Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000774.1 Hibiscus syriacus cultivar Beakdansim tig00001502_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: 105336
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:399 original size:165 final size:164
Alignment explanation
Indices: 222--652 Score: 465
Period size: 165 Copynumber: 2.6 Consensus size: 164
212 CTTAGCTCCA
* * * * * * * *
222 AGGCATATCATTTGCAGCACA-CTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTCTGAGT
1 AGGCACATCATTTGCAACACAGCTCAAGGCAAGAAAGGCTATCTGCCAACAAAAGACCTCTGAGT
* * *
286 TCGACTACGCTCAGCT-CAACGACACATCATTTTGCAGCATAGCTTAAGTCGATAAGGGCTATCT
66 TCGACTACGCTCAGCTCCAA-GACACATCA-TTTGCAGCATAGCTTAAGTCGAGAAAGGCTAGCT
* *
350 GCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCG
129 GCCAAAGACCCCCGAGTTCAATTACACTCAACTTCG
* * * *
386 AGGGCACATCATTTGCAACATAGCTCAAGGCAAGAAAGGCTATTTGCCAACGAAAGACCTTTGAG
1 A-GGCACATCATTTGCAACACAGCTCAAGGCAAGAAAGGCTATCTGCCAACAAAAGACCTCTGAG
* *
451 TTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAAGGCTAGCTG
65 TTCGACTACGCTCAGCTCCAAGACACATCATTTGCAGCATAGCTTAAGTCGAGAAAGGCTAGCTG
516 CCAAAGACCCCCGAGTTCAATTACACTCAACTTCG
130 CCAAAGACCCCCGAGTTCAATTACACTCAACTTCG
* * * * * * * * ** ** *
551 AGGTACATCA-TTACAATATAACTCAAGGCTAGAAGGGTTATCTATCTCCAAAGGACCT-TCGAG
1 AGGCACATCATTTGCAACACAGCTCAAGGCAAGAAAGGCTATCTGCCAACAAAAGACCTCT-GAG
* * * * *
614 TTTGACTACACTCAGCTGCAAGGCACATCATTTACAGCA
65 TTCGACTACGCTCAGCTCCAAGACACATCATTTGCAGCA
653 AGCCCAAGGC
Statistics
Matches: 225, Mismatches: 38, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
162 1 0.00
163 72 0.32
164 9 0.04
165 82 0.36
166 58 0.26
167 3 0.01
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.24
Consensus pattern (164 bp):
AGGCACATCATTTGCAACACAGCTCAAGGCAAGAAAGGCTATCTGCCAACAAAAGACCTCTGAGT
TCGACTACGCTCAGCTCCAAGACACATCATTTGCAGCATAGCTTAAGTCGAGAAAGGCTAGCTGC
CAAAGACCCCCGAGTTCAATTACACTCAACTTCG
Found at i:454 original size:166 final size:163
Alignment explanation
Indices: 264--652 Score: 476
Period size: 163 Copynumber: 2.4 Consensus size: 163
254 AAGGGTTGTC
264 TGCCAACAAAAGACCTCTGAGTTCGACTACGCTCAGCT-CAACGACACATCATTTTGCAGCATAG
1 TGCCAACAAAAGACCTCTGAGTTCGACTACGCTCAGCTCCAA-GACACATCA-TTTGCAGCATAG
* * * * *
328 CTTAAGTCGATAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
64 CTTAAGTCGAGAAAGGCTAGCTGCCAAAGACCCCCGAGTTCAATTACACTCAACTTCGA-GGCAC
* *
393 ATCATTTGCAACATAGCTCAAGGCAAGAAAGGCTATT
128 ATCA-TTACAACATAACTCAAGGCAAGAAAGGCTATT
* * * *
430 TGCCAACGAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCT
1 TGCCAACAAAAGACCTCTGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAGCATAGCT
*
495 TAAGTCGAGAAAGGCTAGCTGCCAAAGACCCCCGAGTTCAATTACACTCAACTTCGAGGTACATC
66 TAAGTCGAGAAAGGCTAGCTGCCAAAGACCCCCGAGTTCAATTACACTCAACTTCGAGGCACATC
* * * * *
560 ATTACAATATAACTCAAGGCTAGAAGGGTTATC
131 ATTACAACATAACTCAAGGCAAGAAAGGCTATT
** ** * * * * * *
593 TATCTCCAAAGGACCT-TCGAGTTTGACTACACTCAGCTGCAAGGCACATCATTTACAGCA
1 TGCCAACAAAAGACCTCT-GAGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAGCA
653 AGCCCAAGGC
Statistics
Matches: 193, Mismatches: 28, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
162 1 0.01
163 72 0.37
164 8 0.04
165 65 0.34
166 44 0.23
167 3 0.02
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.23
Consensus pattern (163 bp):
TGCCAACAAAAGACCTCTGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAGCATAGCT
TAAGTCGAGAAAGGCTAGCTGCCAAAGACCCCCGAGTTCAATTACACTCAACTTCGAGGCACATC
ATTACAACATAACTCAAGGCAAGAAAGGCTATT
Found at i:524 original size:246 final size:242
Alignment explanation
Indices: 26--518 Score: 691
Period size: 246 Copynumber: 2.0 Consensus size: 242
16 TTTGTATCCA
* * *
26 ACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGTATACTTAAGTC
1 ACAAAAGACCTCTGAGTTCGACTACGCTCAGCTCAACGACACATCATTTGCAGCATACTTAAGTC
*
91 GAGAAGGGTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTAC
66 GAGAAGGGTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAC
* * * * * * *
156 TCATAACTCAAGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTTGACTACGCTTAGCTCC
131 ACATAACTCAAGCAAGAAAGGCTATCTGCCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCC
* * * *
221 AAGGCATATCATTTGCAGCACACTTAAGTCTAGAAGGGTTGTCTGCC
196 AAGGCACATCATTTGCAGCACACTTAAGTCGAGAAGGCTAGTCTGCC
268 AACAAAAGACCTCTGAGTTCGACTACGCTCAGCTCAACGACACATCATTTTGCAGCATAGCTTAA
1 -ACAAAAGACCTCTGAGTTCGACTACGCTCAGCTCAACGACACATCA-TTTGCAGCATA-CTTAA
*
333 GTCGATAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
63 GTCGAGAAGGG-TATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
* * * * *
398 TTGCAACATAGCTCAAGGCAAGAAAGGCTATTTGCCAACGAAAGACCTTTGAGTTCGACTACGCT
127 TTAC-ACATAACTCAA-GCAAGAAAGGCTATCTGCC-ACCAAAGACCTTCGAGTTCGACTACGCT
* *
463 CAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAAGGCTAG-CTGCC
189 CAGCTCCAAGGCACATCATTTGCAGCACA-CTTAAGTCGAG-AAGGCTAGTCTGCC
518 A
1 A
519 AAGACCCCCG
Statistics
Matches: 219, Mismatches: 23, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
243 44 0.20
244 10 0.05
245 15 0.07
246 55 0.25
247 9 0.04
248 14 0.06
249 51 0.23
250 15 0.07
251 6 0.03
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (242 bp):
ACAAAAGACCTCTGAGTTCGACTACGCTCAGCTCAACGACACATCATTTGCAGCATACTTAAGTC
GAGAAGGGTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAC
ACATAACTCAAGCAAGAAAGGCTATCTGCCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCC
AAGGCACATCATTTGCAGCACACTTAAGTCGAGAAGGCTAGTCTGCC
Found at i:1398 original size:35 final size:33
Alignment explanation
Indices: 1359--1585 Score: 164
Period size: 35 Copynumber: 6.7 Consensus size: 33
1349 CGAAAATAAG
1359 TATATATATATAGTTTTTGAAAACATTTTAAAATC
1 TATATATATATAGTTTTT-AAAACATTTTAAAA-C
* * * *
1394 TATATAGATATGGTTTTGAAAAATATTTTGAAAAC
1 TATATATATATAGTTTT-TAAAACATTTT-AAAAC
* * *
1429 ATTTATATATTTATAGTTTTTTAAAACATTTTGAAAG
1 ---TATATATATATAG-TTTTTAAAACATTTTAAAAC
1466 TATATAATATATAGTTTTTTAAAACATTTTAAAAC
1 TATAT-ATATATAG-TTTTTAAAACATTTTAAAAC
*
1501 -ATATAT-TATA-----TAAAACATTTTTGAAAC
1 TATATATATATAGTTTTTAAAACA-TTTTAAAAC
* * *
1528 ATTTATATTATATAGTTTTT-AAACATTTTGAAAG
1 -TATATA-TATATAGTTTTTAAAACATTTTAAAAC
*
1562 TATATAATATATAGTTTTAAAAAC
1 TATAT-ATATATAGTTTTTAAAAC
1586 CTATATTATA
Statistics
Matches: 154, Mismatches: 19, Indels: 39
0.73 0.09 0.18
Matches are distributed among these distances:
26 7 0.05
27 8 0.05
29 4 0.03
30 1 0.01
31 4 0.03
32 4 0.03
33 17 0.11
34 22 0.14
35 56 0.36
36 5 0.03
37 3 0.02
38 19 0.12
39 4 0.03
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.45
Consensus pattern (33 bp):
TATATATATATAGTTTTTAAAACATTTTAAAAC
Found at i:1438 original size:73 final size:73
Alignment explanation
Indices: 1336--1512 Score: 191
Period size: 73 Copynumber: 2.4 Consensus size: 73
1326 ATAATTTTCG
*
1336 GAAAAATGATTTTCGAAAATA-AGTATATATATATAGTTTTTGAAAACATTTTAAAATCTATAT-
1 GAAAAAT-ATTTT-GAAAACATA-TATATATATATAGTTTTTGAAAACATTTTAAAA-CTATATA
*
1399 AGATATGGTTTT
62 AGATATAGTTTT
* * * * * *
1411 GAAAAATATTTTGAAAACATTTATATATTTATAGTTTTTTAAAACATTTTGAAAGTATATAATAT
1 GAAAAATATTTTGAAAACATATATATATATATAGTTTTTGAAAACATTTTAAAACTATATAAGAT
1476 ATAGTTTT
66 ATAGTTTT
** *
1484 TTAAAACATTTT-AAAACATATAT-TATATA
1 GAAAAATATTTTGAAAACATATATATATATA
1513 AAACATTTTT
Statistics
Matches: 87, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
71 5 0.06
72 15 0.17
73 55 0.63
74 5 0.06
75 7 0.08
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (73 bp):
GAAAAATATTTTGAAAACATATATATATATATAGTTTTTGAAAACATTTTAAAACTATATAAGAT
ATAGTTTT
Found at i:1516 original size:26 final size:28
Alignment explanation
Indices: 1485--1541 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 28
1475 TATAGTTTTT
1485 TAAAACA-TTTTAAAACA-TATATTATA
1 TAAAACATTTTTAAAACATTATATTATA
*
1511 TAAAACATTTTTGAAACATTTATATTATA
1 TAAAACATTTTTAAAACA-TTATATTATA
1540 TA
1 TA
1542 GTTTTTAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 7 0.26
27 9 0.33
29 11 0.41
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (28 bp):
TAAAACATTTTTAAAACATTATATTATA
Found at i:1523 original size:62 final size:61
Alignment explanation
Indices: 1450--1574 Score: 155
Period size: 62 Copynumber: 2.0 Consensus size: 61
1440 TATAGTTTTT
* *
1450 TAAAACATTTTGAAA-GTATATAATATATAGTTTTTTAAAACATTTT-AAAACATATATTATA
1 TAAAACATTTTGAAACATATATAATATATAG-TTTTT-AAACATTTTGAAAACATATAATATA
* * **
1511 TAAAACATTTTTGAAACATTTATATTATATAGTTTTTAAACATTTTGAAAGTATATAATATA
1 TAAAACA-TTTTGAAACATATATAATATATAGTTTTTAAACATTTTGAAAACATATAATATA
1573 TA
1 TA
1575 GTTTTAAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
61 16 0.29
62 27 0.49
63 12 0.22
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.44
Consensus pattern (61 bp):
TAAAACATTTTGAAACATATATAATATATAGTTTTTAAACATTTTGAAAACATATAATATA
Found at i:1593 original size:85 final size:88
Alignment explanation
Indices: 1492--1660 Score: 215
Period size: 85 Copynumber: 1.9 Consensus size: 88
1482 TTTTAAAACA
*
1492 TTTTAAAACATATATTATATAAAACA-TTTTTG-AAACATT-TATATTATAT-AGTTTTT-AAAC
1 TTTTAAAACATATATTATAT-AAACATTTTTTGAAAAC-TTATATAATATATAAGTTTTTAAAAC
*
1552 ATTTTG-AAAGTATATAATATATAG
64 ATTTTGAAAACTATATAATATATAG
* *
1576 TTTTAAAAACCTATATTATATAAACATTTTTTTGAAAACTTATATAATATATAATTTTTTAAAAA
1 TTTT-AAAACATATATTATATAAACA-TTTTTTGAAAACTTATATAATATATAAGTTTTT-AAAA
1641 CATTTTGAAAACTATATAAT
63 CATTTTGAAAACTATATAAT
1661 TTTGAAAACA
Statistics
Matches: 72, Mismatches: 4, Indels: 11
0.83 0.05 0.13
Matches are distributed among these distances:
84 9 0.12
85 15 0.21
86 8 0.11
87 13 0.18
88 6 0.08
90 10 0.14
91 11 0.15
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (88 bp):
TTTTAAAACATATATTATATAAACATTTTTTGAAAACTTATATAATATATAAGTTTTTAAAACAT
TTTGAAAACTATATAATATATAG
Found at i:1613 original size:29 final size:28
Alignment explanation
Indices: 1576--1641 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 28
1566 TAATATATAG
*
1576 TTTTAAAAACCTATATTATATAAACATTT
1 TTTTAAAAACCTATATAATATAAA-ATTT
* * *
1605 TTTTGAAAACTTATATAATATATAA-TT
1 TTTTAAAAACCTATATAATATAAAATTT
1632 TTTTAAAAAC
1 TTTTAAAAAC
1642 ATTTTGAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 11 0.34
28 1 0.03
29 20 0.62
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (28 bp):
TTTTAAAAACCTATATAATATAAAATTT
Found at i:1727 original size:34 final size:36
Alignment explanation
Indices: 1653--1745 Score: 104
Period size: 34 Copynumber: 2.6 Consensus size: 36
1643 TTTTGAAAAC
*
1653 TATATAATTTTGAAAACATTTTTTAAAAAGTATATAA
1 TATATAATTTTGAAAATA-TTTTTAAAAAGTATATAA
* *
1690 TATATAATTTT-AAAATATTTTT-GAAA-T-TATAT
1 TATATAATTTTGAAAATATTTTTAAAAAGTATATAA
*
1722 TATATAGGTTTTGAAAATATTTTT
1 TATATA-ATTTTGAAAATATTTTT
1746 TATATATAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
32 10 0.20
33 5 0.10
34 14 0.28
35 5 0.10
36 5 0.10
37 11 0.22
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.49
Consensus pattern (36 bp):
TATATAATTTTGAAAATATTTTTAAAAAGTATATAA
Found at i:3028 original size:15 final size:13
Alignment explanation
Indices: 2995--3051 Score: 53
Period size: 15 Copynumber: 4.2 Consensus size: 13
2985 ACTTTTTGTT
*
2995 TTATTCATTTTATTT
1 TTATT-ATTTT-TTA
3010 TTATTATTTCTTGTA
1 TTATTATTT-TT-TA
3025 TTATT-TTTTTTA
1 TTATTATTTTTTA
*
3037 TTATTATTATTTA
1 TTATTATTTTTTA
3050 TT
1 TT
3052 TTTTTTACTA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
12 7 0.19
13 10 0.27
14 8 0.22
15 12 0.32
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (13 bp):
TTATTATTTTTTA
Found at i:4482 original size:22 final size:22
Alignment explanation
Indices: 4454--4584 Score: 223
Period size: 22 Copynumber: 6.1 Consensus size: 22
4444 AATTTACTTG
4454 TTACTCATTTCTCTCTCTCTAA
1 TTACTCATTTCTCTCTCTCTAA
4476 TTACTCATTTCTCTCTCTCTAA
1 TTACTCATTTCTCTCTCTCTAA
*
4498 TTACTCATTTCTCTCTATCTAA
1 TTACTCATTTCTCTCTCTCTAA
4520 TTACTCATTTCTCTCTCTCTAA
1 TTACTCATTTCTCTCTCTCTAA
4542 TTACT-A-TT-TCTCTCTCTAA
1 TTACTCATTTCTCTCTCTCTAA
*
4561 TTACTCATTTCTCTCTCTTTAA
1 TTACTCATTTCTCTCTCTCTAA
4583 TT
1 TT
4585 GTTAAATACC
Statistics
Matches: 103, Mismatches: 3, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
19 16 0.16
20 3 0.03
21 3 0.03
22 81 0.79
ACGTcount: A:0.19, C:0.29, G:0.00, T:0.52
Consensus pattern (22 bp):
TTACTCATTTCTCTCTCTCTAA
Found at i:10244 original size:2 final size:2
Alignment explanation
Indices: 10237--10268 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
10227 CCTAATGTAA
10237 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
10269 TTAGTTTCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16668 original size:17 final size:17
Alignment explanation
Indices: 16615--16668 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 17
16605 TATAATACAG
* * *
16615 TATTTTTATTTTAACAT
1 TATTTTTAATTTAATAA
16632 TATTTTTAATATTATAATAA
1 TATTTTT-A-ATT-TAATAA
16652 TATTTTTAATTTAATAA
1 TATTTTTAATTTAATAA
16669 ATAATTAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 13 0.42
18 4 0.13
19 3 0.10
20 11 0.35
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTTTTAATTTAATAA
Found at i:16671 original size:21 final size:21
Alignment explanation
Indices: 16647--16739 Score: 72
Period size: 21 Copynumber: 4.6 Consensus size: 21
16637 TTAATATTAT
*
16647 AATAATATTTTTAATTTAATA
1 AATAATATTTATAATTTAATA
* *
16668 AATAAT-TAATATAA-TTGATA
1 AATAATAT-TTATAATTTAATA
*
16688 ATATAATATTTATATTTTAATA
1 A-ATAATATTTATAATTTAATA
*
16710 AATAAT-TAATATAATTT--TA
1 AATAATAT-TTATAATTTAATA
16729 AAT-ATATTTAT
1 AATAATATTTAT
16740 TCTAATAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
18 5 0.09
19 6 0.11
20 8 0.14
21 31 0.54
22 7 0.12
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (21 bp):
AATAATATTTATAATTTAATA
Found at i:16808 original size:13 final size:13
Alignment explanation
Indices: 16792--16855 Score: 51
Period size: 13 Copynumber: 4.8 Consensus size: 13
16782 GTAGATATAA
16792 TATTTAATAATAT
1 TATTTAATAATAT
*
16805 TATTAAATAA-AT
1 TATTTAATAATAT
*
16817 TATTATAATAATTT
1 TATT-TAATAATAT
**
16831 TAAAATAA-AATAT
1 T-ATTTAATAATAT
16844 TATTTTAATAAT
1 TA-TTTAATAAT
16856 TAATATTATT
Statistics
Matches: 38, Mismatches: 8, Indels: 9
0.69 0.15 0.16
Matches are distributed among these distances:
12 7 0.18
13 22 0.58
14 8 0.21
15 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATTTAATAATAT
Found at i:16844 original size:24 final size:26
Alignment explanation
Indices: 16790--16846 Score: 75
Period size: 24 Copynumber: 2.3 Consensus size: 26
16780 TTGTAGATAT
*
16790 AATATT-TAATAATATTATTAAATAA
1 AATATTATAATAATATTATAAAATAA
*
16815 ATTATTATAATAAT-TT-TAAAATAA
1 AATATTATAATAATATTATAAAATAA
16839 AATATTAT
1 AATATTAT
16847 TTTAATAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 14 0.50
25 7 0.25
26 7 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
AATATTATAATAATATTATAAAATAA
Found at i:16850 original size:18 final size:18
Alignment explanation
Indices: 16827--16866 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
16817 TATTATAATA
16827 ATTTTAA-AATAAAATATT
1 ATTTTAATAAT-AAATATT
*
16845 ATTTTAATAATTAATATT
1 ATTTTAATAATAAATATT
16863 ATTT
1 ATTT
16867 ATTATATCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTAATAATAAATATT
Found at i:17144 original size:16 final size:18
Alignment explanation
Indices: 17112--17146 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
17102 ATATGCACCA
17112 AATAAATTTATATATTTT
1 AATAAATTTATATATTTT
17130 AATAAA-TTA-ATATTTT
1 AATAAATTTATATATTTT
17146 A
1 A
17147 TTCATATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AATAAATTTATATATTTT
Found at i:17467 original size:22 final size:22
Alignment explanation
Indices: 17425--17467 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
17415 AAATATTAAA
*
17425 TAAAAATTATATAATTGTTTTT
1 TAAAAATTATATAATTATTTTT
*
17447 TAAATATTA-ATATATTATTTT
1 TAAAAATTATATA-ATTATTTT
17468 ATCATGTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TAAAAATTATATAATTATTTTT
Found at i:18223 original size:25 final size:26
Alignment explanation
Indices: 18167--18235 Score: 113
Period size: 25 Copynumber: 2.7 Consensus size: 26
18157 CTATTCATTC
*
18167 AACAATGATAATAGGTTAGATAAAAA
1 AACAATAATAATAGGTTAGATAAAAA
*
18193 AGCAATAATAATAGGTTA-ATAAAAA
1 AACAATAATAATAGGTTAGATAAAAA
18218 AACAATAATAATAGGTTA
1 AACAATAATAATAGGTTA
18236 TTTTAAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
25 24 0.60
26 16 0.40
ACGTcount: A:0.58, C:0.04, G:0.13, T:0.25
Consensus pattern (26 bp):
AACAATAATAATAGGTTAGATAAAAA
Found at i:18243 original size:25 final size:25
Alignment explanation
Indices: 18167--18245 Score: 97
Period size: 26 Copynumber: 3.1 Consensus size: 25
18157 CTATTCATTC
*
18167 AACAATGATAATAGGTTAGA-TAAAA
1 AACAATAATAATAGGTTA-ATTAAAA
*
18192 AAGCAATAATAATAGGTTAATAAAAA
1 AA-CAATAATAATAGGTTAATTAAAA
*
18218 AACAATAATAATAGGTTATTTTAAAA
1 AACAATAATAATAGGTTA-ATTAAAA
18244 AA
1 AA
18246 ATAGGTGAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
25 19 0.40
26 28 0.60
ACGTcount: A:0.58, C:0.04, G:0.11, T:0.27
Consensus pattern (25 bp):
AACAATAATAATAGGTTAATTAAAA
Found at i:18740 original size:21 final size:21
Alignment explanation
Indices: 18730--18792 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
18720 ACGAAAATGT
*
18730 TAAGCCCTTTCATCAAAAGGA
1 TAAGTCCTTTCATCAAAAGGA
18751 TAAGTCCTTTCATCAAAAGGA
1 TAAGTCCTTTCATCAAAAGGA
*
18772 TAAGTCCTTTCATCGAAAGGA
1 TAAGTCCTTTCATCAAAAGGA
18793 CTTAACCCTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.27
Consensus pattern (21 bp):
TAAGTCCTTTCATCAAAAGGA
Found at i:19208 original size:3 final size:3
Alignment explanation
Indices: 19202--19232 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
19192 ACAATAATAT
*
19202 TTA TTA TTA TTA TTA TTA TTA TTA TTT TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
19233 CTCAGATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:21128 original size:21 final size:19
Alignment explanation
Indices: 21090--21128 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
21080 TTTATTAAAA
*
21090 TTTTAAAATTATTAATTTT
1 TTTTAAAATTAATAATTTT
21109 TTTTAATAATTTAATAATTT
1 TTTTAA-AA-TTAATAATTT
21129 AATGATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 2 0.12
21 9 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTAAAATTAATAATTTT
Found at i:21890 original size:37 final size:37
Alignment explanation
Indices: 21830--21917 Score: 99
Period size: 35 Copynumber: 2.4 Consensus size: 37
21820 CGTTATAAAG
*
21830 AATATAACATTTTTTACTGTCAATAAAAAATGTTACGAA
1 AATATAACA-TTTTGACTGTCAATAAAAAA-GTTACGAA
*
21869 TAATATAACATTTTGA-T-TCAATAAAAAAGTTAGGAA
1 -AATATAACATTTTGACTGTCAATAAAAAAGTTACGAA
* *
21905 AAAATAACGTTTT
1 AATATAACATTTT
21918 AAGTTATGCC
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
35 11 0.25
36 7 0.16
37 11 0.25
38 1 0.02
39 5 0.11
40 9 0.20
ACGTcount: A:0.48, C:0.08, G:0.09, T:0.35
Consensus pattern (37 bp):
AATATAACATTTTGACTGTCAATAAAAAAGTTACGAA
Found at i:26000 original size:105 final size:106
Alignment explanation
Indices: 25844--26074 Score: 295
Period size: 107 Copynumber: 2.2 Consensus size: 106
25834 TGACCATCTA
* * * * *
25844 TTCGATACAATTATCAATATAATTTGAGATGAATTTGTCTGATACTAAAAATATA-TTTTGTGAC
1 TTCGATACTATTATCAATATAAATTGAGATAAATTTATCTGACACTAAAAATATATTTTTGTGAC
*
25908 CATCAATATTGTCACACTAAGTATTTTTTAGTGACAAAATG
66 CACCAATATTGTCACACTAAGTATTTTTTAGTGACAAAATG
* * * *
25949 TTTGATACTATTATCAATATAAATT-ATGATAAATTTATTTGACACTGAAAATATATTTTTTTTG
1 TTCGATACTATTATCAATATAAATTGA-GATAAATTTATCTGACACTAAAAATATA-TTTTTGTG
* * *
26013 ACCACCAATGTTGTCACACTAAGTGTTTTTTAGTGACCAAATG
64 ACCACCAATATTGTCACACTAAGTATTTTTTAGTGACAAAATG
* *
26056 TTCGACATTATTATCAATA
1 TTCGATACTATTATCAATA
26075 ACTTATTCAT
Statistics
Matches: 107, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
104 1 0.01
105 45 0.42
107 61 0.57
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (106 bp):
TTCGATACTATTATCAATATAAATTGAGATAAATTTATCTGACACTAAAAATATATTTTTGTGAC
CACCAATATTGTCACACTAAGTATTTTTTAGTGACAAAATG
Found at i:27092 original size:20 final size:21
Alignment explanation
Indices: 27067--27107 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
27057 GTTGTGGACG
27067 TTTCTAGCCG-TTGGGGATGA
1 TTTCTAGCCGTTTGGGGATGA
27087 TTTCTAGCCGTTTGGGGATGA
1 TTTCTAGCCGTTTGGGGATGA
27108 AATCTCTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.15, C:0.15, G:0.34, T:0.37
Consensus pattern (21 bp):
TTTCTAGCCGTTTGGGGATGA
Found at i:28819 original size:20 final size:20
Alignment explanation
Indices: 28780--28817 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28770 TTCTAAATCA
*
28780 TTTTTCAAAATTTCATTTTG
1 TTTTTCAAAATCTCATTTTG
28800 TTTTTCAAAATCT-ATTTT
1 TTTTTCAAAATCTCATTTT
28818 TGCTTTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.26, C:0.11, G:0.03, T:0.61
Consensus pattern (20 bp):
TTTTTCAAAATCTCATTTTG
Found at i:31619 original size:2 final size:2
Alignment explanation
Indices: 31614--31650 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
31604 TAAAAAAATG
31614 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
31651 GGTATTTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31684 original size:13 final size:13
Alignment explanation
Indices: 31661--31694 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
31651 GGTATTTAAT
31661 AAAAT-AAGTAAA
1 AAAATAAAGTAAA
31673 AAAATAAAGTAAA
1 AAAATAAAGTAAA
*
31686 ATAATAAAG
1 AAAATAAAG
31695 ATGTATACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.18
Consensus pattern (13 bp):
AAAATAAAGTAAA
Found at i:31789 original size:3 final size:3
Alignment explanation
Indices: 31781--31811 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
31771 ATAAAAGGAA
31781 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
31812 GTTACAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:31913 original size:16 final size:16
Alignment explanation
Indices: 31892--31929 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
31882 AATAAGAAAT
31892 AAAATAAAAAATTATA
1 AAAATAAAAAATTATA
*
31908 AAAATAATAAATTATA
1 AAAATAAAAAATTATA
*
31924 ATAATA
1 AAAATA
31930 CGAGGATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATAAAAAATTATA
Found at i:33941 original size:9 final size:9
Alignment explanation
Indices: 33927--33960 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
33917 GCCTACCTCA
33927 TTCTTCTTT
1 TTCTTCTTT
33936 TTCTTCTTT
1 TTCTTCTTT
33945 TTCTTCTTT
1 TTCTTCTTT
*
33954 TGCTTCT
1 TTCTTCT
33961 CTTCGTCTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.00, C:0.24, G:0.03, T:0.74
Consensus pattern (9 bp):
TTCTTCTTT
Found at i:34703 original size:83 final size:82
Alignment explanation
Indices: 34486--34896 Score: 493
Period size: 83 Copynumber: 4.9 Consensus size: 82
34476 TTTTGTTGGT
** * *
34486 AGATAACCCTTCTCGCCTTGAACTATGCTTCAAATGATGTGCCTTTGATCTGAGTGTAATCGAAC
1 AGATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
*
34551 TCGAAGGTCTTAGCTGAC
66 TCGAAGGTCTT-GTTGAC
* * * * *
34569 AAATAACCCTTATTGCCTTGAGTTATGTTGTAAATTGGATGTGCCTTTGAGCTGAGTGTAATCGA
1 AGATAACCCTTCTCGCCTTGAGTTATGCTGCAAA-T-GATGTGCCTTTGAGCTGAGTGTAATCGA
34634 ACTCGAAGGTCTT-TTGAC
64 ACTCGAAGGTCTTGTTGAC
* * * * *
34652 AGATAAACCTTCTCGCCTTGAGTTATACTACACAATTGATATGCCTTTGAGCTGAATGTAATCGA
1 AGATAACCCTTCTCGCCTTGAGTTATGCTGCA-AA-TGATGTGCCTTTGAGCTGAGTGTAATCGA
34717 ACTCGAAGGTCTTGATTGAC
64 ACTCGAAGGTCTTG-TTGAC
* * * *
34737 AGATAACCCTT-TCCACCTTGAGTTATGTTGTAAATGATATGCCTTTGAGCTGAGTGTAATCGAA
1 AGATAACCCTTCT-CGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
*
34801 CTCGAAGGTCTTTTGTTGGC
65 CTCGAAGGTC--TTGTTGAC
* * * * *
34821 ATATAGCCCTTCTCGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAATGTAATTGAAC
1 AGATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
*
34886 TCAAAGGTCTT
66 TCGAAGGTCTT
34897 TTGTTGAAGG
Statistics
Matches: 281, Mismatches: 38, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
82 2 0.01
83 132 0.47
84 74 0.26
85 73 0.26
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (82 bp):
AGATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
TCGAAGGTCTTGTTGAC
Found at i:35891 original size:97 final size:98
Alignment explanation
Indices: 35681--35916 Score: 302
Period size: 97 Copynumber: 2.4 Consensus size: 98
35671 GGCTAGCTGG
* *
35681 ATCCATAAAGCCAGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAATATCATTGTATAGATA
1 ATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAATATCATTATATAGATA
35746 TTATAATCACCTTTATCAGGCTAGCTAAATATT
66 TTATAATCACCTTTATCAGGCTAGCTAAATATT
* * * *
35779 ATCCATAACA-TCGGGGCTTTTAACCAATTGCTCTAGCA-GGACAACTCGAGCT-TTATTATATA
1 ATCCATAA-AGCCGGGGCATTTAACCAATTGCTCTAG-AGGGACAACTC-A-ATATCATTATATA
* * *
35841 -TTA-TATAATCACCTTTATCAGGCTAGCTGAATCTT
62 GATATTATAATCACCTTTATCAGGCTAGCTAAATATT
* *
35876 ATCTATAAAGCCGGGGCATTTAACCAATTGCTTTAGAGGGA
1 ATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGA
35917 GCTTTATTGT
Statistics
Matches: 119, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
96 2 0.02
97 63 0.53
98 42 0.35
99 11 0.09
100 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (98 bp):
ATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAATATCATTATATAGATA
TTATAATCACCTTTATCAGGCTAGCTAAATATT
Found at i:38715 original size:15 final size:16
Alignment explanation
Indices: 38683--38716 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
38673 ATTTGAAATT
*
38683 TTAAAATTTATACAAA
1 TTAAAATTGATACAAA
38699 TTAAAATTGAT-CAAA
1 TTAAAATTGATACAAA
38714 TTA
1 TTA
38717 GAGCATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (16 bp):
TTAAAATTGATACAAA
Found at i:39549 original size:42 final size:42
Alignment explanation
Indices: 39430--39567 Score: 159
Period size: 42 Copynumber: 3.3 Consensus size: 42
39420 TTCACTTTAA
* * *
39430 TAGTAACAAAAATAATTTTCGTTATAAATCACCAACTAAGAT
1 TAGTAACAAAAATAATTGTCGTCATAAATCACCAACTAAGAC
* * * * *
39472 TAGTGAAAAAAAACAATTGCCGTCACAAATAACCAACTAAGAC
1 TAGT-AACAAAAATAATTGTCGTCATAAATCACCAACTAAGAC
* * *
39515 TAGTAACAAAAATGACTGTCGTCATAAATCACCAACAAAGAC
1 TAGTAACAAAAATAATTGTCGTCATAAATCACCAACTAAGAC
*
39557 TAGTGACAAAA
1 TAGTAACAAAA
39568 TATTTTTGCC
Statistics
Matches: 78, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
42 44 0.56
43 34 0.44
ACGTcount: A:0.49, C:0.18, G:0.11, T:0.22
Consensus pattern (42 bp):
TAGTAACAAAAATAATTGTCGTCATAAATCACCAACTAAGAC
Found at i:40878 original size:21 final size:20
Alignment explanation
Indices: 40849--40887 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
40839 TAGGTCAGAG
*
40849 TATCAATATTGGGATGAACAA
1 TATCAATATT-AGATGAACAA
*
40870 TATCGATATTAGATGAAC
1 TATCAATATTAGATGAAC
40888 TGAGGCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (20 bp):
TATCAATATTAGATGAACAA
Found at i:61775 original size:39 final size:39
Alignment explanation
Indices: 61731--61808 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
61721 TGTAAAAGGA
61731 AAATGTTGTGCTTAAGGTGAATGAGAATTCA-AAATACTC
1 AAATGTTGTGCTTAAGGTGAATGAGAATTCAGAAA-ACTC
61770 AAATGTTGTGCTTAAGGTGAATGAGAATTCAGAAAACTC
1 AAATGTTGTGCTTAAGGTGAATGAGAATTCAGAAAACTC
61809 TCTCTATTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 35 0.92
40 3 0.08
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.29
Consensus pattern (39 bp):
AAATGTTGTGCTTAAGGTGAATGAGAATTCAGAAAACTC
Found at i:62309 original size:17 final size:16
Alignment explanation
Indices: 62287--62320 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
62277 TAAAAACAGT
62287 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
62304 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
62320 A
1 A
62321 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:72089 original size:17 final size:16
Alignment explanation
Indices: 72067--72100 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
72057 TAAAAACAGT
72067 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
72084 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
72100 A
1 A
72101 TCCTCATGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:72619 original size:24 final size:24
Alignment explanation
Indices: 72575--72621 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
72565 ATAAAGAACC
*
72575 AAAATAAACTTAAGTATACCATTA
1 AAAATAAACTTAAATATACCATTA
*
72599 AAAATAAAGTTTAAATA-ACCATT
1 AAAATAAA-CTTAAATATACCATT
72622 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.55, C:0.11, G:0.04, T:0.30
Consensus pattern (24 bp):
AAAATAAACTTAAATATACCATTA
Found at i:79495 original size:138 final size:140
Alignment explanation
Indices: 79185--79533 Score: 377
Period size: 138 Copynumber: 2.5 Consensus size: 140
79175 AACTTAAGGG
* *** * ** * * *
79185 ATTAAACCTAAGATGTTGGCTCTAATATTAAAACCTAAAGAATTTTAACATTTTAGTGGATCGAA
1 ATTAAACCTAAAATGAAAGCTCTAATATTTAAACCTAATCAATTTTAACAATTTAATGGATTGAA
* ***
79250 TAATTAATTCGAAGCCTCGAGCATAAAGGTGAGAACCAAATTAAAAATTCTCCTAAACTAAAGGA
66 TAATTAATTCGAAGCCTCGAGCAAAAAGCAAAGAACCAAATTAAAAATTCTCCTAAACTAAAGGA
79315 CTAAAATGAA
131 CTAAAATGAA
* * * * *
79325 ATTAAACCTAAGATGAAGGCTCTAAT-GTTAAACCTATTCAATTTTAACAATTTATTGGATTGAA
1 ATTAAACCTAAAATGAAAGCTCTAATATTTAAACCTAATCAATTTTAACAATTTAATGGATTGAA
* * *
79389 TAATTAATATGGAA-CCTCG-GCAGAAAAGCAAAGAA-CAAATTAAAAATTCTCTTAAATTAAAG
66 TAATTAAT-TCGAAGCCTCGAGCA-AAAAGCAAAGAACCAAATTAAAAATTCTCCTAAACTAAAG
*
79451 GACTAAAGTGAA
129 GACTAAAATGAA
** * *
79463 ATT-AATGTAAAATGAAAGCTCTAATATTTAAACCTAATCAATGTTAACACA-TTAATGGATTAA
1 ATTAAACCTAAAATGAAAGCTCTAATATTTAAACCTAATCAATTTTAACA-ATTTAATGGATTGA
*
79526 ACAATTAA
65 ATAATTAA
79534 AATAAAACCT
Statistics
Matches: 177, Mismatches: 28, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
137 18 0.10
138 79 0.45
139 52 0.29
140 28 0.16
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (140 bp):
ATTAAACCTAAAATGAAAGCTCTAATATTTAAACCTAATCAATTTTAACAATTTAATGGATTGAA
TAATTAATTCGAAGCCTCGAGCAAAAAGCAAAGAACCAAATTAAAAATTCTCCTAAACTAAAGGA
CTAAAATGAA
Found at i:81166 original size:57 final size:57
Alignment explanation
Indices: 81060--81185 Score: 146
Period size: 57 Copynumber: 2.2 Consensus size: 57
81050 ATTTTGCACT
* * * * * *
81060 GGATTTTATCCCCGTCCTGATTCTTCATGGGATTATATTCACGTCTTGATTCTATATG
1 GGATTATAT-CCCGTCCTAATTCTACATGAGATAATATTCACGTCTTGATTCTACATG
* *
81118 GGATTATATCCCGTCCTAATTCTACATGAGATAATA-TCATCGTGTTGATTCTGCATG
1 GGATTATATCCCGTCCTAATTCTACATGAGATAATATTCA-CGTCTTGATTCTACATG
*
81175 AGATTATATCC
1 GGATTATATCC
81186 TCATCCTGAT
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
56 3 0.05
57 47 0.81
58 8 0.14
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.40
Consensus pattern (57 bp):
GGATTATATCCCGTCCTAATTCTACATGAGATAATATTCACGTCTTGATTCTACATG
Found at i:81195 original size:29 final size:29
Alignment explanation
Indices: 81061--81206 Score: 123
Period size: 29 Copynumber: 5.1 Consensus size: 29
81051 TTTTGCACTG
* * * *
81061 GATTTTATCCCCGTCCTGATTCTTCATGG
1 GATTATATCCTCGTCCTGATTCTACATGA
* * * * *
81090 GATTATATTCACGTCTTGATTCTATATGG
1 GATTATATCCTCGTCCTGATTCTACATGA
*
81119 GATTATATCC-CGTCCTAATTCTACATGA
1 GATTATATCCTCGTCCTGATTCTACATGA
* * ** *
81147 GATAATATCATCGTGTTGATTCTGCATGA
1 GATTATATCCTCGTCCTGATTCTACATGA
* * *
81176 GATTATATCCTCATCCTGATTTTATATGA
1 GATTATATCCTCGTCCTGATTCTACATGA
81205 GA
1 GA
81207 CTAGATCCCC
Statistics
Matches: 91, Mismatches: 25, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
28 22 0.24
29 69 0.76
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (29 bp):
GATTATATCCTCGTCCTGATTCTACATGA
Found at i:87698 original size:31 final size:32
Alignment explanation
Indices: 87663--87727 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
87653 ATACTTTTAT
87663 AAGT-AAAAAAAAGACTCAAATAGAATATCTA
1 AAGTAAAAAAAAAGACTCAAATAGAATATCTA
87694 AAGTAAAAAAAAAGACTCAAATAGAATATCTA
1 AAGTAAAAAAAAAGACTCAAATAGAATATCTA
87726 AA
1 AA
87728 TAATTTCACC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 4 0.12
32 29 0.88
ACGTcount: A:0.63, C:0.09, G:0.09, T:0.18
Consensus pattern (32 bp):
AAGTAAAAAAAAAGACTCAAATAGAATATCTA
Found at i:88556 original size:60 final size:60
Alignment explanation
Indices: 88460--88608 Score: 176
Period size: 60 Copynumber: 2.5 Consensus size: 60
88450 CTGATGACTA
* * * *
88460 TTTTATAACTTTTATTAGTCAATAGACTCAGGAAAATAATATCTTATAATCAAA-AGACCG
1 TTTTATAACTTTTAATAGTCAACAGACTCAGCAAAATAATATCATATAATCAAAGAGA-CG
* * * *
88520 TTTTATAACTTTTAATAGTCAACAGACTCTA-CAAAATAATGTCATATAGTCAAAGGGATG
1 TTTTATAACTTTTAATAGTCAACAGACTC-AGCAAAATAATATCATATAATCAAAGAGACG
* *
88580 TTTCATAACTTTTAATAGTCAAGAGACTC
1 TTTTATAACTTTTAATAGTCAACAGACTC
88609 GATAAAGAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
60 74 0.96
61 3 0.04
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (60 bp):
TTTTATAACTTTTAATAGTCAACAGACTCAGCAAAATAATATCATATAATCAAAGAGACG
Found at i:88628 original size:60 final size:60
Alignment explanation
Indices: 88519--88632 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
88509 TCAAAAGACC
* * *
88519 GTTTTATAACTTTTAATAGTCAACAGACTCTACAAAATAATGTCATATAGTCAAAGGGAT
1 GTTTCATAACTTTTAATAGTCAACAGACTCGACAAAATAACGTCATATAGTCAAAGGGAT
* * *
88579 GTTTCATAACTTTTAATAGTCAAGAGACTCGATAAAGA-AACGTCCTATAGTCAA
1 GTTTCATAACTTTTAATAGTCAACAGACTCGACAAA-ATAACGTCATATAGTCAA
88633 GAGATCATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
60 46 0.98
61 1 0.02
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (60 bp):
GTTTCATAACTTTTAATAGTCAACAGACTCGACAAAATAACGTCATATAGTCAAAGGGAT
Found at i:90680 original size:3 final size:3
Alignment explanation
Indices: 90621--90664 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
90611 TTATTTCATG
90621 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
90665 CTCGTACATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:93058 original size:33 final size:31
Alignment explanation
Indices: 93000--93079 Score: 79
Period size: 32 Copynumber: 2.5 Consensus size: 31
92990 AACTAACTTG
* * * *
93000 AACCGAAAACAACCAGAACTGAATTTTAACCC
1 AACCGAAAGCAACCTGAAC-CAAATTTAACCC
*
93032 AATCCGAAAGCAACCTGAACCAAATTTAATCC
1 AA-CCGAAAGCAACCTGAACCAAATTTAACCC
*
93064 GACCTGAAAGCAACCT
1 AACC-GAAAGCAACCT
93080 AAATAGAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
31 2 0.05
32 23 0.57
33 15 0.38
ACGTcount: A:0.44, C:0.29, G:0.11, T:0.16
Consensus pattern (31 bp):
AACCGAAAGCAACCTGAACCAAATTTAACCC
Found at i:93674 original size:14 final size:14
Alignment explanation
Indices: 93651--93680 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
93641 TTACATTGAG
93651 TTTCTCAATAAAAC
1 TTTCTCAATAAAAC
*
93665 TTTCTTAATAAAAC
1 TTTCTCAATAAAAC
93679 TT
1 TT
93681 AAGATCAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (14 bp):
TTTCTCAATAAAAC
Found at i:96882 original size:18 final size:17
Alignment explanation
Indices: 96865--96912 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
96855 TTGAATAATA
96865 AATTAATTTATAAAAAT
1 AATTAATTTATAAAAAT
**
96882 AGGTAATTTATTAAAAAT
1 AATTAATTTA-TAAAAAT
96900 -ATTAGATTTATAA
1 AATTA-ATTTATAA
96913 TAAAAAAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (17 bp):
AATTAATTTATAAAAAT
Found at i:97433 original size:13 final size:12
Alignment explanation
Indices: 97415--97448 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
97405 TAGCATTGGG
97415 AAAAGAAAATAA
1 AAAAGAAAATAA
97427 TAAAAGAAAATAA
1 -AAAAGAAAATAA
97440 AGAAAGAAA
1 A-AAAGAAA
97449 GATTTAGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 1 0.05
13 19 0.95
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (12 bp):
AAAAGAAAATAA
Found at i:104835 original size:14 final size:13
Alignment explanation
Indices: 104818--104869 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 13
104808 AATTATAATC
104818 ATTAAATTAATTTT
1 ATTAAATTAA-TTT
*
104832 ATT-AATTTATTT
1 ATTAAATTAATTT
104844 ATTGAACATT-ATTT
1 ATT-AA-ATTAATTT
104858 ATTAAATTAATT
1 ATTAAATTAATT
104870 ATAATTATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
12 9 0.27
13 10 0.30
14 11 0.33
15 3 0.09
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (13 bp):
ATTAAATTAATTT
Found at i:104877 original size:18 final size:17
Alignment explanation
Indices: 104856--104938 Score: 51
Period size: 19 Copynumber: 4.5 Consensus size: 17
104846 TGAACATTAT
104856 TTATTAAATTAATTATAA
1 TTATTAAATTAA-TATAA
104874 TTATTACAAGTTAA-ATAA
1 TTATTA-AA-TTAATATAA
* * *
104892 TTTATTGGAATTGAACATGA
1 -TTATT-AAATT-AATATAA
104912 TTAATTAAATTAATTATAA
1 TT-ATTAAATTAA-TATAA
*
104931 TCATTAAA
1 TTATTAAA
104939 AGTTAAAATA
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
18 20 0.39
19 21 0.41
20 10 0.20
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (17 bp):
TTATTAAATTAATATAA
Found at i:104909 original size:57 final size:56
Alignment explanation
Indices: 104834--104982 Score: 212
Period size: 57 Copynumber: 2.7 Consensus size: 56
104824 TTAATTTTAT
* * * * *
104834 TAATTTATTTATTGAACATTATTTATTAAATTAATTATAATTATTACAAGTT-AAA
1 TAATTTATTAATTGAACATGATTAATTAAATTAATTATAATCATTAAAAGTTAAAA
104889 TAATTTATTGGAATTGAACATGATTAATTAAATTAATTATAATCATTAAAAGTTAAAA
1 TAATTTATT--AATTGAACATGATTAATTAAATTAATTATAATCATTAAAAGTTAAAA
*
104947 TAATTTATTTATTGAACATGATTAATTAAA-TAATTA
1 TAATTTATTAATTGAACATGATTAATTAAATTAATTA
104983 ATTTAAATAT
Statistics
Matches: 85, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
55 15 0.18
56 20 0.24
57 38 0.45
58 12 0.14
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (56 bp):
TAATTTATTAATTGAACATGATTAATTAAATTAATTATAATCATTAAAAGTTAAAA
Done.