Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002784.1 Hibiscus syriacus cultivar Beakdansim tig00005738_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: 60799
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1828 original size:69 final size:65
Alignment explanation
Indices: 1719--1844 Score: 180
Period size: 69 Copynumber: 1.9 Consensus size: 65
1709 GAATTTCTTG
* *
1719 CACATAAGGTCGTGCCACCTACACTAAGTGTCTTGGGTATACACTCTAGTGCTAATCAAATATGA
1 CACATAAGGTCGTGCCACCTACACTAAGTGTCTTGAGTATACAATCTAGTGCTAATCAAATATGA
* *
1784 CACATAAGGTCGTGCCCACCACCTGCATTAAGTGTCTTGAGTATACAATCTAGTGCTAATC
1 CACATAAGGTCGTG----CCACCTACACTAAGTGTCTTGAGTATACAATCTAGTGCTAATC
1845 CAGATATGCA
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
65 14 0.26
69 39 0.74
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (65 bp):
CACATAAGGTCGTGCCACCTACACTAAGTGTCTTGAGTATACAATCTAGTGCTAATCAAATATGA
Found at i:3260 original size:21 final size:21
Alignment explanation
Indices: 3209--3260 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
3199 CAAAATGGCC
*
3209 CAATTTC-ATACTCTTAACAT
1 CAATTTCAACACTCTTAACAT
3229 CAATTTCAACACTC-TAACAT
1 CAATTTCAACACTCTTAACAT
*
3249 TAATTTCTAACA
1 CAATTTC-AACA
3261 TAGTACATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 19 0.68
21 9 0.32
ACGTcount: A:0.38, C:0.25, G:0.00, T:0.37
Consensus pattern (21 bp):
CAATTTCAACACTCTTAACAT
Found at i:9052 original size:24 final size:24
Alignment explanation
Indices: 9020--9065 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
9010 AGAGAAACAA
*
9020 AGAAAAGAAAAAATAATAAAAATG
1 AGAAAAGAAAAAATAAGAAAAATG
* *
9044 AGAATAGAAGAAATAAGAAAAA
1 AGAAAAGAAAAAATAAGAAAAA
9066 AGGAAAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (24 bp):
AGAAAAGAAAAAATAAGAAAAATG
Found at i:10556 original size:44 final size:44
Alignment explanation
Indices: 10496--10608 Score: 190
Period size: 44 Copynumber: 2.6 Consensus size: 44
10486 AATCAACGTG
*
10496 TCCAGATTTGATCTTCCTTGAAGAGTAGGAAATCATATCATTTT
1 TCCATATTTGATCTTCCTTGAAGAGTAGGAAATCATATCATTTT
*
10540 TCCATATTTGATCTTCCTTGAAGAGTAGGAAATCATGTCATTTT
1 TCCATATTTGATCTTCCTTGAAGAGTAGGAAATCATATCATTTT
* *
10584 TTCATATTTGATCTTCCTTAAAGAG
1 TCCATATTTGATCTTCCTTGAAGAG
10609 AAATAGAGCA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 65 1.00
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (44 bp):
TCCATATTTGATCTTCCTTGAAGAGTAGGAAATCATATCATTTT
Found at i:10738 original size:130 final size:131
Alignment explanation
Indices: 10580--10871 Score: 318
Period size: 130 Copynumber: 2.2 Consensus size: 131
10570 AATCATGTCA
* * *
10580 TTTTTTCATATTTGATCTTCCTTAAAGAGAAATAGAGCAAATCTACCT-CAATTCAATCTTCCCT
1 TTTTTCCATATTTGATCTTCCCTGAAGAGAAATAGAGCAAATCTACCTGC-ATTCAATCTTCCCT
** * ** * *
10644 AAAGAGTAGTAAAGTGAATCAACGTTTCCAAATATGATCTACCCTGAAGAGCAGTGAAGCAGAT-
65 AAAGAACAATAAAGTGAATCAAAATTTCCAAATATGATCTACCCTGAAGAACAGTGAAGCAAATC
10708 CC
130 CC
* * * * * * *
10710 TTTTTCCATATTTGATCTTCCCTGAAGAGCAGTGGAGCAAATCTACTTGCATTTAATCTTCCTTG
1 TTTTTCCATATTTGATCTTCCCTGAAGAGAAATAGAGCAAATCTACCTGCATTCAATCTTCCCTA
* * * * * * *
10775 AAGAACAATAAAGTGAATCAAAATTTCTAGATTTGATTTTCCTTGAAGAACAGTGGAGCAAATCC
66 AAGAACAATAAAGTGAATCAAAATTTCCAAATATGATCTACCCTGAAGAACAGTGAAGCAAATCC
10840 C
131 C
***
10841 TTTTAGTATATTTGATCTTCCCTGAAGAGAA
1 TTTTTCCATATTTGATCTTCCCTGAAGAGAA
10872 GTGAAACAAA
Statistics
Matches: 132, Mismatches: 28, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
130 102 0.77
131 30 0.23
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (131 bp):
TTTTTCCATATTTGATCTTCCCTGAAGAGAAATAGAGCAAATCTACCTGCATTCAATCTTCCCTA
AAGAACAATAAAGTGAATCAAAATTTCCAAATATGATCTACCCTGAAGAACAGTGAAGCAAATCC
C
Found at i:11064 original size:3 final size:3
Alignment explanation
Indices: 11056--11094 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
11046 ACCCAGATCT
11056 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
11095 ATAATTATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:14590 original size:27 final size:27
Alignment explanation
Indices: 14560--14621 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
14550 TAAAACATTA
14560 AAAATAATATATACAATTTATAAAAGT
1 AAAATAATATATACAATTTATAAAAGT
*
14587 AAAATAATATATATAATTTATAAAAGT
1 AAAATAATATATACAATTTATAAAAGT
14614 AAAATAAT
1 AAAATAAT
14622 TATTTATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (27 bp):
AAAATAATATATACAATTTATAAAAGT
Found at i:14611 original size:21 final size:20
Alignment explanation
Indices: 14586--14637 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
14576 TTTATAAAAG
14586 TAAAATAATATATATAATTTA
1 TAAAATAATATA-ATAATTTA
* *
14607 TAAAAGTAAAATAATTATTTA
1 TAAAA-TAATATAATAATTTA
*
14628 TTAAA-AATAT
1 TAAAATAATAT
14638 CAGAAAATAG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 4 0.15
21 16 0.62
22 6 0.23
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
TAAAATAATATAATAATTTA
Found at i:15086 original size:11 final size:11
Alignment explanation
Indices: 15070--15100 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
15060 AGTATTTATC
15070 CTAAATATTTA
1 CTAAATATTTA
15081 CTAAATATTTA
1 CTAAATATTTA
15092 CTAAATATT
1 CTAAATATT
15101 AACAGGGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (11 bp):
CTAAATATTTA
Found at i:15433 original size:33 final size:33
Alignment explanation
Indices: 15390--15476 Score: 156
Period size: 33 Copynumber: 2.6 Consensus size: 33
15380 GTTAGAGGCC
*
15390 GGCCACCACCAGCCACCGTTCTACGACGGTGAT
1 GGCCATCACCAGCCACCGTTCTACGACGGTGAT
*
15423 GGCCATCACCAGCCACCGTTCTACGGCGGTGAT
1 GGCCATCACCAGCCACCGTTCTACGACGGTGAT
15456 GGCCATCACCAGCCACCGTTC
1 GGCCATCACCAGCCACCGTTC
15477 GATCTAAATA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.20, C:0.40, G:0.24, T:0.16
Consensus pattern (33 bp):
GGCCATCACCAGCCACCGTTCTACGACGGTGAT
Found at i:16142 original size:3 final size:3
Alignment explanation
Indices: 16130--16190 Score: 74
Period size: 3 Copynumber: 21.0 Consensus size: 3
16120 GTGTCATTAT
16130 TAA TAA -AA TAA TAA T-A TAAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
* *
16174 T-A TGA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
16191 AAATTTAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
2 6 0.12
3 43 0.84
4 2 0.04
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:16597 original size:73 final size:74
Alignment explanation
Indices: 16348--16944 Score: 943
Period size: 73 Copynumber: 8.1 Consensus size: 74
16338 ATGTCTTATG
*
16348 GATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTTTGAAAACATCGTGCACTGT
1 GATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGC-TTTTTTGAAAACATCATGCACTGT
* *
16413 AGGCCTTACG
65 AGGTCTTACA
* *
16423 GATGACCCTGAGGCTTTAGAATCAAAAAGCTCCCGAGGGC-TTTTTGAAAACATCATGCACT-TA
1 GATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTTGAAAACATCATGCACTGTA
16486 GGTCTTACA
66 GGTCTTACA
* *
16495 GATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGC-TTTTTGAAAACATCGTGCACTGTA
1 GATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTTGAAAACATCATGCACTGTA
16559 GGTCTTACA
66 GGTCTTACA
* * *
16568 GATGACCCTGAGGCTTTAGAATCAAAAAGCTCCCAAAAGC-TTTTTGAAAACATCATGCACTGTA
1 GATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTTGAAAACATCATGCACTGTA
16632 GGTCTTACA
66 GGTCTTACA
*
16641 GATGACCCCGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTTGAAAACATCATGCACTGTA
1 GATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTTGAAAACATCATGCACTGTA
16706 GGTCTTACA
66 GGTCTTACA
*
16715 GATTACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTTGAAAACATCATGCACTGTA
1 GATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTTGAAAACATCATGCACTGTA
16780 GGTCTTACA
66 GGTCTTACA
* *
16789 GATAACCCCGAGGCTTTAAAAAAACATCAAAAAGCTCCCGAAGGCTTTTTTGAAAACATCATGCA
1 GATGACCCTGAGGCTTT----AAA-ATCAAAAAGCTCCCGAAGGCTTTTTTGAAAACATCATGCA
16854 CTGTAGGTCTTACA
61 CTGTAGGTCTTACA
* * * *
16868 GATGACCATGAGGCTCTAAGATCAAAAAGCTCCCGAAGGC-TTTTTGAAAACATCATGCAATGTA
1 GATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTTGAAAACATCATGCACTGTA
16932 GGTCTTACA
66 GGTCTTACA
16941 GATG
1 GATG
16945 TGGGAAATAA
Statistics
Matches: 487, Mismatches: 28, Indels: 16
0.92 0.05 0.03
Matches are distributed among these distances:
72 66 0.14
73 171 0.35
74 140 0.29
75 40 0.08
78 3 0.01
79 67 0.14
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (74 bp):
GATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTTGAAAACATCATGCACTGTA
GGTCTTACA
Found at i:16741 original size:147 final size:147
Alignment explanation
Indices: 16348--16944 Score: 955
Period size: 147 Copynumber: 4.0 Consensus size: 147
16338 ATGTCTTATG
* *
16348 GATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTTTGAAAACATCGTGCACTGT
1 GATGACCCCGAGGCTTTAAAATCAAAAAGCTCCCGAAGGC-TTTTTTGAAAACATCATGCACTGT
* * * *
16413 AGGCCTTACGGATGACCCTGAGGCTTTAGAATCAAAAAGCTCCCGAGGGCTTTTTGAAAACATCA
65 AGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCA
16478 TGCACT-TAGGTCTTACA
130 TGCACTGTAGGTCTTACA
* * *
16495 GATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGC-TTTTTGAAAACATCGTGCACTGTA
1 GATGACCCCGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTTGAAAACATCATGCACTGTA
* * *
16559 GGTCTTACAGATGACCCTGAGGCTTTAGAATCAAAAAGCTCCCAAAAGCTTTTTGAAAACATCAT
66 GGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCAT
16624 GCACTGTAGGTCTTACA
131 GCACTGTAGGTCTTACA
16641 GATGACCCCGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTTGAAAACATCATGCACTGTA
1 GATGACCCCGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTTGAAAACATCATGCACTGTA
*
16706 GGTCTTACAGATTACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTTGAAAACATCA
66 GGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGC-TTTTTGAAAACATCA
16771 TGCACTGTAGGTCTTACA
130 TGCACTGTAGGTCTTACA
*
16789 GATAACCCCGAGGCTTTAAAAAAACATCAAAAAGCTCCCGAAGGCTTTTTTGAAAACATCATGCA
1 GATGACCCCGAGGCTTT----AAA-ATCAAAAAGCTCCCGAAGGCTTTTTTGAAAACATCATGCA
* * *
16854 CTGTAGGTCTTACAGATGACCATGAGGCTCTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAAC
61 CTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAAC
*
16919 ATCATGCAATGTAGGTCTTACA
126 ATCATGCACTGTAGGTCTTACA
16941 GATG
1 GATG
16945 TGGGAAATAA
Statistics
Matches: 422, Mismatches: 20, Indels: 11
0.93 0.04 0.02
Matches are distributed among these distances:
145 89 0.21
146 49 0.12
147 107 0.25
148 49 0.12
152 38 0.09
153 90 0.21
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (147 bp):
GATGACCCCGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTTGAAAACATCATGCACTGTA
GGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCAT
GCACTGTAGGTCTTACA
Found at i:17631 original size:21 final size:22
Alignment explanation
Indices: 17607--17658 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
17597 TAAGGTTTTT
*
17607 ATCTTTGAAAAGA-AATCTATC
1 ATCTTTGAAAAGAGAATATATC
**
17628 ATCTTTGAGGAGAGAATATATC
1 ATCTTTGAAAAGAGAATATATC
17650 ATCTTTGAA
1 ATCTTTGAA
17659 GAGTGTAGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (22 bp):
ATCTTTGAAAAGAGAATATATC
Found at i:18113 original size:54 final size:55
Alignment explanation
Indices: 18026--18158 Score: 155
Period size: 54 Copynumber: 2.5 Consensus size: 55
18016 TAATTGGTTC
* * *
18026 GTAAAACATTTGACAAAACATTCA-TCATCTCATGTG-GTTTATGCTCAGATGCTA
1 GTAAAACATTTGACAAAACATTCATTCATCTCATGCGACTTT-TGCACAGATGCTA
* * * * *
18080 GTAAAACATTTGACAACACGTTCATTC-TTTCATGCGACTTTTGCACAGATGTTT
1 GTAAAACATTTGACAAAACATTCATTCATCTCATGCGACTTTTGCACAGATGCTA
*
18134 GTAAAACATTTGACAATACATTCAT
1 GTAAAACATTTGACAAAACATTCAT
18159 CCAGTTGTGG
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
54 62 0.93
55 5 0.07
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (55 bp):
GTAAAACATTTGACAAAACATTCATTCATCTCATGCGACTTTTGCACAGATGCTA
Found at i:21199 original size:17 final size:16
Alignment explanation
Indices: 21177--21232 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
21167 ATTGGTTCAA
*
21177 TTTTTTCCTTTTTCCT
1 TTTTTTTCTTTTTCCT
*
21193 TTTTTTTCTTTTTTTCT
1 TTTTTTTC-TTTTTCCT
21210 TTTTCTTT-TTTCTTCCT
1 TTTT-TTTCTTT-TTCCT
21227 TTTTTT
1 TTTTTT
21233 CAAGTATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 12 0.35
17 19 0.56
18 3 0.09
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTTTCTTTTTCCT
Found at i:21213 original size:25 final size:25
Alignment explanation
Indices: 21177--21233 Score: 82
Period size: 24 Copynumber: 2.3 Consensus size: 25
21167 ATTGGTTCAA
*
21177 TTTTTTCCTTTTTCCTTTTTT-TT-C
1 TTTTTTTCTTTTT-CTTTTTTCTTCC
21201 TTTTTTTCTTTTTCTTTTTTCTTCC
1 TTTTTTTCTTTTTCTTTTTTCTTCC
21226 TTTTTTTC
1 TTTTTTTC
21234 AAGTATAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 7 0.23
24 14 0.47
25 9 0.30
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (25 bp):
TTTTTTTCTTTTTCTTTTTTCTTCC
Found at i:26932 original size:29 final size:29
Alignment explanation
Indices: 26899--26962 Score: 114
Period size: 27 Copynumber: 2.3 Consensus size: 29
26889 TAAAACATTA
26899 AAAATAATATATATATAATTTATAAAAGT
1 AAAATAATATATATATAATTTATAAAAGT
26928 AAAAT-A-ATATATATAATTTATAAAAGT
1 AAAATAATATATATATAATTTATAAAAGT
26955 AAAATAAT
1 AAAATAAT
26963 TATTTATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
27 26 0.79
28 2 0.06
29 5 0.15
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAATAATATATATATAATTTATAAAAGT
Found at i:28458 original size:3 final size:3
Alignment explanation
Indices: 28446--28508 Score: 69
Period size: 3 Copynumber: 22.0 Consensus size: 3
28436 GTGTAATTAT
* * * *
28446 TAA TAA -AA TAA TAA TAC T-A TTA TAA TAA TAA TAA TAA T-A TGA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
28491 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
28509 AAAGGAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
2 5 0.10
3 46 0.90
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:28475 original size:20 final size:20
Alignment explanation
Indices: 28443--28504 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
28433 TTGGTGTAAT
*
28443 TATTAATAA-AATAATAATAC
1 TATT-ATAATAATAATAATAA
28463 TATTATAATAATAATAATAA
1 TATTATAATAATAATAATAA
* *
28483 TATGATATTAATAATAATAA
1 TATTATAATAATAATAATAA
28503 TA
1 TA
28505 ATAAAAAGGA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 4 0.11
20 34 0.89
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (20 bp):
TATTATAATAATAATAATAA
Found at i:28478 original size:23 final size:24
Alignment explanation
Indices: 28441--28507 Score: 97
Period size: 23 Copynumber: 2.9 Consensus size: 24
28431 GCTTGGTGTA
28441 ATTATTAATAA-AATAATAATACT-
1 ATTATTAATAATAATAATAATA-TG
28464 ATTA-TAATAATAATAATAATATG
1 ATTATTAATAATAATAATAATATG
28487 A-TATTAATAATAATAATAATA
1 ATTATTAATAATAATAATAATA
28508 AAAAGGAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
22 9 0.22
23 32 0.78
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (24 bp):
ATTATTAATAATAATAATAATATG
Found at i:31497 original size:74 final size:75
Alignment explanation
Indices: 31375--31520 Score: 231
Period size: 74 Copynumber: 2.0 Consensus size: 75
31365 TATAATCATT
* * * *
31375 CAGGATTATTAAAAATATATACCCACCATGACCAAAACTATATTACTTATCAATATACCATATTC
1 CAGGATTATTAAAAAAATATACCCACCATGACCAAAACTATATAACTTATCAATATACCAAATTA
31440 TGGACTCTCA
66 TGGACTCTCA
* *
31450 CAGGATTATTAAAAAAATATA-CCACCATGACTAAAACTATGTAACTTATCAATATACCAAATTA
1 CAGGATTATTAAAAAAATATACCCACCATGACCAAAACTATATAACTTATCAATATACCAAATTA
31514 TGGACTC
66 TGGACTC
31521 ACATCTAGTA
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
74 45 0.69
75 20 0.31
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (75 bp):
CAGGATTATTAAAAAAATATACCCACCATGACCAAAACTATATAACTTATCAATATACCAAATTA
TGGACTCTCA
Found at i:33752 original size:8 final size:9
Alignment explanation
Indices: 33737--33764 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
33727 ATTATAACTC
33737 AATAAAAAT
1 AATAAAAAT
33746 AATAAAAAT
1 AATAAAAAT
33755 AATAAAAAT
1 AATAAAAAT
33764 A
1 A
33765 GGAAAATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AATAAAAAT
Found at i:36352 original size:21 final size:21
Alignment explanation
Indices: 36328--36400 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
36318 TATGCCACCA
36328 CCACAGGGTTACATTCCTAGC
1 CCACAGGGTTACATTCCTAGC
* * *
36349 CCACAGGGGTACATACCCAGC
1 CCACAGGGTTACATTCCTAGC
* *
36370 CCGCAAGGTTACATTCCTAGC
1 CCACAGGGTTACATTCCTAGC
36391 CC-CTAGGGTT
1 CCAC-AGGGTT
36401 TTATGACACC
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 1 0.02
21 41 0.98
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (21 bp):
CCACAGGGTTACATTCCTAGC
Found at i:36848 original size:19 final size:19
Alignment explanation
Indices: 36804--36848 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
36794 GTTGTATTTC
*
36804 AATTTTAATGTAATTTTGT
1 AATTTTTATGTAATTTTGT
36823 AATTTTTATGTAATTTTGT
1 AATTTTTATGTAATTTTGT
36842 AATTTTT
1 AATTTTT
36849 TTAAATGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (19 bp):
AATTTTTATGTAATTTTGT
Found at i:36937 original size:18 final size:18
Alignment explanation
Indices: 36914--36950 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
36904 TTAAATTATG
*
36914 TAATGTTTTTTAAATGTT
1 TAATGTTTGTTAAATGTT
*
36932 TAATGTTTGTTGAATGTT
1 TAATGTTTGTTAAATGTT
36950 T
1 T
36951 TTAAAATGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.59
Consensus pattern (18 bp):
TAATGTTTGTTAAATGTT
Found at i:40972 original size:26 final size:28
Alignment explanation
Indices: 40935--40998 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
40925 TATGTATTTG
40935 TTTCTA-ATATTT-CAATGTAAT-TGCAT
1 TTTCTACATATTTCCAATGT-ATGTGCAT
*
40961 TTTCTACA-ATTTCCCAATGTATGTGTAT
1 TTTCTACATATTT-CCAATGTATGTGCAT
40989 TTTCTACATA
1 TTTCTACATA
40999 AATTTCCCAC
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
26 10 0.31
27 3 0.09
28 18 0.56
29 1 0.03
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (28 bp):
TTTCTACATATTTCCAATGTATGTGCAT
Found at i:41091 original size:25 final size:24
Alignment explanation
Indices: 41063--41179 Score: 83
Period size: 25 Copynumber: 4.6 Consensus size: 24
41053 CTTACCCTAA
*
41063 ACCACTTTAACCTACACAACCCTT
1 ACCACTTTAACCTACAAAACCCTT
* * * *
41087 GACCACTCTCACCTTAAATAAACCCTAA
1 -ACCACTTTAACC-TACA-AAACCCT-T
*
41115 ACCACTTTAACCTACAAAATCCTT
1 ACCACTTTAACCTACAAAACCCTT
*
41139 CACCACTTTTACCTTA-ACAAACCCTAT
1 -ACCACTTTAACC-TACA-AAACCCT-T
*
41166 ATCACTTTAACCTA
1 ACCACTTTAACCTA
41180 AAATCACTCC
Statistics
Matches: 71, Mismatches: 14, Indels: 14
0.72 0.14 0.14
Matches are distributed among these distances:
25 30 0.42
26 24 0.34
27 17 0.24
ACGTcount: A:0.36, C:0.36, G:0.01, T:0.27
Consensus pattern (24 bp):
ACCACTTTAACCTACAAAACCCTT
Found at i:41144 original size:52 final size:51
Alignment explanation
Indices: 41056--41179 Score: 167
Period size: 52 Copynumber: 2.4 Consensus size: 51
41046 ATTGAACCTT
* * *
41056 ACCCTAAACCACTTTAACCTACACAACCCTTGACCACTCTCACCTTAAATAA
1 ACCCTAAACCACTTTAACCTACAAAACCCTTCACCACTCTCACCTT-AACAA
* * *
41108 ACCCTAAACCACTTTAACCTACAAAATCCTTCACCACTTTTACCTTAACAA
1 ACCCTAAACCACTTTAACCTACAAAACCCTTCACCACTCTCACCTTAACAA
* *
41159 ACCCTATATCACTTTAACCTA
1 ACCCTAAACCACTTTAACCTA
41180 AAATCACTCC
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
51 23 0.36
52 41 0.64
ACGTcount: A:0.36, C:0.36, G:0.01, T:0.27
Consensus pattern (51 bp):
ACCCTAAACCACTTTAACCTACAAAACCCTTCACCACTCTCACCTTAACAA
Found at i:42331 original size:39 final size:39
Alignment explanation
Indices: 42273--42354 Score: 137
Period size: 39 Copynumber: 2.1 Consensus size: 39
42263 GGTGGTCTAA
*
42273 TTCATATTTTAATACCATATTGTTAAATGGAAATCGTGC
1 TTCATATTTTAATACCATATTGTTAAATGAAAATCGTGC
**
42312 TTCATATTTTAATGGCATATTGTTAAATGAAAATCGTGC
1 TTCATATTTTAATACCATATTGTTAAATGAAAATCGTGC
42351 TTCA
1 TTCA
42355 GTGGAATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.41
Consensus pattern (39 bp):
TTCATATTTTAATACCATATTGTTAAATGAAAATCGTGC
Found at i:43119 original size:23 final size:23
Alignment explanation
Indices: 43076--43122 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
43066 TGTATCACAA
* *
43076 AAACAGAGATAAACGTGCAACAC
1 AAACAGAGATAAACATACAACAC
43099 AAACAGAGATAAACATACAACAC
1 AAACAGAGATAAACATACAACAC
43122 A
1 A
43123 TGTAGAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.57, C:0.21, G:0.13, T:0.09
Consensus pattern (23 bp):
AAACAGAGATAAACATACAACAC
Found at i:47846 original size:32 final size:31
Alignment explanation
Indices: 47809--47868 Score: 93
Period size: 32 Copynumber: 1.9 Consensus size: 31
47799 TCACTATTAT
*
47809 TATTTATAATTGTGATAATAACAATTTTTTTC
1 TATTTATAATTGTGACAATAAC-ATTTTTTTC
*
47841 TATTTATAATTGTGACAGTAACATTTTT
1 TATTTATAATTGTGACAATAACATTTTT
47869 CACTAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 6 0.23
32 20 0.77
ACGTcount: A:0.33, C:0.07, G:0.08, T:0.52
Consensus pattern (31 bp):
TATTTATAATTGTGACAATAACATTTTTTTC
Found at i:48809 original size:21 final size:21
Alignment explanation
Indices: 48780--48846 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
48770 TTGTGGTTAA
*
48780 AATAAAAAATAAGAATTAAAT
1 AATACAAAATAAGAATTAAAT
* *
48801 AATACAAAAAAATAATTAAAT
1 AATACAAAATAAGAATTAAAT
*
48822 AA-ACAAATTAAAGAGATTAAGAT
1 AATACAAAAT-AAGA-ATTAA-AT
48845 AA
1 AA
48847 AGAGAAACTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
20 5 0.14
21 23 0.62
22 5 0.14
23 4 0.11
ACGTcount: A:0.69, C:0.03, G:0.06, T:0.22
Consensus pattern (21 bp):
AATACAAAATAAGAATTAAAT
Found at i:49507 original size:19 final size:19
Alignment explanation
Indices: 49451--49513 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
49441 CTATTTAAAC
**
49451 TAAAATACTAAAAAAATAAT
1 TAAAATACT-AAAACCTAAT
* * *
49471 ATAATATTCTAAATCCTAAT
1 -TAAAATACTAAAACCTAAT
*
49491 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
49510 TAAA
1 TAAA
49514 CTAAAATACA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 7 0.21
21 7 0.21
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:49541 original size:64 final size:66
Alignment explanation
Indices: 49416--49603 Score: 197
Period size: 64 Copynumber: 2.8 Consensus size: 66
49406 CTAAACATCT
* * *
49416 TAAATCTTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACTAAA-A-AAATAATATAATAT
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATAC-AAAGATAAATAATAAAATAT
**
49478 -TC
64 AAA
*
49480 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAA-GATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAATAATAAAATATAA
49544 A
66 A
*
49545 AAATATCCTAAACTTAATTAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAA
1 TAA-ATCCT-AA-TT-A--AAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAA
49604 ATATAATGTT
Statistics
Matches: 106, Mismatches: 7, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
63 8 0.08
64 44 0.42
65 5 0.05
66 5 0.05
67 2 0.02
68 2 0.02
69 1 0.01
71 7 0.07
72 32 0.30
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.29
Consensus pattern (66 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAATAATAAAATATAA
A
Found at i:51373 original size:53 final size:48
Alignment explanation
Indices: 51294--51391 Score: 142
Period size: 52 Copynumber: 1.9 Consensus size: 48
51284 TCCGCTGTGT
51294 ATTTTTCTGCAATCGAACCAAATCAGTTTTTTCTGCACTGTTATGTTCAA
1 ATTTTTCTGCAATCGAACCAAATCAG-TTTTTCTGCACTGTT-TGTTCAA
*
51344 ATTTTTCTGCACAGTTCGAACCAAGTCAGTTTTTCTGCACTGTTTGTT
1 ATTTTTCTGCA-A--TCGAACCAAATCAGTTTTTCTGCACTGTTTGTT
51392 TTTCGTTAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
50 11 0.25
51 5 0.11
52 15 0.34
53 13 0.30
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.43
Consensus pattern (48 bp):
ATTTTTCTGCAATCGAACCAAATCAGTTTTTCTGCACTGTTTGTTCAA
Found at i:51452 original size:15 final size:15
Alignment explanation
Indices: 51432--51460 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
51422 CTGTTCAGAA
51432 AAAATAAAATTAATC
1 AAAATAAAATTAATC
51447 AAAATAAAATTAAT
1 AAAATAAAATTAAT
51461 AGAATGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAATAAAATTAATC
Found at i:57145 original size:18 final size:18
Alignment explanation
Indices: 57122--57169 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
57112 GTTGTGGTTA
*
57122 AAATAAAAAATAAGAATT
1 AAATAAAAAATAAAAATT
57140 AAATAAAAGAA-AAAAATT
1 AAATAAAA-AATAAAAATT
57158 AAATAAAGAAAT
1 AAATAAA-AAAT
57170 TAAAGATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 23 0.88
19 3 0.12
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (18 bp):
AAATAAAAAATAAAAATT
Found at i:57815 original size:64 final size:73
Alignment explanation
Indices: 57797--57936 Score: 187
Period size: 74 Copynumber: 1.9 Consensus size: 73
57787 TACTAAAAAA
* *
57797 ATAATATAATATTCTAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACAAAGATA
1 ATAA-ATAATATCCTAAATCTTAATTAAAATACTTAAAACCTATTTAAACTAAAATACAAAGATA
57861 AAGATAAAAT
65 AAGAT-AAAT
* *
57871 ATAAAAATAATATCCTAAA-ATTAATTAAAATACTAAAAACCTATTTAAACT-AAATACAAAGAT
1 AT--AAATAATATCCTAAATCTTAATTAAAATACTTAAAACCTATTTAAACTAAAATACAAAGAT
57934 AAA
64 AAA
57937 ATATAATGTT
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
74 29 0.49
75 28 0.47
76 2 0.03
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.29
Consensus pattern (73 bp):
ATAAATAATATCCTAAATCTTAATTAAAATACTTAAAACCTATTTAAACTAAAATACAAAGATAA
AGATAAAT
Found at i:57838 original size:19 final size:19
Alignment explanation
Indices: 57782--57844 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
57772 CTATTTAAAC
**
57782 TAAAATACTAAAAAAATAAT
1 TAAAATACT-AAAACCTAAT
* * *
57802 ATAATATTCTAAATCCTAAT
1 -TAAAATACTAAAACCTAAT
*
57822 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
57841 TAAA
1 TAAA
57845 CTAAAATACA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 7 0.21
21 7 0.21
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:57903 original size:74 final size:74
Alignment explanation
Indices: 57818--57963 Score: 224
Period size: 74 Copynumber: 2.0 Consensus size: 74
57808 TTCTAAATCC
57818 TAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAGATAAAAT-ATAAAAATAA
1 TAATTAAAATACTAAAAACCTATTTAAACT-AAATACAAAGATAAA-ATAAAATGATAAAAATAA
57881 TATCCTAAAAT
64 TATCCTAAAAT
* * * *
57892 TAATTAAAATACTAAAAACCTATTTAAACTAAATACAAAGATAAAATATAATGTTTAAAATATTA
1 TAATTAAAATACTAAAAACCTATTTAAACTAAATACAAAGATAAAATAAAATGATAAAAATAATA
57957 TCCTAAA
66 TCCTAAA
57964 TTTGAGTTTA
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
73 6 0.09
74 44 0.67
75 16 0.24
ACGTcount: A:0.58, C:0.10, G:0.03, T:0.29
Consensus pattern (74 bp):
TAATTAAAATACTAAAAACCTATTTAAACTAAATACAAAGATAAAATAAAATGATAAAAATAATA
TCCTAAAAT
Done.