Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002274.1 Hibiscus syriacus cultivar Beakdansim tig00004623_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: 77337
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:8992 original size:11 final size:11
Alignment explanation
Indices: 8976--9002 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
8966 TCACCTAAAG
8976 AAAAAAAGAAA
1 AAAAAAAGAAA
8987 AAAAAAAGAAA
1 AAAAAAAGAAA
8998 AAAAA
1 AAAAA
9003 TAAAATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:15051 original size:21 final size:21
Alignment explanation
Indices: 15025--15064 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
15015 CCCCCTTTGA
*
15025 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
15046 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
15065 TGGGGTTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:17378 original size:66 final size:66
Alignment explanation
Indices: 17300--17438 Score: 260
Period size: 66 Copynumber: 2.1 Consensus size: 66
17290 AAGTGTGCTT
*
17300 TTAAAATGATAAATGAGAGAGGTGTTAAAGTAAGGGGGAGTAATTTCAAAACTTGATTTCAAAAT
1 TTAAAATGATAAATGAGAGAAGTGTTAAAGTAAGGGGGAGTAATTTCAAAACTTGATTTCAAAAT
17365 C
66 C
*
17366 TTAAAATGATAAATGGGAGAAGTGTTAAAGTAAGGGGGAGTAATTTCAAAACTTGATTTCAAAAT
1 TTAAAATGATAAATGAGAGAAGTGTTAAAGTAAGGGGGAGTAATTTCAAAACTTGATTTCAAAAT
17431 C
66 C
17432 TTAAAAT
1 TTAAAAT
17439 TACTAAAATG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 71 1.00
ACGTcount: A:0.43, C:0.06, G:0.22, T:0.29
Consensus pattern (66 bp):
TTAAAATGATAAATGAGAGAAGTGTTAAAGTAAGGGGGAGTAATTTCAAAACTTGATTTCAAAAT
C
Found at i:19071 original size:135 final size:136
Alignment explanation
Indices: 18865--19225 Score: 517
Period size: 135 Copynumber: 2.7 Consensus size: 136
18855 TTCTTTCCAA
* * * *
18865 ATTTGATATTCCCTGAGGAACAGTGGAACAAGTTTGCCTCGATTCAATCTTCCTTGAAGAACAGT
1 ATTTGATCTTCCCTGAGGAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAAGAACAAT
* * *
18930 GGAATAAATCAACATTTCCAAATCTGATTTTCTCTCAAGAAGCAGTGGAACATATCCC-AGTTTT
66 AGAATAAATCAACATTTCCAAATCTGATTTTCCCTCAAGAAGCAGCGGAACATATCCCTAGTTTT
18994 TTCTAG
131 TTCTAG
* * *
19000 ATTTGATCTTCCCTAAGGAACAGTGGAACAAGTCTACCTTGATTCAATCTTCCCTGAAGAACAAT
1 ATTTGATCTTCCCTGAGGAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAAGAACAAT
* ** * **
19065 ACAATAAATCAACATTTCCTGATCTGATTTTCCCTCAAGAAGCAGCGGAATATATCCCTCTTTTT
66 AGAATAAATCAACATTTCCAAATCTGATTTTCCCTCAAGAAGCAGCGGAACATATCCCTAGTTTT
*
19130 TTTTAG
131 TTCTAG
* * * *
19136 ATTTGATCTTCCCCGAGGAACAGTGAAACAAGTCTGCCTCGATTCAATCTTCTCTGAAGAACAAC
1 ATTTGATCTTCCCTGAGGAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAAGAACAAT
*
19201 AGAATGAATCAACATTTCCAAATCT
66 AGAATAAATCAACATTTCCAAATCT
19226 CTTTTTAGAC
Statistics
Matches: 197, Mismatches: 28, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
135 109 0.55
136 88 0.45
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (136 bp):
ATTTGATCTTCCCTGAGGAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAAGAACAAT
AGAATAAATCAACATTTCCAAATCTGATTTTCCCTCAAGAAGCAGCGGAACATATCCCTAGTTTT
TTCTAG
Found at i:19419 original size:3 final size:3
Alignment explanation
Indices: 19411--19471 Score: 52
Period size: 3 Copynumber: 20.0 Consensus size: 3
19401 TTCGTCCCGC
* * * *
19411 TAT TAT TAT TAT TAT TAG TAT AAT AAT TAT TAT TAT TCT TAAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT
*
19456 TAT TTT TATT TAT TAT
1 TAT TAT TA-T TAT TAT
19472 GCAGGCCTAT
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
2 2 0.04
3 40 0.85
4 5 0.11
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:19555 original size:22 final size:23
Alignment explanation
Indices: 19527--19569 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
19517 GTAATTCGAC
19527 CCAAAACTC-GAGCCCAACAGAA
1 CCAAAACTCAGAGCCCAACAGAA
19549 CCAAAACTCAGAGCCCAACAG
1 CCAAAACTCAGAGCCCAACAG
19570 GATCGACCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.44, C:0.37, G:0.14, T:0.05
Consensus pattern (23 bp):
CCAAAACTCAGAGCCCAACAGAA
Found at i:21593 original size:130 final size:131
Alignment explanation
Indices: 21303--21658 Score: 520
Period size: 130 Copynumber: 2.7 Consensus size: 131
21293 CGATATTAAG
*
21303 AATAATAATATCAT-TTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCAT
1 AATAATGATATC-TCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCAT
* * * * *
21367 TTATTCTCGATTAGAAATAATTCGATATTA-CTGTTTTCTCTTGAATCAATATTGATTTTTAAGA
65 TTATTCTCGATT-GAAATAATTAGATATTATCTGGTTTCACTCGAATCAATATTGAGTTTTAAGA
*
21431 CGG
129 CGA
* *
21434 AATAATGATATCTCTTTATTTCGATTGGAGTAATAAATGTCTGCTTTAAGGCATGAGAGGTCATT
1 AATAATGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATT
* * *
21499 TATTCTTGATTGAAATCATTATATATTATC-GGTTTCACTCGAATCAATATTGAGTTTTAAGACG
66 TATTCTCGATTGAAATAATTAGATATTATCTGGTTTCACTCGAATCAATATTGAGTTTTAAGACG
21563 A
131 A
* * *
21564 AATATTGATATGTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGACATGAGAGGTCATT
1 AATAATGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATT
*
21629 TATTCTCGATCAGAAATAATTAGATATTAT
66 TATTCTCGAT-TGAAATAATTAGATATTAT
21659 TGTTTTCTTC
Statistics
Matches: 201, Mismatches: 21, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
130 114 0.57
131 87 0.43
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (131 bp):
AATAATGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATT
TATTCTCGATTGAAATAATTAGATATTATCTGGTTTCACTCGAATCAATATTGAGTTTTAAGACG
A
Found at i:25166 original size:18 final size:19
Alignment explanation
Indices: 25143--25180 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
25133 GATTCAGTTT
*
25143 ACAA-CCGGTTTAGGCCCA
1 ACAACCCGGTTCAGGCCCA
25161 ACAACCCGGTTCAGGCCCA
1 ACAACCCGGTTCAGGCCCA
25180 A
1 A
25181 TCCCAACAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.29, C:0.37, G:0.21, T:0.13
Consensus pattern (19 bp):
ACAACCCGGTTCAGGCCCA
Found at i:29142 original size:3 final size:3
Alignment explanation
Indices: 29134--29165 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
29124 CCGGAGACCG
29134 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
29166 TCTTACAGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:33660 original size:14 final size:13
Alignment explanation
Indices: 33636--33677 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
33626 AATTAACAGC
33636 TTTTTCATTTGCA
1 TTTTTCATTTGCA
33649 TTTTTCATTTTGCA
1 TTTTTCA-TTTGCA
* *
33663 TCTAT-ATTTGCA
1 TTTTTCATTTGCA
33675 TTT
1 TTT
33678 GCATTATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 8 0.32
13 8 0.32
14 9 0.36
ACGTcount: A:0.17, C:0.14, G:0.07, T:0.62
Consensus pattern (13 bp):
TTTTTCATTTGCA
Found at i:36665 original size:54 final size:54
Alignment explanation
Indices: 36600--36936 Score: 505
Period size: 54 Copynumber: 6.2 Consensus size: 54
36590 TTTATTAAGA
* * * * *
36600 TGCACATATAGTGCCTATACGG-TAGTTCATTAACTCATAATGAATTCCATGAAT
1 TGCACACATAGTGCCTGTACGGTTA-TTCATCAACTCATGATGAATTCCGTGAAT
* * *
36654 TGCACACATAGTGCCTTTATGGTTATTCATCAACTCATGATGAATTACGTGAAT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAT
* * *
36708 TCCACACATAGTGCCTGTACGGTTGTTCATCAACTCATGATGAATTCCATGAAT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAT
* * *
36762 TGCACACATAGTACATGTACGGTTATTCATCAACTCATGATTAATTCCGTGAAT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAT
36816 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAT
* * *
36870 TGCACACATAGTGCTTGTATGGTTATTCATTAACTCATGATGAATTCCGTGAAT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAT
36924 TGCACACATAGTG
1 TGCACACATAGTG
36937 ATATACAATT
Statistics
Matches: 257, Mismatches: 25, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
54 255 0.99
55 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (54 bp):
TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAT
Found at i:49200 original size:20 final size:20
Alignment explanation
Indices: 49175--49223 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
49165 GTGATCAATG
49175 GTATCGATA-CCTTC-CTCATA
1 GTATCGATACCCTTCTCTC--A
49195 GTATCGATACCCTTCTCTCA
1 GTATCGATACCCTTCTCTCA
49215 GTATCGATA
1 GTATCGATA
49224 TTGATTGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 19 0.70
21 5 0.19
22 3 0.11
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.35
Consensus pattern (20 bp):
GTATCGATACCCTTCTCTCA
Found at i:54211 original size:54 final size:54
Alignment explanation
Indices: 54153--54516 Score: 435
Period size: 54 Copynumber: 6.8 Consensus size: 54
54143 TATACGATAG
* * * *
54153 TTCATTAACTTATAATAAATTCCGTGAATTGCACACATAGTGTC-TGTACGGTTA
1 TTCATCAACTCATGATAAATTCCGTGAATTGCACACATAGT-TCATATACGGTTA
* * * * *
54207 TTCATCAACTCATGAT-GATTCAGTGAATTGCACACATAGTTCCTATATGGTTG
1 TTCATCAACTCATGATAAATTCCGTGAATTGCACACATAGTTCATATACGGTTA
* * * *
54260 TTCATCAACTCATGATGAATTCCGTGAATTGCACACATAATACATGTACGGTTA
1 TTCATCAACTCATGATAAATTCCGTGAATTGCACACATAGTTCATATACGGTTA
* * *
54314 TTCATCAACTCATGATAAATTCCATGAATTGCACACATAGTGCTTATACGGTTA
1 TTCATCAACTCATGATAAATTCCGTGAATTGCACACATAGTTCATATACGGTTA
* * * * * *
54368 TTCATCAACTCATGATTAATTCTGTGAATTGAACAGATAGTGCATGTACGGTTA
1 TTCATCAACTCATGATAAATTCCGTGAATTGCACACATAGTTCATATACGGTTA
* * * * * *
54422 TTCATCAGCTCATGATGAATTTCGTTAATTGCACACATAGTTCCTATACAGTTA
1 TTCATCAACTCATGATAAATTCCGTGAATTGCACACATAGTTCATATACGGTTA
* *
54476 TTCATCAACTCATGATCAATTCCGTGAATTACACACATAGT
1 TTCATCAACTCATGATAAATTCCGTGAATTGCACACATAGT
54517 CCTTGTAGTA
Statistics
Matches: 263, Mismatches: 45, Indels: 4
0.84 0.14 0.01
Matches are distributed among these distances:
52 2 0.01
53 45 0.17
54 216 0.82
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.35
Consensus pattern (54 bp):
TTCATCAACTCATGATAAATTCCGTGAATTGCACACATAGTTCATATACGGTTA
Found at i:54414 original size:108 final size:106
Alignment explanation
Indices: 54170--54516 Score: 480
Period size: 108 Copynumber: 3.2 Consensus size: 106
54160 ACTTATAATA
*
54170 AATTCCGTGAATTGCACACATAGTGTC-TGTACGGTTATTCATCAACTCATGATGATTCAGTGAA
1 AATTCCGTGAATTGCACACATAGTG-CATGTACGGTTATTCATCAACTCATGATAATTCA-TGAA
* * *
54234 TTGCACACATAGTTCCTATATGGTTGTTCATCAACTCATGATG
64 TTGCACACATAGTTCCTATACGGTTATTCATCAACTCATGATC
* *
54277 AATTCCGTGAATTGCACACATAATACATGTACGGTTATTCATCAACTCATGATAAATTCCATGAA
1 AATTCCGTGAATTGCACACATAGTGCATGTACGGTTATTCATCAACTCATGAT-AATT-CATGAA
* * *
54342 TTGCACACATAGTGCTTATACGGTTATTCATCAACTCATGATT
64 TTGCACACATAGTTCCTATACGGTTATTCATCAACTCATGATC
* * * * * *
54385 AATTCTGTGAATTGAACAGATAGTGCATGTACGGTTATTCATCAGCTCATGATGAATTTCGTTAA
1 AATTCCGTGAATTGCACACATAGTGCATGTACGGTTATTCATCAACTCATGAT-AA-TTCATGAA
*
54450 TTGCACACATAGTTCCTATACAGTTATTCATCAACTCATGATC
64 TTGCACACATAGTTCCTATACGGTTATTCATCAACTCATGATC
*
54493 AATTCCGTGAATTACACACATAGT
1 AATTCCGTGAATTGCACACATAGT
54517 CCTTGTAGTA
Statistics
Matches: 211, Mismatches: 25, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
106 1 0.00
107 49 0.23
108 157 0.74
109 4 0.02
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (106 bp):
AATTCCGTGAATTGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATAATTCATGAATT
GCACACATAGTTCCTATACGGTTATTCATCAACTCATGATC
Found at i:54481 original size:162 final size:160
Alignment explanation
Indices: 54136--54516 Score: 485
Period size: 162 Copynumber: 2.4 Consensus size: 160
54126 CCAGTTCACT
* * * * * *
54136 TAGTGCCTATACGATAGTTCATTAACTTATAATAAATTCCGTGAATTGCACACATAGTGTCTGTA
1 TAGTACCTATACGTTA-TTCATCAACTCATGATAAATTCCGTGAATTGCACACATAGTGTCTATA
* * * * * *
54201 CGGTTATTCATCAACTCATGATGATTCAGTGAATTGCACACATAGTTCCTATATGGTTGTTCATC
65 CGGTTATTCATCAACTCATGATAATTCAGTGAATTGAACACATAGTGCATATACGGTTATTCATC
54266 AACTCATGATGAATTCCGTGAATTGCACACA
130 AACTCATGATGAATTCCGTGAATTGCACACA
* * * *
54297 TAATACATGTACGGTTATTCATCAACTCATGATAAATTCCATGAATTGCACACATAGTG-CTTAT
1 TAGTACCTATAC-GTTATTCATCAACTCATGATAAATTCCGTGAATTGCACACATAGTGTC-TAT
* * *
54361 ACGGTTATTCATCAACTCATGATTAATTCTGTGAATTGAACAGATAGTGCATGTACGGTTATTCA
64 ACGGTTATTCATCAACTCATGA-TAATTCAGTGAATTGAACACATAGTGCATATACGGTTATTCA
* * *
54426 TCAGCTCATGATGAATTTCGTTAATTGCACACA
128 TCAACTCATGATGAATTCCGTGAATTGCACACA
* * *
54459 TAGTTCCTATACAGTTATTCATCAACTCATGATCAATTCCGTGAATTACACACATAGT
1 TAGTACCTATAC-GTTATTCATCAACTCATGATAAATTCCGTGAATTGCACACATAGT
54517 CCTTGTAGTA
Statistics
Matches: 187, Mismatches: 30, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
160 1 0.01
161 70 0.37
162 116 0.62
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.34
Consensus pattern (160 bp):
TAGTACCTATACGTTATTCATCAACTCATGATAAATTCCGTGAATTGCACACATAGTGTCTATAC
GGTTATTCATCAACTCATGATAATTCAGTGAATTGAACACATAGTGCATATACGGTTATTCATCA
ACTCATGATGAATTCCGTGAATTGCACACA
Found at i:57211 original size:134 final size:133
Alignment explanation
Indices: 56977--57348 Score: 424
Period size: 134 Copynumber: 2.8 Consensus size: 133
56967 GTAAATCGAT
** * * * * *
56977 CTCGATTCAATCAGCCCTGAAGAACAGTTGAATGAATCAACATTTTCAGATCTGATCTACCGTAA
1 CTCGATTCAATCTTCCCTAAAGAACA-ATGAATGAATCAACATTTCCAGTTCTGATCTACCATAA
* * * * *
57042 AGAATCAGCGGAGAAGATCCTTTTTTTCTAGATTTGATCTTCTC-TTAAGAAACAATGGAACAAA
65 AGAATCAGCGGAGCAGATCCATTTTTTCCATATTTGATCTTC-CATGAAGAAACAATGGAACAAA
57106 TCTGC
129 TCTGC
* * *
57111 TTCGATTCAATCTTCCCTAAAGAACAATGAAATGAATCAACATTTCCAGTTTTGATCTACCATGA
1 CTCGATTCAATCTTCCCTAAAGAACAATG-AATGAATCAACATTTCCAGTTCTGATCTACCATAA
* * * *
57176 AGAAGCAGCGGAGCATATCCCTTTTTTCCATATTTGATCTTCCATGAAGAAGCAATGGAACAAAT
65 AGAATCAGCGGAGCAGATCCATTTTTTCCATATTTGATCTTCCATGAAGAAACAATGGAACAAAT
*
57241 CTTC
130 CTGC
* * * * ** * *
57245 CTCGATTCAATCTTCCTTTAATAACAGTGGAATGAATCAATGTTTCCA-TATCTGATTTACCCTA
1 CTCGATTCAATCTTCCCTAAAGAACAAT-GAATGAATCAACATTTCCAGT-TCTGATCTACCATA
*
57309 AAGAATCAACGGAGCAGATCCATTTTTTCCATATTTGATC
64 AAGAATCAGCGGAGCAGATCCATTTTTTCCATATTTGATC
57349 CCTTTTTTCC
Statistics
Matches: 200, Mismatches: 34, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
133 4 0.02
134 195 0.98
135 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.32
Consensus pattern (133 bp):
CTCGATTCAATCTTCCCTAAAGAACAATGAATGAATCAACATTTCCAGTTCTGATCTACCATAAA
GAATCAGCGGAGCAGATCCATTTTTTCCATATTTGATCTTCCATGAAGAAACAATGGAACAAATC
TGC
Found at i:57354 original size:20 final size:20
Alignment explanation
Indices: 57325--57368 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
57315 CAACGGAGCA
57325 GATCCATTTTTTCCATATTT
1 GATCCATTTTTTCCATATTT
*
57345 GATCCCTTTTTTCCATATTT
1 GATCCATTTTTTCCATATTT
57365 GATC
1 GATC
57369 TTCCCTAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.18, C:0.23, G:0.07, T:0.52
Consensus pattern (20 bp):
GATCCATTTTTTCCATATTT
Found at i:57620 original size:132 final size:132
Alignment explanation
Indices: 57353--57629 Score: 319
Period size: 132 Copynumber: 2.1 Consensus size: 132
57343 TTGATCCCTT
* * * *
57353 TTTTCCATATTTGATCTTCCCTAAAGAAACATTGGAACAAATCTGCCTCGATTCAATATTACCTG
1 TTTTCCAGATTTGAGCTTCCCTAAAGAAACAGTGGAACAAATCTACCTCGATTCAATATTACCTG
* ** * * * *
57418 AAGAACAGTAGAAGGAATCAATGTTTCCAATCTGATTTACCTTGAAGAAGCAGTGGAGATGATAC
66 AAGAACAATAGAAGGAATCAACATTTCCAATCTGATTTACCCTGAAAAAACAGTGGAGATAATAC
57483 CC
131 CC
* * * * *
57485 TTTTCCCAGATTTGAGCTTCCCT-GAGGAACAGTGGAATAAATCTACCTTGATTCAATATTCCCT
1 TTTT-CCAGATTTGAGCTTCCCTAAAGAAACAGTGGAACAAATCTACCTCGATTCAATATTACCT
* * *
57549 GAAGAACAATAGAATGAATCAACATTTCCAAATCTTATTTACCCTGAAAAAACGGTGGAGCA-AA
65 GAAGAACAATAGAAGGAATCAACATTTCC-AATCTGATTTACCCTGAAAAAACAGTGGAG-ATAA
*
57613 T-CTC
128 TACCC
57617 TTTT-CAGATTTGA
1 TTTTCCAGATTTGA
57630 TTTTCAAAAA
Statistics
Matches: 122, Mismatches: 20, Indels: 8
0.81 0.13 0.05
Matches are distributed among these distances:
130 9 0.07
132 69 0.57
133 43 0.35
134 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (132 bp):
TTTTCCAGATTTGAGCTTCCCTAAAGAAACAGTGGAACAAATCTACCTCGATTCAATATTACCTG
AAGAACAATAGAAGGAATCAACATTTCCAATCTGATTTACCCTGAAAAAACAGTGGAGATAATAC
CC
Found at i:57814 original size:3 final size:3
Alignment explanation
Indices: 57806--57856 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
57796 CCGGAGATTG
57806 TTA TTA TTA 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 TTA TTA TTA
57854 TTA
1 TTA
57857 GGGTAAAGTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:60856 original size:29 final size:28
Alignment explanation
Indices: 60796--60854 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
60786 TTTGATATAA
*
60796 TTTAATTTAACCATGTAATTTATTTTAT
1 TTTAATTTAACCACGTAATTTATTTTAT
* *
60824 TTTAATTTGGACCACGTATTTTA-TTTAT
1 TTTAATTT-AACCACGTAATTTATTTTAT
60852 TTT
1 TTT
60855 TATTCATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 16 0.59
29 11 0.41
ACGTcount: A:0.27, C:0.08, G:0.07, T:0.58
Consensus pattern (28 bp):
TTTAATTTAACCACGTAATTTATTTTAT
Found at i:63743 original size:16 final size:16
Alignment explanation
Indices: 63722--63752 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
63712 TCAACTTCGA
63722 CTCGTTGCTCGTTAAG
1 CTCGTTGCTCGTTAAG
63738 CTCGTTGCTCGTTAA
1 CTCGTTGCTCGTTAA
63753 ATTCACTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.26, G:0.23, T:0.39
Consensus pattern (16 bp):
CTCGTTGCTCGTTAAG
Found at i:66633 original size:5 final size:5
Alignment explanation
Indices: 66623--66648 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
66613 TCGAAATCAA
66623 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
66649 CTCAGACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:67450 original size:29 final size:29
Alignment explanation
Indices: 67418--67473 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
67408 TTATGCCCTT
67418 TATTTTGTAAACATATACGTTATATAATA
1 TATTTTGTAAACATATACGTTATATAATA
*
67447 TATTTTGTAAACATATACGTTGTATAA
1 TATTTTGTAAACATATACGTTATATAA
67474 CATTTTTTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (29 bp):
TATTTTGTAAACATATACGTTATATAATA
Found at i:67488 original size:27 final size:29
Alignment explanation
Indices: 67418--67481 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
67408 TTATGCCCTT
*
67418 TATTTTGTAAACATATACGTTATATAATA
1 TATTTTGTAAACATATACGTTATATAACA
*
67447 TATTTTGTAAACATATACGTTGTATAACA
1 TATTTTGTAAACATATACGTTATATAACA
*
67476 TTTTTT
1 TATTTT
67482 ACCCATAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (29 bp):
TATTTTGTAAACATATACGTTATATAACA
Found at i:68492 original size:131 final size:131
Alignment explanation
Indices: 68308--68550 Score: 337
Period size: 131 Copynumber: 1.9 Consensus size: 131
68298 AATATCGATT
* * * *
68308 TTTTTAGACGGAATATTAATATCTCTTTATTTCAATTGATATAATAAATGATTGTTTTAATGCAC
1 TTTTAAGACGAAATAGTAATATCTCTTTATTTCAATTGAGATAATAAATGATTGTTTTAATGCAC
* * *
68373 AAAATGTCGTTTATTCTCGATT-GAAAATCATTAGATATTATCATTTTTGTTCGAATCGCTATGT
66 AAAATGTCATTTATTCTCGATTAG-AAATAATCAGATATTATCATTTTTGTTCGAATCGCTATGT
68437 AA
130 AA
* * *
68439 TTTTAAGACGAAATAGTAATAT-TCCTTTATTTCAATTGGGGTACTAAATGATTGTTTTAATGCA
1 TTTTAAGACGAAATAGTAATATCT-CTTTATTTCAATTGAGATAATAAATGATTGTTTTAATGCA
* * *
68503 CAAAATGTTATTTGTTCTCGATTAGAAATAATCAGATATTATCGTTTT
65 CAAAATGTCATTTATTCTCGATTAGAAATAATCAGATATTATCATTTT
68551 CACTCTTAAA
Statistics
Matches: 97, Mismatches: 13, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
130 1 0.01
131 95 0.98
132 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (131 bp):
TTTTAAGACGAAATAGTAATATCTCTTTATTTCAATTGAGATAATAAATGATTGTTTTAATGCAC
AAAATGTCATTTATTCTCGATTAGAAATAATCAGATATTATCATTTTTGTTCGAATCGCTATGTA
A
Found at i:70028 original size:2 final size:2
Alignment explanation
Indices: 70021--70058 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
70011 TAAATTCTTT
70021 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
70059 ATTTTTCATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:70834 original size:38 final size:35
Alignment explanation
Indices: 70790--70865 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 35
70780 TTTTTATATT
70790 TTTAATTTTATAAAAAAAAATTATATAA-ATATTATGAA
1 TTTAATTTT-TAAAAAAAAA-TATATAATAT-TTAT-AA
* *
70828 TTTAATTTTTTAAAGAAAATATATAATATTTATAA
1 TTTAATTTTTAAAAAAAAATATATAATATTTATAA
70863 TTT
1 TTT
70866 GTAATATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
35 5 0.14
36 11 0.31
37 10 0.29
38 9 0.26
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (35 bp):
TTTAATTTTTAAAAAAAAATATATAATATTTATAA
Done.