Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006157.1 Kokia drynarioides strain JFW-HI SEQ_120706, 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: 227659
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 92 characters in sequence are not A, C, G, or T
Found at i:604 original size:221 final size:221
Alignment explanation
Indices: 24--1811 Score: 2721
Period size: 221 Copynumber: 8.0 Consensus size: 221
14 CATTTTATTG
* * *
24 AATCATTTTCCATTGAAGAAGAGAAAGAATTGTATGAAACAGGGATATTATCCCTTTCCTATAGT
1 AATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGT
* *
89 TTTATGCCACACCAACAATTTCATCCTGAATTTCAAGATTTTAATTTTAATTTGATTTTTTCAGG
66 TTTATGCCACACTAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGG
* * **
154 ATGAAAATGTTTATATTAAGAATGAAAATACTGATGTGGCGTAAAAC-AATTGGAAAAAAGACAC
131 ATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTAA-TGGAAAAGGGACAC
*
218 -AATAACGTGGTGTCACTGTTTCATTC
195 AAATGACGTGGTGTCACTGTTTCATTC
*
244 AATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCATTAGT
1 AATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGT
*
309 TTTATGCCACAAC-AACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTGTTTTTA
66 TTTATGCCAC-ACTAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATT-TTTTCA
*
373 GGATGAAAATGTTGAAATTAAGGATGAAAATACTGATGTGGCGTAAAACTAATGGAAAAGGGACA
129 GGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTAATGGAAAAGGGACA
438 CAAATGACGTGGTGTCACTGTTTCATTC
194 CAAATGACGTGGTGTCACTGTTTCATTC
* *
466 AACCCTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGAAATTATCCCTTTCCAATAGT
1 AATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGT
* * * * *
531 TTTATGCCACACTAACATTTTCATCCTAAATTTTAGGATTTTAATTTGAATTTTATTTTTTCAGG
66 TTTATGCCACACTAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGG
* ** **
596 ATGAAAATGATGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTGTTGGAAAAGGGACGGA
131 ATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTAATGGAAAAGGGACACA
*
661 AATGACGTTGTGTCACTGTTTCATTC
196 AATGACGTGGTGTCACTGTTTCATTC
* **
687 AATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATGACACAAAGATATTATCCCTTTCCAATAGT
1 AATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGT
** * *
752 TTTATTTCACA-TCAACAATTTCATCTTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAA
66 TTTATGCCACACT-AACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAG
*
816 GATGAAAATGTTGAAATTAAGAATGAAAATACGGATGTGGCGTAAAACTAATGGAAAAGGGACAC
130 GATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTAATGGAAAAGGGACAC
*
881 AAATGACGTGGTGTCACTGTTTTATTC
195 AAATGACGTGGTGTCACTGTTTCATTC
* * *
908 AGTCCTTTTCCATTGAAGAAGAGAAAGTATTGTATGAAACAGGGATATTATCCCTTTCTAATAGT
1 AATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGT
* *
973 TTTATGCTACA-TCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCTG
66 TTTATGCCACACT-AACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAG
* * *
1037 GATGAAAATGTTGAAATTAAGAATGAAAATACTGTTGTGGCGTAAAACTATTGGAAAATGGACAC
130 GATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTAATGGAAAAGGGACAC
1102 AAATGACGTGGTGTCACTGTTTCATTC
195 AAATGACGTGGTGTCACTGTTTCATTC
*
1129 AATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGT
1 AATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGT
* * *
1194 TTTATGCCACACCAACAATTTCATCTTGTATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGG
66 TTTATGCCACACTAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGG
*
1259 ATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTGGAAAAGGGACACA
131 ATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTAATGGAAAAGGGACACA
1324 AATGACGTGGTGTCACTGTTTTATTCAATCCTTCTCC
196 AATGACGTGGTGTCACTG---T-TTC-A----T-T-C
1361 ATTTTATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTT
1 A----A-TC---C-TTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTT
* * * *
1426 TCCAATAGTTTTATGCCATAGC-AACAATTTCATCTTGAATTTCCA-GATTTTAATTTTATTTTT
57 TCCAATAGTTTTATGCCACA-CTAACAATTTCATCCTGAATTT-CAGGATTTTAATTTTAATTTG
* *
1489 ATTTTTTCAGGATGAAAATGTTGAAATTAAGGATGAAAATACTGATGTGGCGTAAAACTGATGGA
120 ATTTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTAATGGA
*
1554 AAAGGGACACAAATGACATGGTGTCACTGTTTCATTC
185 AAAGGGACACAAATGACGTGGTGTCACTGTTTCATTC
* *
1591 AATCCTTTTCCGTTGAAGAAGAGAAAGGATTGTATGAAACAGGGAAATTATCCCTTTCCAATAGT
1 AATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGT
1656 TTTATGCCACA-TCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAG
66 TTTATGCCACACT-AACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAG
*
1720 GAT-AAAAGTGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTGGAAAAGGGACA
130 GATGAAAA-TGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTAATGGAAAAGGGACA
*
1784 CAAATGACGTGGTGTCACTGTTTTATTC
194 CAAATGACGTGGTGTCACTGTTTCATTC
1812 TTAATTTAGA
Statistics
Matches: 1437, Mismatches: 98, Indels: 65
0.90 0.06 0.04
Matches are distributed among these distances:
220 121 0.08
221 955 0.66
222 139 0.10
224 1 0.00
225 5 0.00
226 2 0.00
230 3 0.00
231 2 0.00
232 3 0.00
236 2 0.00
237 5 0.00
238 1 0.00
240 1 0.00
241 194 0.14
242 3 0.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (221 bp):
AATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGT
TTTATGCCACACTAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGG
ATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTAATGGAAAAGGGACACA
AATGACGTGGTGTCACTGTTTCATTC
Found at i:1367 original size:20 final size:20
Alignment explanation
Indices: 1342--1383 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1332 GGTGTCACTG
*
1342 TTTTATTCAATCCTTCTCCA
1 TTTTATTCAATCATTCTCCA
*
1362 TTTTATTCAATCATTTTCCA
1 TTTTATTCAATCATTCTCCA
1382 TT
1 TT
1384 GAAGAAGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.24, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTATTCAATCATTCTCCA
Found at i:1764 original size:462 final size:462
Alignment explanation
Indices: 900--1811 Score: 1587
Period size: 462 Copynumber: 2.0 Consensus size: 462
890 GGTGTCACTG
* * *
900 TTTTATTCAGTCCTTTTCCATTGAAGAAGAGAAAGTATTGTATGAAACAGGGATATTATCCCTTT
1 TTTTATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTT
* * *
965 CTAATAGTTTTATGCTACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATT
66 CCAATAGTTTTATGCCACAGCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATT
* *
1030 TTTTCTGGATGAAAATGTTGAAATTAAGAATGAAAATACTGTTGTGGCGTAAAACTATTGGAAAA
131 TTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTGGAAAA
* *
1095 TGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATT
196 GGGACACAAATGACATGGTGTCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATT
* * *
1160 GTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACACCAACAATTTCATCTTGTAT
261 GTATAAAACAGGGAAATTATCCCTTTCCAATAGTTTTATGCCACACCAACAATTTCATCCTGAAT
1225 TTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATAC
326 TTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATAC
1290 TGATGTGGCGTAAAACTATTGGAAAAGGGACACAAATGACGTGGTGTCACTGTTTTATTCAATCC
391 TGATGTGGCGTAAAACTATTGGAAAAGGGACACAAATGACGTGGTGTCACTGTTTTATTCAATCC
1355 TTCTCCA
456 TTCTCCA
1362 TTTTATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTT
1 TTTTATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTT
* * * *
1427 CCAATAGTTTTATGCCATAGCAACAATTTCATCTTGAATTTCCA-GATTTTAATTTTATTTTTAT
66 CCAATAGTTTTATGCCACAGCAACAATTTCATCCTGAATTT-CAGGATTTTAATTTTAATTTGAT
*
1491 TTTTTCAGGATGAAAATGTTGAAATTAAGGATGAAAATACTGATGTGGCGTAAAACTGA-TGGAA
130 TTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACT-ATTGGAA
*
1555 AAGGGACACAAATGACATGGTGTCACTGTTTCATTCAATCCTTTTCCGTTGAAGAAGAGAAAGGA
194 AAGGGACACAAATGACATGGTGTCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGA
* *
1620 TTGTATGAAACAGGGAAATTATCCCTTTCCAATAGTTTTATGCCACATCAACAATTTCATCCTGA
259 TTGTATAAAACAGGGAAATTATCCCTTTCCAATAGTTTTATGCCACACCAACAATTTCATCCTGA
1685 ATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGGAT-AAAAGTGTTGAAATTAAGAATGAAAA
324 ATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATGAAAA-TGTTGAAATTAAGAATGAAAA
1749 TACTGATGTGGCGTAAAACTATTGGAAAAGGGACACAAATGACGTGGTGTCACTGTTTTATTC
388 TACTGATGTGGCGTAAAACTATTGGAAAAGGGACACAAATGACGTGGTGTCACTGTTTTATTC
1812 TTAATTTAGA
Statistics
Matches: 426, Mismatches: 21, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
461 4 0.01
462 419 0.98
463 3 0.01
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (462 bp):
TTTTATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTT
CCAATAGTTTTATGCCACAGCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATT
TTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTGGAAAA
GGGACACAAATGACATGGTGTCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATT
GTATAAAACAGGGAAATTATCCCTTTCCAATAGTTTTATGCCACACCAACAATTTCATCCTGAAT
TTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATAC
TGATGTGGCGTAAAACTATTGGAAAAGGGACACAAATGACGTGGTGTCACTGTTTTATTCAATCC
TTCTCCA
Found at i:13137 original size:14 final size:14
Alignment explanation
Indices: 13118--13144 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13108 CTTTTATTTA
13118 AAAAGAAAAGAAAG
1 AAAAGAAAAGAAAG
13132 AAAAGAAAAGAAA
1 AAAAGAAAAGAAA
13145 TTTAATTAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:21366 original size:13 final size:14
Alignment explanation
Indices: 21343--21371 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
21333 TTACCTCTCA
21343 AATTGTAATATTTT
1 AATTGTAATATTTT
21357 AATT-TAATATTTT
1 AATTGTAATATTTT
21370 AA
1 AA
21372 AAATTATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (14 bp):
AATTGTAATATTTT
Found at i:21407 original size:22 final size:22
Alignment explanation
Indices: 21357--21409 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
21347 GTAATATTTT
* *
21357 AATTTAATATTTTAAAAATTAT
1 AATTTAATATTGTAAAAATTAC
* *
21379 ATTTTTATTATTGTAAAAATTAC
1 A-ATTTAATATTGTAAAAATTAC
21402 AATTTAAT
1 AATTTAAT
21410 TTCAATACCC
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
AATTTAATATTGTAAAAATTAC
Found at i:22420 original size:9 final size:8
Alignment explanation
Indices: 22395--22419 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
22385 TTTGCCTAGC
22395 TAGTTTTT
1 TAGTTTTT
22403 TAGTTTTT
1 TAGTTTTT
22411 TAGTTTTT
1 TAGTTTTT
22419 T
1 T
22420 TTTTTTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (8 bp):
TAGTTTTT
Found at i:22773 original size:6 final size:6
Alignment explanation
Indices: 22765--22804 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
22755 TGCAGGAGCC
*
22765 GATGCC GATGCT GATGCT GATGCT GATGCT GATGCT GATG
1 GATGCT GATGCT GATGCT GATGCT GATGCT GATGCT GATG
22805 AGTGCCTGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.17, C:0.17, G:0.35, T:0.30
Consensus pattern (6 bp):
GATGCT
Found at i:29970 original size:51 final size:51
Alignment explanation
Indices: 29911--30180 Score: 330
Period size: 51 Copynumber: 5.5 Consensus size: 51
29901 TAAACGAAAG
29911 GGTCCGATGACTAAGTGTCATCGTGAGCAAATGAATCCTTTATGGATTAAT
1 GGTCCGATGACTAAGTGTCATCGTGAGCAAATGAATCCTTTATGGATTAAT
29962 GGTCCGATGAC----TG--A--GT--G--AATGAATCCTTTATGGATTAAT
1 GGTCCGATGACTAAGTGTCATCGTGAGCAAATGAATCCTTTATGGATTAAT
* * * *
30001 GGTTCAATGACTAAGTGTCATCGTGGGCAAATAAATCCTTTATGGATTAAT
1 GGTCCGATGACTAAGTGTCATCGTGAGCAAATGAATCCTTTATGGATTAAT
**
30052 GGTCCGATGACTAAGTGTCATCGTGAGTGAATGAATCCTTTATGGATTAAT
1 GGTCCGATGACTAAGTGTCATCGTGAGCAAATGAATCCTTTATGGATTAAT
* * * * * *
30103 GGTTCAATGACTAAGTGTCATCATGAGTAAATGAATCTTTTATGGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGCAAATGAATCCTTTATGGATTAAT
* *
30154 GATCCGATGACTAAGTGTTATCGTGAG
1 GGTCCGATGACTAAGTGTCATCGTGAG
30181 TTTATGGATT
Statistics
Matches: 187, Mismatches: 20, Indels: 24
0.81 0.09 0.10
Matches are distributed among these distances:
39 31 0.17
41 1 0.01
43 4 0.02
45 2 0.01
47 4 0.02
49 1 0.01
51 144 0.77
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (51 bp):
GGTCCGATGACTAAGTGTCATCGTGAGCAAATGAATCCTTTATGGATTAAT
Found at i:29992 original size:39 final size:39
Alignment explanation
Indices: 29940--30017 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
29930 ATCGTGAGCA
* *
29940 AATGAATCCTTTATGGATTAATGGTCCGATGACTGAGTG
1 AATGAATCCTTTATGGATTAATGGTCCAATGACTAAGTG
*
29979 AATGAATCCTTTATGGATTAATGGTTCAATGACTAAGTG
1 AATGAATCCTTTATGGATTAATGGTCCAATGACTAAGTG
30018 TCATCGTGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.35
Consensus pattern (39 bp):
AATGAATCCTTTATGGATTAATGGTCCAATGACTAAGTG
Found at i:30239 original size:102 final size:101
Alignment explanation
Indices: 29973--30228 Score: 244
Period size: 102 Copynumber: 2.5 Consensus size: 101
29963 GTCCGATGAC
* ** * * * * * * *
29973 TGAGTGAATGAATCCTTTATGGATTAATGGTTCAATGACTAAGTGTCATCGTGGGCAAATAAATC
1 TGAGTGAATGAATCCTATATGGAACAAAGGTCCAATGACTAAGTATCATCATGAG-TAATGAATC
* *
30038 CTTTATGGATTAATGGTCCGATGACTAAGTGTCATCG
65 CTTTATGGATTAAAGATCCGATGACTAAGTGTCATCG
* ** * * *
30075 TGAGTGAATGAATCCTTTATGGATTAATGGTTCAATGACTAAGTGTCATCATGAGTAAATGAATC
1 TGAGTGAATGAATCCTATATGGAACAAAGGTCCAATGACTAAGTATCATCATGAGT-AATGAATC
* *
30140 TTTTATGGATTAAAGATCCGATGACTAAGTGTTATCG
65 CTTTATGGATTAAAGATCCGATGACTAAGTGTCATCG
** * *
30177 TGAGTTTATGGATTCCTATATGGAACAAGAGGTCCGATGACTATA-TATCATC
1 TGAGTGAAT-GAATCCTATATGGAACAA-AGGTCCAATGACTA-AGTATCATC
30229 GTTAGTATGA
Statistics
Matches: 132, Mismatches: 18, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
102 100 0.76
103 14 0.11
104 17 0.13
105 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.34
Consensus pattern (101 bp):
TGAGTGAATGAATCCTATATGGAACAAAGGTCCAATGACTAAGTATCATCATGAGTAATGAATCC
TTTATGGATTAAAGATCCGATGACTAAGTGTCATCG
Found at i:33787 original size:40 final size:41
Alignment explanation
Indices: 33709--33981 Score: 281
Period size: 40 Copynumber: 6.8 Consensus size: 41
33699 TATAACTTTA
**
33709 GGGGTAAAAGATTGAATTAT-TTCAATCTGCCC-CATGATT
1 GGGGTAAAAGATTGAATGGTCTTCAATCTGCCCTCATGATT
*
33748 GGGGTAAGAGATTGAATGGTCTTCAATCTGCCCTC-TGATT
1 GGGGTAAAAGATTGAATGGTCTTCAATCTGCCCTCATGATT
* * * * *
33788 AGGGTAAAAGATTGGATGGTTTTTAATCTGCCC-CATGATC
1 GGGGTAAAAGATTGAATGGTCTTCAATCTGCCCTCATGATT
* * * *
33828 GGGGTAAGAGATCGAATAGTCTTCAATCTGCCTTC-TGATT
1 GGGGTAAAAGATTGAATGGTCTTCAATCTGCCCTCATGATT
* * * *
33868 AGGGTAAAAGATTGGATGATCTTCAATCTGCCCTC-TAATT
1 GGGGTAAAAGATTGAATGGTCTTCAATCTGCCCTCATGATT
* * * * *
33908 AGGGTAAAATATTGAATAGTTTTCAATCTG-CCTCATGATC
1 GGGGTAAAAGATTGAATGGTCTTCAATCTGCCCTCATGATT
* * *
33948 GGGGTAAGAGATCGGATGGTCTTCAATCTGCCCT
1 GGGGTAAAAGATTGAATGGTCTTCAATCTGCCCT
33982 TTAGTCTATC
Statistics
Matches: 188, Mismatches: 40, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
39 22 0.12
40 161 0.86
41 5 0.03
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (41 bp):
GGGGTAAAAGATTGAATGGTCTTCAATCTGCCCTCATGATT
Found at i:33825 original size:80 final size:80
Alignment explanation
Indices: 33710--33980 Score: 332
Period size: 80 Copynumber: 3.4 Consensus size: 80
33700 ATAACTTTAG
* ** *
33710 GGGTAAAAGATTGAATTAT-TTCAATCTGCCCCATGATTGGGGTAAGAGATTGAATGGTCTTCAA
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCCATGATTGGGGTAAGAGATTGAATAGTCTTCAA
33774 TCTGCCCTCTGATTA
66 TCTGCCCTCTGATTA
* * * *
33789 GGGTAAAAGATTGGATGGTTTTTAATCTGCCCCATGATCGGGGTAAGAGATCGAATAGTCTTCAA
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCCATGATTGGGGTAAGAGATTGAATAGTCTTCAA
*
33854 TCTGCCTTCTGATTA
66 TCTGCCCTCTGATTA
* * * * * *
33869 GGGTAAAAGATTGGATGATCTTCAATCTGCCCTC-TAATTAGGGTAAAATATTGAATAGTTTTCA
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCC-CATGATTGGGGTAAGAGATTGAATAGTCTTCA
**
33933 ATCTG-CCTCATGATCG
65 ATCTGCCCTC-TGATTA
* *
33949 GGGTAAGAGATCGGATGGTCTTCAATCTGCCC
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCC
33981 TTTAGTCTAT
Statistics
Matches: 165, Mismatches: 24, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
79 19 0.12
80 145 0.88
81 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (80 bp):
GGGTAAAAGATTGGATGGTCTTCAATCTGCCCCATGATTGGGGTAAGAGATTGAATAGTCTTCAA
TCTGCCCTCTGATTA
Found at i:33945 original size:120 final size:120
Alignment explanation
Indices: 33729--33980 Score: 371
Period size: 120 Copynumber: 2.1 Consensus size: 120
33719 ATTGAATTAT
* * * *
33729 TTCAATCTGCCCCATGATTGGGGTAAGAGATTGAATGGTCTTCAATCTGCCCTCTGATTAGGGTA
1 TTCAATCTGCCCCATGATTAGGGTAAAAGATTGAATGATCTTCAATCTGCCCTCTAATTAGGGTA
* * *
33794 AAAGATTGGATGGTTTTTAATCTGCCCCATGATCGGGGTAAGAGATCGAATAGTC
66 AAAGATTGAATAGTTTTCAATCTGCCCCATGATCGGGGTAAGAGATCGAATAGTC
* *
33849 TTCAATCTGCCTTC-TGATTAGGGTAAAAGATTGGATGATCTTCAATCTGCCCTCTAATTAGGGT
1 TTCAATCTGCC-CCATGATTAGGGTAAAAGATTGAATGATCTTCAATCTGCCCTCTAATTAGGGT
* * * *
33913 AAAATATTGAATAGTTTTCAATCTGCCTCATGATCGGGGTAAGAGATCGGATGGTC
65 AAAAGATTGAATAGTTTTCAATCTGCCCCATGATCGGGGTAAGAGATCGAATAGTC
33969 TTCAATCTGCCC
1 TTCAATCTGCCC
33981 TTTAGTCTAT
Statistics
Matches: 117, Mismatches: 14, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
120 116 0.99
121 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.32
Consensus pattern (120 bp):
TTCAATCTGCCCCATGATTAGGGTAAAAGATTGAATGATCTTCAATCTGCCCTCTAATTAGGGTA
AAAGATTGAATAGTTTTCAATCTGCCCCATGATCGGGGTAAGAGATCGAATAGTC
Found at i:42587 original size:77 final size:75
Alignment explanation
Indices: 42456--43068 Score: 647
Period size: 77 Copynumber: 7.9 Consensus size: 75
42446 ATTTTACAGG
* * * *
42456 TCTCTTACCCCAATCATAGGGTAGATCGAAGCATCCAAATCTCTTACCCTAATCA-AAGGGCAGA
1 TCTCTTACCCCGATCAT-GGGCAGATTGAAGCATCC-AATCTCTTACCTTAATCAGAA-GGCAGA
* * *
42520 TTAAAAACCGCCAA
63 TTGAAGACTG-CAA
* * *
42534 TCTCTTACCCCGATCATGGGACAGATTGAAACATCTAATCTTTTACCTTAATCAGAAGGCAGATT
1 TCTCTTACCCCGATCATGGG-CAGATTGAAGCATCCAATCTCTTACCTTAATCAGAAGGCAGATT
42599 GAAGACAT-CTAA
65 GAAGAC-TGC-AA
*
42611 TCTCTTACCCTGATCATGGGGCAGATTGAAGCATCCAATCTCTTACCTTAATCAGAAGGCAGATT
1 TCTCTTACCCCGATCAT-GGGCAGATTGAAGCATCCAATCTCTTACCTTAATCAGAAGGCAGATT
*
42676 GAAAACATGCAA
65 GAAGAC-TGCAA
* * * * * * *
42688 TCTCTTACCCCAATCATGAGACAGATTGAAGCATCAAATTTCTTACCTTAATCAAAAGGTAGATC
1 TCTCTTACCCCGATCATG-GGCAGATTGAAGCATCCAATCTCTTACCTTAATCAGAAGGCAGATT
*
42753 GAAGACATACAA
65 GAAGAC-TGCAA
*
42765 TCTCTTACCCCGATCATGGGGCGGATTGAAGCATCCAATCTCTTACCTTAATCAGAAGGCAGATT
1 TCTCTTACCCCGATCAT-GGGCAGATTGAAGCATCCAATCTCTTACCTTAATCAGAAGGCAGATT
*
42830 GAAGACATGTAA
65 GAAGAC-TGCAA
* * *
42842 TCTCTTACCCCGATCATAAGGCAGATTGAAGTATCCAATCTCTTACCTTAATCAGAAGACAGATT
1 TCTCTTACCCCGATCAT-GGGCAGATTGAAGCATCCAATCTCTTACCTTAATCAGAAGGCAGATT
* * *
42907 AAAGATATGTAA
65 GAAGA-CTGCAA
* * * * * * *
42919 TCTCTTACCCCGATCATAGGGCTGATTGAAGCATCCATTCTTTTACCCTAATTAGAGGGTAGATT
1 TCTCTTACCCCGATCAT-GGGCAGATTGAAGCATCCAATCTCTTACCTTAATCAGAAGGCAGATT
42984 GAAGACATGCCAA
65 GAAGAC-TG-CAA
* * * ** *
42997 TCTCTTACCCCGATCATGGGGCAAATTGAAAACATCCAATCTCTTATCTCGATCATG-GGGCAGA
1 TCTCTTACCCCGATCAT-GGGCAGATTG-AAGCATCCAATCTCTTACCTTAATCA-GAAGGCAGA
43061 TTGAAGAC
63 TTGAAGAC
43069 ACATTAATTT
Statistics
Matches: 455, Mismatches: 67, Indels: 25
0.83 0.12 0.05
Matches are distributed among these distances:
76 2 0.00
77 359 0.79
78 61 0.13
79 32 0.07
80 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (75 bp):
TCTCTTACCCCGATCATGGGCAGATTGAAGCATCCAATCTCTTACCTTAATCAGAAGGCAGATTG
AAGACTGCAA
Found at i:42737 original size:154 final size:155
Alignment explanation
Indices: 42456--43014 Score: 716
Period size: 154 Copynumber: 3.6 Consensus size: 155
42446 ATTTTACAGG
* * *
42456 TCTCTTACCCCAATCATAGGGTAGATCGAAGCATCCAAATCTCTTACCCTAATCA-AAGGGCAGA
1 TCTCTTACCCCGATCATAGGGCAGATTGAAGCATCC-AATCTCTTACCCTAATCAGAA-GGCAGA
* * * * *
42520 TTAAAAAC-CGCCAATCTCTTACCCCGATCATGGGACAGATTGAAACATCTAATCTT-TTACCTT
64 TTGAAAACATGCCAATCTCTTACCCCGATCATGAGACAGATTGAAGCATCAAAT-TTCTTACCTT
42583 AATCAGAAGGCAGATTGAAGACATCTAA
128 AATCAGAAGGCAGATTGAAGACATCTAA
* * *
42611 TCTCTTACCCTGATCATGGGGCAGATTGAAGCATCCAATCTCTTACCTTAATCAGAAGGCAGATT
1 TCTCTTACCCCGATCATAGGGCAGATTGAAGCATCCAATCTCTTACCCTAATCAGAAGGCAGATT
*
42676 GAAAACATG-CAATCTCTTACCCCAATCATGAGACAGATTGAAGCATCAAATTTCTTACCTTAAT
66 GAAAACATGCCAATCTCTTACCCCGATCATGAGACAGATTGAAGCATCAAATTTCTTACCTTAAT
* * *
42740 CAAAAGGTAGATCGAAGACATAC-AA
131 CAGAAGGCAGATTGAAGACAT-CTAA
* * *
42765 TCTCTTACCCCGATCATGGGGCGGATTGAAGCATCCAATCTCTTACCTTAATCAGAAGGCAGATT
1 TCTCTTACCCCGATCATAGGGCAGATTGAAGCATCCAATCTCTTACCCTAATCAGAAGGCAGATT
* * * * * * *
42830 GAAGACATG-TAATCTCTTACCCCGATCATAAGGCAGATTGAAGTATCCAATCTCTTACCTTAAT
66 GAAAACATGCCAATCTCTTACCCCGATCATGAGACAGATTGAAGCATCAAATTTCTTACCTTAAT
* * * *
42894 CAGAAGACAGATTAAAGATATGTAA
131 CAGAAGGCAGATTGAAGACATCTAA
* * * * * *
42919 TCTCTTACCCCGATCATAGGGCTGATTGAAGCATCCATTCTTTTACCCTAATTAGAGGGTAGATT
1 TCTCTTACCCCGATCATAGGGCAGATTGAAGCATCCAATCTCTTACCCTAATCAGAAGGCAGATT
*
42984 GAAGACATGCCAATCTCTTACCCCGATCATG
66 GAAAACATGCCAATCTCTTACCCCGATCATG
43015 GGGCAAATTG
Statistics
Matches: 356, Mismatches: 42, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
153 2 0.01
154 300 0.84
155 54 0.15
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (155 bp):
TCTCTTACCCCGATCATAGGGCAGATTGAAGCATCCAATCTCTTACCCTAATCAGAAGGCAGATT
GAAAACATGCCAATCTCTTACCCCGATCATGAGACAGATTGAAGCATCAAATTTCTTACCTTAAT
CAGAAGGCAGATTGAAGACATCTAA
Found at i:42867 original size:231 final size:231
Alignment explanation
Indices: 42456--43069 Score: 804
Period size: 231 Copynumber: 2.6 Consensus size: 231
42446 ATTTTACAGG
* * * *
42456 TCTCTTACCCCAATCATAGGGTAGATCGAAGCATCCAAATCTCTTACCCTAATCAAAGGGCAGAT
1 TCTCTTACCCCAATCATAGGGCAGATTGAAGCAT-CAAATTTCTTACCCTAATCAAAGGGTAGAT
* * ** * * *
42521 TAAAAACCGCCAATCTCTTACCCCGATCATGGGACAGATTGAAACATCTAATCTTTTACCTTAAT
65 TGAAGACATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAACATCCAATCTCTTACCTTAAT
* **
42586 CAGAAGGCAGATTGAAGACATCTAATCTCTTACCCTGATCATGGGGCAGATTGAAGCATCCAATC
130 CAGAAGGCAGATTGAAGACATCTAATCTCTTACCCCGATCATAAGGCAGATTGAAGCATCCAATC
*
42651 TCTTACCTTAATCAGAAGGCAGATTGAAA-ACATGCAA
195 TCTTACCTTAATCAGAAGACAGATT-AAAGACATGCAA
* * *
42688 TCTCTTACCCCAATCAT-GAGACAGATTGAAGCATCAAATTTCTTACCTTAATCAAAAGGTAGAT
1 TCTCTTACCCCAATCATAG-GGCAGATTGAAGCATCAAATTTCTTACCCTAATCAAAGGGTAGAT
* * * *
42752 CGAAGACATACAATCTCTTACCCCGATCATGGGGCGGATTGAAGCATCCAATCTCTTACCTTAAT
65 TGAAGACATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAACATCCAATCTCTTACCTTAAT
* *
42817 CAGAAGGCAGATTGAAGACATGTAATCTCTTACCCCGATCATAAGGCAGATTGAAGTATCCAATC
130 CAGAAGGCAGATTGAAGACATCTAATCTCTTACCCCGATCATAAGGCAGATTGAAGCATCCAATC
* *
42882 TCTTACCTTAATCAGAAGACAGATTAAAGATATGTAA
195 TCTTACCTTAATCAGAAGACAGATTAAAGACATGCAA
* * * * * *
42919 TCTCTTACCCCGATCATAGGGCTGATTGAAGCATC-CATTCTTTTACCCTAATTAGAGGGTAGAT
1 TCTCTTACCCCAATCATAGGGCAGATTGAAGCATCAAATT-TCTTACCCTAATCAAAGGGTAGAT
* * **
42983 TGAAGACATGCCAATCTCTTACCCCGATCATGGGGCAAATTGAAAACATCCAATCTCTTATCTCG
65 TGAAGACAT-CCAATCTCTTACCCCGATCATGGGGCAGATTG-AAACATCCAATCTCTTACCTTA
*
43048 ATCATG-GGGCAGATTGAAGACA
128 ATCA-GAAGGCAGATTGAAGACA
43070 CATTAATTTT
Statistics
Matches: 331, Mismatches: 44, Indels: 13
0.85 0.11 0.03
Matches are distributed among these distances:
230 6 0.02
231 228 0.69
232 59 0.18
233 37 0.11
234 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (231 bp):
TCTCTTACCCCAATCATAGGGCAGATTGAAGCATCAAATTTCTTACCCTAATCAAAGGGTAGATT
GAAGACATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAACATCCAATCTCTTACCTTAATC
AGAAGGCAGATTGAAGACATCTAATCTCTTACCCCGATCATAAGGCAGATTGAAGCATCCAATCT
CTTACCTTAATCAGAAGACAGATTAAAGACATGCAA
Found at i:43050 original size:39 final size:40
Alignment explanation
Indices: 42493--43065 Score: 179
Period size: 39 Copynumber: 14.8 Consensus size: 40
42483 GAAGCATCCA
** ** * * *
42493 AATCTCTTACCCTAATCAAAGGGCAGATTAAAAAC-CGCC
1 AATCTCTTACCCCGATCATGGGGCAAATTGAAAACATGCC
* * *
42532 AATCTCTTACCCCGATCATGGGACAGATTG-AAACAT-CT
1 AATCTCTTACCCCGATCATGGGGCAAATTGAAAACATGCC
* *** * * * *
42570 AATCTTTTACCTTAATCA-GAAGGCAGATTGAAGACAT-CT
1 AATCTCTTACCCCGATCATG-GGGCAAATTGAAAACATGCC
* * *
42609 AATCTCTTACCCTGATCATGGGGCAGATTG-AAGCAT-CC
1 AATCTCTTACCCCGATCATGGGGCAAATTGAAAACATGCC
*** * *
42647 AATCTCTTACCTTAATCA-GAAGGCAGATTGAAAACATG-C
1 AATCTCTTACCCCGATCATG-GGGCAAATTGAAAACATGCC
* * * * * *
42686 AATCTCTTACCCCAATCATGAGACAGATTG-AAGCAT-CA
1 AATCTCTTACCCCGATCATGGGGCAAATTGAAAACATGCC
* *** *** * * * * *
42724 AATTTCTTACCTTAATCAAAAGGTAGATCGAAGACAT-AC
1 AATCTCTTACCCCGATCATGGGGCAAATTGAAAACATGCC
** *
42763 AATCTCTTACCCCGATCATGGGGCGGATTG-AAGCAT-CC
1 AATCTCTTACCCCGATCATGGGGCAAATTGAAAACATGCC
*** * * * *
42801 AATCTCTTACCTTAATCA-GAAGGCAGATTGAAGACATG-T
1 AATCTCTTACCCCGATCATG-GGGCAAATTGAAAACATGCC
** * **
42840 AATCTCTTACCCCGATCATAAGGCAGATTG-AAGTAT-CC
1 AATCTCTTACCCCGATCATGGGGCAAATTGAAAACATGCC
*** * * * * *
42878 AATCTCTTACCTTAATCA-GAAGACAGATT-AAAGATATG-T
1 AATCTCTTACCCCGATCATG-GGGCAAATTGAAA-ACATGCC
* ** *
42917 AATCTCTTACCCCGATCATAGGGCTGATTG-AAGCAT-CC
1 AATCTCTTACCCCGATCATGGGGCAAATTGAAAACATGCC
* * ** * * * *
42955 ATTCTTTTACCCTAATTA-GAGGGTAGATTGAAGACATGCC
1 AATCTCTTACCCCGATCATG-GGGCAAATTGAAAACATGCC
42995 AATCTCTTACCCCGATCATGGGGCAAATTGAAAACAT-CC
1 AATCTCTTACCCCGATCATGGGGCAAATTGAAAACATGCC
* * *
43034 AATCTCTTATCTCGATCATGGGGCAGATTGAA
1 AATCTCTTACCCCGATCATGGGGCAAATTGAA
43066 GACACATTAA
Statistics
Matches: 398, Mismatches: 110, Indels: 52
0.71 0.20 0.09
Matches are distributed among these distances:
37 3 0.01
38 163 0.41
39 200 0.50
40 31 0.08
41 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (40 bp):
AATCTCTTACCCCGATCATGGGGCAAATTGAAAACATGCC
Found at i:51681 original size:41 final size:41
Alignment explanation
Indices: 51624--51705 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
51614 CAGATTTAGA
* * *
51624 ATGATTTAGCTATCCGTTGTCACTTTATATGTTTATCTAGC
1 ATGATTTAGCTATCCGTTGTCACTTCATACGTTTACCTAGC
51665 ATGATTTAGCTATCCGTTGTCACTTCATACGTTTACCTAGC
1 ATGATTTAGCTATCCGTTGTCACTTCATACGTTTACCTAGC
51706 TCTAGCCAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.22, C:0.21, G:0.15, T:0.43
Consensus pattern (41 bp):
ATGATTTAGCTATCCGTTGTCACTTCATACGTTTACCTAGC
Found at i:56818 original size:22 final size:22
Alignment explanation
Indices: 56746--56820 Score: 82
Period size: 22 Copynumber: 3.4 Consensus size: 22
56736 CATCAACAAA
56746 TAATTTTAAAATTATTAAAATTAT
1 TAATTTTAAAA-TA-TAAAATTAT
** *
56770 T--TTTTAAAATATAATTTTTT
1 TAATTTTAAAATATAAAATTAT
*
56790 TATTTTTAAAATATAAAATTAT
1 TAATTTTAAAATATAAAATTAT
56812 TAATTTTAA
1 TAATTTTAA
56821 TTTCCAATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
20 7 0.17
21 2 0.05
22 32 0.76
24 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATTTTAAAATATAAAATTAT
Found at i:57654 original size:11 final size:11
Alignment explanation
Indices: 57638--57726 Score: 86
Period size: 11 Copynumber: 8.6 Consensus size: 11
57628 GATAATGATT
57638 ATAATTTTAAA
1 ATAATTTTAAA
57649 ATAATTTTAAA
1 ATAATTTTAAA
*
57660 TTAATTTTAAA
1 ATAATTTTAAA
57671 ATAATTTT--A
1 ATAATTTTAAA
57680 ATAATTTT---
1 ATAATTTTAAA
57688 AT-ATTTTAAAAA
1 ATAATTTT--AAA
57700 ATAATTTT--A
1 ATAATTTTAAA
57709 ATAATTTTAAA
1 ATAATTTTAAA
*
57720 ATTATTT
1 ATAATTT
57727 GCTGACGTGT
Statistics
Matches: 67, Mismatches: 3, Indels: 16
0.78 0.03 0.19
Matches are distributed among these distances:
7 5 0.07
8 2 0.03
9 18 0.27
11 35 0.52
12 2 0.03
13 5 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
ATAATTTTAAA
Found at i:57702 original size:20 final size:22
Alignment explanation
Indices: 57679--57720 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
57669 AAATAATTTT
57679 AATAATTTT-AT-ATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
57699 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
57721 TTATTTGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 2 0.10
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:60660 original size:16 final size:16
Alignment explanation
Indices: 60636--60667 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
60626 AATATTGTTT
60636 TATACTTTTTAATTTA
1 TATACTTTTTAATTTA
*
60652 TATATTTTTTAATTTA
1 TATACTTTTTAATTTA
60668 AAAAACTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (16 bp):
TATACTTTTTAATTTA
Found at i:60808 original size:9 final size:9
Alignment explanation
Indices: 60796--60833 Score: 67
Period size: 9 Copynumber: 4.1 Consensus size: 9
60786 TTTCTTTTTA
60796 TTTATAATT
1 TTTATAATT
60805 TTTATACATT
1 TTTATA-ATT
60815 TTTATAATT
1 TTTATAATT
60824 TTTATAATT
1 TTTATAATT
60833 T
1 T
60834 AAAAAGCTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 19 0.68
10 9 0.32
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (9 bp):
TTTATAATT
Found at i:60820 original size:19 final size:18
Alignment explanation
Indices: 60796--60833 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
60786 TTTCTTTTTA
60796 TTTATAATTTTTATACATT
1 TTTATAATTTTTATA-ATT
60815 TTTATAATTTTTATAATT
1 TTTATAATTTTTATAATT
60833 T
1 T
60834 AAAAAGCTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTATAATTTTTATAATT
Found at i:62677 original size:21 final size:22
Alignment explanation
Indices: 62629--62687 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
62619 GAAAAGATGA
**
62629 ATGAATAGTGAATAATCTCTTGC
1 ATGAATAGTGAAT-ATCTCTAAC
*
62652 CTGAATAGTGAAT-TCTCTAAC
1 ATGAATAGTGAATATCTCTAAC
*
62673 ATGAACAGTGAATAT
1 ATGAATAGTGAATAT
62688 TTTTTGCAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 17 0.57
22 1 0.03
23 12 0.40
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (22 bp):
ATGAATAGTGAATATCTCTAAC
Found at i:62725 original size:23 final size:23
Alignment explanation
Indices: 62673--62734 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
62663 ATTCTCTAAC
* *
62673 ATGAACAGTGAATATTTTTTGCA
1 ATGAACAGTGAAAATTATTTGCA
* * *
62696 ATAAACAGTAAAAATTATTTGCT
1 ATGAACAGTGAAAATTATTTGCA
*
62719 ATGAACAATGAAAATT
1 ATGAACAGTGAAAATT
62735 CTCTGAAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (23 bp):
ATGAACAGTGAAAATTATTTGCA
Found at i:66579 original size:20 final size:18
Alignment explanation
Indices: 66554--66592 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
66544 TCTCAAGCTC
66554 CTTCTTTAAATTATCTATTT
1 CTTCTTTAAA-TATCT-TTT
*
66574 CTTCTTTCAATATCTTTT
1 CTTCTTTAAATATCTTTT
66592 C
1 C
66593 CTCCTCTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 5 0.28
20 9 0.50
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.59
Consensus pattern (18 bp):
CTTCTTTAAATATCTTTT
Found at i:70466 original size:19 final size:17
Alignment explanation
Indices: 70434--70468 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
70424 AGTTTAGGAA
70434 TCAAAAATTATATTATC
1 TCAAAAATTATATTATC
70451 TCAAATAATATATATTAT
1 TCAAA-AAT-TATATTAT
70469 ACTCCCTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (17 bp):
TCAAAAATTATATTATC
Found at i:76249 original size:52 final size:52
Alignment explanation
Indices: 76106--76292 Score: 261
Period size: 52 Copynumber: 3.6 Consensus size: 52
76096 AATGAAAAAG
*
76106 GGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTAAGGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTAAGGATTATGA
* * *
76158 GGTCCGGTGAC--TGTGTCATTGTGAGTATATGAATCCTTTATGGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTAAGGATTATGA
* * * * *
76208 GGTCCGATGGCTATGTGTCATCGTGAGTATAAGAATTCTTTACGAATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTAAGGATTATGA
* *
76260 GGTCCGGTGGCTATGTGTCATCGTGAGTATATG
1 GGTCCGATGACTATGTGTCATCGTGAGTATATG
76293 GATGAAATGA
Statistics
Matches: 120, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
50 45 0.38
52 75 0.62
ACGTcount: A:0.24, C:0.13, G:0.28, T:0.35
Consensus pattern (52 bp):
GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTAAGGATTATGA
Found at i:77937 original size:14 final size:14
Alignment explanation
Indices: 77914--77943 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
77904 TCATATTCCC
77914 TTTATATTTTTAAT
1 TTTATATTTTTAAT
*
77928 TTTATGTTTTTAAT
1 TTTATATTTTTAAT
77942 TT
1 TT
77944 AATTTTTCAA
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:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (14 bp):
TTTATATTTTTAAT
Found at i:85021 original size:43 final size:41
Alignment explanation
Indices: 84965--85081 Score: 128
Period size: 41 Copynumber: 2.8 Consensus size: 41
84955 AGTTTTCTCG
*
84965 ATTGCAATCTTATTTCAGTTCATTTCTTTCCTTAGGTTTCTCA
1 ATTGCAATTTTATTTCAGTTCATTTCTTTCCTTAGG-TT-TCA
** * * * *
85008 ATTGTGATTTTATTTCAGTTTACTCCATTT-TTTAGGTTTCA
1 ATTGCAATTTTATTTCAGTTCATTTC-TTTCCTTAGGTTTCA
*
85049 ATTGCAATTTTATTTCAGTTGATTTCTTTCCTT
1 ATTGCAATTTTATTTCAGTTCATTTCTTTCCTT
85082 TCTAGAATAG
Statistics
Matches: 59, Mismatches: 13, Indels: 6
0.76 0.17 0.08
Matches are distributed among these distances:
40 3 0.05
41 26 0.44
42 2 0.03
43 25 0.42
44 3 0.05
ACGTcount: A:0.19, C:0.16, G:0.10, T:0.55
Consensus pattern (41 bp):
ATTGCAATTTTATTTCAGTTCATTTCTTTCCTTAGGTTTCA
Found at i:85062 original size:41 final size:43
Alignment explanation
Indices: 84952--85068 Score: 123
Period size: 43 Copynumber: 2.8 Consensus size: 43
84942 CTACTTGAGA
* * * * *
84952 CTTAGTTTTCTCGATTGCAATCTTATTTCAGTTCATTTCTTTC
1 CTTAGGTTTCTCAATTGCAATTTTATTTCAGTTCACTCCTTTC
** *
84995 CTTAGGTTTCTCAATTGTGATTTTATTTCAGTTTACTCCATTT-
1 CTTAGGTTTCTCAATTGCAATTTTATTTCAGTTCACTCC-TTTC
*
85038 TTTAGG-TT-TCAATTGCAATTTTATTTCAGTT
1 CTTAGGTTTCTCAATTGCAATTTTATTTCAGTT
85069 GATTTCTTTC
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 21 0.34
42 2 0.03
43 36 0.58
44 3 0.05
ACGTcount: A:0.19, C:0.16, G:0.11, T:0.54
Consensus pattern (43 bp):
CTTAGGTTTCTCAATTGCAATTTTATTTCAGTTCACTCCTTTC
Found at i:90569 original size:60 final size:60
Alignment explanation
Indices: 90434--90569 Score: 182
Period size: 60 Copynumber: 2.3 Consensus size: 60
90424 CAATTTGATC
* ** ** *
90434 CTAAATCTAAAAATTCGATAAATTTAGCCCTCAATGTTTACAAAATTTGTTATTTTAGTT
1 CTAATTCTAAAAATTTAATAAATTTAGCCCTCAACATTTACAAAATTTGTTACTTTAGTT
** * *
90494 CCGATTTTAAAAATTTAATAAATTTATCCCTCAACATTTACAAAATTTGTTACTTTAGTT
1 CTAATTCTAAAAATTTAATAAATTTAGCCCTCAACATTTACAAAATTTGTTACTTTAGTT
90554 CTAATTCTAAAAATTT
1 CTAATTCTAAAAATTT
90570 GAAATTTTTT
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.43
Consensus pattern (60 bp):
CTAATTCTAAAAATTTAATAAATTTAGCCCTCAACATTTACAAAATTTGTTACTTTAGTT
Found at i:93186 original size:3 final size:3
Alignment explanation
Indices: 93178--93214 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
93168 CTCCAACAAT
93178 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
93215 ACTAAGAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:93788 original size:2 final size:2
Alignment explanation
Indices: 93776--93807 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
93766 TCTTTTCAAA
93776 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT A
93808 ACTCAATTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:94889 original size:22 final size:24
Alignment explanation
Indices: 94861--94905 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
94851 CAAATACGGT
*
94861 TTTAATAT-CATTT-GGTCCTTGG
1 TTTAATATCCATTTAAGTCCTTGG
94883 TTTAATATCCATTTAAGTCCTTG
1 TTTAATATCCATTTAAGTCCTTG
94906 TTCAATTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
23 5 0.25
24 7 0.35
ACGTcount: A:0.22, C:0.16, G:0.13, T:0.49
Consensus pattern (24 bp):
TTTAATATCCATTTAAGTCCTTGG
Found at i:95940 original size:25 final size:23
Alignment explanation
Indices: 95912--95957 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
95902 GTTGGATTCA
95912 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
95937 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
95958 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:98275 original size:23 final size:23
Alignment explanation
Indices: 98246--98291 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
98236 TCACAATTGC
98246 TTTTTCACCTGAGATTGATTCAT
1 TTTTTCACCTGAGATTGATTCAT
98269 TTTTTCACCTGAGATTGATTCAT
1 TTTTTCACCTGAGATTGATTCAT
98292 AGGTTCCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.17, G:0.13, T:0.48
Consensus pattern (23 bp):
TTTTTCACCTGAGATTGATTCAT
Found at i:106815 original size:24 final size:23
Alignment explanation
Indices: 106776--106822 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
106766 ATGGATGTTC
*
106776 AACCTTTATCTCCTTTGACCTTT
1 AACCTTTATCTCCTTTAACCTTT
*
106799 AACCTTTCATCTTCTTTAACCTTT
1 AACCTTT-ATCTCCTTTAACCTTT
106823 CATATTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.19, C:0.30, G:0.02, T:0.49
Consensus pattern (23 bp):
AACCTTTATCTCCTTTAACCTTT
Found at i:111793 original size:51 final size:51
Alignment explanation
Indices: 111724--111855 Score: 203
Period size: 51 Copynumber: 2.6 Consensus size: 51
111714 AAAAGGTCCA
* *
111724 ATGACTAAGTGTTATCGTGAGTAAATGAATCCTTTACGGATTAGAGGTC-T
1 ATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTACAGGTCGT
*
111774 GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTACAGGTCGT
1 -ATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTACAGGTCGT
* *
111826 ATGACTAATTGTCATCGTGAGTATATGAAT
1 ATGACTAAGTGTCATCGTGAGTAAATGAAT
111856 TCTTATATGA
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
51 74 0.99
52 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.34
Consensus pattern (51 bp):
ATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTACAGGTCGT
Found at i:112519 original size:21 final size:24
Alignment explanation
Indices: 112494--112550 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 24
112484 GACTTGAGTT
112494 GTATCGGTAGTTAAAT-TAT-G-A
1 GTATCGGTAGTTAAATGTATAGAA
* **
112515 GTATCGATAGTTGTATGTATAGAA
1 GTATCGGTAGTTAAATGTATAGAA
112539 GTATCGGTAGTT
1 GTATCGGTAGTT
112551 TGCATACTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 13 0.45
22 3 0.10
23 1 0.03
24 12 0.41
ACGTcount: A:0.30, C:0.05, G:0.26, T:0.39
Consensus pattern (24 bp):
GTATCGGTAGTTAAATGTATAGAA
Found at i:114522 original size:17 final size:17
Alignment explanation
Indices: 114502--114542 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
114492 TCCCTTGACT
114502 TTTAACCTTCCATCTTC
1 TTTAACCTTCCATCTTC
* *
114519 TTTAACCTTTCATGTTC
1 TTTAACCTTCCATCTTC
114536 TTGTAAC
1 TT-TAAC
114543 TACTTTTTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.20, C:0.27, G:0.05, T:0.49
Consensus pattern (17 bp):
TTTAACCTTCCATCTTC
Found at i:118204 original size:2 final size:2
Alignment explanation
Indices: 118199--118244 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
118189 CAAAAAAGTA
118199 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
118241 AT AT
1 AT AT
118245 TATGTTTAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:122568 original size:5 final size:5
Alignment explanation
Indices: 122558--122587 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
122548 CGCAGATACC
122558 AAGGG AAGGG AAGGG AAGGG AAGGG AAGGG
1 AAGGG AAGGG AAGGG AAGGG AAGGG AAGGG
122588 TAGTGAGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (5 bp):
AAGGG
Found at i:126554 original size:25 final size:25
Alignment explanation
Indices: 126524--126573 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
126514 AAATTTAATT
126524 TACGTTACTAAGAAAGTATGAAAAA
1 TACGTTACTAAGAAAGTATGAAAAA
126549 TACGTTACTAAGAAAGTATGAAAAA
1 TACGTTACTAAGAAAGTATGAAAAA
126574 AAAAATCTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.08, G:0.16, T:0.24
Consensus pattern (25 bp):
TACGTTACTAAGAAAGTATGAAAAA
Found at i:131224 original size:25 final size:24
Alignment explanation
Indices: 131190--131237 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
131180 TGGAAATTAA
* *
131190 AAAATATATAGAATTTTTAAAAAAT
1 AAAACATATA-AATTTATAAAAAAT
131215 AAAACATATAAATTTATAAAAAA
1 AAAACATATAAATTTATAAAAAA
131238 ACCTAAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (24 bp):
AAAACATATAAATTTATAAAAAAT
Found at i:131238 original size:25 final size:25
Alignment explanation
Indices: 131190--131238 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
131180 TGGAAATTAA
* *
131190 AAAATATATAGAATTTTTAAAAAAT
1 AAAACATATAGAATTTTAAAAAAAT
131215 AAAACATATA-AATTTATAAAAAAA
1 AAAACATATAGAATTT-TAAAAAAA
131239 CCTAAACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (25 bp):
AAAACATATAGAATTTTAAAAAAAT
Found at i:139002 original size:113 final size:113
Alignment explanation
Indices: 138857--139086 Score: 390
Period size: 113 Copynumber: 2.0 Consensus size: 113
138847 CCATTAGCCC
* *
138857 AAAGAAACTTAACGGAAAGAAGATATTGGAACCAAAGATATTGAATCTTTTGGTTAATAGGTTTT
1 AAAGAAACTTAACGGAAAGAAGATATTAGAACCAAAGATATTGAATCTTTTGATTAATAGGTTTT
* * * *
138922 AAAGATTCAAGCTTTGAGATAGATTTGTAACTAAAGATATTGGAATCA
66 AAAGATTCAAGCTTTGAAACAGATTTGTAACTAAAAATACTGGAATCA
138970 AAAGAAACTTAAC-GAAGAGAAGATATTAGAACCAAAGATATTGAATCTTTTGATTAATAGGTTT
1 AAAGAAACTTAACGGAA-AGAAGATATTAGAACCAAAGATATTGAATCTTTTGATTAATAGGTTT
139034 TAAAGATTCAAGCTTTGAAACAGATTTGTAACTAAAAATACTGGAATCA
65 TAAAGATTCAAGCTTTGAAACAGATTTGTAACTAAAAATACTGGAATCA
139083 AAAG
1 AAAG
139087 GGATGAAGAT
Statistics
Matches: 110, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
112 3 0.03
113 107 0.97
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.30
Consensus pattern (113 bp):
AAAGAAACTTAACGGAAAGAAGATATTAGAACCAAAGATATTGAATCTTTTGATTAATAGGTTTT
AAAGATTCAAGCTTTGAAACAGATTTGTAACTAAAAATACTGGAATCA
Found at i:139099 original size:6 final size:6
Alignment explanation
Indices: 139088--139113 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
139078 AATCAAAAGG
139088 GATGAA GATGAA GATGAA GATGAA GA
1 GATGAA GATGAA GATGAA GATGAA GA
139114 AGAGAAATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.35, T:0.15
Consensus pattern (6 bp):
GATGAA
Found at i:139204 original size:16 final size:16
Alignment explanation
Indices: 139167--139207 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
139157 TTAGGGTTTA
* *
139167 AAATTTTTAATTAATT
1 AAATATTTATTTAATT
139183 -AA-ATTTATTTAATT
1 AAATATTTATTTAATT
139197 AAATATTTATT
1 AAATATTTATT
139208 CTCAAGTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 10 0.48
15 4 0.19
16 7 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AAATATTTATTTAATT
Found at i:144287 original size:24 final size:24
Alignment explanation
Indices: 144258--144305 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
144248 CATGATTAAA
*
144258 ATCACGCACCACTAAATTTCCATC
1 ATCACGCACCACTAAACTTCCATC
*
144282 ATCACGCATCACTAAACTTCCATC
1 ATCACGCACCACTAAACTTCCATC
144306 TTGGCCTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.33, C:0.38, G:0.04, T:0.25
Consensus pattern (24 bp):
ATCACGCACCACTAAACTTCCATC
Found at i:152045 original size:18 final size:19
Alignment explanation
Indices: 152022--152061 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
152012 AATCCAACAC
152022 AAATATA-AATAATACA-AA
1 AAATATATAA-AATACATAA
152040 AAATATATAAAATACATAA
1 AAATATATAAAATACATAA
152059 AAA
1 AAA
152062 GCATGTGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (19 bp):
AAATATATAAAATACATAA
Found at i:162479 original size:17 final size:17
Alignment explanation
Indices: 162439--162480 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
162429 TAAAGAAATT
*
162439 TTATTAAAATTAGAAACA
1 TTATT-AAATTAGAAAAA
*
162457 -TGTTAAATTAGAAAAA
1 TTATTAAATTAGAAAAA
162473 TTATTAAA
1 TTATTAAA
162481 AATAAATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (17 bp):
TTATTAAATTAGAAAAA
Found at i:163077 original size:10 final size:10
Alignment explanation
Indices: 163064--163099 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
163054 AATAAAAATC
163064 TATATTTTTT
1 TATATTTTTT
*
163074 TATAATTTTT
1 TATATTTTTT
163084 T-TATTTTTT
1 TATATTTTTT
163093 TATATTT
1 TATATTT
163100 CATAAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (10 bp):
TATATTTTTT
Found at i:163276 original size:18 final size:18
Alignment explanation
Indices: 163250--163305 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
163240 TTAATATTAT
*
163250 ATTTCATAATTTTTAA-A
1 ATTTTATAATTTTTAATA
*
163267 CATTTTATAATATTTAATA
1 -ATTTTATAATTTTTAATA
*
163286 GTTTTAATAATTTTT-ATA
1 ATTTT-ATAATTTTTAATA
163304 AT
1 AT
163306 ATTTTTTATG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
18 22 0.71
19 9 0.29
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (18 bp):
ATTTTATAATTTTTAATA
Found at i:166191 original size:93 final size:94
Alignment explanation
Indices: 166058--166241 Score: 273
Period size: 93 Copynumber: 2.0 Consensus size: 94
166048 ATGGTATTTA
* * *
166058 TTGACCAAGATAGCTTTTCTTGTAATGGTTCATGGACACTGGACTTAAATATTGACTCTTCT-AG
1 TTGACCAAGATAGCTTGTCTTGTAATGGCTCATAGACACTGGACTTAAATATTGACTCTTCTAAG
** *
166122 CGGTTGTTTATTATGCATGTATGTGATTG
66 CGGTCATTTATTATGCATGGATGTGATTG
166151 TTGACCAAGATAGCTTGTCTTGTAGA-GGCTCATAGACACTGGACTTAAATATTGACTCTTCTAA
1 TTGACCAAGATAGCTTGTCTTGTA-ATGGCTCATAGACACTGGACTTAAATATTGACTCTTCTAA
* *
166215 GTGGTCATTTATTGTGCATGGATGTGA
65 GCGGTCATTTATTATGCATGGATGTGA
166242 GTCCATCTTG
Statistics
Matches: 81, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
93 57 0.70
94 24 0.30
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (94 bp):
TTGACCAAGATAGCTTGTCTTGTAATGGCTCATAGACACTGGACTTAAATATTGACTCTTCTAAG
CGGTCATTTATTATGCATGGATGTGATTG
Found at i:178547 original size:19 final size:17
Alignment explanation
Indices: 178501--178548 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
178491 TGTTTCGTTT
178501 TTTTTAATTTCTCTTTA
1 TTTTTAATTTCTCTTTA
* *
178518 TTTTGTTATTTTTCTATTA
1 TTTT-TAATTTCTCT-TTA
178537 TATTTTAATTTC
1 T-TTTTAATTTC
178549 ATTTGAAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
17 4 0.17
18 8 0.33
19 9 0.38
20 3 0.12
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.71
Consensus pattern (17 bp):
TTTTTAATTTCTCTTTA
Found at i:184534 original size:12 final size:12
Alignment explanation
Indices: 184482--184526 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
184472 TTTTTTTTTT
*
184482 TATTTCAAATAA
1 TATTTTAAATAA
**
184494 TATTCAAAATAAA
1 TATTTTAAAT-AA
184507 TATTTTAAATAA
1 TATTTTAAATAA
184519 TATTTTAA
1 TATTTTAA
184527 TACATATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 18 0.64
13 10 0.36
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (12 bp):
TATTTTAAATAA
Found at i:184818 original size:19 final size:19
Alignment explanation
Indices: 184794--184831 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
184784 TAATATTATA
*
184794 TATTTTTAAATTTAATTTT
1 TATTTTTAAATTAAATTTT
*
184813 TATTTTTTAATTAAATTTT
1 TATTTTTAAATTAAATTTT
184832 ACCTTTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TATTTTTAAATTAAATTTT
Found at i:187579 original size:16 final size:17
Alignment explanation
Indices: 187559--187592 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
187549 TTATATTTTT
187559 ATTTTT-ATT-AATTTG
1 ATTTTTAATTAAATTTG
187574 ATTTTTAATTAAATTTG
1 ATTTTTAATTAAATTTG
187591 AT
1 AT
187593 CTCAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 3 0.18
17 8 0.47
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
ATTTTTAATTAAATTTG
Found at i:187776 original size:2 final size:2
Alignment explanation
Indices: 187769--187793 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
187759 GTCAGACATT
187769 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 T
187794 TCATTTTGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:192472 original size:18 final size:18
Alignment explanation
Indices: 192451--192498 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
192441 CTCACTTGAA
192451 GCTGTGAGCTCATCCAAT
1 GCTGTGAGCTCATCCAAT
* * * *
192469 GCTGCGAGCCCATTCATT
1 GCTGTGAGCTCATCCAAT
*
192487 ACTGTGAGCTCA
1 GCTGTGAGCTCA
192499 AACGAAACTA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (18 bp):
GCTGTGAGCTCATCCAAT
Found at i:197714 original size:66 final size:66
Alignment explanation
Indices: 197608--197736 Score: 213
Period size: 66 Copynumber: 2.0 Consensus size: 66
197598 AATAATGAAG
* *
197608 CACATCCATTAACAAAGAAGTTGATCTATAGCATTGATCTAGAACTAAAGAACCATCAATCCAGG
1 CACATCCATTAACAAAAAAGGTGATCTATAGCATTGATCTAGAACTAAAGAACCATCAATCCAGG
197673 T
66 T
* * *
197674 CACATTCATTAACAAAAAAGGTGATCTATTGCATTGATCTAGAACTAAAGAACCATCAGTCCA
1 CACATCCATTAACAAAAAAGGTGATCTATAGCATTGATCTAGAACTAAAGAACCATCAATCCA
197737 CTTAAATTTG
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.25
Consensus pattern (66 bp):
CACATCCATTAACAAAAAAGGTGATCTATAGCATTGATCTAGAACTAAAGAACCATCAATCCAGG
T
Found at i:204803 original size:11 final size:11
Alignment explanation
Indices: 204788--204867 Score: 53
Period size: 10 Copynumber: 7.7 Consensus size: 11
204778 TCAGACATAT
*
204788 TAAAAATATTT
1 TAAAAATATTA
204799 TAAAAA-ATTA
1 TAAAAATATTA
*
204809 TATAAATATTA
1 TAAAAATATTA
*
204820 TAAAAA-CTTA
1 TAAAAATATTA
* *
204830 TAAGAA-ATTC
1 TAAAAATATTA
*
204840 TAATAA-ATTA
1 TAAAAATATTA
**
204850 TATTAAT-TTA
1 TAAAAATATTA
204860 TAAAAATA
1 TAAAAATA
204868 ATAAGAAAAA
Statistics
Matches: 54, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
10 39 0.72
11 15 0.28
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (11 bp):
TAAAAATATTA
Found at i:205075 original size:7 final size:7
Alignment explanation
Indices: 205063--205087 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
205053 TTTATTAATA
205063 ATTTATT
1 ATTTATT
205070 ATTTATT
1 ATTTATT
205077 ATTTATT
1 ATTTATT
205084 ATTT
1 ATTT
205088 TAAATTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
ATTTATT
Found at i:205094 original size:14 final size:14
Alignment explanation
Indices: 205054--205087 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
205044 CCTCTCTTTT
*
205054 TTATTAATAATTTA
1 TTATTTATAATTTA
*
205068 TTATTTATTATTTA
1 TTATTTATAATTTA
205082 TTATTT
1 TTATTT
205088 TAAATTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTATTTATAATTTA
Found at i:205712 original size:10 final size:9
Alignment explanation
Indices: 205663--205768 Score: 79
Period size: 9 Copynumber: 11.3 Consensus size: 9
205653 CTTAAGATTA
205663 TTTATAAGTT
1 TTTATAA-TT
* **
205673 ATTATAACA
1 TTTATAATT
205682 TTTATAATTT
1 TTTATAA-TT
* *
205692 TTTGTGATT
1 TTTATAATT
205701 TTTATAAGTT
1 TTTATAA-TT
*
205711 TTTATGATTT
1 TTTAT-AATT
205721 TTTATAATT
1 TTTATAATT
*
205730 TTTATAATA
1 TTTATAATT
*
205739 TTT-TAATA
1 TTTATAATT
205747 TTTATAATTT
1 TTTATAA-TT
*
205757 TTTATAAAT
1 TTTATAATT
205766 TTT
1 TTT
205769 CTTTAAAAAA
Statistics
Matches: 76, Mismatches: 15, Indels: 11
0.75 0.15 0.11
Matches are distributed among these distances:
8 8 0.11
9 34 0.45
10 33 0.43
11 1 0.01
ACGTcount: A:0.32, C:0.01, G:0.05, T:0.62
Consensus pattern (9 bp):
TTTATAATT
Found at i:205733 original size:19 final size:19
Alignment explanation
Indices: 205682--205768 Score: 81
Period size: 19 Copynumber: 4.6 Consensus size: 19
205672 TATTATAACA
*
205682 TTTATAATTTTTTGTGA-TT
1 TTTATAA-TTTTTATGATTT
205701 TTTATAAGTTTTTATGATTT
1 TTTATAA-TTTTTATGATTT
* *
205721 TTTATAATTTTTAT-AATA
1 TTTATAATTTTTATGATTT
* *
205739 TTT-TAATATTTATAATTT
1 TTTATAATTTTTATGATTT
205757 TTTATAAATTTT
1 TTTAT-AATTTT
205769 CTTTAAAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
17 9 0.16
18 10 0.18
19 23 0.41
20 14 0.25
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (19 bp):
TTTATAATTTTTATGATTT
Found at i:205742 original size:29 final size:30
Alignment explanation
Indices: 205682--205768 Score: 58
Period size: 29 Copynumber: 3.1 Consensus size: 30
205672 TATTATAACA
* *
205682 TTTATAATTTTTTGTGATT-TTTATAAGTT
1 TTTATAATATTTTATGATTATTTATAAGTT
* * * *
205711 TTTATGATTTTTTATAATT-TTTATAA-TA
1 TTTATAATATTTTATGATTATTTATAAGTT
* * *
205739 TTT-TAATA-TTTATAATTTTTTATAAATT
1 TTTATAATATTTTATGATTATTTATAAGTT
205767 TT
1 TT
205769 CTTTAAAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
26 9 0.18
27 10 0.20
28 7 0.14
29 23 0.47
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (30 bp):
TTTATAATATTTTATGATTATTTATAAGTT
Found at i:205750 original size:17 final size:17
Alignment explanation
Indices: 205725--205760 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
205715 TGATTTTTTA
*
205725 TAATTTTTATAATATTT
1 TAATATTTATAATATTT
*
205742 TAATATTTATAATTTTT
1 TAATATTTATAATATTT
205759 TA
1 TA
205761 TAAATTTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TAATATTTATAATATTT
Found at i:206118 original size:21 final size:20
Alignment explanation
Indices: 206093--206145 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
206083 CTTTTGTGAT
206093 TTTTAT-ATTTTGCATAAATAA
1 TTTTATAATTTT-CA-AAATAA
*
206114 TTTTATAATTTTTAAAATAA
1 TTTTATAATTTTCAAAATAA
206134 TTTTATAATTTT
1 TTTTATAATTTT
206146 TTTATATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 18 0.60
21 7 0.23
22 5 0.17
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (20 bp):
TTTTATAATTTTCAAAATAA
Found at i:206133 original size:20 final size:20
Alignment explanation
Indices: 206108--206146 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
206098 TATTTTGCAT
206108 AAATAATTTTATAATTTTTA
1 AAATAATTTTATAATTTTTA
206128 AAATAATTTTATAATTTTT
1 AAATAATTTTATAATTTTT
206147 TTATATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
AAATAATTTTATAATTTTTA
Found at i:206164 original size:17 final size:18
Alignment explanation
Indices: 206133--206182 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
206123 TTTTAAAATA
*
206133 ATTTTATAATTTTTTTAT
1 ATTTTATAATATTTTTAT
*
206151 ATTTT-TAATATTTTCAT
1 ATTTTATAATATTTTTAT
206168 -TTTTATAA-ATTTTTA
1 ATTTTATAATATTTTTA
206183 ATGATATTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 10 0.36
17 13 0.46
18 5 0.18
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTTTATAATATTTTTAT
Found at i:211617 original size:22 final size:22
Alignment explanation
Indices: 211579--211622 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
211569 CAGCAAATAA
*
211579 TTTTAAAATTATTAAAATTATTT
1 TTTTAAAATTA-TAAAAATATTT
211602 TTTTAAAA-TATAAAAATATTT
1 TTTTAAAATTATAAAAATATTT
211623 AAAATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 10 0.50
22 2 0.10
23 8 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTTAAAATTATAAAAATATTT
Found at i:211642 original size:29 final size:31
Alignment explanation
Indices: 211582--211650 Score: 108
Period size: 29 Copynumber: 2.3 Consensus size: 31
211572 CAAATAATTT
211582 TAAAATTA-TTAAAATTATTTTTTTAAAATA
1 TAAAATTATTTAAAATTATTTTTTTAAAATA
*
211612 TAAAAATATTTAAAA-TA-TTTTTTAAAATA
1 TAAAATTATTTAAAATTATTTTTTTAAAATA
211641 TAAAATTATT
1 TAAAATTATT
211651 AAATAATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
29 21 0.58
30 9 0.25
31 6 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
TAAAATTATTTAAAATTATTTTTTTAAAATA
Found at i:211659 original size:28 final size:28
Alignment explanation
Indices: 211582--211660 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 28
211572 CAAATAATTT
*
211582 TAAAATTATTAAAATTATTTTTTTAAAATA
1 TAAAATTATT-AAA-TAATTTTTTAAAATA
*
211612 TAAAAATATTTAAA-ATATTTTTTAAAATA
1 TAAAATTA-TTAAATA-ATTTTTTAAAATA
211641 TAAAATTATTAAATAATTTT
1 TAAAATTATTAAATAATTTT
211661 AATTTTTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
28 11 0.26
29 20 0.47
30 10 0.23
31 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
TAAAATTATTAAATAATTTTTTAAAATA
Found at i:212503 original size:29 final size:30
Alignment explanation
Indices: 212478--212550 Score: 121
Period size: 29 Copynumber: 2.4 Consensus size: 30
212468 ATTAAAATTA
212478 TTTAATAATTTTATTATTTCAAAAAAATAAT
1 TTTAATAATTTTA-TATTTCAAAAAAATAAT
*
212509 TTTAATAATTTTATATTT-TAAAAAATAAT
1 TTTAATAATTTTATATTTCAAAAAAATAAT
212538 TTTAATAATTTTA
1 TTTAATAATTTTA
212551 AAATAATTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 23 0.56
30 5 0.12
31 13 0.32
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (30 bp):
TTTAATAATTTTATATTTCAAAAAAATAAT
Found at i:212537 original size:20 final size:22
Alignment explanation
Indices: 212512--212553 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
212502 AAATAATTTT
212512 AATAATTTT-AT-ATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
212532 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
212554 TAATTTGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 2 0.10
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:212554 original size:20 final size:20
Alignment explanation
Indices: 212503--212559 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
212493 ATTTCAAAAA
212503 AATAATTTT--AATAATTTT
1 AATAATTTTAAAATAATTTT
212521 -AT-ATTTTAAAAAATAATTTT
1 AATAATTTT--AAAATAATTTT
212541 AATAATTTTAAAATAATTT
1 AATAATTTTAAAATAATTT
212560 GCTGACGTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
16 5 0.15
17 2 0.06
20 19 0.58
21 2 0.06
22 5 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATAATTTTAAAATAATTTT
Found at i:216113 original size:18 final size:18
Alignment explanation
Indices: 216092--216131 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
216082 ATTCTAAATC
216092 TTCTAGCTCAT-TGTCACA
1 TTCTAGCTCATCT-TCACA
*
216110 TTCTAGTTCATCTTCACA
1 TTCTAGCTCATCTTCACA
216128 TTCT
1 TTCT
216132 GGTTCTTGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.20, C:0.28, G:0.07, T:0.45
Consensus pattern (18 bp):
TTCTAGCTCATCTTCACA
Found at i:216177 original size:165 final size:164
Alignment explanation
Indices: 215996--216515 Score: 871
Period size: 165 Copynumber: 3.2 Consensus size: 164
215986 GCTCTCCCAT
* * * *
215996 AGATTCTAATAATTCTAAGGGTTCTGGTTTAGGTCATGGGGGTTCTATTTCCTCTACAACTTCTA
1 AGATTCTAACAATTCTAAGGATTCTGGTTTAGGTCATGGGGATTCTACTTCCTCTA-AACTTCTA
216061 GTTCTTTATCAGGTTCTAGCCATTCTAAATCTTCTAGCTCATTGTCACATTCTAGTTCATCTTCA
65 GTTCTTTATCAGGTTCTAGCCATTCTAAATCTTCTAGCTCATTGTCACATTCTAGTTCATCTTCA
* *
216126 CATTCTGGTTCTTGGAAGGGTTCCAGCTCATTAGA
130 CATTCTGGTTCTTGGAAGGGTTCTAGCTCATTAGG
** *
216161 AGATTCTAACAATTCTAAGGATTCTGGTTTAGGTCATGGGGATTCTGGTCCCTCTAAACCTTCTA
1 AGATTCTAACAATTCTAAGGATTCTGGTTTAGGTCATGGGGATTCTACTTCCTCTAAA-CTTCTA
* *
216226 GTTCTTTATCAGG-CCGTAGCCATTCTAAATCTTCTAGCTCATTGTCACATTCTAGCTCATCTTC
65 GTTCTTTATCAGGTTC-TAGCCATTCTAAATCTTCTAGCTCATTGTCACATTCTAGTTCATCTTC
216290 ACATTCTGGTTCTTGGAAGGGTTCTAGCTCATTAGG
129 ACATTCTGGTTCTTGGAAGGGTTCTAGCTCATTAGG
216326 AGATTCTAACAATTCTAAGGATTCTGGTTTAGGTCATGGGGATTCTACTTCCTCTAAAACTTCTA
1 AGATTCTAACAATTCTAAGGATTCTGGTTTAGGTCATGGGGATTCTACTTCCTCT-AAACTTCTA
*
216391 GTTCTTTATCAGGTTCTAGCAATTCTAAATCTTCTAGCTCATTGTCACATTCTAGTTCATCTTCA
65 GTTCTTTATCAGGTTCTAGCCATTCTAAATCTTCTAGCTCATTGTCACATTCTAGTTCATCTTCA
* *
216456 CATTCTGGTTCTTGGAAGGGTTCTAGCTCACTCGG
130 CATTCTGGTTCTTGGAAGGGTTCTAGCTCATTAGG
216491 AGATTCTAACAATTCTAAGGATTCT
1 AGATTCTAACAATTCTAAGGATTCT
216516 AGTTCTACTA
Statistics
Matches: 333, Mismatches: 18, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
164 3 0.01
165 326 0.98
166 4 0.01
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.38
Consensus pattern (164 bp):
AGATTCTAACAATTCTAAGGATTCTGGTTTAGGTCATGGGGATTCTACTTCCTCTAAACTTCTAG
TTCTTTATCAGGTTCTAGCCATTCTAAATCTTCTAGCTCATTGTCACATTCTAGTTCATCTTCAC
ATTCTGGTTCTTGGAAGGGTTCTAGCTCATTAGG
Found at i:216278 original size:18 final size:18
Alignment explanation
Indices: 216257--216296 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
216247 ATTCTAAATC
216257 TTCTAGCTCAT-TGTCACA
1 TTCTAGCTCATCT-TCACA
216275 TTCTAGCTCATCTTCACA
1 TTCTAGCTCATCTTCACA
216293 TTCT
1 TTCT
216297 GGTTCTTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.20, C:0.30, G:0.07, T:0.42
Consensus pattern (18 bp):
TTCTAGCTCATCTTCACA
Found at i:216443 original size:18 final size:18
Alignment explanation
Indices: 216422--216461 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
216412 ATTCTAAATC
216422 TTCTAGCTCAT-TGTCACA
1 TTCTAGCTCATCT-TCACA
*
216440 TTCTAGTTCATCTTCACA
1 TTCTAGCTCATCTTCACA
216458 TTCT
1 TTCT
216462 GGTTCTTGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.20, C:0.28, G:0.07, T:0.45
Consensus pattern (18 bp):
TTCTAGCTCATCTTCACA
Found at i:216939 original size:18 final size:18
Alignment explanation
Indices: 216918--216954 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
216908 TTCTGGCTCA
*
216918 TCTTCACATTCTAATTCT
1 TCTTCACATTCCAATTCT
216936 TCTTCACATTCCAATTCT
1 TCTTCACATTCCAATTCT
216954 T
1 T
216955 TTAAGCATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.30, G:0.00, T:0.49
Consensus pattern (18 bp):
TCTTCACATTCCAATTCT
Found at i:216963 original size:18 final size:18
Alignment explanation
Indices: 216918--216964 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
216908 TTCTGGCTCA
* *
216918 TCTTCACATTCTAATTCT
1 TCTTAACATTCCAATTCT
*
216936 TCTTCACATTCCAATTCT
1 TCTTAACATTCCAATTCT
216954 T-TTAAGCATTC
1 TCTTAA-CATTC
216965 AAGTTTTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 3 0.12
18 23 0.88
ACGTcount: A:0.23, C:0.28, G:0.02, T:0.47
Consensus pattern (18 bp):
TCTTAACATTCCAATTCT
Found at i:217480 original size:192 final size:190
Alignment explanation
Indices: 217236--217805 Score: 556
Period size: 192 Copynumber: 3.0 Consensus size: 190
217226 TAGTGCTACT
* * * * * **
217236 ACAAACTTGGGTTCCAACAATTCTAAAGATACTGGTTCTACTACTACTTCTCAGTCTTCATTAAA
1 ACAAAC-TAGGTTCCAACAATTCTAAGGATTCTGATTCTATTACGGCTTCTCAGTCTTCATTAAA
** *
217301 TCATAAGGCTTCTAATTCCTCTGCAAGTTCTAGTTCTTTATCAGGTTCTAGCAATTATACAGCTT
65 TCATGGGGCTTCTAATTCCTCTACAAGTTCTAGTTCTTTATCAGGTTCTAGCAATTATA-AGCTT
* * * *
217366 CAGGCTTATCCACAGATTCCAATTCATCTTTACATTCTGGTTCTAGTGCTACTAACTCATCC
129 CTGGCTCATCCTCAAATTCCAATTCATCTTTACATTCTGGTTCTAGTGCTACTAACTCATCC
* *
217428 ACAAACTCAGGTTCCAACTATTCTAAGGATTCTGATTCTATTACGGCTTCTCAGTCTTTATTAAA
1 ACAAACT-AGGTTCCAACAATTCTAAGGATTCTGATTCTATTACGGCTTCTCAGTCTTCATTAAA
* ** * * ** * *
217493 TCATGGGGCTACTCCTTCCTCCACAAGTTCTCA-TTCTTTATCAGGTTCAAATAGTTCTAAGGCT
65 TCATGGGGCTTCTAATTCCTCTACAAGTTCT-AGTTCTTTATCAGGTTCTAGCAATTATAA-GCT
* * * * * * * * *
217557 TTTGGCTCATCTTTACATTCCAGTTC-T-TTTAAGCATTCTGGTTCTGGTAC-ATCTAAATCTTC
128 TCTGGCTCATCCTCAAATTCCAATTCATCTTT-A-CATTCTGGTTCTAGTGCTA-CTAACTCATC
217619 C
190 C
* * * *
217620 ACAAACATAGGTTCCAACAATTCTAAGGATTCTAATTCTATTGCGG-TTACTCAGTCTACACTAA
1 ACAAAC-TAGGTTCCAACAATTCTAAGGATTCTGATTCTATTACGGCTT-CTCAGTCTTCATTAA
* * * *
217684 ATCACGGGGCTTCTAATTCCTCTTCAAGTTCTGGTTCTTTATCCGGTTCTAGCAATTATAAGACT
64 ATCATGGGGCTTCTAATTCCTCTACAAGTTCTAGTTCTTTATCAGGTTCTAGCAATTATAAG-CT
* ** * ** * *
217749 TCTGGGTCATCCTCAAATTTTATTTCATCTACACATTCCGGTTCTAGTGCTATTAAC
128 TCTGGCTCATCCTCAAATTCCAATTCATCTTTACATTCTGGTTCTAGTGCTACTAAC
217806 CATGAGGCTT
Statistics
Matches: 298, Mismatches: 67, Indels: 26
0.76 0.17 0.07
Matches are distributed among these distances:
190 3 0.01
191 8 0.03
192 281 0.94
193 5 0.02
194 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (190 bp):
ACAAACTAGGTTCCAACAATTCTAAGGATTCTGATTCTATTACGGCTTCTCAGTCTTCATTAAAT
CATGGGGCTTCTAATTCCTCTACAAGTTCTAGTTCTTTATCAGGTTCTAGCAATTATAAGCTTCT
GGCTCATCCTCAAATTCCAATTCATCTTTACATTCTGGTTCTAGTGCTACTAACTCATCC
Found at i:218078 original size:210 final size:210
Alignment explanation
Indices: 217806--218270 Score: 609
Period size: 210 Copynumber: 2.2 Consensus size: 210
217796 TGCTATTAAC
*
217806 CATGAGGCTTCTAATTCCTCTGCAAGTTCTGGTTCTTTATCAGGTTCTAGTAATCATAAGGCTTT
1 CATGAGGCTTCTAATTCCTCTACAAGTTCTGGTTCTTTATCAGGTTCTAGTAATCATAAGGCTTT
* * * * * *
217871 AGGTTCATTCTCAAATTCCAGTTCATCTTCACATTTTGGTTCTTTTAAGCA-TTCTGGTTCTAGT
66 AGGCTCATCCTCAAAATCCAATTCATCTTCACATTCTGGTTCTTTTAAGCACGT-TGGTTCTAGT
* *
217935 GCTGCTAACTCATCCA-CAA-ATTCTAGTTCCAACAATTGTAAAGATTCT-GATTCTACTACGAC
130 GATGCTAACTCAT-CAGCAATA-TCTAGTTCCAACAATTGTAAAGATTCTAG-TCCTACTACGAC
217997 TTCTCAA-TCTTCATTA-AA
192 TTCT-AAGTCTTCATTAGAA
* **
218015 TCATGAGGCTTCTAATTCTTCTACAAGTTCTGGTTCTTTATCAGGTTCTAGTAATTTTAAGGCTT
1 -CATGAGGCTTCTAATTCCTCTACAAGTTCTGGTTCTTTATCAGGTTCTAGTAATCATAAGGCTT
* * * *
218080 TTGGCTCATCCTCAAAATCTAATTCATCTTCACATTCTGGTTCTTTTAAGCACGTTGGTTTTGGT
65 TAGGCTCATCCTCAAAATCCAATTCATCTTCACATTCTGGTTCTTTTAAGCACGTTGGTTCTAGT
* * * * *
218145 GATTCTAACTCATCAGCAATATCTGGTTCCAACAATTTTAAGGATTCTAGTCCTACTATGACTTC
130 GATGCTAACTCATCAGCAATATCTAGTTCCAACAATTGTAAAGATTCTAGTCCTACTACGACTTC
218210 TAAGTCTTCATTAGAA
195 TAAGTCTTCATTAGAA
* ** *
218226 CATGAAGCTTCTGGTTCCTCTACAAGTTCTGGTTCTTTTTCAGGT
1 CATGAGGCTTCTAATTCCTCTACAAGTTCTGGTTCTTTATCAGGT
218271 ACTAAGGCTT
Statistics
Matches: 223, Mismatches: 26, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
209 4 0.02
210 214 0.96
211 5 0.02
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (210 bp):
CATGAGGCTTCTAATTCCTCTACAAGTTCTGGTTCTTTATCAGGTTCTAGTAATCATAAGGCTTT
AGGCTCATCCTCAAAATCCAATTCATCTTCACATTCTGGTTCTTTTAAGCACGTTGGTTCTAGTG
ATGCTAACTCATCAGCAATATCTAGTTCCAACAATTGTAAAGATTCTAGTCCTACTACGACTTCT
AAGTCTTCATTAGAA
Found at i:218372 original size:18 final size:18
Alignment explanation
Indices: 218349--218410 Score: 81
Period size: 18 Copynumber: 3.4 Consensus size: 18
218339 TTTCTCTTTG
*
218349 TCACATTCAAGTTCAGCT
1 TCACATTCAAGTTCAACT
*
218367 TCACATCCAAGTTCAACT
1 TCACATTCAAGTTCAACT
*
218385 TCACATTCTAGTTCATA-T
1 TCACATTCAAGTTCA-ACT
218403 TCACATTC
1 TCACATTC
218411 TGGTTCTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
18 38 0.97
19 1 0.03
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.35
Consensus pattern (18 bp):
TCACATTCAAGTTCAACT
Found at i:218428 original size:18 final size:18
Alignment explanation
Indices: 218407--218441 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
218397 TCATATTCAC
*
218407 ATTCTGGTTCTTTTAAGA
1 ATTCGGGTTCTTTTAAGA
218425 ATTCGGGTTCTTTTAAG
1 ATTCGGGTTCTTTTAAG
218442 GGATCTGGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.11, G:0.20, T:0.49
Consensus pattern (18 bp):
ATTCGGGTTCTTTTAAGA
Found at i:220753 original size:195 final size:195
Alignment explanation
Indices: 220421--221148 Score: 988
Period size: 213 Copynumber: 3.5 Consensus size: 195
220411 GACGTTAATT
*
220421 CTTCCACAACTAATAGCCATAAGGGATTTGATCATACAAGTTCAAGCAATATCGCTCACTCTGGT
1 CTTCCACAACTAATAGCCATAAGGGATTTGATCATACAAGTTCAAGCAATTTCGCTCACTCTGGT
*
220486 TCGTATACAACTTCTGGTCACTCTTCCGCAAGTCATAGTTCTAGTCCTAGTACTAAAGATACAAG
66 TCGTATACAACTTCTGGTCACTCTTCCGCAAGTCATAGTTCTAGTCCTAGTACTAAAGATACAGG
* * *
220551 TACTTCCACAGGCACTAGTACTTCTGTAACAAATGGTCCTACAACTTTTGCTCTTTCTTCGAGCC
131 TACTTCCACAGGCACTAGTACTTCTATGACAAATGGTCCTACAGCTTTTGCTCTTTCTTCGAGCC
220616 CTTCCACAACTAATAGCCATAAGGGATTTGATCATACAAGTTCAAGCAATTTCGCTCACTCTGGT
1 CTTCCACAACTAATAGCCATAAGGGATTTGATCATACAAGTTCAAGCAATTTCGCTCACTCTGGT
* * *
220681 TCGTATACAACTTCTGGTCACTCTTTCGCAAGTCATAGTTCTAGTGCTAGTACTAAAGATACTGG
66 TCGTATACAACTTCTGGTCACTCTTCCGCAAGTCATAGTTCTAGTCCTAGTACTAAAGATACAGG
*
220746 TACTTCCACAGGCACTAGTACTTCTATGACAAATGGTCCTACAGCTTTTGCTCCTTCTTCGAGCC
131 TACTTCCACAGGCACTAGTACTTCTATGACAAATGGTCCTACAGCTTTTGCTCTTTCTTCGAG--
220811 CTTCCACAGGC
194 ------C---C
220822 GTTAGTTCTTCCACAACTAATAGCCATAAGGGATTTGATCATACAAGTTCAAGCAATTTCGCTCA
1 -------CTTCCACAACTAATAGCCATAAGGGATTTGATCATACAAGTTCAAGCAATTTCGCTCA
* *
220887 CTCTGGCTCGTATACAACTTCTGGTCACTCTTCCGCAAGTCATAGTTCTAGTCCTAGAACTAAAG
59 CTCTGGTTCGTATACAACTTCTGGTCACTCTTCCGCAAGTCATAGTTCTAGTCCTAGTACTAAAG
*
220952 ATACAGGTACTTCCACAGGCATTAGTACTTCTATGACAAATGGTCCTACAGCTTTTGCTCCTTCT
124 ATACAGGTACTTCCACAGGCACTAGTACTTCTATGACAAATGGTCCTACAGCTTTTG---C-TCT
**
221017 TTAAGCCCTTCCACAGGCATTAGTA
185 TT-----CTT---C--G----AGCC
*
221042 CTTCCACAACTAATAGCCATAAGGGATTTGATCATACAAGTTCAAGCAATTTCGCTCACTCCGGT
1 CTTCCACAACTAATAGCCATAAGGGATTTGATCATACAAGTTCAAGCAATTTCGCTCACTCTGGT
*
221107 TCGTATACAACTTCTGGTCACACTTCCGCAAGTCATAGTTCT
66 TCGTATACAACTTCTGGTCACTCTTCCGCAAGTCATAGTTCT
221149 GGTTTTAAAA
Statistics
Matches: 476, Mismatches: 21, Indels: 54
0.86 0.04 0.10
Matches are distributed among these distances:
195 184 0.39
203 1 0.00
206 1 0.00
213 278 0.58
216 1 0.00
217 4 0.01
222 3 0.01
225 1 0.00
227 1 0.00
231 2 0.00
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (195 bp):
CTTCCACAACTAATAGCCATAAGGGATTTGATCATACAAGTTCAAGCAATTTCGCTCACTCTGGT
TCGTATACAACTTCTGGTCACTCTTCCGCAAGTCATAGTTCTAGTCCTAGTACTAAAGATACAGG
TACTTCCACAGGCACTAGTACTTCTATGACAAATGGTCCTACAGCTTTTGCTCTTTCTTCGAGCC
Found at i:221651 original size:18 final size:18
Alignment explanation
Indices: 221630--221670 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
221620 AAAATCTGGC
* *
221630 TCTTCTACACATACAGGT
1 TCTTCTAAACACACAGGT
*
221648 TCTTCTAAACACACTGGT
1 TCTTCTAAACACACAGGT
221666 TCTTC
1 TCTTC
221671 CACAACCTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.29, G:0.10, T:0.37
Consensus pattern (18 bp):
TCTTCTAAACACACAGGT
Found at i:221887 original size:198 final size:197
Alignment explanation
Indices: 221544--222785 Score: 1681
Period size: 198 Copynumber: 6.5 Consensus size: 197
221534 ATCCACATAG
* * * * *
221544 CTACCGGTTCTATTTCGAGCCACTATTCAGGTTCTACTTCTCATAAGAGTAATAGTCACACAACT
1 CTACTGGTTCTATTTCGAGCCACTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACACGACT
* * *
221609 TCTACTCATACAAAATCTGGCTCTTCTACACATACAGGTTCTTCTAAACACACTGGTTCTTCCAC
66 TCTGCTCATACAAAATCTGGCTCTTCTACACACACAGGTTCTTC-AAACACATTGGTTCTTCCAC
* * * * * *
221674 AACCTCTGGTTCCAAAACTTTAGGCTCTTCCACAAACATTGGTTCTACTACGACTAATGGCCATA
130 AACCTCTGGTTCCAAAACTTCAGGCTCTTCCACAAGCACTGGTTCTGCTACGACTGATGGCCATG
221739 CAA
195 CAA
* *
221742 CTACTGGTTCTATTTCGAGCCACTCTTCAGGTTCTAATTCTCATAAGACTAATAGTCACATGACT
1 CTACTGGTTCTATTTCGAGCCACTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACACGACT
* ** *
221807 TTTGCTCATACAGGATCTGGCTCTTCTACACACGCAGGTTCTTCTAAACACATTGGTTCTTCCAC
66 TCTGCTCATACAAAATCTGGCTCTTCTACACACACAGGTTCTTC-AAACACATTGGTTCTTCCAC
* * * * * *
221872 AACCTCTGGTTCCAAAACTTCGGGCTCTTCCATAAACACTGGTTCTGTTACGACTAATGACCATG
130 AACCTCTGGTTCCAAAACTTCAGGCTCTTCCACAAGCACTGGTTCTGCTACGACTGATGGCCATG
221937 CAA
195 CAA
* *
221940 CTACTGGTTCTATTTCGAGCCACTTTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACACAACT
1 CTACTGGTTCTATTTCGAGCCACTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACACGACT
*
222005 TCTGCTCATACAAAATCTGGCTCTTCTACACACACAGGTTCATCCAAACACATTGGTTCTTCCAC
66 TCTGCTCATACAAAATCTGGCTCTTCTACACACACAGGTTC-TTCAAACACATTGGTTCTTCCAC
* *
222070 AACCTCTGGTTCCAAAACTTCGGGCTCTTCCACAAGCACTGGTTCTGCTACAACTGATGGCCATG
130 AACCTCTGGTTCCAAAACTTCAGGCTCTTCCACAAGCACTGGTTCTGCTACGACTGATGGCCATG
222135 CAA
195 CAA
* * *
222138 CTACTAGTTCTATTTCGAGCCACTCTTCAGATTCTAGTTCTCATAAGACTAATAGTCACAAGACT
1 CTACTGGTTCTATTTCGAGCCACTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACACGACT
* * * *
222203 TCTGCTCATACAGAATTTGGCTCTTCTAAACACACAGGTTCTTCCAAACACATTGGTTCTTACAC
66 TCTGCTCATACAAAATCTGGCTCTTCTACACACACAGGTTCTT-CAAACACATTGGTTCTTCCAC
* * * * *
222268 AACCTCTGGTTCCAAAACTTCGGGCTCTTCCACAATCACTGGTTCTGCCACAACTGATGGTCATG
130 AACCTCTGGTTCCAAAACTTCAGGCTCTTCCACAAGCACTGGTTCTGCTACGACTGATGGCCATG
222333 CAA
195 CAA
* * *
222336 CTACTGGTTCTATTTCGAGCCACTCTACGGGTTCTAGTTCTCATAAGACTAATAGTCATACGACT
1 CTACTGGTTCTATTTCGAGCCACTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACACGACT
222401 TCTGCTCATACAAAATCTGGCTCTTCTACACACACAGG---TT------C-----TTC-T--ACA
66 TCTGCTCATACAAAATCTGGCTCTTCTACACACACAGGTTCTTCAAACACATTGGTTCTTCCACA
*
222449 ACCTCTGGTTCCAAAACTTCAGGCTCTTCCACAAGCACTGGTTCTACTACGACTGATGGCCATGC
131 ACCTCTGGTTCCAAAACTTCAGGCTCTTCCACAAGCACTGGTTCTGCTACGACTGATGGCCATGC
222514 AA
196 AA
* *
222516 CTACTGGTTCTATTTCGAGCCACTCTTTAGGTTCTACTTCTCATAAGACTAATAGTCACACGACT
1 CTACTGGTTCTATTTCGAGCCACTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACACGACT
*
222581 TCTGCTCATACAGAATCTGGCTCTTCT------ACA-------C--ACACA--GGTTCTTCCACA
66 TCTGCTCATACAAAATCTGGCTCTTCTACACACACAGGTTCTTCAAACACATTGGTTCTTCCACA
*
222629 ATCTCTGGTTCCAAAACTTCAGGCTCTTCCACAAGCACTGGTTCTGCTACGACTGATGGCCATGC
131 ACCTCTGGTTCCAAAACTTCAGGCTCTTCCACAAGCACTGGTTCTGCTACGACTGATGGCCATGC
222694 AA
196 AA
** * *
222696 CTACTGGTTCTATTTCGAGCCACTCTTCAGGTTCTAGTTCTCATAAGGTTGATAGTCAGA-GCAC
1 CTACTGGTTCTATTTCGAGCCACTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACACG-AC
* *
222760 TTCTGCTCCTACAAAATCTTGCTCTT
65 TTCTGCTCATACAAAATCTGGCTCTT
222786 GCACTTGCAC
Statistics
Matches: 950, Mismatches: 81, Indels: 44
0.88 0.08 0.04
Matches are distributed among these distances:
174 4 0.00
177 3 0.00
178 1 0.00
179 1 0.00
180 297 0.31
182 1 0.00
183 3 0.00
188 1 0.00
195 2 0.00
197 1 0.00
198 634 0.67
199 2 0.00
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (197 bp):
CTACTGGTTCTATTTCGAGCCACTCTTCAGGTTCTAGTTCTCATAAGACTAATAGTCACACGACT
TCTGCTCATACAAAATCTGGCTCTTCTACACACACAGGTTCTTCAAACACATTGGTTCTTCCACA
ACCTCTGGTTCCAAAACTTCAGGCTCTTCCACAAGCACTGGTTCTGCTACGACTGATGGCCATGC
AA
Found at i:222260 original size:18 final size:18
Alignment explanation
Indices: 222219--222263 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
222209 CATACAGAAT
* *
222219 TTGGCTCTTCTAAACACA
1 TTGGTTCTTCCAAACACA
**
222237 CAGGTTCTTCCAAACACA
1 TTGGTTCTTCCAAACACA
222255 TTGGTTCTT
1 TTGGTTCTT
222264 ACACAACCTC
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.36
Consensus pattern (18 bp):
TTGGTTCTTCCAAACACA
Found at i:222559 original size:180 final size:179
Alignment explanation
Indices: 222257--222785 Score: 844
Period size: 180 Copynumber: 2.9 Consensus size: 179
222247 CAAACACATT
* * * *
222257 GGTTCTTACACAACCTCTGGTTCCAAAACTTCGGGCTCTTCCACAATCACTGGTTCTGCCACAAC
1 GGTTCTT-CACAACCTCTGGTTCCAAAACTTCAGGCTCTTCCACAAGCACTGGTTCTGCTACGAC
* * *
222322 TGATGGTCATGCAACTACTGGTTCTATTTCGAGCCACTCTACGGGTTCTAGTTCTCATAAGACTA
65 TGATGGCCATGCAACTACTGGTTCTATTTCGAGCCACTCTTCAGGTTCTAGTTCTCATAAGACTA
*
222387 ATAGTCATACGACTTCTGCTCATACAAAATCTGGCTCTTCTACACACACA
130 ATAGTCACACGACTTCTGCTCATACAAAATCTGGCTCTTCTACACACACA
*
222437 GGTTCTTCTACAACCTCTGGTTCCAAAACTTCAGGCTCTTCCACAAGCACTGGTTCTACTACGAC
1 GGTTCTTC-ACAACCTCTGGTTCCAAAACTTCAGGCTCTTCCACAAGCACTGGTTCTGCTACGAC
* *
222502 TGATGGCCATGCAACTACTGGTTCTATTTCGAGCCACTCTTTAGGTTCTACTTCTCATAAGACTA
65 TGATGGCCATGCAACTACTGGTTCTATTTCGAGCCACTCTTCAGGTTCTAGTTCTCATAAGACTA
*
222567 ATAGTCACACGACTTCTGCTCATACAGAATCTGGCTCTTCTACACACACA
130 ATAGTCACACGACTTCTGCTCATACAAAATCTGGCTCTTCTACACACACA
*
222617 GGTTCTTCCACAATCTCTGGTTCCAAAACTTCAGGCTCTTCCACAAGCACTGGTTCTGCTACGAC
1 GGTTCTT-CACAACCTCTGGTTCCAAAACTTCAGGCTCTTCCACAAGCACTGGTTCTGCTACGAC
** *
222682 TGATGGCCATGCAACTACTGGTTCTATTTCGAGCCACTCTTCAGGTTCTAGTTCTCATAAGGTTG
65 TGATGGCCATGCAACTACTGGTTCTATTTCGAGCCACTCTTCAGGTTCTAGTTCTCATAAGACTA
* * *
222747 ATAGTCAGA-GCACTTCTGCTCCTACAAAATCTTGCTCTT
130 ATAGTCACACG-ACTTCTGCTCATACAAAATCTGGCTCTT
222786 GCACTTGCAC
Statistics
Matches: 323, Mismatches: 23, Indels: 6
0.92 0.07 0.02
Matches are distributed among these distances:
179 2 0.01
180 320 0.99
181 1 0.00
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (179 bp):
GGTTCTTCACAACCTCTGGTTCCAAAACTTCAGGCTCTTCCACAAGCACTGGTTCTGCTACGACT
GATGGCCATGCAACTACTGGTTCTATTTCGAGCCACTCTTCAGGTTCTAGTTCTCATAAGACTAA
TAGTCACACGACTTCTGCTCATACAAAATCTGGCTCTTCTACACACACA
Found at i:222894 original size:333 final size:333
Alignment explanation
Indices: 222471--223118 Score: 1043
Period size: 333 Copynumber: 1.9 Consensus size: 333
222461 AAAACTTCAG
* *
222471 GCTCTTCCACAAGCACTGGTTCTACTACGACTGATGGCCATGCAACTACTGGTTCTATTTCGAGC
1 GCTCTTCCACAAGCACTGGTTCTACTACGACTGATGGCCATACAACTACTGGTTCTAATTCGAGC
*
222536 CACTCTTTAGGTTCTACTTCTCATAAGACTAATAGTCACACGACTTCTGCTCATACAGAATCTGG
66 CACTCTTCAGGTTCTACTTCTCATAAGACTAATAGTCACACGACTTCTGCTCATACAGAATCTGG
* *
222601 CTCTTCTACACACAC-AGGTTCTTCCACAATCTCTGGTTCCAAAACTTCAGGCTCTTCCACAAGC
131 CTCTTCTACACAC-CTAGGTTCTTCCACAACCTCTGGTTCCAAAACTTCAGGCTCCTCCACAAGC
* * * *
222665 ACTGGTTCTGCTACGACTGATGGCCATGCAACTACTGGTTCTATTTCGAGCCACTCTTCAGGTTC
195 ACTGGTTCTGCTACAACTAATGGCCATACAACTACTGGTTCTATTTCAAGCCACTCTTCAGGTTC
* * * * *
222730 TAGTTCTCATAAG-GTTGATAGTCAGA-GCACTTCTGCTCCTACAAAATCTTGCTCTTGCACTTG
260 TACTTCTCATAAGAG-TAATAGTCACACG-ACTTCTGCTCATACAAAATCTGGCTCTTGCACTTG
222793 CACACCTATCA
323 CACACCTATCA
* * *
222804 GCTCTTCCACAAGCACTGGTTCTGCTATGACTGATGGCCATACAACTACTGGTTCTAATTCGAGG
1 GCTCTTCCACAAGCACTGGTTCTACTACGACTGATGGCCATACAACTACTGGTTCTAATTCGAGC
* *
222869 CACTCTTCAGGTTCTAGC-TCTCATAAGACTAATAGTCACATGACTTCTGCTCATACAGAATTTG
66 CACTCTTCAGGTTCTA-CTTCTCATAAGACTAATAGTCACACGACTTCTGCTCATACAGAATCTG
222933 GCTCTTCTACACACCTAGGTTCTTCCACAACCTCTGGTTCCAAAACTTCAGGCTCCTCCACAAGC
130 GCTCTTCTACACACCTAGGTTCTTCCACAACCTCTGGTTCCAAAACTTCAGGCTCCTCCACAAGC
* *
222998 ACTGGTTCTGGTACAACTAATGGCCATACAACTACTGGTTCTATTTCAAGCCACTCTTTAGGTTC
195 ACTGGTTCTGCTACAACTAATGGCCATACAACTACTGGTTCTATTTCAAGCCACTCTTCAGGTTC
223063 TACTTCTCATAAGAGTAATAGTCACACGACTTCTGCTCATACAAAATCTGGCTCTT
260 TACTTCTCATAAGAGTAATAGTCACACGACTTCTGCTCATACAAAATCTGGCTCTT
223119 CTACACATAC
Statistics
Matches: 290, Mismatches: 21, Indels: 8
0.91 0.07 0.03
Matches are distributed among these distances:
332 1 0.00
333 286 0.99
334 3 0.01
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.31
Consensus pattern (333 bp):
GCTCTTCCACAAGCACTGGTTCTACTACGACTGATGGCCATACAACTACTGGTTCTAATTCGAGC
CACTCTTCAGGTTCTACTTCTCATAAGACTAATAGTCACACGACTTCTGCTCATACAGAATCTGG
CTCTTCTACACACCTAGGTTCTTCCACAACCTCTGGTTCCAAAACTTCAGGCTCCTCCACAAGCA
CTGGTTCTGCTACAACTAATGGCCATACAACTACTGGTTCTATTTCAAGCCACTCTTCAGGTTCT
ACTTCTCATAAGAGTAATAGTCACACGACTTCTGCTCATACAAAATCTGGCTCTTGCACTTGCAC
ACCTATCA
Found at i:222937 original size:153 final size:153
Alignment explanation
Indices: 222651--222938 Score: 445
Period size: 153 Copynumber: 1.9 Consensus size: 153
222641 AAAACTTCAG
* *
222651 GCTCTTCCACAAGCACTGGTTCTGCTACGACTGATGGCCATGCAACTACTGGTTCTATTTCGAGC
1 GCTCTTCCACAAGCACTGGTTCTGCTACGACTGATGGCCATACAACTACTGGTTCTAATTCGAGC
* ** * * *
222716 CACTCTTCAGGTTCTAGTTCTCATAAGGTTGATAGTCAGAGCACTTCTGCTCCTACAAAATCTTG
66 CACTCTTCAGGTTCTAGCTCTCATAAGACTAATAGTCACAGCACTTCTGCTCATACAAAATCTTG
222781 CTCTTGCACTTGCACACCTATCA
131 CTCTTGCACTTGCACACCTATCA
* *
222804 GCTCTTCCACAAGCACTGGTTCTGCTATGACTGATGGCCATACAACTACTGGTTCTAATTCGAGG
1 GCTCTTCCACAAGCACTGGTTCTGCTACGACTGATGGCCATACAACTACTGGTTCTAATTCGAGC
*
222869 CACTCTTCAGGTTCTAGCTCTCATAAGACTAATAGTCACATG-ACTTCTGCTCATACAGAAT-TT
66 CACTCTTCAGGTTCTAGCTCTCATAAGACTAATAGTCACA-GCACTTCTGCTCATACAAAATCTT
222932 GGCTCTT
130 -GCTCTT
222939 CTACACACCT
Statistics
Matches: 122, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
152 2 0.02
153 119 0.98
154 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (153 bp):
GCTCTTCCACAAGCACTGGTTCTGCTACGACTGATGGCCATACAACTACTGGTTCTAATTCGAGC
CACTCTTCAGGTTCTAGCTCTCATAAGACTAATAGTCACAGCACTTCTGCTCATACAAAATCTTG
CTCTTGCACTTGCACACCTATCA
Found at i:223117 original size:180 final size:181
Alignment explanation
Indices: 222804--223350 Score: 604
Period size: 198 Copynumber: 2.9 Consensus size: 181
222794 ACACCTATCA
* * * *
222804 GCTCTTCCACAAGCACTGGTTCTGCTATGACTGATGGCCATACAACTACTGGTTCTAATTCGAGG
1 GCTCTTCCACAAGCACTGGTTCTGCTATAACTAATGGCCATACAACTACTGGTTCTATTTCGAGC
* * *
222869 CACTCTTCAGGTTCTAGC-TCTCATAAGACTAATAGTCACATGACTTCTGCTCATACAGAATTTG
66 CACTCTTCAGGTTCTA-CTTCTCATAAGACTAATAGTCACACGACTTCTGCTCATACAAAATCTG
222933 GCTCTTCTACACACCT-AGGTTCTTCCACAACCTCTGGTTCCAAAACTTCAG
130 GCTCTTCTACACACCTCAGGTTCTTCCACAACCTCTGGTTCCAAAACTTCAG
* * * *
222984 GCTCCTCCACAAGCACTGGTTCTGGTACAACTAATGGCCATACAACTACTGGTTCTATTTCAAGC
1 GCTCTTCCACAAGCACTGGTTCTGCTATAACTAATGGCCATACAACTACTGGTTCTATTTCGAGC
* *
223049 CACTCTTTAGGTTCTACTTCTCATAAGAGTAATAGTCACACGACTTCTGCTCATACAAAATCTGG
66 CACTCTTCAGGTTCTACTTCTCATAAGACTAATAGTCACACGACTTCTGCTCATACAAAATCTGG
223114 CTCTTCTACACATACAGGTTCTTCCAAACACACTGGTTCTTCCACAACCTCTGGTTCCAAAACTT
131 CTCTTCTACAC--AC-----C-T-------CA--GGTTCTTCCACAACCTCTGGTTCCAAAACTT
*
223179 TAG
179 CAG
* * *
223182 GCTCTTCCACAAACACTGGTTCTACTATAACTAATGGCCATACAGCTACTGGTTCTACTTT-GAG
1 GCTCTTCCACAAGCACTGGTTCTGCTATAACTAATGGCCATACAACTACTGGTTCTA-TTTCGAG
* * * * * *
223246 TCACTCTTCAGGTTTTAGTTCTCATGAGACTAATAGTCGTACAC-A-TTTTTCTCATACAAAATC
65 CCACTCTTCAGGTTCTACTTCTCATAAGACTAATAGTC--ACACGACTTCTGCTCATACAAAATC
* * * *
223309 TGGCCCTTCCACACA-CTCCGGTTCTTCCA-AACACACTGGTTC
128 TGGCTCTTCTACACACCTCAGGTTCTTCCACAAC-CTCTGGTTC
223351 TTTCACAACC
Statistics
Matches: 311, Mismatches: 33, Indels: 46
0.80 0.08 0.12
Matches are distributed among these distances:
179 4 0.01
180 144 0.46
182 3 0.01
187 1 0.00
188 1 0.00
189 1 0.00
190 1 0.00
196 2 0.01
198 146 0.47
199 4 0.01
200 4 0.01
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (181 bp):
GCTCTTCCACAAGCACTGGTTCTGCTATAACTAATGGCCATACAACTACTGGTTCTATTTCGAGC
CACTCTTCAGGTTCTACTTCTCATAAGACTAATAGTCACACGACTTCTGCTCATACAAAATCTGG
CTCTTCTACACACCTCAGGTTCTTCCACAACCTCTGGTTCCAAAACTTCAG
Found at i:223151 original size:18 final size:18
Alignment explanation
Indices: 223130--223170 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
223120 TACACATACA
223130 GGTTCTTCCA-AACACACT
1 GGTTCTTCCACAAC-CACT
*
223148 GGTTCTTCCACAACCTCT
1 GGTTCTTCCACAACCACT
223166 GGTTC
1 GGTTC
223171 CAAAACTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.20, C:0.34, G:0.15, T:0.32
Consensus pattern (18 bp):
GGTTCTTCCACAACCACT
Found at i:223337 original size:18 final size:18
Alignment explanation
Indices: 223314--223357 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
223304 AAATCTGGCC
*
223314 CTTCCACACACTCCGGTT
1 CTTCCACACACACCGGTT
* *
223332 CTTCCAAACACACTGGTT
1 CTTCCACACACACCGGTT
*
223350 CTTTCACA
1 CTTCCACA
223358 ACCTCTGGTC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.39, G:0.09, T:0.30
Consensus pattern (18 bp):
CTTCCACACACACCGGTT
Done.