Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003759.1 Hibiscus syriacus cultivar Beakdansim tig00008051_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: 52647
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:268 original size:21 final size:21
Alignment explanation
Indices: 243--306 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
233 CCCCTTATGC
* *
243 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
264 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
285 CTATC-AGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
305 CT
1 CT
307 TGATTGTCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 17 0.43
21 23 0.57
ACGTcount: A:0.16, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:2554 original size:20 final size:19
Alignment explanation
Indices: 2508--2554 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
2498 TCCGGTATCG
2508 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
* *
2527 TTGATACCGGTTTTATTATAT
1 TT-TTACCGGTTTTATCAT-T
2548 TTTTACC
1 TTTTACC
2555 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.15, G:0.11, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:2779 original size:181 final size:182
Alignment explanation
Indices: 2475--2947 Score: 687
Period size: 181 Copynumber: 2.6 Consensus size: 182
2465 CGTACTTACG
*
2475 AAAGTATCGACACTTTCAATATATCCGGTATCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * * *
2540 TATTATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* *
2605 AAGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
131 AAGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCATTATATT
*
2656 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCAGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
2721 TATCATATTTTTACATGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* ** * *
2786 AGGATTTAAAACTGTTTCTCTTTTAAATTCACGAAGTGTCGATCATTATATT
131 AAGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCATTATATT
* * * * * * * * *
2838 AAAGTACCGACACTTTAAATGTATCCGATAGCGCTTTACCGGTTTTATTATTTTAATACCGTTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
2903 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
2948 AATTTGGATC
Statistics
Matches: 260, Mismatches: 31, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
181 164 0.63
182 96 0.37
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AAGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCATTATATT
Found at i:9445 original size:28 final size:30
Alignment explanation
Indices: 9364--9446 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 30
9354 TTATTTTTCT
* *
9364 AAAAACAACCT-TAAATTCTTTTAAAATATA
1 AAAAACACCCTCTAAATT-TTCTAAAATATA
* * *
9394 AAAAACACCCTCTAAAATTGCTAAAATATC
1 AAAAACACCCTCTAAATTTTCTAAAATATA
*
9424 AGAAAC-CCC-CTAAATTTTCTAAA
1 AAAAACACCCTCTAAATTTTCTAAA
9447 CACCCAATAC
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
28 12 0.27
29 3 0.07
30 24 0.55
31 5 0.11
ACGTcount: A:0.49, C:0.20, G:0.02, T:0.28
Consensus pattern (30 bp):
AAAAACACCCTCTAAATTTTCTAAAATATA
Found at i:9529 original size:120 final size:120
Alignment explanation
Indices: 9375--9619 Score: 400
Period size: 120 Copynumber: 2.0 Consensus size: 120
9365 AAAACAACCT
*
9375 TAAATTCTTTTAAAATATAAAAAACACCCTCTAAAATTGCTAAAATATCAGAAACCCCCTAAATT
1 TAAATTCTTTTAAAATATAAAAAACACCCTCTAAAATTGATAAAATATCAGAAACCCCCTAAATT
9440 TTCTAAACACCCAATACTTGCTGACCATTCCTTGCAGCCCGCAACCATCGCCCCC
66 TTCTAAACACCCAATACTTGCTGACCATTCCTTGCAGCCCGCAACCATCGCCCCC
* * *
9495 TAAATTCTTTTAAAATATCAAAAACACCCTCTAAAATTTATAAAATATCAGAAACTCCCTAAATT
1 TAAATTCTTTTAAAATATAAAAAACACCCTCTAAAATTGATAAAATATCAGAAACCCCCTAAATT
* * * **
9560 TTGTAAACACCCAATACTTGCTGACCATTCCTTGCCGTCCGCCCCCATCGCCCCC
66 TTCTAAACACCCAATACTTGCTGACCATTCCTTGCAGCCCGCAACCATCGCCCCC
*
9615 AAAAT
1 TAAAT
9620 CTCTACTCAT
Statistics
Matches: 115, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
120 115 1.00
ACGTcount: A:0.36, C:0.30, G:0.07, T:0.27
Consensus pattern (120 bp):
TAAATTCTTTTAAAATATAAAAAACACCCTCTAAAATTGATAAAATATCAGAAACCCCCTAAATT
TTCTAAACACCCAATACTTGCTGACCATTCCTTGCAGCCCGCAACCATCGCCCCC
Found at i:9566 original size:28 final size:29
Alignment explanation
Indices: 9491--9566 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 29
9481 CAACCATCGC
*
9491 CCCCTAAATTCTTTTAAAATATCAAAAACA
1 CCCCTAAATT-TTATAAAATATCAAAAACA
* *
9521 CCCTCTAAAATTTATAAAATATCAGAAAC-
1 CCC-CTAAATTTTATAAAATATCAAAAACA
* *
9550 TCCCTAAATTTTGTAAA
1 CCCCTAAATTTTATAAA
9567 CACCCAATAC
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 12 0.31
29 2 0.05
30 19 0.49
31 6 0.15
ACGTcount: A:0.45, C:0.21, G:0.03, T:0.32
Consensus pattern (29 bp):
CCCCTAAATTTTATAAAATATCAAAAACA
Found at i:10080 original size:13 final size:14
Alignment explanation
Indices: 10046--10093 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
10036 TTAAAAAAGC
* *
10046 TTAATAATATTATA
1 TTAATAAAAATATA
*
10060 TTATTAAAAAT-TA
1 TTAATAAAAATATA
*
10073 TTAATAAAAATATT
1 TTAATAAAAATATA
10087 TTAATAA
1 TTAATAA
10094 TTAGAGTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
13 12 0.43
14 16 0.57
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TTAATAAAAATATA
Found at i:14297 original size:30 final size:29
Alignment explanation
Indices: 14247--14323 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 29
14237 TCATTTTTTA
*
14247 AATATATTCGGTCATTTTTAGCGCCTAAT
1 AATATTTTCGGTCATTTTTAGCGCCTAAT
* *
14276 AATATTTTCGGTTATTTTTTAGCGCTTAAT
1 AATATTTTCGGTCA-TTTTTAGCGCCTAAT
14306 AATA-TTTCTGGTCATTTT
1 AATATTTTC-GGTCATTTT
14324 CGGTCATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 20 0.48
30 22 0.52
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.49
Consensus pattern (29 bp):
AATATTTTCGGTCATTTTTAGCGCCTAAT
Found at i:17741 original size:19 final size:19
Alignment explanation
Indices: 17717--17753 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
17707 AATATTTCAG
*
17717 ATTTTAGTATAAATATAAA
1 ATTTTAGGATAAATATAAA
*
17736 ATTTTAGGATACATATAA
1 ATTTTAGGATAAATATAA
17754 TATCATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (19 bp):
ATTTTAGGATAAATATAAA
Found at i:17964 original size:3 final size:3
Alignment explanation
Indices: 17956--17990 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
17946 TAGTTTAGTT
*
17956 TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
17991 TTTAATGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:21609 original size:60 final size:60
Alignment explanation
Indices: 21472--21597 Score: 164
Period size: 60 Copynumber: 2.1 Consensus size: 60
21462 GAACATATGA
* * * *
21472 ATAGTCG-AGTGACCATTTTGTAACTTTTAATAGTCGAGGGACTCAACAGAGCAATGTCCT
1 ATAGTCGTA-TGACCATTTTGTAACTTTCAATAGTCGAGAGACTCAACAGAACAATATCCT
* * * *
21532 ATAGTCGTATGATCATTTTGTAACTTTCAATAGTCGAGAGACTCAATAGAACACTATCTT
1 ATAGTCGTATGACCATTTTGTAACTTTCAATAGTCGAGAGACTCAACAGAACAATATCCT
21592 ATAGTC
1 ATAGTC
21598 TTGAGACCAT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 56 0.98
61 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (60 bp):
ATAGTCGTATGACCATTTTGTAACTTTCAATAGTCGAGAGACTCAACAGAACAATATCCT
Found at i:22510 original size:2 final size:2
Alignment explanation
Indices: 22503--22541 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
22493 ACTACGATCA
22503 AT AT 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 AT AT A
22542 ATTTTTAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:22598 original size:22 final size:22
Alignment explanation
Indices: 22527--22601 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
22517 ATATATATAT
* *
22527 ATATATATATATATAATTTTTA
1 ATATATTTATATTTAATTTTTA
22549 ATA-ATTTA-ATTT-ATTTTTA
1 ATATATTTATATTTAATTTTTA
* * *
22568 GTATTTTTATATTTAATTTTTT
1 ATATATTTATATTTAATTTTTA
*
22590 CTATATTTATAT
1 ATATATTTATAT
22602 AGTTTAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
19 9 0.21
20 7 0.16
21 8 0.19
22 19 0.44
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (22 bp):
ATATATTTATATTTAATTTTTA
Found at i:22898 original size:3 final size:3
Alignment explanation
Indices: 22892--22921 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
22882 ATGAGTTAAC
*
22892 ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
22922 TAAAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:27192 original size:29 final size:29
Alignment explanation
Indices: 27160--27216 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
27150 CATCGAATTG
27160 AGTTTCGCTAAAAACTATCCCTACACCTC
1 AGTTTCGCTAAAAACTATCCCTACACCTC
*
27189 AGTTTCGTTAAAAACTATCCCTACACCT
1 AGTTTCGCTAAAAACTATCCCTACACCT
27217 AATTGGAGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.32, G:0.07, T:0.30
Consensus pattern (29 bp):
AGTTTCGCTAAAAACTATCCCTACACCTC
Found at i:33104 original size:64 final size:63
Alignment explanation
Indices: 33036--33265 Score: 210
Period size: 64 Copynumber: 3.6 Consensus size: 63
33026 TTGGAATACT
* *** *
33036 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAGAAATAGCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGA-AAAAAGCC
** * **
33100 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAAATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAAAGCC
* * * * * * ** *
33164 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAATTCA
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAA-AAAAGCC
* *
33228 TCGATGCATCGATGCATGGACTGATGCATCGGTGCATG
1 T-GATGCATCGATGCATGGAGTG-TGCATCGATGCATG
33266 CCTTTGAATA
Statistics
Matches: 136, Mismatches: 25, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
63 4 0.03
64 70 0.51
65 62 0.46
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (63 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAAGCC
Found at i:33188 original size:19 final size:19
Alignment explanation
Indices: 33164--33214 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
33154 GAAAAAATTC
33164 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
33183 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
33202 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
33215 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:33256 original size:65 final size:64
Alignment explanation
Indices: 33058--33265 Score: 210
Period size: 65 Copynumber: 3.2 Consensus size: 64
33048 GCACCAAGTG
* * * ** *
33058 TGCATCGATGCATGAAATGCATTCGATGTTTGAGAAATAGCCTGATGCATCGATGCATGG-CTTG
1 TGCATCGGTGCATGAAATGCATTCGATGTTTCA-AAAAATTCAGATGCATCGATGCATGGAC-TG
33122 -
64 A
* * *
33122 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAAATTCAGAGTGCATCGATGCATGGA--G
1 TGCATCGGTGCATGAAATGCATTCGATG-TTTCAAAAAATTCAGA-TGCATCGATGCATGGACTG
33185 A
64 A
* **
33186 GTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAATTCATCGATGCATCGATGCATGGACT
1 -TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAAAATTCA--GATGCATCGATGCATGGACT
33250 GA
63 GA
33252 TGCATCGGTGCATG
1 TGCATCGGTGCATG
33266 CCTTTGAATA
Statistics
Matches: 124, Mismatches: 11, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
63 11 0.09
64 50 0.40
65 61 0.49
66 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.29
Consensus pattern (64 bp):
TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAAAATTCAGATGCATCGATGCATGGACTGA
Found at i:41678 original size:64 final size:63
Alignment explanation
Indices: 41610--41839 Score: 210
Period size: 64 Copynumber: 3.6 Consensus size: 63
41600 TTGGAACACT
* *** *
41610 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAGAAATAGCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGA-AAAAAGCC
** * **
41674 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAAATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAAAGCC
* * * * * * ** *
41738 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAATTCA
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAA-AAAAGCC
* *
41802 TCGATGCATCGATGCATGGACTGATGCATCGGTGCATG
1 T-GATGCATCGATGCATGGAGTG-TGCATCGATGCATG
41840 CCTTTGAATA
Statistics
Matches: 136, Mismatches: 25, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
63 4 0.03
64 70 0.51
65 62 0.46
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (63 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAAGCC
Found at i:41762 original size:19 final size:19
Alignment explanation
Indices: 41738--41788 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
41728 GAAAAAATTC
41738 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
41757 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
41776 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
41789 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:41830 original size:65 final size:64
Alignment explanation
Indices: 41632--41839 Score: 210
Period size: 65 Copynumber: 3.2 Consensus size: 64
41622 GCACCAAGTG
* * * ** *
41632 TGCATCGATGCATGAAATGCATTCGATGTTTGAGAAATAGCCTGATGCATCGATGCATGG-CTTG
1 TGCATCGGTGCATGAAATGCATTCGATGTTTCA-AAAAATTCAGATGCATCGATGCATGGAC-TG
41696 -
64 A
* * *
41696 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAAATTCAGAGTGCATCGATGCATGGA--G
1 TGCATCGGTGCATGAAATGCATTCGATG-TTTCAAAAAATTCAGA-TGCATCGATGCATGGACTG
41759 A
64 A
* **
41760 GTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAATTCATCGATGCATCGATGCATGGACT
1 -TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAAAATTCA--GATGCATCGATGCATGGACT
41824 GA
63 GA
41826 TGCATCGGTGCATG
1 TGCATCGGTGCATG
41840 CCTTTGAATA
Statistics
Matches: 124, Mismatches: 11, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
63 11 0.09
64 50 0.40
65 61 0.49
66 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.29
Consensus pattern (64 bp):
TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAAAATTCAGATGCATCGATGCATGGACTGA
Found at i:49111 original size:2 final size:2
Alignment explanation
Indices: 49104--49130 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
49094 TTTGATAGTG
49104 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
49131 TAAAATGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:50312 original size:157 final size:157
Alignment explanation
Indices: 50026--50345 Score: 613
Period size: 157 Copynumber: 2.0 Consensus size: 157
50016 GAAGGAAGTT
*
50026 ATCAACAATGCCCATGTAAACATGGTAAGATGAATATTTCAAATTCTAGTATTGGATGGTTCTTT
1 ATCAACAATGCCCATGTAAACATGGTAAGATGAATATTCCAAATTCTAGTATTGGATGGTTCTTT
*
50091 AAGTTAATCTTATTTTGGCATCTCCTCTATTTGTGGAGACCTCTACTACTAGACCAGAAAAACCT
66 AAGTTAATCTTATTTCGGCATCTCCTCTATTTGTGGAGACCTCTACTACTAGACCAGAAAAACCT
50156 GTAGAATACAAGAAAACATATTTAGAG
131 GTAGAATACAAGAAAACATATTTAGAG
*
50183 ATCAACAATGCCCATGTAAACATGGTAAGATGAATATTCCAAATTCTAGTATTGGATTGTTCTTT
1 ATCAACAATGCCCATGTAAACATGGTAAGATGAATATTCCAAATTCTAGTATTGGATGGTTCTTT
50248 AAGTTAATCTTATTTCGGCATCTCCTCTATTTGTGGAGACCTCTACTACTAGACCAGAAAAACCT
66 AAGTTAATCTTATTTCGGCATCTCCTCTATTTGTGGAGACCTCTACTACTAGACCAGAAAAACCT
50313 GTAGAATACAAGAAAACATATTTAGAG
131 GTAGAATACAAGAAAACATATTTAGAG
50340 ATCAAC
1 ATCAAC
50346 TCCGATGATG
Statistics
Matches: 160, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
157 160 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Consensus pattern (157 bp):
ATCAACAATGCCCATGTAAACATGGTAAGATGAATATTCCAAATTCTAGTATTGGATGGTTCTTT
AAGTTAATCTTATTTCGGCATCTCCTCTATTTGTGGAGACCTCTACTACTAGACCAGAAAAACCT
GTAGAATACAAGAAAACATATTTAGAG
Done.