Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002796.1 Hibiscus syriacus cultivar Beakdansim tig00005757_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: 103822
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:10260 original size:18 final size:18
Alignment explanation
Indices: 10189--10261 Score: 62
Period size: 18 Copynumber: 4.1 Consensus size: 18
10179 TTATAAATTT
10189 TATTAAAATTTTA-AAAA
1 TATTAAAATTTTATAAAA
*
10206 TATTGAAATTTTTATAAAA
1 TATT-AAAATTTTATAAAA
***
10225 -ATTAAAAACCCTATAAAA
1 TATT-AAAATTTTATAAAA
10243 TATTATAAATTTTA-AAAA
1 TATTA-AAATTTTATAAAA
10261 T
1 T
10262 CAAAAGTTAT
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
17 4 0.09
18 27 0.63
19 12 0.28
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (18 bp):
TATTAAAATTTTATAAAA
Found at i:10477 original size:556 final size:552
Alignment explanation
Indices: 9388--10500 Score: 2165
Period size: 556 Copynumber: 2.0 Consensus size: 552
9378 TTTATATTTT
9388 TAATTATATTAGTTTTTTTTAAAACTGATTTAATTGTGTTAAAGTCATCTTTTGATGATCTATCT
1 TAATTATATTAGTTTTTTTTAAAACTGATTTAATTGTGTTAAAGTCATCTTTTGATGATCTATCT
9453 GTTACGATGTTGACATGCCAATTAACTATGCTAATGCCACAATTCATTCTGATGACATAACAATC
66 GTTACGATGTTGACATGCCAATTAACTATGCTAATGCCACAATTCATTCTGATGACATAACAATC
9518 CATATGTGAATGATGAAATAACAAAAGAGTTTAATTGATTTTTAGTCGAGTTCAAAATATAATTG
131 CATATGTGAATGATGAAATAACAAAAGAGTTTAATTGATTTTTAGTCGAGTTCAAAATATAATTG
9583 ATTTTAACTGAAAATACAAATATTTTTAATATTTAAGGAAAAATTATAAATTTTATTAAAATTTT
196 ATTTTAACTGAAAATACAAATATTTTTAATATTTAAGGAAAAATTATAAATTTTATTAAAATTTT
9648 AAAAATATTGAAATTTTTATAAAAATTAAAAACCCTATAAAATATTAAAATTTTAAAAATCAAAA
261 AAAAATATTGAAATTTTTATAAAAATTAAAAACCCTATAAAATATTAAAATTTTAAAAATCAAAA
9713 GTTATAAAATGATAAGTTATAAATATAAAAGTAAAATTTAAAAATATTTATAAAGTATTAAAAAA
326 GTTATAAAATGATAAGTTATAAATATAAAAGTAAAATTTAAAAATATTTATAAAGTATTAAAAAA
9778 TTTGATATTTCATTGAAAAAGTTTTCAACAATCTCTTATTAGGCTGTGTCTACTCCTCTTCTTTC
391 TTTGATATTTCATTGAAAAAGTTTTCAACAATCTCTTATTAGGCTGTGTCTACTCCTCTTCTTTC
9843 AACATACTTTTAGTAGAATTAATTTTATAATAGGGTAACAATAAAACTCAAATTTCCTTCGATTT
456 AACATACTTTTAGTAGAATTAATTTTATAATAGGGTAACAATAAAACTCAAATTTCCTTCGATTT
9908 ATTACACCAAATATTAATGAAAATTTGAGAAC
521 ATTACACCAAATATTAATGAAAATTTGAGAAC
9940 TAATTATATTAGTTTTTTTTAAAACTGATTTAATTGTGTTAAAGTCATCTTTTGATGATCTATCT
1 TAATTATATTAGTTTTTTTTAAAACTGATTTAATTGTGTTAAAGTCATCTTTTGATGATCTATCT
10005 GTTACGATGTTGACATGCCAATTAACTATGCTAATGCCACAATTCATTCTGATGACATAACAATC
66 GTTACGATGTTGACATGCCAATTAACTATGCTAATGCCACAATTCATTCTGATGACATAACAATC
10070 CATATGTGAATGATGAAATAACAAAAGAGTTTAATTGATTTTTAGTCGAGTTCAAAAATATAATT
131 CATATGTGAATGATGAAATAACAAAAGAGTTTAATTGATTTTTAGTCGAGTTC-AAAATATAATT
10135 GATTTTAACTGAAAATACAAA-ATATTTTAATATTTAAGGAAAAATTATAAATTTTATTAAAATT
195 GATTTTAACTGAAAATACAAATAT-TTTTAATATTTAAGGAAAAATTATAAATTTTATTAAAATT
10199 TTAAAAATATTGAAATTTTTATAAAAATTAAAAACCCTATAAAATATTATAAATTTTAAAAATCA
259 TTAAAAATATTGAAATTTTTATAAAAATTAAAAACCCTATAAAATATTA-AAATTTTAAAAATCA
10264 AAAGTTATAAAATGATAAGTTATAAATATATAAAAGTAAAATTTAAAAATATTTATAAAGTATTA
323 AAAGTTATAAAATGATAAGTTAT-AA-ATATAAAAGTAAAATTTAAAAATATTTATAAAGTATTA
10329 AAAAATTTGATATTTCATTGAAAAAGTTTTCAACAATCTCTTATTAGGCTGTGTCTACTCCTCTT
386 AAAAATTTGATATTTCATTGAAAAAGTTTTCAACAATCTCTTATTAGGCTGTGTCTACTCCTCTT
10394 CTTTCAACATACTTTTAGTAGAATTAATTTTATAATAGGGTAACAATAAAACTCAAATTTCCTTC
451 CTTTCAACATACTTTTAGTAGAATTAATTTTATAATAGGGTAACAATAAAACTCAAATTTCCTTC
10459 GATTTATTACACCAAATATTAATGAAAATTTGAGAAC
516 GATTTATTACACCAAATATTAATGAAAATTTGAGAAC
*
10496 CAATT
1 TAATT
10501 TAGTGTAACA
Statistics
Matches: 555, Mismatches: 1, Indels: 6
0.99 0.00 0.01
Matches are distributed among these distances:
552 185 0.33
553 121 0.22
554 38 0.07
555 2 0.00
556 209 0.38
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (552 bp):
TAATTATATTAGTTTTTTTTAAAACTGATTTAATTGTGTTAAAGTCATCTTTTGATGATCTATCT
GTTACGATGTTGACATGCCAATTAACTATGCTAATGCCACAATTCATTCTGATGACATAACAATC
CATATGTGAATGATGAAATAACAAAAGAGTTTAATTGATTTTTAGTCGAGTTCAAAATATAATTG
ATTTTAACTGAAAATACAAATATTTTTAATATTTAAGGAAAAATTATAAATTTTATTAAAATTTT
AAAAATATTGAAATTTTTATAAAAATTAAAAACCCTATAAAATATTAAAATTTTAAAAATCAAAA
GTTATAAAATGATAAGTTATAAATATAAAAGTAAAATTTAAAAATATTTATAAAGTATTAAAAAA
TTTGATATTTCATTGAAAAAGTTTTCAACAATCTCTTATTAGGCTGTGTCTACTCCTCTTCTTTC
AACATACTTTTAGTAGAATTAATTTTATAATAGGGTAACAATAAAACTCAAATTTCCTTCGATTT
ATTACACCAAATATTAATGAAAATTTGAGAAC
Found at i:11020 original size:2 final size:2
Alignment explanation
Indices: 11008--11045 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
10998 GTAACTTACT
11008 TA TA T- TA TA TA 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 TA TA TA TA TA TA T
11046 TAGATTAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:21355 original size:16 final size:16
Alignment explanation
Indices: 21334--21370 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
21324 GGATATTTGT
21334 TATTGATGCTTTGGAA
1 TATTGATGCTTTGGAA
21350 TATTGATGCTTTGGAA
1 TATTGATGCTTTGGAA
21366 TATTG
1 TATTG
21371 TATTCTAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.24, C:0.05, G:0.24, T:0.46
Consensus pattern (16 bp):
TATTGATGCTTTGGAA
Found at i:36124 original size:2 final size:2
Alignment explanation
Indices: 36119--36161 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
36109 GCCTTTTTTA
36119 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
36161 A
1 A
36162 ATTTTTTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42417 original size:17 final size:17
Alignment explanation
Indices: 42364--42418 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 17
42354 CGATAAACCG
*
42364 AACCGAATCGAACCGAAA
1 AACCGAACCGAACC-AAA
42382 AATCCGAACCGTTAA--AAA
1 AA-CCGAACCG--AACCAAA
42400 AACCGAACCGAACCAAA
1 AACCGAACCGAACCAAA
42417 AA
1 AA
42419 AACCGATTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 11
0.72 0.02 0.26
Matches are distributed among these distances:
15 2 0.06
17 13 0.42
18 7 0.23
19 7 0.23
21 2 0.06
ACGTcount: A:0.53, C:0.27, G:0.13, T:0.07
Consensus pattern (17 bp):
AACCGAACCGAACCAAA
Found at i:42417 original size:19 final size:19
Alignment explanation
Indices: 42364--42424 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
42354 CGATAAACCG
* *
42364 AACCGAATCGAACCGAAAA
1 AACCGAACCGAACCAAAAA
* **
42383 ATCCGAACCG--TTAAAAA
1 AACCGAACCGAACCAAAAA
42400 AACCGAACCGAACCAAAAA
1 AACCGAACCGAACCAAAAA
42419 AACCGA
1 AACCGA
42425 TTTCGATTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
17 13 0.41
19 19 0.59
ACGTcount: A:0.52, C:0.28, G:0.13, T:0.07
Consensus pattern (19 bp):
AACCGAACCGAACCAAAAA
Found at i:51397 original size:2 final size:2
Alignment explanation
Indices: 51333--51382 Score: 63
Period size: 2 Copynumber: 27.0 Consensus size: 2
51323 TTTTTTCTAA
*
51333 AT AT -T AT A- AT AT AT TT A- AT -T 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
51371 AT AT AT AT AT AT
1 AT AT AT AT AT AT
51383 TAGCATTATA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
1 4 0.10
2 38 0.90
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:51485 original size:2 final size:2
Alignment explanation
Indices: 51473--51552 Score: 153
Period size: 2 Copynumber: 40.5 Consensus size: 2
51463 ACTTATATGT
51473 TA TA T- 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
51514 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
51553 GTGTGTGTGT
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 76 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:51623 original size:19 final size:18
Alignment explanation
Indices: 51586--51660 Score: 57
Period size: 18 Copynumber: 4.1 Consensus size: 18
51576 GTATTTTATC
*
51586 TTATTATTTCTTTACTTTT
1 TTATTATTTATTTA-TTTT
51605 TTATTATTATATTTA-TTT
1 TTATTATT-TATTTATTTT
* *
51623 TCATTATTTAGTTT-TTCTA
1 TTATTATTTA-TTTATT-TT
*
51642 TTATTA-TTATATATTTT
1 TTATTATTTATTTATTTT
51659 TT
1 TT
51661 CCTCTCTCTC
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
17 7 0.16
18 19 0.42
19 14 0.31
20 5 0.11
ACGTcount: A:0.23, C:0.05, G:0.01, T:0.71
Consensus pattern (18 bp):
TTATTATTTATTTATTTT
Found at i:51791 original size:29 final size:30
Alignment explanation
Indices: 51718--51792 Score: 75
Period size: 30 Copynumber: 2.5 Consensus size: 30
51708 TATATGTTTT
* *
51718 TATTAATTTTATTTATTTTACTTTATACGC
1 TATTATTTTTATTTATTTTACTATATACGC
*
51748 TATTATTTTACATTT-TTTTA-TATATACG-
1 TATTATTTT-TATTTATTTTACTATATACGC
51776 TATGTATGTTTTATTTA
1 TAT-TAT-TTTTATTTA
51793 ATTCTTATTG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
28 3 0.08
29 14 0.38
30 16 0.43
31 4 0.11
ACGTcount: A:0.27, C:0.07, G:0.05, T:0.61
Consensus pattern (30 bp):
TATTATTTTTATTTATTTTACTATATACGC
Found at i:52515 original size:18 final size:18
Alignment explanation
Indices: 52492--52532 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
52482 TAATGAAAAG
52492 GGTAAGTTTGAACTTTAA
1 GGTAAGTTTGAACTTTAA
52510 GGTAAGTTTGAACTTTAA
1 GGTAAGTTTGAACTTTAA
52528 GGTAA
1 GGTAA
52533 TTTCCAGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (18 bp):
GGTAAGTTTGAACTTTAA
Found at i:57317 original size:78 final size:78
Alignment explanation
Indices: 57173--57324 Score: 191
Period size: 78 Copynumber: 1.9 Consensus size: 78
57163 AATACTTCGC
* * * * *
57173 TTAGGATGAAAACCCGAGAGGGTGTCCTAAGTTTAAAAAAAAAAGAAAAAAAATGAAAAAAGAAG
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAAAAGAAAAAAAATGAAAAAAGAAG
57238 AAGAAAAGAACGT
66 AAGAAAAGAACGT
* *
57251 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTGAGAAAAGAAAAAGAGGAAAAAA-GAACAAAA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGA-AAAA-AAAAAGA-AAAAAAATGAA-AAAA
57315 GAAG-AGAAAA
62 GAAGAAGAAAA
57325 TAAGGTGGGT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
78 29 0.46
79 4 0.06
80 16 0.25
81 14 0.22
ACGTcount: A:0.56, C:0.09, G:0.24, T:0.11
Consensus pattern (78 bp):
TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAAAAGAAAAAAAATGAAAAAAGAAG
AAGAAAAGAACGT
Found at i:58225 original size:43 final size:43
Alignment explanation
Indices: 58164--58324 Score: 117
Period size: 43 Copynumber: 3.4 Consensus size: 43
58154 ATTTCCCAAT
58164 TTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAG
* ** ** *
58207 TTCAACTTCACGACGAAGGGACCGCTGACTGTCAACTTCTCAATTTCAG-AGCCAAT
1 TTCAACTTCACAACGAA-GGA----T-A-T-TGGA---CTCAA-GACAGTA--CAAG
*
58263 TTCAACTTCACAACGAAGGATATTGGACTCAAGATAGTACAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAG
*
58306 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
58325 GACCGCTGAC
Statistics
Matches: 89, Mismatches: 14, Indels: 30
0.67 0.11 0.23
Matches are distributed among these distances:
43 37 0.42
44 5 0.06
45 6 0.07
48 3 0.03
49 2 0.02
50 2 0.02
51 3 0.03
54 6 0.07
55 6 0.07
56 19 0.21
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.23
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAG
Found at i:58287 original size:99 final size:99
Alignment explanation
Indices: 58060--58641 Score: 734
Period size: 99 Copynumber: 5.9 Consensus size: 99
58050 AGGTTTTACC
* **
58060 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAATACAAGTTCAACTTCACG
* * * ** * ***
58125 ATGAAGAGACCACTGGTTATCAA-TAAACAATTT
66 ACGAAGGGACCGCTGACTGTCAACTTCTCAATTT
*
58158 C----CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAATACAAGTTCAACTTCACG
58219 ACGAAGGGACCGCTGACTGTCAACTTCTCAATTT
66 ACGAAGGGACCGCTGACTGTCAACTTCTCAATTT
* *
58253 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGATAGTACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAATACAAGTTCAACTTCACG
58318 ACGAAGGGACCGCTGACTGTCAAACAAACAACTTCTCAATTT
66 ACGAAGGGACCGCTGACTGT--------CAACTTCTCAATTT
* * * **
58360 CAGGGCCAATTTCAACTGCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAATACAAGTTCAACTTCACG
** * *** *
58425 ACGAAGGGACCGCTGGTTATCAA-TAAACATTTT
66 ACGAAGGGACCGCTGACTGTCAACTTCTCAATTT
*
58458 C----CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAATACAAGTTCAACTTCACG
*
58519 ACGAAGGGACCGTTGACTGTCAACTTCTCAATTT
66 ACGAAGGGACCGCTGACTGTCAACTTCTCAATTT
* *
58553 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAATACAAGTTCAACTTCACG
*
58618 ACGAAGGGACCGCTGATTGTCAAC
66 ACGAAGGGACCGCTGACTGTCAAC
58642 GAACAATACT
Statistics
Matches: 420, Mismatches: 46, Indels: 35
0.84 0.09 0.07
Matches are distributed among these distances:
94 147 0.35
95 15 0.04
98 8 0.02
99 161 0.38
107 89 0.21
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.23
Consensus pattern (99 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAATACAAGTTCAACTTCACG
ACGAAGGGACCGCTGACTGTCAACTTCTCAATTT
Found at i:58608 original size:300 final size:300
Alignment explanation
Indices: 58064--58640 Score: 1055
Period size: 300 Copynumber: 1.9 Consensus size: 300
58054 TTTACCCAGA
* *
58064 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGA
1 GCCAATTTCAACTGCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
58129 AGAGACCACTGGTTATCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTC
66 AGAGACCACTGGTTATCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTC
58194 AAGACAGTACAAGTTCAACTTCACGACGAAGGGACCGCTGACTGTCAACTTCTCAATTTCAGAGC
131 AAGACAGTACAAGTTCAACTTCACGACGAAGGGACCGCTGACTGTCAACTTCTCAATTTCAGAGC
* *
58259 CAATTTCAACTTCACAACGAAGGATATTGGACTCAAGATAGTACAAGTTCAACTTCACGACGAAG
196 CAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAATACAAGTTCAACTTCACGACGAAG
58324 GGACCGCTGACTGTCAAACAAACAACTTCTCAATTTCAGG
261 GGACCGCTGACTGTCAAACAAACAACTTCTCAATTTCAGG
58364 GCCAATTTCAACTGCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTGCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
* * *
58429 AGGGACCGCTGGTTATCAATAAACATTTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTC
66 AGAGACCACTGGTTATCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTC
*
58494 AAGACAGTACAAGTTCAACTTCACGACGAAGGGACCGTTGACTGTCAACTTCTCAATTTCAGAGC
131 AAGACAGTACAAGTTCAACTTCACGACGAAGGGACCGCTGACTGTCAACTTCTCAATTTCAGAGC
* *
58559 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAG
196 CAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAATACAAGTTCAACTTCACGACGAAG
*
58624 GGACCGCTGATTGTCAA
261 GGACCGCTGACTGTCAA
58641 CGAACAATAC
Statistics
Matches: 266, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
300 266 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (300 bp):
GCCAATTTCAACTGCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
AGAGACCACTGGTTATCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTC
AAGACAGTACAAGTTCAACTTCACGACGAAGGGACCGCTGACTGTCAACTTCTCAATTTCAGAGC
CAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAATACAAGTTCAACTTCACGACGAAG
GGACCGCTGACTGTCAAACAAACAACTTCTCAATTTCAGG
Found at i:58622 original size:193 final size:194
Alignment explanation
Indices: 58065--58633 Score: 736
Period size: 193 Copynumber: 2.9 Consensus size: 194
58055 TTACCCAGAG
* *** *
58065 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCACGACGAA
* * ** * ***
58130 GAGACCACTGGTTATCAA-TAAACAATTTC---CCAATTTCAACTTCACAACGAAGGATATTGGA
66 GGGACCGCTGACTGTCAACTTCTCAATTTCAGGCCAATTTCAACTTCACAACGAAGGATATTGGA
* * * * ***
58191 CTCAAGACAGTACAAGTTCAACTTCACGACGAAGGGACCGCTGACTGTCAACTTCTCAATTTCAG
131 CTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGACTATCAACTAAACAATTTC--
58256 A
194 A
*
58257 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGATAGTACAAGTTCAACTTCACGACGA
1 -CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCACGACGA
*
58322 AGGGACCGCTGACTGTCAAACAAACAACTTCTCAATTTCAGGGCCAATTTCAACTGCACAACGAA
65 AGGGACCGCTGACTGT--------CAACTTCTCAATTTCA-GGCCAATTTCAACTTCACAACGAA
* **
58387 GGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTATCAA-TAA
121 GGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGACTATCAACTAA
*
58451 ACATTTTC-
186 ACAATTTCA
58459 CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCACGACGAA
*
58524 GGGACCGTTGACTGTCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 GGGACCGCTGACTGTCAACTTCTCAATTTCAG-GCCAATTTCAACTTCACAACGAAGGATATTGG
58589 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGA
130 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGA
58634 TTGTCAACGA
Statistics
Matches: 331, Mismatches: 31, Indels: 28
0.85 0.08 0.07
Matches are distributed among these distances:
192 1 0.00
193 159 0.48
201 81 0.24
202 8 0.02
205 7 0.02
206 75 0.23
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.23
Consensus pattern (194 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCACGACGAA
GGGACCGCTGACTGTCAACTTCTCAATTTCAGGCCAATTTCAACTTCACAACGAAGGATATTGGA
CTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGACTATCAACTAAACAATTTCA
Found at i:60213 original size:2 final size:2
Alignment explanation
Indices: 60200--60384 Score: 82
Period size: 2 Copynumber: 98.0 Consensus size: 2
60190 TTTTTTCTAA
60200 AT AT -T AT A- AT AT AT -T A- AT -T 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
* *
60237 AT AT AT AT AT AT AT AT AT AGC AT -T AT AT AT -T TT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
* * * * * * *
60277 -T AT -T AGT TT TT TT TT CACT CT CGT AT AT AT GT AT -T AT -T AGT
1 AT AT AT A-T AT AT AT AT -A-T AT -AT AT AT AT AT AT AT AT AT A-T
* *
60318 AT AT -T AT -T AT -T TT ACT -T AT AT GT -T AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
60355 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
60385 GTGTGTATAT
Statistics
Matches: 146, Mismatches: 12, Indels: 50
0.70 0.06 0.24
Matches are distributed among these distances:
1 18 0.12
2 121 0.83
3 6 0.04
4 1 0.01
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (2 bp):
AT
Found at i:60445 original size:19 final size:18
Alignment explanation
Indices: 60408--60482 Score: 57
Period size: 18 Copynumber: 4.1 Consensus size: 18
60398 GTATTTTATC
*
60408 TTATTATTTCTTTACTTTT
1 TTATTATTTATTTA-TTTT
60427 TTATTATTATATTTA-TTT
1 TTATTATT-TATTTATTTT
* *
60445 TCATTATTTAGTTT-TTCTA
1 TTATTATTTA-TTTATT-TT
*
60464 TTATTA-TTATATATTTT
1 TTATTATTTATTTATTTT
60481 TT
1 TT
60483 CCTTTCTCTC
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
17 7 0.16
18 19 0.42
19 14 0.31
20 5 0.11
ACGTcount: A:0.23, C:0.05, G:0.01, T:0.71
Consensus pattern (18 bp):
TTATTATTTATTTATTTT
Found at i:63109 original size:2 final size:2
Alignment explanation
Indices: 63102--63127 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
63092 CCATGCAAAG
63102 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
63128 TCCCACCTGT
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:72199 original size:12 final size:12
Alignment explanation
Indices: 72184--72237 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 12
72174 ACATATCATC
72184 ATCATTATCACT
1 ATCATTATCACT
*
72196 ATCATTATCATT
1 ATCATTATCACT
**
72208 ATCAACATCACT
1 ATCATTATCACT
* *
72220 ATCATTATTATT
1 ATCATTATCACT
72232 ATCATT
1 ATCATT
72238 CATTGTTCAT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.44
Consensus pattern (12 bp):
ATCATTATCACT
Found at i:72217 original size:18 final size:18
Alignment explanation
Indices: 72177--72237 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
72167 TATATATACA
*
72177 TATCATCATCATTATCAC
1 TATCATTATCATTATCAC
72195 TATCATTATCATTATCAAC
1 TATCATTATCATTATC-AC
* * *
72214 -ATCACTATCATTATTAT
1 TATCATTATCATTATCAC
72231 TATCATT
1 TATCATT
72238 CATTGTTCAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 1 0.03
18 33 0.92
19 2 0.06
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.44
Consensus pattern (18 bp):
TATCATTATCATTATCAC
Found at i:72422 original size:46 final size:46
Alignment explanation
Indices: 72370--72460 Score: 155
Period size: 46 Copynumber: 2.0 Consensus size: 46
72360 AAGTGCCACA
72370 TAGAAATGTCCCAAAGGACCACATAGTATTGTCCAGAAAGACCGCG
1 TAGAAATGTCCCAAAGGACCACATAGTATTGTCCAGAAAGACCGCG
* * *
72416 TAGAAATGTCCCGAAGGACCACATAGTATTGTCCCGAATGACCGC
1 TAGAAATGTCCCAAAGGACCACATAGTATTGTCCAGAAAGACCGC
72461 ATAAAACCCT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.19
Consensus pattern (46 bp):
TAGAAATGTCCCAAAGGACCACATAGTATTGTCCAGAAAGACCGCG
Found at i:72451 original size:23 final size:23
Alignment explanation
Indices: 72357--72463 Score: 99
Period size: 23 Copynumber: 4.7 Consensus size: 23
72347 ATAAATTGCA
72357 CCGAAGTG-CCACATAGAAATGTC
1 CCGAAG-GACCACATAGAAATGTC
* * *
72380 CCAAAGGACCACATAGTATTGTC
1 CCGAAGGACCACATAGAAATGTC
* * * *
72403 CAGAAAGACCGCGTAGAAATGTC
1 CCGAAGGACCACATAGAAATGTC
* *
72426 CCGAAGGACCACATAGTATTGTC
1 CCGAAGGACCACATAGAAATGTC
* *
72449 CCGAATGACCGCATA
1 CCGAAGGACCACATA
72464 AAACCCTTGA
Statistics
Matches: 65, Mismatches: 18, Indels: 2
0.76 0.21 0.02
Matches are distributed among these distances:
22 1 0.02
23 64 0.98
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.18
Consensus pattern (23 bp):
CCGAAGGACCACATAGAAATGTC
Found at i:72643 original size:45 final size:45
Alignment explanation
Indices: 72589--72736 Score: 172
Period size: 45 Copynumber: 3.3 Consensus size: 45
72579 CCATTGTCAA
* * *
72589 ATAGCTTATATCACATTTTTAGATTTTCACCTAGTTCAATATCAC
1 ATAGTTTATATCACATTTTTAGATTTTCACGTAGTTCGATATCAC
* * * * *
72634 AGAGTTTATATCACA-TGTTCGCTTGTTCACGTAGTTTGATATCAC
1 ATAGTTTATATCACATTTTTAGATT-TTCACGTAGTTCGATATCAC
* * *
72679 ATAGTTTATATCACATGTTTACATGTTCACGTAGTTCGATATCAC
1 ATAGTTTATATCACATTTTTAGATTTTCACGTAGTTCGATATCAC
*
72724 ATAGCTTATATCA
1 ATAGTTTATATCA
72737 TTTTCTTATG
Statistics
Matches: 84, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
44 6 0.07
45 75 0.89
46 3 0.04
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (45 bp):
ATAGTTTATATCACATTTTTAGATTTTCACGTAGTTCGATATCAC
Found at i:72691 original size:14 final size:14
Alignment explanation
Indices: 72660--72736 Score: 57
Period size: 15 Copynumber: 5.2 Consensus size: 14
72650 GTTCGCTTGT
*
72660 TCACGTAGTTTGATA
1 TCACATAGTTT-ATA
72675 TCACATAGTTTATA
1 TCACATAGTTTATA
*
72689 TCACAT-GTTTACATGT
1 TCACATAGTTT--AT-A
* *
72705 TCACGTAGTTCGATA
1 TCACATAGTT-TATA
*
72720 TCACATAGCTTATA
1 TCACATAGTTTATA
72734 TCA
1 TCA
72737 TTTTCTTATG
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
13 4 0.08
14 15 0.31
15 20 0.41
16 7 0.14
17 3 0.06
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (14 bp):
TCACATAGTTTATA
Found at i:77453 original size:20 final size:21
Alignment explanation
Indices: 77428--77478 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
77418 CTTCAAAGAG
77428 TATCGATACTC-G-GGGTCTAA
1 TATCGATACTCTGAGGGTC-AA
*
77448 TATCGATACTCTGATGGTCAA
1 TATCGATACTCTGAGGGTCAA
77469 TATCGATACT
1 TATCGATACT
77479 GAGGTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 11 0.39
21 13 0.46
22 4 0.14
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (21 bp):
TATCGATACTCTGAGGGTCAA
Found at i:90672 original size:64 final size:63
Alignment explanation
Indices: 90539--90695 Score: 158
Period size: 64 Copynumber: 2.4 Consensus size: 63
90529 TAATGAAGGT
* * * ** *
90539 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTACTGGG
1 ATGCATCGATGCA-TACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
* *
90603 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATT-TTAAA-A
1 ATGCATCGATGCAT-ACTAATGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATTAAAGA
90665 G
63 G
*
90666 AGTGCATCGATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCA-TACTAATGCATCGAT
90696 ACACCTTCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
63 3 0.04
64 68 0.86
65 8 0.10
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCATACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
Found at i:97593 original size:64 final size:63
Alignment explanation
Indices: 97441--97593 Score: 166
Period size: 63 Copynumber: 2.4 Consensus size: 63
97431 TAATGAAGGT
* * * * **
97441 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTACTGA
1 ATGCATCGATGCATTACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGA
* * *
97504 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATT-TTAAAAG
1 ATGCATCGATGCATTACTAATGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATT-AAAG
97567 A
63 A
* *
97568 GTGCATCGATGCATTACCAATGCATC
1 ATGCATCGATGCATTACTAATGCATC
97594 AATACACCTT
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
63 43 0.57
64 32 0.43
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCATTACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGA
Found at i:99006 original size:21 final size:20
Alignment explanation
Indices: 98980--99028 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
98970 TATCTAATCT
98980 ATAATATAAATAATAAAAAAA
1 ATAATATAAATAA-AAAAAAA
* *
99001 ATAATAT-TATAAATAAAAA
1 ATAATATAAATAAAAAAAAA
99020 ATGAATATA
1 AT-AATATA
99029 TTTCTTGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 8 0.33
20 9 0.38
21 7 0.29
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (20 bp):
ATAATATAAATAAAAAAAAA
Found at i:99665 original size:12 final size:12
Alignment explanation
Indices: 99644--99673 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
99634 CCTACCAATA
*
99644 ATGCATCTTATG
1 ATGCACCTTATG
99656 ATGCACCTTATG
1 ATGCACCTTATG
99668 ATGCAC
1 ATGCAC
99674 ATAATGTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (12 bp):
ATGCACCTTATG
Done.