Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004366.1 Hibiscus syriacus cultivar Beakdansim tig00009566_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: 64547
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:8038 original size:30 final size:31
Alignment explanation
Indices: 8002--8059 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
7992 AATTCAATGT
* * *
8002 AAAATCACCTTTAGATAA-TTAATACCACTC
1 AAAATCACATTAAAATAACTTAATACCACTC
8032 AAAATCACATTAAAATAACTTAATACCA
1 AAAATCACATTAAAATAACTTAATACCA
8060 AATATCTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 15 0.62
31 9 0.38
ACGTcount: A:0.50, C:0.21, G:0.02, T:0.28
Consensus pattern (31 bp):
AAAATCACATTAAAATAACTTAATACCACTC
Found at i:10683 original size:20 final size:21
Alignment explanation
Indices: 10652--10690 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
10642 TATTGATACC
10652 ACCTCTGAGTATCAATACTGG
1 ACCTCTGAGTATCAATACTGG
*
10673 ACCTC-GAGTATCGATACT
1 ACCTCTGAGTATCAATACT
10691 CCTTGAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (21 bp):
ACCTCTGAGTATCAATACTGG
Found at i:11275 original size:19 final size:21
Alignment explanation
Indices: 11224--11273 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
11214 CTACAATTCA
*
11224 AAACTCTACAAAAAATAGATT
1 AAACTCCACAAAAAATAGATT
11245 AAACTCCACAAAAAATAGATT
1 AAACTCCACAAAAAATAGATT
11266 AAACTCCA
1 AAACTCCA
11274 AAGTCTCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.56, C:0.20, G:0.04, T:0.20
Consensus pattern (21 bp):
AAACTCCACAAAAAATAGATT
Found at i:23259 original size:23 final size:22
Alignment explanation
Indices: 23217--23261 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
23207 AAAACAACAA
*
23217 AAAAAAAATCAGTGAAAAAACT
1 AAAAAAAATCAGTAAAAAAACT
23239 AAAAAAAATACA-TAAAGAAAACT
1 AAAAAAAAT-CAGTAAA-AAAACT
23262 CGGAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.71, C:0.09, G:0.07, T:0.13
Consensus pattern (22 bp):
AAAAAAAATCAGTAAAAAAACT
Found at i:23652 original size:2 final size:2
Alignment explanation
Indices: 23645--23670 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
23635 CGGCTTTTCC
23645 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
23671 TATCCTTTTC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:29128 original size:58 final size:58
Alignment explanation
Indices: 29052--29277 Score: 285
Period size: 58 Copynumber: 3.9 Consensus size: 58
29042 TAATAGCCGA
* *
29052 GGACTCAACAAAATATCATCATATAGTCAAAGACCATTTTGTAACTTTTGATATTCAG
1 GGACTCAACAAAACAACATCATATAGTCAAAGACCATTTTGTAACTTTTGATATTCAG
* * *
29110 GGACTCAATAAAACATCATCATATAGTCAAAGACTATTTTGTAACTTTTGATATTCAG
1 GGACTCAACAAAACAACATCATATAGTCAAAGACCATTTTGTAACTTTTGATATTCAG
* * * * *
29168 GAACTCAACAAAACAACACCA-ATAATCAAAGGACCATTTTGTAACTTTAGATACTCAAG
1 GGACTCAACAAAACAACATCATATAGTCAAA-GACCATTTTGTAACTTTTGATATTC-AG
* * *
29227 TGACTCAACAAAGCAACATCATATAGTCAATGGACCATTTT-TATACTTTTG
1 GGACTCAACAAAACAACATCATATAGTCAA-AGACCATTTTGTA-ACTTTTG
29278 CCCCATTGTA
Statistics
Matches: 145, Mismatches: 18, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
57 8 0.06
58 94 0.65
59 21 0.14
60 22 0.15
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.31
Consensus pattern (58 bp):
GGACTCAACAAAACAACATCATATAGTCAAAGACCATTTTGTAACTTTTGATATTCAG
Found at i:31177 original size:2 final size:2
Alignment explanation
Indices: 31172--31206 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
31162 TTTCTACTCT
31172 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 T
31207 GTAGACACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31367 original size:39 final size:37
Alignment explanation
Indices: 31276--31518 Score: 153
Period size: 38 Copynumber: 6.5 Consensus size: 37
31266 ATATATACAT
* * *
31276 ATTTTGAAACTACGTATATAATATATAGTTTT-TAATA-
1 ATTTTGAAAATA--TATATAATATATAGTTTTAAAAAAC
* *
31313 GTTTTTAAAATTATAT--AATATATAGTTTTAAAAAAAC
1 ATTTTGAAAA-TATATATAATATATAGTTTT-AAAAAAC
* * *
31350 ATTTTAGAAAATATATATAATATATAATTTTTAAAATC
1 ATTTT-GAAAATATATATAATATATAGTTTTAAAAAAC
* **
31388 ATTTGGAAAACT-TATATATATATATAGTTTTTGAAAAC
1 ATTTTGAAAA-TATATATA-ATATATAGTTTTAAAAAAC
* * *
31426 ATTTTTGAAAACATATAT-AT-TATAGTTTT-GAAAGC
1 A-TTTTGAAAATATATATAATATATAGTTTTAAAAAAC
* * * *
31461 ATTTTGAAAACATTTATATTATATAGTTTT-TAAAAC
1 ATTTTGAAAATATATATAATATATAGTTTTAAAAAAC
* *
31497 GTTTTGGGAAAATTTATATAAT
1 ATTTT--GAAAATATATATAAT
31519 CTTTTTTGAA
Statistics
Matches: 165, Mismatches: 26, Indels: 29
0.75 0.12 0.13
Matches are distributed among these distances:
34 28 0.17
35 7 0.04
36 32 0.19
37 29 0.18
38 44 0.27
39 25 0.15
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.44
Consensus pattern (37 bp):
ATTTTGAAAATATATATAATATATAGTTTTAAAAAAC
Found at i:31391 original size:38 final size:37
Alignment explanation
Indices: 31290--31542 Score: 168
Period size: 34 Copynumber: 6.9 Consensus size: 37
31280 TGAAACTACG
* * * *
31290 TATATAATATATAGTTTTTAATA-GTTTT-TAAAAT-
1 TATATAATATATAATTTTTAAAACATTTTGGAAAATA
* * *
31324 TATATAATATATAGTTTTAAAAAAACATTTTAGAAAATA
1 TATATAATATATAATTTT--TAAAACATTTTGGAAAATA
31363 TATATAATATATAATTTTTAAAATCA-TTTGGAAAACT-
1 TATATAATATATAATTTTTAAAA-CATTTTGGAAAA-TA
* * *
31400 TATATATATATATAGTTTTTGAAAACATTTTTGAAAACA
1 TATATA-ATATATAATTTTT-AAAACATTTTGGAAAATA
* * * *
31439 TATAT-AT-TATAGTTTTGAAAGCATTTT-GAAAACA
1 TATATAATATATAATTTTTAAAACATTTTGGAAAATA
* * * * *
31473 TTTATATTATATAGTTTTTAAAACGTTTTGGGAAAATT
1 TATATAATATATAATTTTTAAAACATTTT-GGAAAATA
* * *
31511 TATATAATCT-T--TTTTGAAAACATGTTGGAAAA
1 TATATAATATATAATTTTTAAAACATTTTGGAAAA
31543 CATTCGTATA
Statistics
Matches: 179, Mismatches: 25, Indels: 30
0.76 0.11 0.13
Matches are distributed among these distances:
34 35 0.20
35 22 0.12
36 29 0.16
37 25 0.14
38 34 0.19
39 34 0.19
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (37 bp):
TATATAATATATAATTTTTAAAACATTTTGGAAAATA
Found at i:31432 original size:12 final size:12
Alignment explanation
Indices: 31415--31439 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31405 ATATATATAG
31415 TTTTTGAAAACA
1 TTTTTGAAAACA
31427 TTTTTGAAAACA
1 TTTTTGAAAACA
31439 T
1 T
31440 ATATATTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTTTGAAAACA
Found at i:31479 original size:36 final size:36
Alignment explanation
Indices: 31345--31557 Score: 152
Period size: 36 Copynumber: 5.8 Consensus size: 36
31335 TAGTTTTAAA
* * * *
31345 AAAACATTTTAGAAAATATATATA-ATATATAATTTTT
1 AAAACATTTT-GAAAACATTTATATAT-TATAGTTTTG
*
31382 AAAATCATTTGGAAAAC-TTATATATATATATAGTTTTTG
1 AAAA-CATTTTGAAAACATT-TATATAT-TATAG-TTTTG
31421 AAAACATTTTTGAAAACA--TATATATTATAGTTTTG
1 AAAACA-TTTTGAAAACATTTATATATTATAGTTTTG
* *
31456 AAAGCATTTTGAAAACATTTATAT-TATATAGTTTTT
1 AAAACATTTTGAAAACATTTATATAT-TATAGTTTTG
* * * * *
31492 AAAACGTTTTGGGAAA-ATTTATATAATCT-TTTTTG
1 AAAACATTTT-GAAAACATTTATATATTATAGTTTTG
* **
31527 AAAACATGTTGGAAAACATTCGTATATTATA
1 AAAACAT-TTTGAAAACATTTATATATTATA
31558 TAGTTTTAAA
Statistics
Matches: 140, Mismatches: 22, Indels: 28
0.74 0.12 0.15
Matches are distributed among these distances:
34 11 0.08
35 25 0.18
36 49 0.35
37 24 0.17
38 14 0.10
39 17 0.12
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.43
Consensus pattern (36 bp):
AAAACATTTTGAAAACATTTATATATTATAGTTTTG
Found at i:31515 original size:72 final size:71
Alignment explanation
Indices: 31322--31569 Score: 221
Period size: 72 Copynumber: 3.4 Consensus size: 71
31312 AGTTTTTAAA
* * * * * *
31322 ATTATATAATATATAGTTTTAAAAAAACATTTTAGAAAATATATATAATATATAATTTTTAAAAT
1 ATTATATATTATATAGTTTT--TAAAACATTTTGGAAAACATATAT-A-ATAT-GTTTTGAAAA-
31387 CATTTGGAAAAC
60 CATTTGGAAAAC
* * *
31399 -TTATATATATATATAGTTTTTGAAAACATTTTTGAAAACATATATATTATAGTTTTGAAAGCAT
1 ATTATATAT-TATATAGTTTTT-AAAACATTTTGGAAAACATATATAATAT-GTTTTGAAAACAT
*
31463 TTTGAAAAC
63 TTGGAAAAC
* ** * *
31472 ATT-TATATTATATAGTTTTTAAAACGTTTTGGGAAAATTTATATAATCTTTTTTGAAAACATGT
1 ATTATATATTATATAGTTTTTAAAACATTTT-GGAAAACATATATAATATGTTTTGAAAACAT-T
31536 TGGAAAAC
64 TGGAAAAC
* *
31544 ATTCGTATATTATATAGTTTTAAAAA
1 ATT-ATATATTATATAGTTTTTAAAA
31570 AAAAAACATT
Statistics
Matches: 145, Mismatches: 19, Indels: 17
0.80 0.10 0.09
Matches are distributed among these distances:
71 20 0.14
72 36 0.25
73 16 0.11
74 33 0.23
75 1 0.01
76 28 0.19
77 11 0.08
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (71 bp):
ATTATATATTATATAGTTTTTAAAACATTTTGGAAAACATATATAATATGTTTTGAAAACATTTG
GAAAAC
Found at i:31636 original size:3 final size:3
Alignment explanation
Indices: 31628--31661 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
31618 TGTATATATA
*
31628 TAT TAT TAT TAT TTT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
31662 TTTCATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:33916 original size:1 final size:1
Alignment explanation
Indices: 33902--33942 Score: 55
Period size: 1 Copynumber: 41.0 Consensus size: 1
33892 AACCCTTTCA
* * *
33902 TTTTTTGTTCTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
33943 GTGTGTTCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.02, G:0.05, T:0.93
Consensus pattern (1 bp):
T
Found at i:34606 original size:19 final size:19
Alignment explanation
Indices: 34572--34616 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
34562 ATTTAGACAT
34572 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
34590 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
34609 TTTGCATT
1 TTTGCATT
34617 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:38241 original size:165 final size:164
Alignment explanation
Indices: 37969--38740 Score: 964
Period size: 165 Copynumber: 4.7 Consensus size: 164
37959 TAAACAAACT
* *
37969 ATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCTGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCCTGAGTTCGATTACACTCA
*
38034 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
66 GCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACC-AAAGACC
38099 TTCGAGTTCGACTACGCTCAGCTCTAAGGCACATC
130 TTCGAGTTCGACTACGCTCAGCTCTAAGGCACATC
*
38134 ATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCCTAAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCCTGAGTTCGATTACACTCA
* *
38199 GCTTCAAGGGCATAACATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
66 GCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACC-AAAGACC
38264 TTCGAGTTCGACTACGCTCAGCTCTAAGGCACATC
130 TTCGAGTTCGACTACGCTCAGCTCTAAGGCACATC
* ** *
38299 ATTTGCAGCATAACTTAAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTAC
1 ATTTGCAGCATAGCTT-AAGTCGAGAAGGGTTATCTG----CCAAAGACCCCTGAGTTCGATTAC
* * * * * * * *
38364 GCTCAGCTCCAA-GGCACATCATTTGCAGAATAGCTTAAGTCAAGAAGGGTTATC--TG-CCAAA
61 ACTCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAA
* * * * *
38425 GACCCTT-AAGTTCGATTACACTCAGCT-TCAAGGGCATAAC
126 GA-CCTTCGAGTTCGACTACGCTCAGCTCT-AA-GGCACATC
* * * * * * ** * *
38465 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGC
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTG---CCAAAGACCCCTGAGTTCGATTACAC
* * *
38530 TCAGC-TCAACGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCATCAAAGA
63 TCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAGA
38594 CCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATC
128 CCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATC
* *
38631 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCTGGGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCCTGAGTTCGATTACACTCA
* * * * * * * *
38696 ACTTCGAGGTCATATCAGTTACAACATAGCTCAAGGCAAGAAGGG
66 GCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGG
38741 CTATTTGTCA
Statistics
Matches: 524, Mismatches: 68, Indels: 31
0.84 0.11 0.05
Matches are distributed among these distances:
163 27 0.05
164 102 0.19
165 216 0.41
166 87 0.17
167 27 0.05
168 1 0.00
169 34 0.06
170 30 0.06
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (164 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCCTGAGTTCGATTACACTCA
GCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAGACCT
TCGAGTTCGACTACGCTCAGCTCTAAGGCACATC
Found at i:38448 original size:250 final size:245
Alignment explanation
Indices: 38017--38740 Score: 1097
Period size: 250 Copynumber: 2.9 Consensus size: 245
38007 AAAGACCCCT
* * *
38017 GAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTA
1 GAGTTCGACTACGCTCAGC-TC-AAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTA
*
38082 TCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAG
64 TCTG-CACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAG
38147 CTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCCTAAGTTCGATTACACTCAGCTTCAAGGGCAT
127 CTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCCTAAGTTCGATTACACTCAGCTTCAAGGGCAT
38212 AACATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTC
192 AACATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACC-AAAGACCTTC
* * * *
38267 GAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTTAAAGTCGAGAAGGGTTA
1 GAGTTCGACTACGCTCAGCTC-AAGGCACATCATTTACAGCATAAC-TCAAGGCTAGAAGGGTTA
* * *
38332 TCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAG
64 TCTG-C-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAG
* *
38397 CTTAAGTCAAGAAGGGTTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCAT
127 CTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCCTAAGTTCGATTACACTCAGCTTCAAGGGCAT
* * *
38462 AACATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTT
192 AACATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAGACCTTC
38516 GAGTTCGACTACGCTCAGCTCAACGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTAT
1 GAGTTCGACTACGCTCAGCTCAA-GGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTAT
*
38581 CTGTCATCAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCT
65 CTG-CACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCT
* ** * * * *
38646 TAAGTCGAGAAGGGCTATCTGCCAAAGACCCCTGGGTTCGATTACACTCAACTTCGAGGTCATAT
129 TAAGTCGAGAAGGGTTATCTGCCAAAGACCCCTAAGTTCGATTACACTCAGCTTCAAGGGCATAA
* * * *
38711 CAGTTACAACATAGCTCAAGGCAAGAAGGG
194 CATTTACAGCATAACTCAAGGCTAGAAGGG
38741 CTATTTGTCA
Statistics
Matches: 431, Mismatches: 40, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
247 138 0.32
248 22 0.05
249 75 0.17
250 193 0.45
251 3 0.01
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (245 bp):
GAGTTCGACTACGCTCAGCTCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATC
TGCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTA
AGTCGAGAAGGGTTATCTGCCAAAGACCCCTAAGTTCGATTACACTCAGCTTCAAGGGCATAACA
TTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAGACCTTC
Found at i:39417 original size:39 final size:37
Alignment explanation
Indices: 39340--39615 Score: 161
Period size: 34 Copynumber: 7.6 Consensus size: 37
39330 TGAAACTACG
* * *
39340 TATATAATATATAGTTTTT-AATA-GTTTT-TAAAAT
1 TATATAATATATAGTTTTTAAAAACATTTTAGAAAAT
*
39374 TATATAATATATAGTTTTAAAAAAACATTTTAGAAAAT
1 TATATAATATATAGTTTT-TAAAAACATTTTAGAAAAT
* * *
39412 ATATATAATATATAATTTTTAAAATCA-TTTGGAAAACT
1 -TATATAATATATAGTTTTTAAAAACATTTTAGAAAA-T
* *
39450 TATATATATATATAGTTTTTGAAAACATTTTTGAAAA-
1 TATATA-ATATATAGTTTTTAAAAACATTTTAGAAAAT
* * *
39487 CATAT-AT-TATAG-TTTTGAAAGCATTTT-GAAAACAT
1 TATATAATATATAGTTTTTAAAAACATTTTAG-AAA-AT
* *
39522 T-TAT-AT-TATAGTTTTT-AAAACGTTTTGGGAAAAT
1 TATATAATATATAGTTTTTAAAAACATTTT-AGAAAAT
** * * *
39556 T-TAT-ATA-ATCTTTTTTGAAAACATGTTGGAAACAT
1 TATATAATATATAGTTTTTAAAAACATTTTAGAAA-AT
* * *
39591 TCGTATATTATATAGTTTTAAAAAA
1 T-ATATAATATATAGTTTTTAAAAA
39616 AAAACATTTT
Statistics
Matches: 195, Mismatches: 26, Indels: 37
0.76 0.10 0.14
Matches are distributed among these distances:
32 1 0.01
33 17 0.09
34 62 0.32
35 20 0.10
36 4 0.02
37 25 0.13
38 31 0.16
39 35 0.18
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (37 bp):
TATATAATATATAGTTTTTAAAAACATTTTAGAAAAT
Found at i:39441 original size:38 final size:39
Alignment explanation
Indices: 39369--39497 Score: 119
Period size: 39 Copynumber: 3.4 Consensus size: 39
39359 AATAGTTTTT
* **
39369 AAAAT-TATATA-ATATATAGTTTTAAAAAAACATTTTAG
1 AAAATATATATATATATATAATTTT-TGAAAACATTTTAG
*
39407 AAAATATATATA-ATATATAATTTTT-AAAATCA-TTTGG
1 AAAATATATATATATATATAATTTTTGAAAA-CATTTTAG
* *
39444 AAAACT-TATATATATATATAGTTTTTGAAAACATTTTTG
1 AAAA-TATATATATATATATAATTTTTGAAAACATTTTAG
*
39483 AAAACATATAT-TATA
1 AAAATATATATATATA
39498 GTTTTGAAAG
Statistics
Matches: 78, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
37 18 0.23
38 26 0.33
39 34 0.44
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (39 bp):
AAAATATATATATATATATAATTTTTGAAAACATTTTAG
Found at i:39482 original size:12 final size:12
Alignment explanation
Indices: 39465--39489 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39455 ATATATATAG
39465 TTTTTGAAAACA
1 TTTTTGAAAACA
39477 TTTTTGAAAACA
1 TTTTTGAAAACA
39489 T
1 T
39490 ATATTATAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTTTGAAAACA
Found at i:39561 original size:68 final size:70
Alignment explanation
Indices: 39454--39602 Score: 160
Period size: 69 Copynumber: 2.1 Consensus size: 70
39444 AAAACTTATA
* * * *
39454 TATATATATAGTTTTTGAAAACATTTTTGAAAACATATATTAT-AGTTTTGAAAGCATTTTGAAA
1 TATAT-TATAGTTTTTGAAAACATTTTGGAAAACATATATAATCAGTTTTGAAAACATGTTGAAA
39518 ACATT-
65 ACATTC
* ** ** *
39523 TATATTATAGTTTTT-AAAACGTTTTGGGAAAATTTATATAATCTTTTTTGAAAACATGTTGGAA
1 TATATTATAGTTTTTGAAAACATTTT-GGAAAACATATATAATCAGTTTTGAAAACATGTTGAAA
39587 ACATTC
65 ACATTC
39593 GTATATTATA
1 -TATATTATA
39603 TAGTTTTAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
67 9 0.14
68 22 0.33
69 26 0.39
71 9 0.14
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.44
Consensus pattern (70 bp):
TATATTATAGTTTTTGAAAACATTTTGGAAAACATATATAATCAGTTTTGAAAACATGTTGAAAA
CATTC
Found at i:39680 original size:3 final size:3
Alignment explanation
Indices: 39672--39709 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
39662 TGTATATATA
39672 TAT TAT TAT TAT TATT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT T
39710 TTTCATTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:50048 original size:29 final size:29
Alignment explanation
Indices: 50005--50087 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 29
49995 CTTACCTAAC
*
50005 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
50035 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
* *
50064 TAAATGGTGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
50088 ATTTAGTTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 44 0.92
30 4 0.08
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:54703 original size:29 final size:29
Alignment explanation
Indices: 54660--54740 Score: 126
Period size: 29 Copynumber: 2.8 Consensus size: 29
54650 CTTACCTAAC
*
54660 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
54690 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
54719 TAAATGATGTAAGTAATGACAT
1 TAAATGATGTAAGCAATGACAT
54741 AAATTTAGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:56411 original size:17 final size:17
Alignment explanation
Indices: 56389--56427 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
56379 ATCGTTAATC
56389 GTTGATGGTTATGGTTT
1 GTTGATGGTTATGGTTT
56406 GTTGATGGTTATGGTTT
1 GTTGATGGTTATGGTTT
56423 GTTGA
1 GTTGA
56428 AGTTTATTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.13, C:0.00, G:0.36, T:0.51
Consensus pattern (17 bp):
GTTGATGGTTATGGTTT
Found at i:56434 original size:17 final size:17
Alignment explanation
Indices: 56389--56434 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
56379 ATCGTTAATC
*
56389 GTTGATGGTTATGGTTT
1 GTTGAAGGTTATGGTTT
*
56406 GTTGATGGTTATGGTTT
1 GTTGAAGGTTATGGTTT
*
56423 GTTGAAGTTTAT
1 GTTGAAGGTTAT
56435 TTCTTCTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.33, T:0.52
Consensus pattern (17 bp):
GTTGAAGGTTATGGTTT
Found at i:63394 original size:23 final size:22
Alignment explanation
Indices: 63368--63441 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 22
63358 CACCACCTCG
63368 TATAATTGCACCGAAGTGCCACA
1 TATAA-TGCACCGAAGTGCCACA
* * *
63391 TATAAATGCACCGGAGTGCCGCG
1 TAT-AATGCACCGAAGTGCCACA
* * *
63414 TAGAATGCACCGTAGTGCCATA
1 TATAATGCACCGAAGTGCCACA
63436 -ATAATG
1 TATAATG
63442 TCCATAAGGA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
21 5 0.12
22 15 0.37
23 19 0.46
24 2 0.05
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (22 bp):
TATAATGCACCGAAGTGCCACA
Found at i:63624 original size:100 final size:102
Alignment explanation
Indices: 63447--63655 Score: 325
Period size: 100 Copynumber: 2.1 Consensus size: 102
63437 TAATGTCCAT
* ** *
63447 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAGTATGTGTCTCACCAG
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAAGATCAGTATGAGTCTCACCAG
63512 ACTTCACACATGTTCAAAAGAATACATATATGT-CCG
66 ACTTCACACATGTTCAAAAGAATACATATATGTCCCG
*
63548 AAGGACCACATATCATTCCTT-A-AATCATATACATATGCCAAAGATCAAGTATGAGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAAGATC-AGTATGAGTCTCACCA
* *
63611 GACTTCACGCATGTTCCAAAGAATACATATATGTCCCG
65 GACTTCACACATGTTCAAAAGAATACATATATGTCCCG
63649 AAGGACC
1 AAGGACC
63656 GCGTAGACCC
Statistics
Matches: 99, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
99 20 0.20
100 48 0.48
101 31 0.31
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (102 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAAGATCAGTATGAGTCTCACCAG
ACTTCACACATGTTCAAAAGAATACATATATGTCCCG
Done.