Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007180.1 Hibiscus syriacus cultivar Beakdansim tig00018857_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: 50297
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:1193 original size:9 final size:9
Alignment explanation
Indices: 1169--1201 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
1159 ATTAATTATT
1169 TTTAATATA
1 TTTAATATA
1178 TTT-ATATA
1 TTTAATATA
1186 TTTAATATA
1 TTTAATATA
1195 TTTAATA
1 TTTAATA
1202 ATAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TTTAATATA
Found at i:1205 original size:3 final size:3
Alignment explanation
Indices: 1197--1260 Score: 87
Period size: 3 Copynumber: 21.7 Consensus size: 3
1187 TTAATATATT
* *
1197 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TTA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1244 TAA TAA T-A TAA TTAA TA
1 TAA TAA TAA TAA -TAA TA
1261 TGGGTAAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
2 4 0.07
3 47 0.87
4 3 0.06
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1855 original size:223 final size:222
Alignment explanation
Indices: 1480--2026 Score: 802
Period size: 223 Copynumber: 2.5 Consensus size: 222
1470 GATAGAATTA
* *
1480 TTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGACGTTCTTCTCATTATGA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA-GTTCTTCTCATTATGA
* * * * *
1545 ACTCTAC-CTGGCAATGTTGATCCATC-AATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTC
65 ACT-TTCTCTGGAAATG-AGATCCATCAAATGATGGATTCAA-CAAAAGATTGAACAAATTCTTC
*
1608 TCATTATGAACTTCTTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACCCTCTCTGGAAAAGCT
127 TCATTATGAACTTCTTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACCCTCTCTGGAAAAGAT
* **
1673 AATCCATCAATTTGATGAATTCAGGT-AAAGG
192 AATCCATCAA-ATGATGAATTCAAATAAAAGG
1704 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA-TATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
*
1768 CTTTCTCTGGAAATGAGATCCATCAAATGATGGATTCAA-ATAAAGGTTGAACAAATTCTTCTCA
66 CTTTCTCTGGAAATGAGATCCATCAAATGATGGATTCAACA-AAAGATTGAACAAATTCTTCTCA
** * *
1832 TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATG
130 TTATGAACTTCTT-TT-CTTCTTCAGATGAGTTCTTCTCATTATGAACCCTCTCTGGAAAAGATA
*
1897 ATCCATCAAATGATGGATTCAAATAAAAGG
193 ATCCATCAAATGATGAATTCAAATAAAAGG
1927 TTGAACAAATTC-TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
*
1991 C-TTCTCTGGAAATGATGATCCATCAAATGATAGATT
66 CTTTCTCTGGAAATGA-GATCCATCAAATGATGGATT
2027 TGAATCTTTG
Statistics
Matches: 297, Mismatches: 18, Indels: 17
0.89 0.05 0.05
Matches are distributed among these distances:
220 1 0.00
221 44 0.15
222 101 0.34
223 105 0.35
224 46 0.15
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (222 bp):
TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTTTCTCTGGAAATGAGATCCATCAAATGATGGATTCAACAAAAGATTGAACAAATTCTTCTCAT
TATGAACTTCTTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACCCTCTCTGGAAAAGATAATC
CATCAAATGATGAATTCAAATAAAAGG
Found at i:1980 original size:112 final size:112
Alignment explanation
Indices: 1480--2026 Score: 815
Period size: 111 Copynumber: 4.9 Consensus size: 112
1470 GATAGAATTA
* *
1480 TTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGACGTTCTTCTCATTATGA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA-GTTCTTCTCATTATGA
* * * * *
1545 ACTCTAC-CTGGCAATGTTGATCCATC-AATGATGAATTCAAGCA-AAAGA
65 ACT-TTCTCTGGAAATGATGATCCATCAAATGATGGATTCAA--ATAAAGG
*
1593 TTGAACAAGTTCTTCTCATTATGAACTTCTT-TT-CTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
** * * * * * **
1656 CCCTCTCTGGAAAAGCTAATCCATCAATTTGATGAATTCAGGTAAAGG
66 CTTTCTCTGGAAATGATGATCCATCAA-ATGATGGATTCAAATAAAGG
1704 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA-TATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1768 CTTTCTCTGGAAATGA-GATCCATCAAATGATGGATTCAAATAAAGG
66 CTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAATAAAGG
1814 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1879 CTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAATAAAAGG
66 CTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAAT-AAAGG
1927 TTGAACAAATTC-TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
*
1991 C-TTCTCTGGAAATGATGATCCATCAAATGATAGATT
66 CTTTCTCTGGAAATGATGATCCATCAAATGATGGATT
2027 TGAATCTTTG
Statistics
Matches: 402, Mismatches: 23, Indels: 20
0.90 0.05 0.04
Matches are distributed among these distances:
109 1 0.00
110 107 0.27
111 113 0.28
112 111 0.28
113 70 0.17
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (112 bp):
TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAATAAAGG
Found at i:3006 original size:90 final size:92
Alignment explanation
Indices: 2814--3090 Score: 517
Period size: 90 Copynumber: 3.1 Consensus size: 92
2804 CTTATTTCTA
*
2814 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTAGTTCCTACC-AACCAGATCAGA
1 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTAGTTCCTACCAAACCAGATCAGA
2878 TAACTCAAAGAACACTTCCAGAAGATG
66 TAACTCAAAGAACACTTCCAGAAGATG
2905 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTT-TGTAGTTCCTACCAAACCAGATCAGA
1 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTAGTTCCTACCAAACCAGATCAGA
2969 TAACTC-AAGAACACTTCCAGAAGATG
66 TAACTCAAAGAACACTTCCAGAAGATG
2995 CTATTAGCAAATTCATCTTCC-AATTCAATGATTGGTTCTGTAGTTCCTACCAAACCAGATCAGA
1 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTAGTTCCTACCAAACCAGATCAGA
3059 TAACTCAAAGAACACTTCCAGAAGATG
66 TAACTCAAAGAACACTTCCAGAAGATG
3086 CTATT
1 CTATT
3091 GAGTTTCCTT
Statistics
Matches: 182, Mismatches: 1, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
89 16 0.09
90 86 0.47
91 80 0.44
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (92 bp):
CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTAGTTCCTACCAAACCAGATCAGA
TAACTCAAAGAACACTTCCAGAAGATG
Found at i:3198 original size:113 final size:113
Alignment explanation
Indices: 2995--3202 Score: 389
Period size: 113 Copynumber: 1.8 Consensus size: 113
2985 CCAGAAGATG
*
2995 CTATTAGCAAATTCATCTTCCAATTCAATGATTGGTTCTGTAGTTCCTACCAAACCAGATCAGAT
1 CTATGAGCAAATTCATCTTCCAATTCAATGATTGGTTCTGTAGTTCCTACCAAACCAGATCAGAT
3060 AACTCAAAGAACACTTCCAGAAGATGCTATTGAGTTTCCTTATTTCTA
66 AACTCAAAGAACACTTCCAGAAGATGCTATTGAGTTTCCTTATTTCTA
* *
3108 CTATGAGCAAATTTATCTTCCAATTCAATGATTGGTTCTGTAGTTCCTACCAAACCAGATTAGAT
1 CTATGAGCAAATTCATCTTCCAATTCAATGATTGGTTCTGTAGTTCCTACCAAACCAGATCAGAT
3173 AACTCAAAGAACACTTCCAGAAGATGCTAT
66 AACTCAAAGAACACTTCCAGAAGATGCTAT
3203 GAGCACATTC
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 92 1.00
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (113 bp):
CTATGAGCAAATTCATCTTCCAATTCAATGATTGGTTCTGTAGTTCCTACCAAACCAGATCAGAT
AACTCAAAGAACACTTCCAGAAGATGCTATTGAGTTTCCTTATTTCTA
Found at i:3380 original size:82 final size:83
Alignment explanation
Indices: 3157--3384 Score: 397
Period size: 83 Copynumber: 2.8 Consensus size: 83
3147 GTAGTTCCTA
* *
3157 CCAAACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCCA
3222 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
3240 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCCA
3305 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* *
3323 CC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-TCAAATTCATCTTCC
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATCTTCC
3385 AGATAATGTT
Statistics
Matches: 140, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
82 55 0.39
83 85 0.61
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.26
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCCA
ATTCAATGATTGGTTCTG
Found at i:4523 original size:1 final size:1
Alignment explanation
Indices: 4519--4562 Score: 61
Period size: 1 Copynumber: 44.0 Consensus size: 1
4509 CTTGACCCCC
* * *
4519 TTTTTTTTTTTTTTTTTTTCTTTTTTTTTTCTTTTTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4563 CTTCAAGCAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:4535 original size:11 final size:11
Alignment explanation
Indices: 4519--4560 Score: 68
Period size: 11 Copynumber: 3.8 Consensus size: 11
4509 CTTGACCCCC
4519 TTTTTTTTT-T
1 TTTTTTTTTCT
4529 TTTTTTTTTCT
1 TTTTTTTTTCT
4540 TTTTTTTTTCT
1 TTTTTTTTTCT
4551 TTTTCTTTTT
1 TTTT-TTTTT
4561 TTCTTCAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 9 0.30
11 16 0.53
12 5 0.17
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:4544 original size:17 final size:17
Alignment explanation
Indices: 4519--4562 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
4509 CTTGACCCCC
4519 TTTT-TTTTTTTTTT-T
1 TTTTCTTTTTTTTTTCT
4534 TTTTCTTTTTTTTTTCT
1 TTTTCTTTTTTTTTTCT
4551 TTTTCTTTTTTT
1 TTTTCTTTTTTT
4563 CTTCAAGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.15
16 10 0.37
17 13 0.48
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (17 bp):
TTTTCTTTTTTTTTTCT
Found at i:15930 original size:13 final size:13
Alignment explanation
Indices: 15886--15932 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
15876 CTGTTCTTTG
*
15886 ATATTGAAAACTAA
1 ATATTTAAAA-TAA
15900 ATA-TTAAAATAA
1 ATATTTAAAATAA
*
15912 TTTATTTAAAATAA
1 -ATATTTAAAATAA
15926 ATATTTA
1 ATATTTA
15933 TTTATTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 3 0.11
13 13 0.46
14 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:17368 original size:3 final size:3
Alignment explanation
Indices: 17360--17417 Score: 98
Period size: 3 Copynumber: 19.3 Consensus size: 3
17350 TTAATATATT
* *
17360 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
17408 TAA TAA TAA T
1 TAA TAA TAA T
17418 TAATTAATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:18332 original size:2 final size:2
Alignment explanation
Indices: 18325--18354 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
18315 ATACTGCCCC
18325 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18355 TATTGTGTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22988 original size:31 final size:31
Alignment explanation
Indices: 22950--23009 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
22940 AAAAACGTTG
22950 GTCAAAGGGCTACATTAAGTTTATTTTATAA
1 GTCAAAGGGCTACATTAAGTTTATTTTATAA
*
22981 GTCAAAGGGCTACATTAGGTTTATTTTAT
1 GTCAAAGGGCTACATTAAGTTTATTTTAT
23010 GAGTTATCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (31 bp):
GTCAAAGGGCTACATTAAGTTTATTTTATAA
Found at i:32763 original size:44 final size:47
Alignment explanation
Indices: 32697--32794 Score: 139
Period size: 44 Copynumber: 2.1 Consensus size: 47
32687 TATTTTCGTT
*
32697 TTTTTCGAATAAATGCATGCGAACTAGGTATCATGCGGTTAGG-TTTA
1 TTTTT-GAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
* *
32744 TTTTTGAAT-AA-GCATGCGAATTAGATATCATGCGGTTAGGATTTC
1 TTTTTGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
32789 TTTTTG
1 TTTTTG
32795 TGGATAACAA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
44 27 0.57
45 11 0.23
46 4 0.09
47 5 0.11
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.40
Consensus pattern (47 bp):
TTTTTGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
Found at i:42527 original size:19 final size:18
Alignment explanation
Indices: 42505--42581 Score: 69
Period size: 16 Copynumber: 4.6 Consensus size: 18
42495 ACGAAAAGGA
42505 AAAAAAGAAGAAAAAATAG
1 AAAAAAGAAGAAAAAAT-G
**
42524 AAAAGGGAAGAAAAAATG
1 AAAAAAGAAGAAAAAATG
*
42542 --AAAA-ATG-AAAAATG
1 AAAAAAGAAGAAAAAATG
42556 AAAAAAG-AG-AAAAATG
1 AAAAAAGAAGAAAAAATG
42572 AAAAAA-AAGA
1 AAAAAAGAAGA
42582 GAAATAAAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
14 7 0.15
15 2 0.04
16 22 0.47
18 1 0.02
19 15 0.32
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.06
Consensus pattern (18 bp):
AAAAAAGAAGAAAAAATG
Found at i:42552 original size:6 final size:7
Alignment explanation
Indices: 42535--42576 Score: 57
Period size: 7 Copynumber: 5.7 Consensus size: 7
42525 AAAGGGAAGA
42535 AAAAATG
1 AAAAATG
42542 AAAAATG
1 AAAAATG
42549 AAAAATG
1 AAAAATG
*
42556 AAAAAAGAG
1 -AAAAA-TG
42565 AAAAATG
1 AAAAATG
42572 AAAAA
1 AAAAA
42577 AAAGAGAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 20 0.65
8 10 0.32
9 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (7 bp):
AAAAATG
Found at i:42567 original size:23 final size:22
Alignment explanation
Indices: 42533--42576 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
42523 GAAAAGGGAA
*
42533 GAAAAAATGAAAAATGAAAAAT
1 GAAAAAAAGAAAAATGAAAAAT
42555 GAAAAAAGAGAAAAATGAAAAA
1 GAAAAAA-AGAAAAATGAAAAA
42577 AAAGAGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (22 bp):
GAAAAAAAGAAAAATGAAAAAT
Found at i:42579 original size:18 final size:16
Alignment explanation
Indices: 42531--42590 Score: 65
Period size: 16 Copynumber: 4.0 Consensus size: 16
42521 TAGAAAAGGG
42531 AAGA-AAAAATG-AAA
1 AAGAGAAAAATGAAAA
*
42545 AA-TGAAAAATGAAAA
1 AAGAGAAAAATGAAAA
42560 AAGAGAAAAATGAAAA
1 AAGAGAAAAATGAAAA
* *
42576 AAAAGAGAAAT-AAAA
1 AAGAGAAAAATGAAAA
42591 GGAGGGTTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
14 9 0.23
15 9 0.23
16 21 0.54
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (16 bp):
AAGAGAAAAATGAAAA
Found at i:43971 original size:51 final size:51
Alignment explanation
Indices: 43910--44469 Score: 594
Period size: 51 Copynumber: 10.8 Consensus size: 51
43900 AAATTCGTTC
43910 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAATTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAATTTT
*
43961 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAATTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAATTTT
* * *
44012 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAATTTT
* * * *
44063 GTTGAATATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC-AGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAATTTT
* * * *
44113 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGAGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAATTTT
* **
44164 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGA-CAATTTT
* * * * * **
44216 ATTGAAGATCGAGTTCTATACTCCCTGAACGG-ATAGGGAGCGAACACGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAA-GGAATAGGGAGCGGACAATTTT
* * *
44267 GTTAAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGAC-CTGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAT-TTT
* * * **
44318 ATTGAAGATTTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGC-GACCGTTTT
1 GTTGAAGA--TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAATTTT
* * * * *
44371 ATT-AAGATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACATTTT
1 GTTGAAGATTG----AGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA-ATTTT
* *
44426 -ATGAAGATTGCTCGAGTCTTATACT-TCCTGAAGGAATAGGGAGC
1 GTTGAAGA-T--T-GAGTCCTATACTCT-CTGAAGGAATAGGGAGC
44470 AGGCTCGTCA
Statistics
Matches: 446, Mismatches: 42, Indels: 38
0.85 0.08 0.07
Matches are distributed among these distances:
49 1 0.00
50 52 0.12
51 240 0.54
52 42 0.09
53 40 0.09
54 34 0.08
55 34 0.08
56 1 0.00
58 1 0.00
59 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (51 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAATTTT
Found at i:44096 original size:27 final size:27
Alignment explanation
Indices: 44065--44147 Score: 66
Period size: 27 Copynumber: 3.2 Consensus size: 27
44055 ACAAGTTCGT
44065 TGAATATTGAGTCCTATACTCTCTGAA
1 TGAATATTGAGTCCTATACTCTCTGAA
** ** * * *
44092 TGAATAGGGAG-CGGACAGT-TC-G-T
1 TGAATATTGAGTCCTATACTCTCTGAA
*
44115 TGAAGATTGAGTCCTATACTCTCTGAA
1 TGAATATTGAGTCCTATACTCTCTGAA
44142 TGAATA
1 TGAATA
44148 GAGAGCGGAC
Statistics
Matches: 36, Mismatches: 16, Indels: 8
0.60 0.27 0.13
Matches are distributed among these distances:
23 8 0.22
24 5 0.14
25 4 0.11
26 5 0.14
27 14 0.39
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (27 bp):
TGAATATTGAGTCCTATACTCTCTGAA
Found at i:44489 original size:55 final size:55
Alignment explanation
Indices: 44278--44471 Score: 168
Period size: 55 Copynumber: 3.6 Consensus size: 55
44268 TTAAAGATTG
* * * * * * *
44278 AGTCCTATACTCTCTGAAAGAATAGGGAGCGGAC-C-TGTTTATTGAAGATT-TTCG
1 AGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACAT-ATTA-TGAAGATTGCTCA
* * * *
44332 AGT-TCTATACTCTCTGAAGGAATAGAGAGC-GAC-CGTTTTATTAAGATTGTTCA
1 AGTCT-TATACTCTCTGAAGGAATAGAGAGCAGACACATATTATGAAGATTGCTCA
* * *
44385 AGTCTTATACTCTCTGAATGAATAGAGAGCAGACACATTTTATGAAGATTGCTCG
1 AGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACATATTATGAAGATTGCTCA
*
44440 AGTCTTATACT-TCCTGAAGGAATAGGGAGCAG
1 AGTCTTATACTCT-CTGAAGGAATAGAGAGCAG
44472 GCTCGTCATT
Statistics
Matches: 121, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
52 7 0.06
53 38 0.31
54 32 0.26
55 44 0.36
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (55 bp):
AGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACATATTATGAAGATTGCTCA
Done.