Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004232.1 Hibiscus syriacus cultivar Beakdansim tig00009270_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: 92151
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1492 original size:20 final size:20
Alignment explanation
Indices: 1467--1592 Score: 156
Period size: 20 Copynumber: 6.6 Consensus size: 20
1457 AGAATAGTTT
1467 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1487 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
*
1503 A--ATCGCAATGCGAAAAGG
1 ACTATCGCAATGCGAAAATG
1521 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
1541 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
**
1561 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
1581 ACTATCGCAATG
1 ACTATCGCAATG
1593 AGAGAATCCA
Statistics
Matches: 95, Mismatches: 5, Indels: 12
0.85 0.04 0.11
Matches are distributed among these distances:
14 7 0.07
16 4 0.04
17 4 0.04
18 4 0.04
20 76 0.80
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:1732 original size:20 final size:20
Alignment explanation
Indices: 1636--1722 Score: 147
Period size: 20 Copynumber: 4.3 Consensus size: 20
1626 GATTCTCTCG
**
1636 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
1656 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1676 TTGCGATAGTCATTTTCACA
1 TTGCGATAGTCATTTTCGCA
1696 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1716 TTGCGAT
1 TTGCGAT
1723 TTTAAGTTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1733 original size:40 final size:40
Alignment explanation
Indices: 1636--1733 Score: 126
Period size: 40 Copynumber: 2.5 Consensus size: 40
1626 GATTCTCTCG
* *
1636 TTGCGATAGTCAA-ATTCGCATTGCGATAGTCATTTTCGCA
1 TTGCGATAGT-AAGTTTCACATTGCGATAGTCATTTTCGCA
* *
1676 TTGCGATAGTCATTTTCACATTGCGATAGTCATTTTCGCA
1 TTGCGATAGTAAGTTTCACATTGCGATAGTCATTTTCGCA
**
1716 TTGCGATTTTAAGTTTCA
1 TTGCGATAGTAAGTTTCA
1734 GATTCTATTC
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
39 1 0.02
40 49 0.98
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.40
Consensus pattern (40 bp):
TTGCGATAGTAAGTTTCACATTGCGATAGTCATTTTCGCA
Found at i:2293 original size:21 final size:21
Alignment explanation
Indices: 2204--2306 Score: 91
Period size: 21 Copynumber: 4.9 Consensus size: 21
2194 CTCACCTGTT
*
2204 ATCGTTCAAGAGGCCTCCCCT-
1 ATCGTTCAAGAGGCC-CCTCTC
*
2225 ATCGTTCAAGAGGCCCCTATC
1 ATCGTTCAAGAGGCCCCTCTC
** * *
2246 ATCCCTCAAGAGTCCCCTCCC
1 ATCGTTCAAGAGGCCCCTCTC
* * *
2267 ACCGTTCAAGAGGCCACTGTC
1 ATCGTTCAAGAGGCCCCTCTC
* *
2288 ATCGTTGAAGAGGTCCCTC
1 ATCGTTCAAGAGGCCCCTC
2307 CCAACATTCT
Statistics
Matches: 62, Mismatches: 19, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
20 3 0.05
21 59 0.95
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.22
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTCTC
Found at i:2299 original size:42 final size:42
Alignment explanation
Indices: 2227--2309 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
2217 CCTCCCCTAT
*
2227 CGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCAC
* ** *
2269 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
2310 ACATTCTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.22, C:0.39, G:0.19, T:0.20
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:3111 original size:20 final size:20
Alignment explanation
Indices: 3086--3127 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
3076 TAAATTATAT
3086 ATCATTGTCTGATTTGAGAG
1 ATCATTGTCTGATTTGAGAG
3106 ATCATTGTCTGATTTGAGAG
1 ATCATTGTCTGATTTGAGAG
3126 AT
1 AT
3128 ATGATTAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.10, G:0.24, T:0.40
Consensus pattern (20 bp):
ATCATTGTCTGATTTGAGAG
Found at i:3701 original size:14 final size:14
Alignment explanation
Indices: 3682--3717 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3672 ATTGTTTAAT
3682 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
3696 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
3710 TGATTTGT
1 TGATTTGT
3718 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3867 original size:33 final size:33
Alignment explanation
Indices: 3830--3947 Score: 200
Period size: 33 Copynumber: 3.5 Consensus size: 33
3820 TCGTAACGCA
** *
3830 GAAATGACTATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGTGAATCGCAATGC
3863 GAAATGAAAATCGCAACGAGTGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGTGAATCGCAATGC
3896 GAAATGAAAATCGCAACGAGTGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGTGAATCGCAATGC
3929 GAAAATGAAAATCGCAACG
1 G-AAATGAAAATCGCAACG
3948 CGAAACTAAT
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
33 64 0.79
34 17 0.21
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.14
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGTGAATCGCAATGC
Found at i:4197 original size:20 final size:20
Alignment explanation
Indices: 4150--4200 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
4140 GATTCTCTTG
* *
4150 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCAGTTCCGCA
4170 TT-CGATAGTCAGTTCCGCA
1 TTGCGATAGTCAGTTCCGCA
4189 TTGCGATAGTCA
1 TTGCGATAGTCA
4201 TTTTCATGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCAGTTCCGCA
Found at i:4212 original size:20 final size:20
Alignment explanation
Indices: 4149--4235 Score: 106
Period size: 20 Copynumber: 4.4 Consensus size: 20
4139 CGATTCTCTT
4149 GTTGCGATAGTCATTTCCGC
1 GTTGCGATAGTCATTTCCGC
*
4169 GTT-CGATAGTCAGTTCCGC
1 GTTGCGATAGTCATTTCCGC
* * **
4188 ATTGCGATAGTCATTTTCAT
1 GTTGCGATAGTCATTTCCGC
4208 GTTGCGATAGTCATATT-CGC
1 GTTGCGATAGTCAT-TTCCGC
4228 GTTGCGAT
1 GTTGCGAT
4236 TTACGCGTTG
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
19 17 0.30
20 37 0.66
21 2 0.04
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCGC
Found at i:4233 original size:40 final size:39
Alignment explanation
Indices: 4149--4235 Score: 104
Period size: 39 Copynumber: 2.2 Consensus size: 39
4139 CGATTCTCTT
*
4149 GTTGCGATAGTCATTTCCGCGTTCGATAGTCAGTTCCGC
1 GTTGCGATAGTCATTTCCACGTTCGATAGTCAGTTCCGC
* * * *
4188 ATTGCGATAGTCATTTTCATGTTGCGATAGTCA-TATTCGC
1 GTTGCGATAGTCATTTCCACGTT-CGATAGTCAGT-TCCGC
4228 GTTGCGAT
1 GTTGCGAT
4236 TTACGCGTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
39 20 0.50
40 20 0.50
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (39 bp):
GTTGCGATAGTCATTTCCACGTTCGATAGTCAGTTCCGC
Found at i:6644 original size:24 final size:24
Alignment explanation
Indices: 6617--6670 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
6607 CTGAAAAATC
6617 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
6641 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
6665 ATCAAA
1 ATCAAA
6671 TTTCAAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:8622 original size:2 final size:2
Alignment explanation
Indices: 8615--8666 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
8605 CTTTTTAATT
8615 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8657 TA TA TA TA TA
1 TA TA TA TA TA
8667 GATTTTATAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25829 original size:18 final size:18
Alignment explanation
Indices: 25806--25866 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
25796 ATTGAAAAAC
25806 CGAAAAACCGAACCGAAT
1 CGAAAAACCGAACCGAAT
*
25824 CGAAAAACCCGAACCG-TT
1 CGAAAAA-CCGAACCGAAT
** *
25842 AAAAAAACCGAACCGAAC
1 CGAAAAACCGAACCGAAT
25860 CGAAAAA
1 CGAAAAA
25867 ACCGGTTTCG
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
17 8 0.24
18 18 0.53
19 8 0.24
ACGTcount: A:0.52, C:0.28, G:0.15, T:0.05
Consensus pattern (18 bp):
CGAAAAACCGAACCGAAT
Found at i:25867 original size:19 final size:19
Alignment explanation
Indices: 25803--25870 Score: 72
Period size: 19 Copynumber: 3.7 Consensus size: 19
25793 TTTATTGAAA
25803 AACCG-AAAAACCGAACCG
1 AACCGAAAAAACCGAACCG
* *
25821 AATCGAAAAACCCGAACCG
1 AACCGAAAAAACCGAACCG
*
25840 TTA---AAAAAACCGAACCG
1 -AACCGAAAAAACCGAACCG
25857 AACCGAAAAAACCG
1 AACCGAAAAAACCG
25871 GTTTCGGTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
16 1 0.03
17 13 0.32
18 4 0.10
19 21 0.52
20 1 0.03
ACGTcount: A:0.51, C:0.29, G:0.15, T:0.04
Consensus pattern (19 bp):
AACCGAAAAAACCGAACCG
Found at i:27409 original size:18 final size:19
Alignment explanation
Indices: 27386--27428 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
27376 AATATTTAAA
*
27386 ATAAAATATTT-AATTTAT
1 ATAAAATATTTGAATATAT
27404 ATAAAA-ATTTGAATATAT
1 ATAAAATATTTGAATATAT
27422 A-AAAATA
1 ATAAAATA
27429 AATAGTATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
ATAAAATATTTGAATATAT
Found at i:29659 original size:23 final size:23
Alignment explanation
Indices: 29633--29678 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
29623 TTTTCTTGTT
29633 AACCAAACTTTTTAATTCTTATC
1 AACCAAACTTTTTAATTCTTATC
29656 AACCAAACTTTTTAATTCTTATC
1 AACCAAACTTTTTAATTCTTATC
29679 TAGCAGGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (23 bp):
AACCAAACTTTTTAATTCTTATC
Found at i:32653 original size:3 final size:3
Alignment explanation
Indices: 32645--32676 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
32635 TTTGTTTCAT
*
32645 TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
32677 CCATGACCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:34988 original size:2 final size:2
Alignment explanation
Indices: 34983--35028 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
34973 ATGTGATAAA
34983 AT AT AT AT AT AT 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 AT AT AT AT AT AT
35025 AT AT
1 AT AT
35029 TTCTGATCTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39302 original size:35 final size:36
Alignment explanation
Indices: 39256--39324 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
39246 CATTTAGGGG
39256 GGAATCGATA-CCCCCCAGGGGGAATCTGTTCCCGA
1 GGAATCGATACCCCCCCAGGGGGAATCTGTTCCCGA
39291 GGAATCGATACCCCCCCAGGGGGAATCTGTTCCC
1 GGAATCGATACCCCCCCAGGGGGAATCTGTTCCC
39325 CCTGCACATA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 10 0.30
36 23 0.70
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (36 bp):
GGAATCGATACCCCCCCAGGGGGAATCTGTTCCCGA
Found at i:48848 original size:2 final size:2
Alignment explanation
Indices: 48841--48866 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
48831 TATCAAAGTA
48841 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
48867 TTATTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49914 original size:2 final size:2
Alignment explanation
Indices: 49907--49931 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
49897 AATTATTTAC
49907 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 T
49932 CTTACAGACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52028 original size:2 final size:2
Alignment explanation
Indices: 52021--52049 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
52011 GATTAAACGA
52021 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
52050 ATCTTGGACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53719 original size:25 final size:25
Alignment explanation
Indices: 53691--53767 Score: 70
Period size: 25 Copynumber: 3.1 Consensus size: 25
53681 TAGAAACAAT
53691 AGTAGCTGTGGCATAAACAAGATGC
1 AGTAGCTGTGGCATAAACAAGATGC
** * * *
53716 AGTATAT-TAGCTATGTAA-AA-ATGT
1 AGTAGCTGTGGC-AT-AAACAAGATGC
53740 AGTAGCTGTGGCATAAACAAGATGC
1 AGTAGCTGTGGCATAAACAAGATGC
53765 AGT
1 AGT
53768 TTATTAGCTT
Statistics
Matches: 37, Mismatches: 10, Indels: 10
0.65 0.18 0.18
Matches are distributed among these distances:
23 2 0.05
24 15 0.41
25 18 0.49
26 2 0.05
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.26
Consensus pattern (25 bp):
AGTAGCTGTGGCATAAACAAGATGC
Found at i:55127 original size:15 final size:15
Alignment explanation
Indices: 55107--55143 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
55097 GAGGTGTCAC
55107 TTTGACTTTTCAAAA
1 TTTGACTTTTCAAAA
55122 TTTGACTTTTCAAAA
1 TTTGACTTTTCAAAA
55137 TTTGACT
1 TTTGACT
55144 CTTAAAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.49
Consensus pattern (15 bp):
TTTGACTTTTCAAAA
Found at i:55519 original size:20 final size:20
Alignment explanation
Indices: 55479--55519 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
55469 TTTGATCATG
*
55479 ATATTTCAATATGCATGTAT
1 ATATTTCAATATGCATATAT
55499 ATATTTC-ATATGACATATAT
1 ATATTTCAATATG-CATATAT
55519 A
1 A
55520 ACCAAGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (20 bp):
ATATTTCAATATGCATATAT
Found at i:55762 original size:15 final size:15
Alignment explanation
Indices: 55738--55772 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
55728 CCGTAGGACC
*
55738 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGA
*
55753 ACTACTTCCCGAAGA
1 ACTACGTCCCGAAGA
55768 ACTAC
1 ACTAC
55773 AGTACCATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.31, C:0.34, G:0.17, T:0.17
Consensus pattern (15 bp):
ACTACGTCCCGAAGA
Found at i:57463 original size:17 final size:17
Alignment explanation
Indices: 57420--57465 Score: 64
Period size: 13 Copynumber: 2.9 Consensus size: 17
57410 ACAATTCTTT
57420 TAACCTGAAAAGATGAG
1 TAACCTGAAAAGATGAG
57437 TAA-C---AAAGATGAG
1 TAACCTGAAAAGATGAG
57450 TAACCTGAAAAGATGA
1 TAACCTGAAAAGATGA
57466 TGCAAAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
13 12 0.48
14 1 0.04
16 1 0.04
17 11 0.44
ACGTcount: A:0.50, C:0.11, G:0.22, T:0.17
Consensus pattern (17 bp):
TAACCTGAAAAGATGAG
Found at i:57911 original size:24 final size:24
Alignment explanation
Indices: 57869--57956 Score: 88
Period size: 24 Copynumber: 3.7 Consensus size: 24
57859 GATATCAGAA
* *
57869 ATCAAAACAGGAATTCAGAACATAT
1 ATCAGAACA-GAATTCAGATCATAT
* * *
57894 ATCAGAACAGAATCCAGATCAGAA
1 ATCAGAACAGAATTCAGATCATAT
* *
57918 ATCAGAATAGAATTCAGGTCATAT
1 ATCAGAACAGAATTCAGATCATAT
*
57942 AT-AGAACATAATTCA
1 ATCAGAACAGAATTCA
57957 AGTCGGAAAT
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
23 11 0.22
24 32 0.63
25 8 0.16
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAGAACAGAATTCAGATCATAT
Found at i:70546 original size:12 final size:13
Alignment explanation
Indices: 70529--70562 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
70519 TGATATTTGA
*
70529 ATCATTGCCA-TG
1 ATCATTGCAACTG
70541 ATCATTGCAACTG
1 ATCATTGCAACTG
70554 ATCATTGCA
1 ATCATTGCA
70563 GCGGCGGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (13 bp):
ATCATTGCAACTG
Found at i:74501 original size:42 final size:40
Alignment explanation
Indices: 74438--74573 Score: 116
Period size: 42 Copynumber: 3.3 Consensus size: 40
74428 AAGTATTATT
* *
74438 TATTGCGGCGTTT-TAGATATAAACGTCGCTAATTTATCACTC
1 TATTACGGCGTTTGT-GGTATAAACG-CGCTAATTTA-CACTC
* * *
74480 TATTGCGGCGTTTGTGGTATAAACGC-C-ACTTTACAAATC
1 TATTACGGCGTTTGTGGTATAAACGCGCTAATTTAC-ACTC
* * *
74519 TATTACGGTGTTTGTGGTATAAACGCCGCTAAATTAACACTA
1 TATTACGGCGTTTGTGGTATAAACG-CGCT-AATTTACACTC
*
74561 TATTACGACGTTT
1 TATTACGGCGTTT
74574 TGGCTGAAAC
Statistics
Matches: 77, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
38 1 0.01
39 31 0.40
40 2 0.03
41 2 0.03
42 35 0.45
43 6 0.08
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (40 bp):
TATTACGGCGTTTGTGGTATAAACGCGCTAATTTACACTC
Found at i:75052 original size:63 final size:67
Alignment explanation
Indices: 74923--75099 Score: 177
Period size: 63 Copynumber: 2.6 Consensus size: 67
74913 TTTGAATGTG
* * * * *
74923 TCAAATTAAAAGGTATTTTCTACCTATTTAACTTTGAATATTAAAGATAATTATATCCTTTTGAA
1 TCAAATTAAAAGATA-TAT-TATCTATTTAACTTTGAATATAAAAGATAATTATATCCTTTCGAA
74988 TATT
64 TATT
* *
74992 TCAAATT-AAA-ATA-A-TATCTATTTAAGTTTGAATAGTAAAAGGTAACTT-TAT-CTTTCGAA
1 TCAAATTAAAAGATATATTATCTATTTAACTTTGAATA-TAAAAGATAA-TTATATCCTTTCGAA
75051 TATT
64 TATT
* *
75055 TTAAATTAAAAGATATTATTATCTATTTAATTTTGAATATTAAAA
1 TCAAATTAAAAGATA-TATTATCTATTTAACTTTGAATA-TAAAA
75100 TATATCTAAT
Statistics
Matches: 91, Mismatches: 10, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
63 35 0.38
64 14 0.15
65 5 0.05
67 3 0.03
68 27 0.30
69 7 0.08
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (67 bp):
TCAAATTAAAAGATATATTATCTATTTAACTTTGAATATAAAAGATAATTATATCCTTTCGAATA
TT
Found at i:75097 original size:34 final size:33
Alignment explanation
Indices: 75006--75104 Score: 85
Period size: 34 Copynumber: 2.9 Consensus size: 33
74996 ATTAAAATAA
* * * *
75006 TATCTATTTAAGTTTGAATAGTAAAAGGTAACTT
1 TATCTATTTAATTTTGAATATTAAAAGAT-ATTT
* *
75040 TATCT-TTCGAATATTTTAA-ATTAAAAGATATTAT
1 TATCTATT-TAAT-TTTGAATATTAAAAGATATT-T
*
75074 TATCTATTTAATTTTGAATATTAAAATATAT
1 TATCTATTTAATTTTGAATATTAAAAGATAT
75105 CTAATTGGAG
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
33 9 0.18
34 35 0.69
35 7 0.14
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.46
Consensus pattern (33 bp):
TATCTATTTAATTTTGAATATTAAAAGATATTT
Found at i:75721 original size:28 final size:28
Alignment explanation
Indices: 75681--75742 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
75671 ATGTTTTTCT
* *
75681 ATTGTTTGGTCGTTGTTTTCACTTATCG
1 ATTGTTTGGTCGTTATTTTCACTTATCA
75709 ATTGTTTGGTCGTTATTTTCACTTATCA
1 ATTGTTTGGTCGTTATTTTCACTTATCA
75737 ATTGTT
1 ATTGTT
75743 CGGACCCTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.15, C:0.13, G:0.18, T:0.55
Consensus pattern (28 bp):
ATTGTTTGGTCGTTATTTTCACTTATCA
Found at i:82633 original size:7 final size:7
Alignment explanation
Indices: 82623--82649 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
82613 TCTTTTGTGA
82623 TTTGAAC
1 TTTGAAC
82630 TTTGAAC
1 TTTGAAC
82637 TTTGAAC
1 TTTGAAC
82644 TTTGAA
1 TTTGAA
82650 GTGTGTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (7 bp):
TTTGAAC
Found at i:88341 original size:13 final size:13
Alignment explanation
Indices: 88323--88347 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
88313 GGTACATCTT
88323 TGCTTTCCTGCTG
1 TGCTTTCCTGCTG
88336 TGCTTTCCTGCT
1 TGCTTTCCTGCT
88348 TCACAGCATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.32, G:0.20, T:0.48
Consensus pattern (13 bp):
TGCTTTCCTGCTG
Done.