Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001066.1 Hibiscus syriacus cultivar Beakdansim tig00002112_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: 58874
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:5363 original size:21 final size:23
Alignment explanation
Indices: 5326--5451 Score: 136
Period size: 23 Copynumber: 5.7 Consensus size: 23
5316 TCGAGGGTTA
* *
5326 TATGTGGTCCTTCGG-G-ATAAT
1 TATGTGGTCCTTCGGTGCAAAAC
*
5347 TATGTGGTCCTTTGG-G-ACAAA-
1 TATGTGGTCCTTCGGTGCA-AAAC
*
5368 TATGTGGTACTTCGGTGCAAAAC
1 TATGTGGTCCTTCGGTGCAAAAC
*
5391 TATGTGGTACTTCGGTGCAAAAC
1 TATGTGGTCCTTCGGTGCAAAAC
* * *
5414 TATGTGGTACTTAGGTGCAAACC
1 TATGTGGTCCTTCGGTGCAAAAC
5437 TATGTGGTCCTTCGG
1 TATGTGGTCCTTCGG
5452 GATAATTATG
Statistics
Matches: 93, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
21 29 0.31
22 6 0.06
23 58 0.62
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (23 bp):
TATGTGGTCCTTCGGTGCAAAAC
Found at i:5421 original size:46 final size:44
Alignment explanation
Indices: 5347--5478 Score: 149
Period size: 46 Copynumber: 3.0 Consensus size: 44
5337 TCGGGATAAT
* * *
5347 TATGTGGTCCTTTGGGACAAA-TATGTGGTACTTCGGTGCAAAAC
1 TATGTGGTACTTCGGGA-AAACTATGTGGTACTTAGGTGCAAAAC
*
5391 TATGTGGTACTTCGGTGCAAAACTATGTGGTACTTAGGTGCAAACC
1 TATGTGGTACTTCGG-G-AAAACTATGTGGTACTTAGGTGCAAAAC
* * * * *
5437 TATGTGGTCCTTCGGGATAATTATGTGGCACTTTGGTGCAAA
1 TATGTGGTACTTCGGGAAAACTATGTGGTACTTAGGTGCAAA
5479 TTACGAGCTG
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
44 35 0.46
45 5 0.07
46 36 0.47
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (44 bp):
TATGTGGTACTTCGGGAAAACTATGTGGTACTTAGGTGCAAAAC
Found at i:5463 original size:21 final size:23
Alignment explanation
Indices: 5368--5478 Score: 145
Period size: 23 Copynumber: 4.9 Consensus size: 23
5358 TTGGGACAAA
5368 TATGTGGTACTTCGGTGCAAAAC
1 TATGTGGTACTTCGGTGCAAAAC
5391 TATGTGGTACTTCGGTGCAAAAC
1 TATGTGGTACTTCGGTGCAAAAC
* *
5414 TATGTGGTACTTAGGTGCAAACC
1 TATGTGGTACTTCGGTGCAAAAC
* * *
5437 TATGTGGTCCTTCGG-G-ATAAT
1 TATGTGGTACTTCGGTGCAAAAC
* *
5458 TATGTGGCACTTTGGTGCAAA
1 TATGTGGTACTTCGGTGCAAA
5479 TTACGAGCTG
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
21 14 0.19
22 2 0.03
23 59 0.79
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (23 bp):
TATGTGGTACTTCGGTGCAAAAC
Found at i:16687 original size:37 final size:37
Alignment explanation
Indices: 16614--16688 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
16604 GTTGAAAAAT
* *
16614 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
16651 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
16688 A
1 A
16689 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:23932 original size:15 final size:15
Alignment explanation
Indices: 23912--23943 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
23902 AAAATCTTTC
*
23912 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTGGAT
23927 TTTCCCGTTCTGGAT
1 TTTCCCGTTCTGGAT
23942 TT
1 TT
23944 CGATCTGCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.25, G:0.16, T:0.53
Consensus pattern (15 bp):
TTTCCCGTTCTGGAT
Found at i:33175 original size:10 final size:10
Alignment explanation
Indices: 33160--33215 Score: 58
Period size: 10 Copynumber: 5.2 Consensus size: 10
33150 TCGTGAACGC
33160 TCGGTTATGT
1 TCGGTTATGT
33170 TCGGTTATGT
1 TCGGTTATGT
*
33180 TCGTTTATGT
1 TCGGTTATGT
33190 TCGTTCGATTATGT
1 TCG---G-TTATGT
*
33204 TCGTTTATGT
1 TCGGTTATGT
33214 TC
1 TC
33216 ATTCATTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 30 0.77
14 9 0.23
ACGTcount: A:0.11, C:0.12, G:0.23, T:0.54
Consensus pattern (10 bp):
TCGGTTATGT
Found at i:33201 original size:14 final size:14
Alignment explanation
Indices: 33178--33208 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
33168 GTTCGGTTAT
*
33178 GTTCGTTTATGTTC
1 GTTCGATTATGTTC
33192 GTTCGATTATGTTC
1 GTTCGATTATGTTC
33206 GTT
1 GTT
33209 TATGTTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.13, G:0.23, T:0.55
Consensus pattern (14 bp):
GTTCGATTATGTTC
Found at i:33201 original size:24 final size:24
Alignment explanation
Indices: 33168--33228 Score: 88
Period size: 24 Copynumber: 2.5 Consensus size: 24
33158 GCTCGGTTAT
*
33168 GTTCGGTTATGTTCGTTTATGTTC
1 GTTCGATTATGTTCGTTTATGTTC
33192 GTTCGATTATGTTCGTTTATGTTC
1 GTTCGATTATGTTCGTTTATGTTC
*
33216 ATTC-ATTTATGTT
1 GTTCGA-TTATGTT
33229 TAACTCAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
23 1 0.03
24 33 0.97
ACGTcount: A:0.13, C:0.11, G:0.20, T:0.56
Consensus pattern (24 bp):
GTTCGATTATGTTCGTTTATGTTC
Found at i:34328 original size:16 final size:16
Alignment explanation
Indices: 34309--34381 Score: 82
Period size: 16 Copynumber: 4.7 Consensus size: 16
34299 CCAATGTTTA
34309 TGTTGATTTATGTTCG
1 TGTTGATTTATGTTCG
*
34325 TGTTCATTTATGTTCG
1 TGTTGATTTATGTTCG
*
34341 TGTTCG-TTTAAGTTCG
1 TGTT-GATTTATGTTCG
34357 TGTTCG-TTTATGTTCG
1 TGTT-GATTTATGTTCG
34373 T-TT-ATTTAT
1 TGTTGATTTAT
34382 TAAATGAACG
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
14 5 0.10
15 2 0.04
16 44 0.86
ACGTcount: A:0.12, C:0.10, G:0.21, T:0.58
Consensus pattern (16 bp):
TGTTGATTTATGTTCG
Found at i:34463 original size:16 final size:16
Alignment explanation
Indices: 34442--34474 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
34432 AAAAAAAATT
34442 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
34458 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
34474 T
1 T
34475 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:38078 original size:25 final size:26
Alignment explanation
Indices: 38036--38088 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
38026 ACTAAGTGCA
*
38036 TATGGTGGGTACGACCTTATGTGTAT
1 TATGGTGGGTACGACCTTATATGTAT
* *
38062 TATGGT-GGTATGGCCTTATATGTAT
1 TATGGTGGGTACGACCTTATATGTAT
38087 TA
1 TA
38089 GCACTTCGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 18 0.75
26 6 0.25
ACGTcount: A:0.21, C:0.09, G:0.28, T:0.42
Consensus pattern (26 bp):
TATGGTGGGTACGACCTTATATGTAT
Found at i:40992 original size:35 final size:34
Alignment explanation
Indices: 40895--40988 Score: 111
Period size: 35 Copynumber: 2.7 Consensus size: 34
40885 CCATTAGTAT
*
40895 ATATATATATATATA-G-TTTGGAATCATTTTGAAA
1 ATATATA-ATATATAGGTTTTGAAAT-ATTTTGAAA
* *
40929 ATTATATAATATATGGGTTTTTTAAATATTTTGAAA
1 A-TATATAATATATAGG-TTTTGAAATATTTTGAAA
40965 ATATATAATATATAGGTTTTGAAA
1 ATATATAATATATAGGTTTTGAAA
40989 ATATATATTA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
34 14 0.27
35 21 0.41
36 10 0.20
37 6 0.12
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.46
Consensus pattern (34 bp):
ATATATAATATATAGGTTTTGAAATATTTTGAAA
Found at i:41010 original size:23 final size:24
Alignment explanation
Indices: 40957--41015 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
40947 TTTTTAAATA
40957 TTTTGAAAATATATAATATATAGG
1 TTTTGAAAATATATAATATATAGG
* *
40981 TTTTGAAAATATATATTATAT-TG
1 TTTTGAAAATATATAATATATAGG
41004 TTTTGAAAATAT
1 TTTTGAAAATAT
41016 TTTGAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
23 13 0.39
24 20 0.61
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.47
Consensus pattern (24 bp):
TTTTGAAAATATATAATATATAGG
Found at i:41019 original size:58 final size:62
Alignment explanation
Indices: 40921--41049 Score: 176
Period size: 60 Copynumber: 2.1 Consensus size: 62
40911 TTTGGAATCA
**
40921 TTTTGAAAATTATATAATATATGGGTTTTTTAAATATTTTG-AAA-ATATATAATATATAGG
1 TTTTGAAAATTATATAATATATGGGTTTTGAAAATATTTTGAAAATATATATAATATATAGG
* * *
40981 TTTTGAAAA-TATATATTATAT-TGTTTTGAAAATATTTTGAAAATATATATAATATATAGT
1 TTTTGAAAATTATATAATATATGGGTTTTGAAAATATTTTGAAAATATATATAATATATAGG
*
41041 TTTTAAAAA
1 TTTTGAAAA
41050 CATTTTTGAA
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
58 15 0.25
59 14 0.23
60 32 0.52
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.47
Consensus pattern (62 bp):
TTTTGAAAATTATATAATATATGGGTTTTGAAAATATTTTGAAAATATATATAATATATAGG
Found at i:41037 original size:36 final size:37
Alignment explanation
Indices: 40980--41266 Score: 256
Period size: 36 Copynumber: 7.9 Consensus size: 37
40970 TAATATATAG
*
40980 GTTTTGAAAATATATAT-TATATTGTTTTGAAAA-TA
1 GTTTTGAAAATATATATATATATAGTTTTGAAAATTA
* **
41015 -TTTTGAAAATATATATAATATATAGTTTTTAAAAACA
1 GTTTTGAAAATATATAT-ATATATAGTTTTGAAAATTA
* *
41052 TTTTTGAAAAACATATATATTATATAGTTTTGAAAATTA
1 GTTTTG-AAAATATATATA-TATATAGTTTTGAAAATTA
* *
41091 GTTTT--TAA-A-A-A-ACATATAGTTTTGAAAATTA
1 GTTTTGAAAATATATATATATATAGTTTTGAAAATTA
* * *
41122 GTTTTTAAAATATTTATAT-TATAATTTTGAAAATTA
1 GTTTTGAAAATATATATATATATAGTTTTGAAAATTA
*
41158 GTTTTTAAAAATATATATATTATATAGTTTTGAAAATTA
1 G-TTTTGAAAATATATATA-TATATAGTTTTGAAAATTA
* * *
41197 TTTTTTAAAATATATAT-TATATGGTTTTGAAAATTA
1 GTTTTGAAAATATATATATATATAGTTTTGAAAATTA
* * ** * *
41233 TTTTTTAAAGCATATAT-TGTATAGTTTTAAAAAT
1 GTTTTGAAAATATATATATATATAGTTTTGAAAAT
41267 GTTTTTCATT
Statistics
Matches: 212, Mismatches: 25, Indels: 29
0.80 0.09 0.11
Matches are distributed among these distances:
31 23 0.11
32 1 0.00
33 3 0.01
34 18 0.08
35 1 0.00
36 81 0.38
37 17 0.08
38 22 0.10
39 46 0.22
ACGTcount: A:0.43, C:0.01, G:0.08, T:0.48
Consensus pattern (37 bp):
GTTTTGAAAATATATATATATATAGTTTTGAAAATTA
Found at i:41078 original size:39 final size:39
Alignment explanation
Indices: 40989--41108 Score: 138
Period size: 39 Copynumber: 3.1 Consensus size: 39
40979 GGTTTTGAAA
* * *
40989 ATATATATTATATTG-TTTTGAAAATA-TTTTG-AAAAT
1 ATATATATTATATAGTTTTTAAAAATATTTTTGAAAAAC
* *
41025 ATATATAATATATAGTTTTTAAAAACATTTTTGAAAAAC
1 ATATATATTATATAGTTTTTAAAAATATTTTTGAAAAAC
* * *
41064 ATATATATTATATAGTTTTGAAAATTAGTTTTTAAAAAAC
1 ATATATATTATATAGTTTTTAAAAATA-TTTTTGAAAAAC
41104 ATATA
1 ATATA
41109 GTTTTGAAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
36 13 0.19
37 9 0.13
38 5 0.07
39 27 0.39
40 16 0.23
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.45
Consensus pattern (39 bp):
ATATATATTATATAGTTTTTAAAAATATTTTTGAAAAAC
Found at i:41108 original size:31 final size:32
Alignment explanation
Indices: 41073--41176 Score: 138
Period size: 31 Copynumber: 3.2 Consensus size: 32
41063 CATATATATT
41073 ATATAGTTTTGAAAATTAGTTTTTAAAAA-AC
1 ATATAGTTTTGAAAATTAGTTTTTAAAAATAC
*
41104 ATATAGTTTTGAAAATTAGTTTTTAAAATATTTAT
1 ATATAGTTTTGAAAATTAGTTTTTAAAA-A--TAC
* *
41139 ATTATAATTTTGAAAATTAGTTTTTAAAAATAT
1 A-TATAGTTTTGAAAATTAGTTTTTAAAAATAC
41172 ATATA
1 ATATA
41177 TTATATAGTT
Statistics
Matches: 66, Mismatches: 2, Indels: 9
0.86 0.03 0.12
Matches are distributed among these distances:
31 28 0.42
32 5 0.08
33 4 0.06
35 3 0.05
36 26 0.39
ACGTcount: A:0.44, C:0.01, G:0.08, T:0.47
Consensus pattern (32 bp):
ATATAGTTTTGAAAATTAGTTTTTAAAAATAC
Found at i:41113 original size:106 final size:106
Alignment explanation
Indices: 40998--41206 Score: 289
Period size: 106 Copynumber: 2.0 Consensus size: 106
40988 AATATATATT
* * *
40998 ATATTGTTTTGAAAA-TA-TTTTGAAAATATATATAATATATAGTTTTTAAAAACA-TTTTTGAA
1 ATATAGTTTTGAAAATTAGTTTTGAAAATATATAT-AT-TATAATTTTGAAAAACAGTTTTT-AA
41060 AAACATATATATTATATAGTTTTGAAAATTAGTTTTTAAAAAAC
63 AAACATATATATTATATAGTTTTGAAAATTAGTTTTTAAAAAAC
* * **
41104 ATATAGTTTTGAAAATTAGTTTTTAAAATATTTATATTATAATTTTGAAAATTAGTTTTTAAAAA
1 ATATAGTTTTGAAAATTAGTTTTGAAAATATATATATTATAATTTTGAAAAACAGTTTTTAAAAA
* *
41169 TATATATATTATATAGTTTTGAAAATTATTTTTTAAAA
66 CATATATATTATATAGTTTTGAAAATTAGTTTTTAAAA
41207 TATATATTAT
Statistics
Matches: 91, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
106 68 0.75
107 9 0.10
108 14 0.15
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.47
Consensus pattern (106 bp):
ATATAGTTTTGAAAATTAGTTTTGAAAATATATATATTATAATTTTGAAAAACAGTTTTTAAAAA
CATATATATTATATAGTTTTGAAAATTAGTTTTTAAAAAAC
Found at i:41167 original size:13 final size:13
Alignment explanation
Indices: 41076--41207 Score: 56
Period size: 13 Copynumber: 10.0 Consensus size: 13
41066 ATATATTATA
*
41076 TAGTTTTGAAAAT
1 TAGTTTTTAAAAT
41089 TAGTTTTTAAAAAACAT
1 TAGTTTTT---AAA-AT
*
41106 ATAGTTTTGAAAAT
1 -TAGTTTTTAAAAT
41120 TAGTTTTTAAAA-
1 TAGTTTTTAAAAT
* **
41132 TA-TTTATATTA-
1 TAGTTTTTAAAAT
* *
41143 TAATTTTGAAAAT
1 TAGTTTTTAAAAT
*
41156 TAGTTTTTAAAAA
1 TAGTTTTTAAAAT
* * **
41169 TA-TATATATTAT
1 TAGTTTTTAAAAT
*
41181 ATAGTTTTGAAAAT
1 -TAGTTTTTAAAAT
*
41195 TATTTTTTAAAAT
1 TAGTTTTTAAAAT
41208 ATATATTATA
Statistics
Matches: 85, Mismatches: 25, Indels: 18
0.66 0.20 0.14
Matches are distributed among these distances:
11 8 0.09
12 12 0.14
13 43 0.51
14 7 0.08
15 3 0.04
16 3 0.04
17 2 0.02
18 7 0.08
ACGTcount: A:0.42, C:0.01, G:0.08, T:0.49
Consensus pattern (13 bp):
TAGTTTTTAAAAT
Found at i:41283 original size:4 final size:4
Alignment explanation
Indices: 41274--41342 Score: 104
Period size: 4 Copynumber: 17.0 Consensus size: 4
41264 AATGTTTTTC
*
41274 ATTT ATTT ATTT ATTT ATCT ATTT ATTT ATTTT ATTT CATTT A-TT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT A-TTT ATTT -ATTT ATTT ATTT
41323 ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT
41343 TAGGTCTATT
Statistics
Matches: 60, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
3 3 0.05
4 49 0.82
5 8 0.13
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:46892 original size:95 final size:95
Alignment explanation
Indices: 46716--46897 Score: 260
Period size: 95 Copynumber: 1.9 Consensus size: 95
46706 ATATTATTTA
* * * * *
46716 TATACAATAAAACTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCTCGGCTTTATGAATAAT
1 TATACAATAAAACTTGAGCTATCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTATGAATAAG
* *
46781 ATTAAGCTAGCCTGATAAAGGTGATTATAC
66 ATTAAGCTAACATGATAAAGGTGATTATAC
*
46811 TATACAATAAAACTTGAGCTATCCCTCTA-AGGCAATTGGTTAAACGCCCCAGCTTTATGGATAA
1 TATACAATAAAACTTGAGCTATCCCTCTAGA-GCAATTGGTTAAACGCCCCAGCTTTATGAATAA
46875 GATTCAA-CTAACATGATAAAGGT
65 GATT-AAGCTAACATGATAAAGGT
46898 ATTTACATAT
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
94 1 0.01
95 74 0.96
96 2 0.03
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (95 bp):
TATACAATAAAACTTGAGCTATCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTATGAATAAG
ATTAAGCTAACATGATAAAGGTGATTATAC
Found at i:48317 original size:36 final size:37
Alignment explanation
Indices: 48260--48340 Score: 119
Period size: 36 Copynumber: 2.2 Consensus size: 37
48250 TAATTTACTC
* * *
48260 AAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTT
1 AAAACAAAGTTTTATCTCTCTTGAGACAGTTCCCCTT
48297 AAAACAAA-TTTTATCTCTCTTGAGACAGTTCCCCTT
1 AAAACAAAGTTTTATCTCTCTTGAGACAGTTCCCCTT
*
48333 TAAACAAA
1 AAAACAAA
48341 ATCTTTGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 32 0.80
37 8 0.20
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (37 bp):
AAAACAAAGTTTTATCTCTCTTGAGACAGTTCCCCTT
Found at i:48410 original size:36 final size:35
Alignment explanation
Indices: 48355--48474 Score: 129
Period size: 36 Copynumber: 3.4 Consensus size: 35
48345 TTGAATCTGT
*
48355 TTTC-CTTGAAACAAATTTTGTCTCCCTTGAGACAG
1 TTTCTCTT-AAACAAATTTTGTCTCTCTTGAGACAG
* * * *
48390 TTTCTTTTAAAACAAATTTTGTCTCTCTTAATACAT
1 TTTCTCTT-AAACAAATTTTGTCTCTCTTGAGACAG
*
48426 TTTCTCTT-AA-AATTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTAAACAAATTTTGTCTCTCTTGAGACAG
*
48459 TTTCCCTTGAAACAAA
1 TTTCTCTT-AAACAAA
48475 AACTTTGAAT
Statistics
Matches: 68, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
33 26 0.38
34 2 0.03
35 6 0.09
36 34 0.50
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.43
Consensus pattern (35 bp):
TTTCTCTTAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:48472 original size:134 final size:138
Alignment explanation
Indices: 48260--48528 Score: 402
Period size: 134 Copynumber: 2.0 Consensus size: 138
48250 TAATTTACTC
*
48260 AAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAATTTTATCTCTCTTGAGACAG
1 AAAACAAAGTTTTGTCTCTCTTAAGACAGTTTCTCTT-AAACAAATTTTATCTCTCTTGAGACAG
* *
48325 TTCCCCTTTAAACAAAATCTTTGAATCTGTTTTCCTTGAAACAAA-TTTTGTCTCCCTTGAGACA
65 TTCCCCTTGAAACAAAAACTTTGAATCTGTTTTCCTTGAAACAAAGTTTTGTCTCCCTTGAGACA
*
48389 GTTTCTTTT
130 ATTTCTTTT
* * * *
48398 AAAACAAA-TTTTGTCTCTCTTAATACATTTTCTCTT-AA-AATTTTTGTCTCTCTTGAGACAGT
1 AAAACAAAGTTTTGTCTCTCTTAAGACAGTTTCTCTTAAACAAATTTTATCTCTCTTGAGACAGT
* * *
48460 TTCCCTTGAAACAAAAACTTTGAATTTGTTTTCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAA
66 TCCCCTTGAAACAAAAACTTTGAATCTGTTTTCCTTGAAACAAAGTTTTGTCTCCCTTGAGACAA
48525 TTTC
131 TTTC
48529 CCATGAAACA
Statistics
Matches: 119, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
134 62 0.52
135 24 0.20
137 25 0.21
138 8 0.07
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (138 bp):
AAAACAAAGTTTTGTCTCTCTTAAGACAGTTTCTCTTAAACAAATTTTATCTCTCTTGAGACAGT
TCCCCTTGAAACAAAAACTTTGAATCTGTTTTCCTTGAAACAAAGTTTTGTCTCCCTTGAGACAA
TTTCTTTT
Found at i:48623 original size:36 final size:36
Alignment explanation
Indices: 48555--48675 Score: 135
Period size: 36 Copynumber: 3.4 Consensus size: 36
48545 TTGAATTAGT
* *
48555 TTTC-CTTGAAACAAAGTTTTGTCTCTCTTGAGATAG
1 TTTCTCTTGAAACAAA-TTTTTTCTCTCTTGAGACAG
* *
48591 TTTCTCTTAAAACAAATTTTTTCTCTCTTGAGACAT
1 TTTCTCTTGAAACAAATTTTTTCTCTCTTGAGACAG
*
48627 TTTCTCTT---A-AAATTTTTGTCCCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTT-TCTCTCTTGAGACAG
*
48660 TTTCCCTTGAAACAAA
1 TTTCTCTTGAAACAAA
48676 AACTTTGAAT
Statistics
Matches: 72, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
32 8 0.11
33 21 0.29
36 30 0.42
37 13 0.18
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.43
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTTTCTCTCTTGAGACAG
Found at i:48654 original size:201 final size:200
Alignment explanation
Indices: 48289--49043 Score: 745
Period size: 201 Copynumber: 3.7 Consensus size: 200
48279 CTTGAGACAG
* * * * *
48289 TTTCTCTTAAAACAAA-TTTTATCTCTCTTGAGACAGTTCCCCTTTAAACAAAATCTTTGAATCT
1 TTTC-CTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCATGAAACAAAATCTTTGAATCT
*
48353 GTTTTCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCT
65 GTTTTCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTCT
* *
48418 TAATACATTTTCTCTTAAAATTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAACTTTGA
130 TAAGACATTTTCTCTTAAAATTTTTGTCCCTCTTGAGACAGTTTCCCTTGAAACAAAAACTTTGA
48483 ATTTGT
195 ATTTGT
*
48489 TTTCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCCCATGAAACAAAATCTTTGAAT-TA
1 TTTCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCATGAAACAAAATCTTTGAATCT-
* * *
48553 GTTTTCCTTGAAACAAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTAAAACAAATTTTTTCTCTC
65 GTTTTCCTTGAAACAAA-TTTTGTCTCCCTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTC
*
48618 TTGAGACATTTTCTCTTAAAATTTTTGTCCCTCTTGAGACAGTTTCCCTTGAAACAAAAACTTTG
129 TTAAGACATTTTCTCTTAAAATTTTTGTCCCTCTTGAGACAGTTTCCCTTGAAACAAAAACTTTG
48683 AATTTGT
194 AATTTGT
* * * * **
48690 TTTCCTTGAAGCAAAGTTTTGTCTCTCTTGAGACAGTTTCTC-TTAAAAAAAAT-TTTGTCTCTC
1 TTTCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCATGAAACAAAATCTTTG--AATC
* * * * *
48753 TTGAGACATTTTCTCTTAAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCT
64 -T--G---TTTTC-CTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTAAAAC-AAAT-T
** * * *
48818 TTG--AATC-T--G---TTTTC-CTTAAAACAAATTTCGTCTCC-CTTGAGACAGTTTCTCTT-A
120 TTGTCTCTCTTAAGACATTTTCTCTT--AA-AATTTTTGTC-CCTCTTGAGACAGTTTCCCTTGA
* * **
48872 AA-ACAAATTTTGTCTCTCTTGATACAT
181 AACAAAAACTTTG--AAT-TTG-----T
* * ***
48899 TTTCTCTTAAAATAAA-TTTTGTCTCTCTTGAGACAGTTTCATTTGAAACAAAATCTTTGAATCT
1 TTTC-CTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCATGAAACAAAATCTTTGAATCT
* * * *
48963 GTTTTCCTTAAAACAAATTTCGTCTCCCTTGAGATAGTTTCTTTTAAAACAAATTTTGTCTCTCT
65 GTTTTCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTCT
*
49028 TGAGACAATTTT-TCTT
130 TAAGAC-ATTTTCTCTT
49044 GAAACAAATC
Statistics
Matches: 463, Mismatches: 53, Indels: 69
0.79 0.09 0.12
Matches are distributed among these distances:
199 15 0.03
200 78 0.17
201 169 0.37
202 44 0.10
203 33 0.07
204 8 0.02
205 1 0.00
206 2 0.00
207 37 0.08
208 14 0.03
209 41 0.09
210 17 0.04
211 4 0.01
ACGTcount: A:0.28, C:0.19, G:0.10, T:0.43
Consensus pattern (200 bp):
TTTCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCATGAAACAAAATCTTTGAATCTG
TTTTCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTCTT
AAGACATTTTCTCTTAAAATTTTTGTCCCTCTTGAGACAGTTTCCCTTGAAACAAAAACTTTGAA
TTTGT
Found at i:48760 original size:36 final size:36
Alignment explanation
Indices: 48571--48682 Score: 113
Period size: 33 Copynumber: 3.1 Consensus size: 36
48561 TGAAACAAAG
* *
48571 TTTTGTCTCTCTTGAGATAGTTTCTCTTAAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTAAAAAAAA
* * *
48607 TTTTTTCTCTCTTGAGACATTTTCTCTT---AAAAT
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTAAAAAAAA
* *
48640 TTTTGTCCCTCTTGAGACAGTTTCCCTTGAAACAAAAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTT-AAA-AAAAA
*
48678 CTTTG
1 TTTTG
48683 AATTTGTTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
33 27 0.45
36 25 0.42
38 8 0.13
ACGTcount: A:0.25, C:0.20, G:0.11, T:0.45
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCTCTTAAAAAAAA
Found at i:48766 original size:36 final size:37
Alignment explanation
Indices: 48706--48820 Score: 171
Period size: 36 Copynumber: 3.1 Consensus size: 37
48696 TGAAGCAAAG
48706 TTTTGTCTCTCTTGAGACAGTTTCTCTT-AAAAAAAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAAAA
* *
48742 TTTTGTCTCTCTTGAGACATTTTCTCTT-AAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAAAA
* *
48778 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAAAA
48815 TCTTTG
1 T-TTTG
48821 AATCTGTTTT
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
36 60 0.85
37 7 0.10
38 4 0.06
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.43
Consensus pattern (37 bp):
TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAAAA
Found at i:48879 original size:36 final size:36
Alignment explanation
Indices: 48828--49057 Score: 212
Period size: 36 Copynumber: 6.6 Consensus size: 36
48818 TTGAATCTGT
* *
48828 TTTC-CTTAAAACAAATTTCGTCTCCCTTGAGACAG
1 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
* *
48863 TTTCTCTTAAAACAAATTTTGTCTCTCTTGATACAT
1 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
*
48899 TTTCTCTTAAAATAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
* * *
48935 TTTCAT-TTGAAACAAA------ATCT-TTGA-ATCTG
1 TTTC-TCTTAAAACAAATTTTGTCTCTCTTGAGA-CAG
* * *
48964 TTT-TCCTTAAAACAAATTTCGTCTCCCTTGAGATAG
1 TTTCT-CTTAAAACAAATTTTGTCTCTCTTGAGACAG
* *
49000 TTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACAA
1 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
* *
49036 TTTTTCTTGAAACAAATCTTTG
1 TTTCTCTTAAAACAAAT-TTTG
49058 AATCTGTTTT
Statistics
Matches: 156, Mismatches: 24, Indels: 28
0.75 0.12 0.13
Matches are distributed among these distances:
27 1 0.01
28 1 0.01
29 18 0.12
30 3 0.02
35 6 0.04
36 120 0.77
37 7 0.04
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.43
Consensus pattern (36 bp):
TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:48903 original size:137 final size:138
Alignment explanation
Indices: 48488--49057 Score: 832
Period size: 137 Copynumber: 4.2 Consensus size: 138
48478 TTTGAATTTG
* * * *
48488 TTTTC-CTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCCCATGAAACAAAATCTTTGAAT-
1 TTTTCTCTTAAAATAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATC
* * * * *
48551 TAGTTTTCCTTGAAACAAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTAAAACAAATTTTTTCTC
65 T-GTTTTCCTTAAAACAAAGTTTCGTCTCCCTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTC
48616 TCTTGAGACA
129 TCTTGAGACA
* * *
48626 TTTTCTCTTAAAAT---TTTTGTCCCTCTTGAGACAGTTTCCCTTGAAACAAAAACTTTGAATTT
1 TTTTCTCTTAAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCT
* * * * *
48688 GTTTTCCTTGAAGCAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAAAAAATTTTGTCTCTC
66 GTTTTCCTTAAAACAAAGTTTCGTCTCCCTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTC
48753 TTGAGACA
131 TTGAGACA
48761 TTTTCTCTTAAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCT
1 TTTTCTCTTAAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCT
48826 GTTTTCCTTAAAACAAA-TTTCGTCTCCCTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTC
66 GTTTTCCTTAAAACAAAGTTTCGTCTCCCTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTC
*
48890 TTGATACA
131 TTGAGACA
**
48898 TTTTCTCTTAAAATAAATTTTGTCTCTCTTGAGACAGTTTCATTTGAAACAAAATCTTTGAATCT
1 TTTTCTCTTAAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCT
* *
48963 GTTTTCCTTAAAACAAA-TTTCGTCTCCCTTGAGATAGTTTCTTTTAAAACAAATTTTGTCTCTC
66 GTTTTCCTTAAAACAAAGTTTCGTCTCCCTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTC
49027 TTGAGACAA
131 TTGAGAC-A
* *
49036 TTTT-TCTTGAAACAAATCTTTG
1 TTTTCTCTTAAAATAAAT-TTTG
49058 AATCTGTTTT
Statistics
Matches: 399, Mismatches: 26, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
135 125 0.31
136 1 0.00
137 193 0.48
138 74 0.19
139 6 0.02
ACGTcount: A:0.28, C:0.18, G:0.11, T:0.42
Consensus pattern (138 bp):
TTTTCTCTTAAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCT
GTTTTCCTTAAAACAAAGTTTCGTCTCCCTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTC
TTGAGACA
Found at i:49102 original size:100 final size:101
Alignment explanation
Indices: 48863--49107 Score: 350
Period size: 101 Copynumber: 2.4 Consensus size: 101
48853 CTTGAGACAG
* * * * *
48863 TTTCTCTTAAAACAAATTTTGTCTCTCTTGATACATTTTCTCTTAAAATAAATTTTGTCTCTCTT
1 TTTC-CTTAAAACAAATTTAGTCTCTCTTGAGATAGTTTCTCTTAAAACAAATTTTGTCTCTCTT
*
48928 GAGACAGTTTCATTTGAAACAAAATCTTTGAATCTGT
65 GAGACAATTTCATTTGAAACAAAATCTTTGAATCTGT
* * *
48965 TTTCCTTAAAACAAATTTCGTCTCCCTTGAGATAGTTTCTTTTAAAACAAATTTTGTCTCTCTTG
1 TTTCCTTAAAACAAATTTAGTCTCTCTTGAGATAGTTTCTCTTAAAACAAATTTTGTCTCTCTTG
*
49030 AGACAATTT-TTCTTGAAAC-AAATCTTTGAATCTGT
66 AGACAATTTCAT-TTGAAACAAAATCTTTGAATCTGT
* *
49065 TTTCCTTTAAACAAATTTAGTCTCTCTCGAGATAGTTTCTCTT
1 TTTCCTTAAAACAAATTTAGTCTCTCTTGAGATAGTTTCTCTT
49108 GAAGCACCAA
Statistics
Matches: 128, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
100 55 0.43
101 69 0.54
102 4 0.03
ACGTcount: A:0.28, C:0.18, G:0.09, T:0.44
Consensus pattern (101 bp):
TTTCCTTAAAACAAATTTAGTCTCTCTTGAGATAGTTTCTCTTAAAACAAATTTTGTCTCTCTTG
AGACAATTTCATTTGAAACAAAATCTTTGAATCTGT
Found at i:49201 original size:34 final size:35
Alignment explanation
Indices: 49124--49249 Score: 141
Period size: 34 Copynumber: 3.6 Consensus size: 35
49114 CCAATATTTA
* *
49124 AAATTGTTTCTCTTGAAACAAAAAAAAAATCTTGGG
1 AAATTGTTTCTCTTGAAACACAAAAAAAA-CTTGTG
* **
49160 ACA--GTTTCTCTTGAAACACAAAAAAGCCTT-TG
1 AAATTGTTTCTCTTGAAACACAAAAAAAACTTGTG
*
49192 AAATTGTTTCTCTTTAAACACACAAAAAAAACTTGTG
1 AAATTGTTTCTC-TTGAA-ACACAAAAAAAACTTGTG
*
49229 AAAATGTTTCTCTTGAAACAC
1 AAATTGTTTCTCTTGAAACAC
49250 TGAATCTTCA
Statistics
Matches: 74, Mismatches: 11, Indels: 11
0.77 0.11 0.11
Matches are distributed among these distances:
32 3 0.04
33 3 0.04
34 28 0.38
35 8 0.11
36 19 0.26
37 13 0.18
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (35 bp):
AAATTGTTTCTCTTGAAACACAAAAAAAACTTGTG
Found at i:49935 original size:36 final size:35
Alignment explanation
Indices: 49895--50209 Score: 115
Period size: 38 Copynumber: 8.9 Consensus size: 35
49885 ATTTTAAATA
49895 TTTTGAAAACATATAATATATAGTTTTTGAAAACAT
1 TTTTGAAAACATATAATATATAG-TTTTGAAAACAT
* * *
49931 TTTTGAAAATATATATTATATTGTTTTG-AAA-AT
1 TTTTGAAAACATATAATATATAGTTTTGAAAACAT
* * * *
49964 ATAT--AAA-ATAT-ATA-GT--TTTTAAAAACAT
1 TTTTGAAAACATATAATATATAGTTTTGAAAACAT
*
49992 TTTTGAAAAACATATATATTATATAGTTTTGAAAATTAGT
1 TTTTG-AAAACATATA-A-TATATAGTTTTGAAAA-CA-T
* *
50032 TTTT---AA-A-A-AACATATAGTTTTGAAAATTAGT
1 TTTTGAAAACATATAATATATAGTTTTGAAAA-CA-T
* * *
50063 TTTT-AAAATATATATATTATATAATTTTGAAAATTAGT
1 TTTTGAAAACATATA-A-TATATAGTTTTGAAAA-CA-T
* * *
50101 TTTTAAAAATATATATATTATATAGTTTTGAAAATTAT
1 TTTTGAAAACATATA-A-TATATAGTTTTGAAAA-CAT
* * * *
50139 ATTTTAAAAAACATA-AATTATATGGGTTTGAAAATTATT
1 -TTTT-GAAAACATATAA-TATATAGTTTTGAAAA-CA-T
* * * *
50178 TTTTTAAAACATATATTGTATAGTTTTAAAAA
1 TTTTGAAAACATATAATATATAGTTTTGAAAA
50210 ATGTTTTTCA
Statistics
Matches: 227, Mismatches: 26, Indels: 51
0.75 0.09 0.17
Matches are distributed among these distances:
26 4 0.02
27 3 0.01
28 5 0.02
29 2 0.01
30 4 0.02
31 30 0.13
32 5 0.02
33 7 0.03
34 6 0.03
35 9 0.04
36 24 0.11
37 21 0.09
38 56 0.25
39 38 0.17
40 13 0.06
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (35 bp):
TTTTGAAAACATATAATATATAGTTTTGAAAACAT
Found at i:49974 original size:23 final size:23
Alignment explanation
Indices: 49931--49974 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
49921 TTGAAAACAT
**
49931 TTTTGAAAATATATATTATATTG
1 TTTTGAAAATATATAAAATATTG
49954 TTTTGAAAATATATAAAATAT
1 TTTTGAAAATATATAAAATAT
49975 ATAGTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (23 bp):
TTTTGAAAATATATAAAATATTG
Found at i:49975 original size:25 final size:23
Alignment explanation
Indices: 49931--49987 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 23
49921 TTGAAAACAT
* *
49931 TTTTGAAAATATATATTATATTG
1 TTTTGAAAATATATAATATATAG
49954 TTTTGAAAATATATAAAATATATAG
1 TTTTGAAAATATAT--AATATATAG
*
49979 TTTTTAAAA
1 TTTTGAAAA
49988 ACATTTTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 14 0.48
25 15 0.52
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.47
Consensus pattern (23 bp):
TTTTGAAAATATATAATATATAG
Found at i:49990 original size:61 final size:61
Alignment explanation
Indices: 49895--50027 Score: 198
Period size: 61 Copynumber: 2.2 Consensus size: 61
49885 ATTTTAAATA
* * *
49895 TTTTGAAAACATATAATATATAGTTTTTGAAAACATTTTTG-AAA-ATATATATTATATTG
1 TTTTGAAAATATATAATATATAGTTTTTAAAAACATTTTTGAAAACATATATATTATATAG
49954 TTTTGAAAATATATAAAATATATAGTTTTTAAAAACATTTTTGAAAAACATATATATTATATAG
1 TTTTGAAAATATAT--AATATATAGTTTTTAAAAACATTTTTG-AAAACATATATATTATATAG
50018 TTTTGAAAAT
1 TTTTGAAAAT
50028 TAGTTTTTAA
Statistics
Matches: 66, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
59 13 0.20
61 26 0.39
63 3 0.05
64 24 0.36
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (61 bp):
TTTTGAAAATATATAATATATAGTTTTTAAAAACATTTTTGAAAACATATATATTATATAG
Found at i:50015 original size:39 final size:40
Alignment explanation
Indices: 49954--50047 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 40
49944 TATTATATTG
* *
49954 TTTTG-AAAATATATAAAATATATAGTTTTTAAAAACA-T
1 TTTTGAAAAACATATAAAATATATAGTTTTGAAAAACAGT
* * **
49992 TTTTGAAAAACATATATATTATATAGTTTTGAAAATTAGT
1 TTTTGAAAAACATATAAAATATATAGTTTTGAAAAACAGT
*
50032 TTTTAAAAAACATATA
1 TTTTGAAAAACATATA
50048 GTTTTGAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
38 5 0.11
39 26 0.55
40 16 0.34
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (40 bp):
TTTTGAAAAACATATAAAATATATAGTTTTGAAAAACAGT
Found at i:50033 original size:13 final size:13
Alignment explanation
Indices: 50015--50071 Score: 51
Period size: 13 Copynumber: 4.0 Consensus size: 13
50005 ATATATTATA
50015 TAGTTTTGAAAAT
1 TAGTTTTGAAAAT
*
50028 TAGTTTTTAAAAAACAT
1 TAG-TTTT--GAAA-AT
50045 ATAGTTTTGAAAAT
1 -TAGTTTTGAAAAT
*
50059 TAGTTTTTAAAAT
1 TAGTTTTGAAAAT
50072 ATATATATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
13 15 0.42
14 6 0.17
15 3 0.08
16 3 0.08
17 6 0.17
18 3 0.08
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.46
Consensus pattern (13 bp):
TAGTTTTGAAAAT
Found at i:50071 original size:108 final size:108
Alignment explanation
Indices: 49953--50153 Score: 298
Period size: 108 Copynumber: 1.9 Consensus size: 108
49943 ATATTATATT
* *
49953 GTTTTGAAAATATATAAAATATATAGTTTTTAAAAACA-TTTTTGAAAAACATATATATTATATA
1 GTTTTGAAAATATATAAAATATATAATTTTGAAAAACAGTTTTT-AAAAACATATATATTATATA
50017 GTTTTGAAAATTAGT-TTTTAAAAAACATATAGTTTTGAAAATTA
65 GTTTTGAAAATTA-TATTTTAAAAAACATATAGTTTTGAAAATTA
* * * ** *
50061 GTTTTTAAAATATATATATTATATAATTTTGAAAATTAGTTTTTAAAAATATATATATTATATAG
1 GTTTTGAAAATATATAAAATATATAATTTTGAAAAACAGTTTTTAAAAACATATATATTATATAG
50126 TTTTGAAAATTATATTTTAAAAAACATA
66 TTTTGAAAATTATATTTTAAAAAACATA
50154 AATTATATGG
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
107 1 0.01
108 77 0.93
109 5 0.06
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (108 bp):
GTTTTGAAAATATATAAAATATATAATTTTGAAAAACAGTTTTTAAAAACATATATATTATATAG
TTTTGAAAATTATATTTTAAAAAACATATAGTTTTGAAAATTA
Found at i:50078 original size:31 final size:31
Alignment explanation
Indices: 50011--50117 Score: 124
Period size: 31 Copynumber: 3.2 Consensus size: 31
50001 ACATATATAT
50011 TATATAGTTTTGAAAATTAGTTTTTAAAAAA
1 TATATAGTTTTGAAAATTAGTTTTTAAAAAA
*
50042 CATATAGTTTTGAAAATTAGTTTTTAAAATATATATA
1 TATATAGTTTTGAAAATTAGTTTTT--AA-A-A-A-A
*
50079 TTATATAATTTTGAAAATTAGTTTTTAAAAATA
1 -TATATAGTTTTGAAAATTAGTTTTTAAAAA-A
50112 TATATA
1 TATATA
50118 TTATATAGTT
Statistics
Matches: 66, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
31 24 0.36
32 6 0.09
33 5 0.08
34 2 0.03
35 2 0.03
36 3 0.05
37 1 0.02
38 23 0.35
ACGTcount: A:0.45, C:0.01, G:0.07, T:0.47
Consensus pattern (31 bp):
TATATAGTTTTGAAAATTAGTTTTTAAAAAA
Found at i:50094 original size:38 final size:38
Alignment explanation
Indices: 50043--50217 Score: 203
Period size: 38 Copynumber: 4.6 Consensus size: 38
50033 TTTAAAAAAC
50043 ATATAGTTTTGAAAATTAGTTTTTAAAATATATATATT
1 ATATAGTTTTGAAAATTAGTTTTTAAAATATATATATT
*
50081 ATATAATTTTGAAAATTAGTTTTTAAAAATATATATATT
1 ATATAGTTTTGAAAATTAGTTTTT-AAAATATATATATT
* * *
50120 ATATAGTTTTGAAAATTA-TATTTTAAAAAACATAAATT
1 ATATAGTTTTGAAAATTAGT-TTTTAAAATATATATATT
* * * * *
50158 ATATGGGTTTGAAAATTATTTTTTTAAA-ACATATATT
1 ATATAGTTTTGAAAATTAGTTTTTAAAATATATATATT
* * *
50195 GTATAGTTTTAAAAAAT-GTTTTT
1 ATATAGTTTTGAAAATTAGTTTTT
50218 CATTTATTTA
Statistics
Matches: 119, Mismatches: 15, Indels: 8
0.84 0.11 0.06
Matches are distributed among these distances:
36 5 0.04
37 20 0.17
38 58 0.49
39 36 0.30
ACGTcount: A:0.43, C:0.01, G:0.08, T:0.48
Consensus pattern (38 bp):
ATATAGTTTTGAAAATTAGTTTTTAAAATATATATATT
Found at i:50136 original size:77 final size:75
Alignment explanation
Indices: 50043--50217 Score: 201
Period size: 77 Copynumber: 2.3 Consensus size: 75
50033 TTTAAAAAAC
* * * *
50043 ATATAGTTTTGAAAATTAGTTTTTAAAATATATATATTATATAATTTTGAAAATTAGTTTTTAAA
1 ATATAGTTTTGAAAATTAGTTTTTAAAAAACATAAATTATATAAGTTTGAAAATTA-TTTTTAAA
*
50108 AATATATATATT
65 AA-ACATATATT
** **
50120 ATATAGTTTTGAAAATTA-TATTTTAAAAAACATAAATTATATGGGTTTGAAAATTATTTTTTTA
1 ATATAGTTTTGAAAATTAGT-TTTTAAAAAACATAAATTATATAAGTTTGAAAATTATTTTTAAA
50184 AAACATATATT
65 AAACATATATT
* * *
50195 GTATAGTTTTAAAAAAT-GTTTTT
1 ATATAGTTTTGAAAATTAGTTTTT
50218 CATTTATTTA
Statistics
Matches: 84, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
74 4 0.05
75 23 0.27
76 9 0.11
77 48 0.57
ACGTcount: A:0.43, C:0.01, G:0.08, T:0.48
Consensus pattern (75 bp):
ATATAGTTTTGAAAATTAGTTTTTAAAAAACATAAATTATATAAGTTTGAAAATTATTTTTAAAA
AACATATATT
Found at i:50217 original size:37 final size:37
Alignment explanation
Indices: 49972--50209 Score: 229
Period size: 39 Copynumber: 6.4 Consensus size: 37
49962 ATATATAAAA
* ** *
49972 TATATAGTTTTTAAAAACATTTTTGAAAAACATATATAT
1 TATATAGTTTTGAAAATTATTTTT-AAAAA-ACATATAT
50011 TATATAGTTTTGAAAATTAGTTTTTAAAAAAC------
1 TATATAGTTTTGAAAATTA-TTTTTAAAAAACATATAT
* *
50043 -ATATAGTTTTGAAAATTAGTTTTTAAAATATATATAT
1 TATATAGTTTTGAAAATTA-TTTTTAAAAAACATATAT
* *
50080 TATATAATTTTGAAAATTAGTTTTTAAAAATATATATAT
1 TATATAGTTTTGAAAATTA-TTTTTAAAAA-ACATATAT
*
50119 TATATAGTTTTGAAAATTATATTTTAAAAAACATAAAT
1 TATATAGTTTTGAAAATTAT-TTTTAAAAAACATATAT
* * **
50157 TATATGGGTTTGAAAATTATTTTTTTAAAACATATAT
1 TATATAGTTTTGAAAATTATTTTTAAAAAACATATAT
* *
50194 TGTATAGTTTTAAAAA
1 TATATAGTTTTGAAAA
50210 ATGTTTTTCA
Statistics
Matches: 169, Mismatches: 20, Indels: 22
0.80 0.09 0.10
Matches are distributed among these distances:
31 29 0.17
37 26 0.15
38 53 0.31
39 56 0.33
40 5 0.03
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.46
Consensus pattern (37 bp):
TATATAGTTTTGAAAATTATTTTTAAAAAACATATAT
Found at i:50228 original size:4 final size:4
Alignment explanation
Indices: 50219--50276 Score: 64
Period size: 4 Copynumber: 14.0 Consensus size: 4
50209 AATGTTTTTC
*
50219 ATTT ATTT ATCT ATTT ATTT ATTTT ATTT CATTT A-TT ATTT ATTTT ATTT
1 ATTT ATTT ATTT ATTT ATTT A-TTT ATTT -ATTT ATTT ATTT A-TTT ATTT
*
50269 TTTT ATTT
1 ATTT ATTT
50277 TGTTTTAGGT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
3 3 0.07
4 31 0.67
5 12 0.26
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:50244 original size:21 final size:21
Alignment explanation
Indices: 50220--50268 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
50210 ATGTTTTTCA
50220 TTTATTT-ATCTATTTATTTAT
1 TTTATTTCATCTA-TTATTTAT
*
50241 TTTATTTCATTTATTATTTAT
1 TTTATTTCATCTATTATTTAT
50262 TTTATTT
1 TTTATTT
50269 TTTTATTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTATTTCATCTATTATTTAT
Found at i:50249 original size:30 final size:29
Alignment explanation
Indices: 50215--50276 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 29
50205 AAAAAATGTT
50215 TTTCATTTATTTATCTA-TTTATTTATTTTA
1 TTTCATTTA-TTATCTATTTTATTT-TTTTA
*
50245 TTTCATTTATTATTTATTTTATTTTTTTA
1 TTTCATTTATTATCTATTTTATTTTTTTA
50274 TTT
1 TTT
50277 TGTTTTAGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 14 0.47
30 16 0.53
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (29 bp):
TTTCATTTATTATCTATTTTATTTTTTTA
Found at i:52795 original size:120 final size:123
Alignment explanation
Indices: 52660--52930 Score: 415
Period size: 122 Copynumber: 2.2 Consensus size: 123
52650 TTATGTTTTG
* * *
52660 AAAAAAATTGAAAGTTTAGTTACTAAAACATACCAAAAGTGAT-GTTTAGGTACTAAATGTGTTA
1 AAAAAAATTGAAAGTTTAGGTACTAAAACAGACCAAAAGTGATAGTTTAGGTACTAAATGCGTTA
*
52724 A-ATTTTTAACGGC-GGATACTAAAATGAAATGAAAGCTAAACATTAGGTATGACTTT
66 AGATTTTTAACGGCGGGATACTAAAATGAAATGAAAACTAAACATTAGGTATGACTTT
* *
52780 AAAAAAATTGAAAGTTTAGGTACTAAAA-GGACCAAAAGTGATAGTTTAGGTGCTAAATGCGTTA
1 AAAAAAATTGAAAGTTTAGGTACTAAAACAGACCAAAAGTGATAGTTTAGGTACTAAATGCGTTA
* * *
52844 AGTTTTTTAACGGCGGGATATTAAAATGAAATGAAAACTAAACATTATGTATGACTTT
66 AGATTTTTAACGGCGGGATACTAAAATGAAATGAAAACTAAACATTAGGTATGACTTT
* *
52902 AAAAAATTTAAAAGTTTAGGTACTAAAAC
1 AAAAAAATTGAAAGTTTAGGTACTAAAAC
52931 TAATAGTTTA
Statistics
Matches: 136, Mismatches: 11, Indels: 5
0.89 0.07 0.03
Matches are distributed among these distances:
119 12 0.09
120 47 0.35
121 11 0.08
122 66 0.49
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.30
Consensus pattern (123 bp):
AAAAAAATTGAAAGTTTAGGTACTAAAACAGACCAAAAGTGATAGTTTAGGTACTAAATGCGTTA
AGATTTTTAACGGCGGGATACTAAAATGAAATGAAAACTAAACATTAGGTATGACTTT
Done.