATT
64204 ATATTAAGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (17 bp):
GAATTTTAAATTCAATT
Found at i:64668 original size:2 final size:2
Alignment explanation
Indices: 64663--64738 Score: 63
Period size: 2 Copynumber: 40.5 Consensus size: 2
64653 AATGAAAATG
* * * * *
64663 AT AT AT AT AT AT AT AT AT AT AT -T AA AT -T AT TT GT AT AC AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
64703 AT -T TT AT -T AT AT A- 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 AT AT AT AT AT A
64739 AATTATAAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
1 5 0.08
2 55 0.92
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:76168 original size:10 final size:10
Alignment explanation
Indices: 76153--76179 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
76143 GAAAATTTCA
76153 GGATGAAACC
1 GGATGAAACC
76163 GGATGAAACC
1 GGATGAAACC
76173 GGATGAA
1 GGATGAA
76180 GACATCAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.15, G:0.33, T:0.11
Consensus pattern (10 bp):
GGATGAAACC
Found at i:80704 original size:21 final size:21
Alignment explanation
Indices: 80678--80800 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 21
80668 TTATGTGCAC
*
80678 TAGGTATCGATACCCCCTTTA
1 TAGGTATCGATACCCCCTTGA
*
80699 TAGGTATCGATACCCCCTTGC
1 TAGGTATCGATACCCCCTTGA
* *
80720 TAGGTATCAATA-CCCCTTCA
1 TAGGTATCGATACCCCCTTGA
*
80740 -ACGTGTATCGATACCCTCTTTGA
1 TA-G-GTATCGATACCC-CCTTGA
* *
80763 -ATGTGTATTGATACCCCCTTGC
1 TA-G-GTATCGATACCCCCTTGA
*
80785 TAGGTATCAATACCCC
1 TAGGTATCGATACCCC
80801 TTCAACGTGT
Statistics
Matches: 83, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
19 1 0.01
20 7 0.08
21 49 0.59
22 7 0.08
23 19 0.23
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (21 bp):
TAGGTATCGATACCCCCTTGA
Found at i:80770 original size:23 final size:22
Alignment explanation
Indices: 80681--80844 Score: 87
Period size: 21 Copynumber: 7.6 Consensus size: 22
80671 TGTGCACTAG
80681 GTATCGATACCCCCTTT--ATAG-
1 GTATCGATA-CCCCTTTGAAT-GT
* *
80702 GTATCGATACCCCCTTG-CTAG-
1 GTATCGATACCCCTTTGAAT-GT
* * *
80723 GTATCAATACCCC-TTCAACGT
1 GTATCGATACCCCTTTGAATGT
80744 GTATCGATACCCTCTTTGAATGT
1 GTATCGATACCC-CTTTGAATGT
* * *
80767 GTATTGATACCCCCTTG-CTAG-
1 GTATCGATACCCCTTTGAAT-GT
* * *
80788 GTATCAATACCCC-TTCAACGT
1 GTATCGATACCCCTTTGAATGT
*
80809 GTATCG-CACCCTCTTTGAATGT
1 GTATCGATACCC-CTTTGAATGT
*
80831 GTATTGATACCCCT
1 GTATCGATACCCCT
80845 ATAAGGGTAC
Statistics
Matches: 109, Mismatches: 23, Indels: 21
0.71 0.15 0.14
Matches are distributed among these distances:
20 16 0.15
21 53 0.49
22 19 0.17
23 21 0.19
ACGTcount: A:0.23, C:0.29, G:0.15, T:0.33
Consensus pattern (22 bp):
GTATCGATACCCCTTTGAATGT
Found at i:80783 original size:65 final size:65
Alignment explanation
Indices: 80681--80843 Score: 262
Period size: 65 Copynumber: 2.6 Consensus size: 65
80671 TGTGCACTAG
* *
80681 GTATCGATACCCCCTTT--ATAG-GTATCGATACCCCCTTGCTAGGTATCAATACCCCTTCAACG
1 GTATCGATACCCTCTTTGAAT-GTGTATTGATACCCCCTTGCTAGGTATCAATACCCCTTCAACG
80743 T
65 T
80744 GTATCGATACCCTCTTTGAATGTGTATTGATACCCCCTTGCTAGGTATCAATACCCCTTCAACGT
1 GTATCGATACCCTCTTTGAATGTGTATTGATACCCCCTTGCTAGGTATCAATACCCCTTCAACGT
*
80809 GTATCG-CACCCTCTTTGAATGTGTATTGATACCCC
1 GTATCGATACCCTCTTTGAATGTGTATTGATACCCC
80844 TATAAGGGTA
Statistics
Matches: 94, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
63 16 0.17
64 29 0.31
65 49 0.52
ACGTcount: A:0.23, C:0.29, G:0.15, T:0.33
Consensus pattern (65 bp):
GTATCGATACCCTCTTTGAATGTGTATTGATACCCCCTTGCTAGGTATCAATACCCCTTCAACGT
Found at i:81342 original size:13 final size:13
Alignment explanation
Indices: 81319--81361 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
81309 AAAACTACAT
81319 ATTGATTTTCAAAC
1 ATTG-TTTTCAAAC
81333 ATTGTTTTCAAAC
1 ATTGTTTTCAAAC
*
81346 ATAGTTTTCAAA-
1 ATTGTTTTCAAAC
81358 ATTG
1 ATTG
81362 CCCATTAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 3 0.11
13 20 0.74
14 4 0.15
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (13 bp):
ATTGTTTTCAAAC
Found at i:83111 original size:13 final size:14
Alignment explanation
Indices: 83080--83113 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
83070 AGGGGGAGTA
83080 ATTTTCAAAAATTG
1 ATTTTCAAAAATTG
83094 A-TTTCAAAAA-TG
1 ATTTTCAAAAATTG
83106 ATTTTCAA
1 ATTTTCAA
83114 TAAGAAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.16
13 15 0.79
14 1 0.05
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (14 bp):
ATTTTCAAAAATTG
Done.