Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003899.1 Hibiscus syriacus cultivar Beakdansim tig00008427_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: 40306
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:307 original size:24 final size:23
Alignment explanation
Indices: 257--307 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
247 ATCCATGTAT
* * *
257 TGACCAATATCAAAGTCGAGTAT
1 TGACCAAGATCAAAGTCGAATAC
*
280 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAA-GTCGAATAC
304 TGAC
1 TGAC
308 TAGTAGTCAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (23 bp):
TGACCAAGATCAAAGTCGAATAC
Found at i:1338 original size:20 final size:20
Alignment explanation
Indices: 1313--1370 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
1303 CATTCATTGA
1313 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1333 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
1353 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
1371 CGCATGCGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1410 original size:31 final size:32
Alignment explanation
Indices: 1375--1438 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 32
1365 GAAAATCGCA
1375 TGCGAATGAAAATCGCATTGCGA-TTTCTCGT
1 TGCGAATGAAAATCGCATTGCGATTTTCTCGT
* *** *
1406 TGCGATTTTCATTCGCATTGCGATTTTCTCGT
1 TGCGAATGAAAATCGCATTGCGATTTTCTCGT
1438 T
1 T
1439 ACGATAGCCA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 18 0.67
32 9 0.33
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.41
Consensus pattern (32 bp):
TGCGAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:1428 original size:18 final size:16
Alignment explanation
Indices: 1387--1436 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 16
1377 CGAATGAAAA
1387 TCGCATTGCGA-TTTC
1 TCGCATTGCGATTTTC
1402 TCG--TTGCGATTTTC
1 TCGCATTGCGATTTTC
1416 ATTCGCATTGCGATTTTC
1 --TCGCATTGCGATTTTC
1434 TCG
1 TCG
1437 TTACGATAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
13 6 0.20
14 4 0.13
15 3 0.10
16 6 0.20
18 11 0.37
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (16 bp):
TCGCATTGCGATTTTC
Found at i:2940 original size:24 final size:23
Alignment explanation
Indices: 2900--2957 Score: 80
Period size: 24 Copynumber: 2.5 Consensus size: 23
2890 GGGGGGGGGA
2900 GAATAGAGGGGGGCCTCTTGAAC
1 GAATAGAGGGGGGCCTCTTGAAC
*
2923 GAATAGGGAGGGGGCCTCTTGAAC
1 GAATAGAG-GGGGGCCTCTTGAAC
* *
2947 GATTGGAGGGG
1 GAATAGAGGGG
2958 ACTCTTGAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 10 0.33
24 20 0.67
ACGTcount: A:0.24, C:0.14, G:0.45, T:0.17
Consensus pattern (23 bp):
GAATAGAGGGGGGCCTCTTGAAC
Found at i:2965 original size:21 final size:24
Alignment explanation
Indices: 2900--2948 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
2890 GGGGGGGGGA
*
2900 GAATAGAG-GGGGGCCTCTTGAAC
1 GAATAGGGAGGGGGCCTCTTGAAC
2923 GAATAGGGAGGGGGCCTCTTGAAC
1 GAATAGGGAGGGGGCCTCTTGAAC
2947 GA
1 GA
2949 TTGGAGGGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.27, C:0.16, G:0.41, T:0.16
Consensus pattern (24 bp):
GAATAGGGAGGGGGCCTCTTGAAC
Found at i:3359 original size:19 final size:20
Alignment explanation
Indices: 3335--3379 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
3325 AAAACTTAAA
3335 ATCGCAACGC-GAAATGACT
1 ATCGCAACGCGGAAATGACT
*
3354 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGGAAATGACT
3374 ATCGCA
1 ATCGCA
3380 TTGCGATAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:3421 original size:20 final size:19
Alignment explanation
Indices: 3380--3424 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
3370 GGCTATCGCA
*
3380 TTGCGATAGCATTTCCGCG
1 TTGCGATAGCATTTCCACG
* *
3399 TTGCGATAGTCATTTTCATG
1 TTGCGATAG-CATTTCCACG
3419 TTGCGA
1 TTGCGA
3425 AAGTAAACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (19 bp):
TTGCGATAGCATTTCCACG
Found at i:3929 original size:18 final size:18
Alignment explanation
Indices: 3903--3947 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
3893 GTCGATCAGA
*
3903 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
3921 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
3939 TGATGGCTC
1 TGATGGCTC
3948 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:5278 original size:20 final size:20
Alignment explanation
Indices: 5253--5290 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5243 AATAGTTTCT
5253 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
5273 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
5291 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:5840 original size:41 final size:41
Alignment explanation
Indices: 5795--5872 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
5785 CGAAGGTCAG
* *
5795 TATCGCATTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* *
5836 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
5873 CCCAATTCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:5861 original size:20 final size:20
Alignment explanation
Indices: 5755--5869 Score: 90
Period size: 20 Copynumber: 5.7 Consensus size: 20
5745 CGCTTTGAAA
*
5755 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
*
5776 ATCGCGTTGCGA-AGGTCAGT
1 ATCGCATTGCGATA-GTCAGT
* *
5796 ATCGCATTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
5816 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
5837 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
5857 ATCGCATTGCGAT
1 ATCGCATTGCGAT
5870 TTTCCCAATT
Statistics
Matches: 73, Mismatches: 18, Indels: 7
0.74 0.18 0.07
Matches are distributed among these distances:
19 3 0.04
20 45 0.62
21 25 0.34
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:5891 original size:21 final size:21
Alignment explanation
Indices: 5858--5950 Score: 91
Period size: 20 Copynumber: 4.5 Consensus size: 21
5848 ATAGTCAGTA
5858 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * * **
5879 TCGCGTTGTGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
5899 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
5920 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
5940 TCGCATTGCGA
1 TCGCATTGCGA
5951 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:5903 original size:41 final size:41
Alignment explanation
Indices: 5858--5950 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
5848 ATAGTCAGTA
*
5858 TCGCATTGCGATTTTCCCAATTCGCGTTGTGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
5899 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
5940 TCGCATTGCGA
1 TCGCATTGCGA
5951 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:6834 original size:50 final size:50
Alignment explanation
Indices: 6709--6834 Score: 153
Period size: 50 Copynumber: 2.5 Consensus size: 50
6699 GTAGCAGTAA
* * *
6709 AGCGCGCCCCCTGAACCGCGCTATACGTTAATTTGGCACCATGTGGGTAT
1 AGCGCGCCCCCTGAACCGCGCTATACGGTAATCTGGCACCACGTGGGTAT
** * * *
6759 AGCGCGCCCCCTGCCCCGCGATATACGGTGATCTGGCGCCACGTGGGTAT
1 AGCGCGCCCCCTGAACCGCGCTATACGGTAATCTGGCACCACGTGGGTAT
* * *
6809 AGCGCGTCCCCTGATCCGAGCTATAC
1 AGCGCGCCCCCTGAACCGCGCTATAC
6835 CTGGGTATCT
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 63 1.00
ACGTcount: A:0.17, C:0.34, G:0.28, T:0.21
Consensus pattern (50 bp):
AGCGCGCCCCCTGAACCGCGCTATACGGTAATCTGGCACCACGTGGGTAT
Found at i:6972 original size:10 final size:10
Alignment explanation
Indices: 6957--6995 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
6947 TTATCACACT
6957 AAATTCTCTC
1 AAATTCTCTC
6967 AAATTCTCT-
1 AAATTCTCTC
6976 AAATTTCTCTC
1 AAA-TTCTCTC
*
6987 AAATACTCT
1 AAATTCTCT
6996 ATCTTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
9 3 0.12
10 20 0.77
11 3 0.12
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.41
Consensus pattern (10 bp):
AAATTCTCTC
Found at i:6985 original size:20 final size:19
Alignment explanation
Indices: 6955--6996 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
6945 TTTTATCACA
*
6955 CTAAATTCTCTCAAATTCT
1 CTAAATTCTCTCAAATACT
6974 CTAAATTTCTCTCAAATACT
1 CTAAA-TTCTCTCAAATACT
6994 CTA
1 CTA
6997 TCTTTTTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.40
Consensus pattern (19 bp):
CTAAATTCTCTCAAATACT
Found at i:7319 original size:111 final size:111
Alignment explanation
Indices: 7122--7452 Score: 590
Period size: 111 Copynumber: 3.0 Consensus size: 111
7112 TGGAAATCAT
*
7122 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACCGTTTTAATTTAATTTAAATTATTAGTA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAA-CGTTTTAATTTAATTTAAATTATTAGTA
* * *
7187 ATATTTAGTTGATTTACTTAATACATGATTATTAGATTAAGAATTAA
65 ATAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
7234 ATATCTCGACACTTTGCTGATACGGTAACATTTTAAAGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
7299 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
7345 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
7410 TAATTAATTGATTTATTTAATGCATGATTATTAGAGTAAGAAT
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAAT
7453 CAATTTTTAT
Statistics
Matches: 211, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
111 176 0.83
112 35 0.17
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.44
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:7632 original size:21 final size:20
Alignment explanation
Indices: 7546--7703 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
7536 AAATGACCAA
**
7546 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
7565 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
7585 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
7605 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
7626 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
7647 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
7667 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
7688 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
7704 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 44 0.43
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:7696 original size:20 final size:20
Alignment explanation
Indices: 7671--7864 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
7661 GATTTTCAAT
* *
7671 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
7691 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
7711 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
7731 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
7751 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
7771 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
7791 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
7811 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
7832 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
7852 AATCGCAACGCGA
1 AATCGCAACGCGA
7865 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:7716 original size:40 final size:39
Alignment explanation
Indices: 7671--7864 Score: 199
Period size: 40 Copynumber: 4.8 Consensus size: 39
7661 GATTTTCAAT
* ** *
7671 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CATA
* * *
7711 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
** * * *
7751 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
* ** *
7791 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT-A
7832 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
7865 TATTTAAAGC
Statistics
Matches: 128, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.01
40 94 0.73
41 33 0.26
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (39 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACCATA
Found at i:7754 original size:60 final size:60
Alignment explanation
Indices: 7671--7863 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
7661 GATTTTCAAT
* ** * *
7671 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
7731 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
7791 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
7852 AATCGCAACGCG
1 AATCGCAACGCG
7864 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:8282 original size:33 final size:33
Alignment explanation
Indices: 8243--8313 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
8233 TTCACTTAGA
*
8243 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
8276 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
8309 TTTCA
1 TTTCA
8314 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:8452 original size:14 final size:14
Alignment explanation
Indices: 8433--8487 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
8423 AGAATGACTG
8433 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
8447 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
8466 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
8480 TCGCAACG
1 TCGCAACG
8488 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:8470 original size:33 final size:33
Alignment explanation
Indices: 8433--8503 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
8423 AGAATGACTG
**
8433 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
8466 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
8499 TCGCA
1 TCGCA
8504 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:8521 original size:19 final size:19
Alignment explanation
Indices: 8499--8596 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
8489 GAAACCAAAA
*
8499 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
8518 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
8532 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
8551 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
8565 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
8584 TCGCGTTGCGATT
1 TCGCGTTGCGATT
8597 CTCGTTGCGA
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:8540 original size:14 final size:14
Alignment explanation
Indices: 8521--8608 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
8511 TTTCATTTCG
8521 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
8535 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
8554 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
8568 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
8585 CGCGTTGCGA-T-TCT
1 --CGTTGCGATTCTCT
8599 CGTTGCGATT
1 CGTTGCGATT
8609 TTCATTTCAA
Statistics
Matches: 61, Mismatches: 2, Indels: 23
0.71 0.02 0.27
Matches are distributed among these distances:
12 8 0.13
13 1 0.02
14 21 0.34
15 1 0.02
16 6 0.10
17 6 0.10
19 18 0.30
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:8546 original size:33 final size:33
Alignment explanation
Indices: 8504--8616 Score: 194
Period size: 33 Copynumber: 3.5 Consensus size: 33
8494 CAAAATCGCA
8504 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
8537 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
8570 TTGCGATTGTCATCTCGCGTTGCGA-T-TCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
8601 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
8617 AACCAAAAGA
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 19 0.25
32 1 0.01
33 56 0.74
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:10630 original size:92 final size:93
Alignment explanation
Indices: 10306--10683 Score: 726
Period size: 93 Copynumber: 4.1 Consensus size: 93
10296 TAGATTGCTT
*
10306 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
10371 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
10399 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
10463 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
10490 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
10554 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
10582 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
10647 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
10675 AGTAAATTT
1 AGTAAATTT
10684 ATCCATTCAA
Statistics
Matches: 282, Mismatches: 1, Indels: 4
0.98 0.00 0.01
Matches are distributed among these distances:
91 91 0.32
92 91 0.32
93 100 0.35
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:10767 original size:19 final size:19
Alignment explanation
Indices: 10727--10855 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
10717 TAGTTTACTT
* *
10727 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
10747 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
10766 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
10785 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
10799 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
10818 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
10832 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
10851 TCGCA
1 TCGCA
10856 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:10806 original size:33 final size:32
Alignment explanation
Indices: 10763--10855 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
10753 CGCGAAACCA
**
10763 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
10795 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
10828 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
10856 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:10853 original size:52 final size:52
Alignment explanation
Indices: 10727--10855 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
10717 TAGTTTACTT
**
10727 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
10779 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
10832 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
10856 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:10873 original size:19 final size:19
Alignment explanation
Indices: 10851--10985 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
10841 GAAACCAAAA
*
10851 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
10870 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
10886 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
10903 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
10919 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
10936 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
10955 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
10975 TCGTGTTGCGA
1 TCGCGTTGCGA
10986 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:10892 original size:14 final size:14
Alignment explanation
Indices: 10873--10929 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
10863 TTTCATTTCG
10873 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
10887 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
10904 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
10920 CGTTGCGATT
1 CGTTGCGATT
10930 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:10898 original size:33 final size:33
Alignment explanation
Indices: 10856--10948 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
10846 CAAAATCGCA
*
10856 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
10889 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
10922 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
10949 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:12900 original size:14 final size:14
Alignment explanation
Indices: 12881--12916 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
12871 ATTGTTTAAT
12881 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
12895 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
12909 TGATTTGT
1 TGATTTGT
12917 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:13090 original size:20 final size:19
Alignment explanation
Indices: 13022--13104 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
13012 CAAAATGACT
13022 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
13041 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
13055 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
13074 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
13094 ATCGCAATGCG
1 ATCGCAATGCG
13105 TTTATAATTT
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 21 0.38
20 19 0.34
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:13153 original size:33 final size:35
Alignment explanation
Indices: 13111--13405 Score: 239
Period size: 33 Copynumber: 8.5 Consensus size: 35
13101 TGCGTTTATA
13111 ATTTCGCATTGCGATT-ATCTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTCATCTCGATTGCGATTTTC
*
13144 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TTCATCTCG-ATTGCGATTTTC
*
13180 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTCATCTCG-ATTGCGATTTTC
*
13215 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TT-CATCTCG-ATTGCGATTTTC
*
13253 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TTCATCTCG-ATTGCGATTTTC
* *
13289 -TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTCATCTCG-ATTGCGATTTTC
13324 ATTTCGCATTGCGATTC-TCTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTCATCTCGATTGCGATTTTC
*
13357 ATTTCCGCATTGCGATT--TCAT-G-TTGGGATTTTC
1 ATTT-CGCATTGCGATTCATC-TCGATTGCGATTTTC
*
13390 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
13406 GTATTTTCCG
Statistics
Matches: 237, Mismatches: 6, Indels: 39
0.84 0.02 0.14
Matches are distributed among these distances:
32 11 0.05
33 96 0.41
34 13 0.05
35 21 0.09
36 23 0.10
37 3 0.01
38 67 0.28
39 3 0.01
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (35 bp):
ATTTCGCATTGCGATTCATCTCGATTGCGATTTTC
Found at i:13157 original size:19 final size:19
Alignment explanation
Indices: 13133--13405 Score: 345
Period size: 19 Copynumber: 15.4 Consensus size: 19
13123 GATTATCTCG
13133 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
13152 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
13171 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
13185 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
13204 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
13223 TTGCGATTTCCATTTCGCA
1 TTGCGATTTTCATTTCGCA
13242 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
13261 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
13280 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
13294 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
13313 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
13332 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
13346 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
13366 TTGCGA-TTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
13379 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
13398 TTGCGATT
1 TTGCGATT
13406 GTATTTTCCG
Statistics
Matches: 224, Mismatches: 8, Indels: 44
0.81 0.03 0.16
Matches are distributed among these distances:
13 5 0.02
14 23 0.10
15 1 0.00
16 23 0.10
17 22 0.10
18 2 0.01
19 142 0.63
20 6 0.03
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:13262 original size:109 final size:105
Alignment explanation
Indices: 13111--13374 Score: 451
Period size: 109 Copynumber: 2.5 Consensus size: 105
13101 TGCGTTTATA
13111 ATTTCGCATTGCGATT-ATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
1 ATTTCGCATTGCGATTCATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
*
13175 GATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
66 GATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
13215 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 ATTTCGCATTGCGA-TT-CATCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
13280 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
62 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
13324 ATTTCGCATTGCGATTC-TCTCGTTGCGATTTTCATTTCCGCATTGCGATTT
1 ATTTCGCATTGCGATTCATCTCGTTGCGATTTTCATTT-CGCATTGCGATTT
13375 CATGTTGGGA
Statistics
Matches: 151, Mismatches: 3, Indels: 11
0.92 0.02 0.07
Matches are distributed among these distances:
104 29 0.19
105 15 0.10
106 4 0.03
107 6 0.04
108 2 0.01
109 95 0.63
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (105 bp):
ATTTCGCATTGCGATTCATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
GATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:13405 original size:52 final size:52
Alignment explanation
Indices: 13111--13374 Score: 447
Period size: 52 Copynumber: 5.0 Consensus size: 52
13101 TGCGTTTATA
*
13111 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
13163 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
13215 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TT-C-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
13272 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
13324 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTT
13375 CATGTTGGGA
Statistics
Matches: 203, Mismatches: 3, Indels: 11
0.94 0.01 0.05
Matches are distributed among these distances:
52 131 0.65
53 15 0.07
54 5 0.02
55 6 0.03
56 2 0.01
57 44 0.22
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:24900 original size:32 final size:32
Alignment explanation
Indices: 24845--24909 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
24835 GCAATAAAAA
*
24845 TAACAATTAATACACATTAACATACATGCCAT
1 TAACAATTAATACACATTAACATACATACCAT
* * * *
24877 TAACAATTACTACATATTGACATATATACCAT
1 TAACAATTAATACACATTAACATACATACCAT
24909 T
1 T
24910 CATATTAAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (32 bp):
TAACAATTAATACACATTAACATACATACCAT
Found at i:27245 original size:18 final size:18
Alignment explanation
Indices: 27222--27269 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 18
27212 TCTGATATTT
*
27222 TTTTCTTCTTATTTTCGA
1 TTTTCTTCTTATTTACGA
*
27240 TTTTCTTC--ATTCACGA
1 TTTTCTTCTTATTTACGA
*
27256 TATTCTTCTTATTT
1 TTTTCTTCTTATTT
27270 CCCATTTCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
16 13 0.54
18 11 0.46
ACGTcount: A:0.15, C:0.19, G:0.04, T:0.62
Consensus pattern (18 bp):
TTTTCTTCTTATTTACGA
Found at i:29261 original size:41 final size:42
Alignment explanation
Indices: 29213--29331 Score: 122
Period size: 39 Copynumber: 2.9 Consensus size: 42
29203 TAGGGTTCAT
*
29213 CTATAGTGACATTTTTCAACAAATGCCGCAACAGAGTAGCA-
1 CTATAGTGGCATTTTTCAACAAATGCCGCAACAGAGTAGCAC
* * * * * *
29254 CTTTAGTGGCATTTTTATAAAAAAT---GCAATAGTGT-TCAC
1 CTATAGTGGCATTTTT-CAACAAATGCCGCAACAGAGTAGCAC
*
29293 CTATAGTGGCATTTTTCAACAAACGCCGCAACAGAGTAG
1 CTATAGTGGCATTTTTCAACAAATGCCGCAACAGAGTAG
29332 TACATTAGCA
Statistics
Matches: 58, Mismatches: 14, Indels: 11
0.70 0.17 0.13
Matches are distributed among these distances:
38 7 0.12
39 23 0.40
41 22 0.38
42 6 0.10
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (42 bp):
CTATAGTGGCATTTTTCAACAAATGCCGCAACAGAGTAGCAC
Found at i:29272 original size:82 final size:80
Alignment explanation
Indices: 29183--29517 Score: 356
Period size: 80 Copynumber: 4.2 Consensus size: 80
29173 TTTAGTAGTG
*
29183 TTTTTATACAAATGTCATAATAGGGTTCATCTATAGTGACATTTTTCAACAAATGCCGCAACAGA
1 TTTTTATACAAATG-C-TAATAGGGTTCATCTATAGTGACATTTTTCAACAAACGCCGCAACAGA
* **
29248 GTAGCACTTTAGTGGCA
64 GTAGTACTTTAGCAGCA
* * * *
29265 TTTTTATAAAAAATGC-AATAGTGTTCACCTATAGTGGCATTTTTCAACAAACGCCGCAACAGAG
1 TTTTTAT-ACAAATGCTAATAGGGTTCATCTATAGTGACATTTTTCAACAAACGCCGCAACAGAG
* * *
29329 TAGTACATTAGCAACG
65 TAGTACTTTAGCAGCA
* * * *
29345 TTTTTATACTAATGTCGTAATAGGGTTTATCTATAGTGACATTTTTCAATAAACGTCGCAACAGA
1 TTTTTATACAAATG-C-TAATAGGGTTCATCTATAGTGACATTTTTCAACAAACGCCGCAACAGA
*
29410 GTAGTACTTTAGTAG-A
64 GTAGTACTTTAGCAGCA
* * * *
29426 GTTTTATACAAACGCTGCAATA-GGTTCATCTATAGTG-CATTTTTCAACAAACACCACAACAGA
1 TTTTTATACAAATGCT--AATAGGGTTCATCTATAGTGACATTTTTCAACAAACGCCGCAACAG-
* **
29489 AG-AGTACTTTAGCGGTG
63 AGTAGTACTTTAGCAGCA
29506 TTTTTATACAAA
1 TTTTTATACAAA
29518 CGCCGCTATA
Statistics
Matches: 210, Mismatches: 35, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
79 38 0.18
80 90 0.43
81 15 0.07
82 61 0.29
83 6 0.03
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (80 bp):
TTTTTATACAAATGCTAATAGGGTTCATCTATAGTGACATTTTTCAACAAACGCCGCAACAGAGT
AGTACTTTAGCAGCA
Found at i:29461 original size:162 final size:161
Alignment explanation
Indices: 29182--29517 Score: 453
Period size: 162 Copynumber: 2.1 Consensus size: 161
29172 CTTTAGTAGT
*
29182 GTTTTTATACAAATGTCATAATAGGGTTCATCTATAGTGACATTTTTCAACAAATGCCGCAACAG
1 GTTTTTATACAAATGTCATAATAGGGTTCATCTATAGTGACATTTTTCAACAAACGCCGCAACAG
* *
29247 AGTAGCACTTTAGTGGCATTTTTATAAAAAATGCAATAGTGTTCACCTATAGTGGCATTTTTCAA
66 AGTAGCACTTTAGTAGCAGTTTTATAAAAAATGCAATAGTGTTCACCTATAGT-GCATTTTTCAA
* *
29312 CAAACGCCGCAACAG-AGTAGTACATTAGCAAC
130 CAAACACCACAACAGAAG-AGTACATTAGCAAC
* * * * *
29344 GTTTTTATACTAATGTCGTAATAGGGTTTATCTATAGTGACATTTTTCAATAAACGTCGCAACAG
1 GTTTTTATACAAATGTCATAATAGGGTTCATCTATAGTGACATTTTTCAACAAACGCCGCAACAG
* ** *
29409 AGTAGTACTTTAGTAG-AGTTTTATACAAACGCTGCAATAG-GTTCATCTATAGTGCATTTTTCA
66 AGTAGCACTTTAGTAGCAGTTTTATA-AAA-AATGCAATAGTGTTCACCTATAGTGCATTTTTCA
* ***
29472 ACAAACACCACAACAGAAGAGTACTTTAGCGGT
129 ACAAACACCACAACAGAAGAGTACATTAGCAAC
29505 GTTTTTATACAAA
1 GTTTTTATACAAA
29518 CGCCGCTATA
Statistics
Matches: 152, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
161 54 0.36
162 90 0.59
163 8 0.05
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Consensus pattern (161 bp):
GTTTTTATACAAATGTCATAATAGGGTTCATCTATAGTGACATTTTTCAACAAACGCCGCAACAG
AGTAGCACTTTAGTAGCAGTTTTATAAAAAATGCAATAGTGTTCACCTATAGTGCATTTTTCAAC
AAACACCACAACAGAAGAGTACATTAGCAAC
Found at i:35448 original size:24 final size:25
Alignment explanation
Indices: 35390--35454 Score: 87
Period size: 26 Copynumber: 2.6 Consensus size: 25
35380 TTCTTTTGAG
35390 TAAATGATATGAACATGAATAAATTA
1 TAAATGATATGAACATGAAT-AATTA
* * *
35416 TAAATGATAGGAACATGAAT-TTTT
1 TAAATGATATGAACATGAATAATTA
35440 TAAATGATATGAACA
1 TAAATGATATGAACA
35455 CGACGAGCTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 16 0.46
26 19 0.54
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.32
Consensus pattern (25 bp):
TAAATGATATGAACATGAATAATTA
Found at i:36410 original size:33 final size:34
Alignment explanation
Indices: 36364--36431 Score: 120
Period size: 33 Copynumber: 2.0 Consensus size: 34
36354 ATAAGGGTAG
36364 AATAAGTTGACTACAGACTCCTTCACAAGGCAAA
1 AATAAGTTGACTACAGACTCCTTCACAAGGCAAA
*
36398 AATAAG-TGACTACAGACTCCTTCGCAAGGCAAA
1 AATAAGTTGACTACAGACTCCTTCACAAGGCAAA
36431 A
1 A
36432 GGCAGCTGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 27 0.82
34 6 0.18
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.19
Consensus pattern (34 bp):
AATAAGTTGACTACAGACTCCTTCACAAGGCAAA
Done.