Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000221.1 Hibiscus syriacus cultivar Beakdansim tig00000391_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: 71788
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:8816 original size:18 final size:19
Alignment explanation
Indices: 8793--8829 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
8783 TCAGTAATCC
8793 TATTCT-CTGATAATCTTT
1 TATTCTACTGATAATCTTT
8811 TATTCTCACTGATAATCTT
1 TATTCT-ACTGATAATCTT
8830 ACATTCCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.24, C:0.19, G:0.05, T:0.51
Consensus pattern (19 bp):
TATTCTACTGATAATCTTT
Found at i:13769 original size:21 final size:22
Alignment explanation
Indices: 13740--13789 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
13730 ATTCACTATA
* *
13740 TTTTCAAAATTATATTTAA-AT
1 TTTTTAAAAATATATTTAATAT
13761 TTTTTAAAAATATATTTAATAT
1 TTTTTAAAAATATATTTAATAT
*
13783 ATTTTAA
1 TTTTTAA
13790 TTTTATTTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
TTTTTAAAAATATATTTAATAT
Found at i:13770 original size:22 final size:22
Alignment explanation
Indices: 13736--13789 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
13726 AGTAATTCAC
*
13736 TATATTTTCAAAATTATATTTAA
1 TATATTTT-AAAAATATATTTAA
*
13759 -ATTTTTTAAAAATATATTTAA
1 TATATTTTAAAAATATATTTAA
13780 TATATTTTAA
1 TATATTTTAA
13790 TTTTATTTCG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
TATATTTTAAAAATATATTTAA
Found at i:14515 original size:28 final size:28
Alignment explanation
Indices: 14471--14527 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
14461 AATATGCTCG
*
14471 ACATCCTCCCTGCTGCTTCAACTCTTCA
1 ACATCCTCCCTGATGCTTCAACTCTTCA
14499 ACATCCTCCCTGATGCTTCAACTCTTCA
1 ACATCCTCCCTGATGCTTCAACTCTTCA
14527 A
1 A
14528 AGCAAGAGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.21, C:0.40, G:0.07, T:0.32
Consensus pattern (28 bp):
ACATCCTCCCTGATGCTTCAACTCTTCA
Found at i:17362 original size:76 final size:75
Alignment explanation
Indices: 17281--17428 Score: 217
Period size: 76 Copynumber: 2.0 Consensus size: 75
17271 TAAACTCAAA
* *
17281 TTTAGGATAATATTTTAAACATTATAT-TTTTTCTTTGTATTTTAGTTTAAATAGGTTTTTAGTA
1 TTTAGGATAATATTTT-AACATTATATCTTTATCTTTGTATTTTAGTTTAAATA-GATTTTAGTA
17345 TTTTAATTAAGT
64 TTTTAATTAAGT
* * * *
17357 TTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGATTTTAGTATT
1 TTTAGGATAATATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGATTTTAGTATT
17422 TTAATTA
66 TTAATTA
17429 GGATTTAGAA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
75 25 0.38
76 40 0.62
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (75 bp):
TTTAGGATAATATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGATTTTAGTATT
TTAATTAAGT
Found at i:17591 original size:64 final size:64
Alignment explanation
Indices: 17393--17563 Score: 317
Period size: 64 Copynumber: 2.7 Consensus size: 64
17383 CTTTATCTTT
17393 GTATTTTAGTTTAAATAGATTTT-AGTATTTTAATTAGGATTTAGAATATTATATTATTTTTTAG
1 GTATTTTAGTTTAAATAG-TTTTAAGTATTTTAATTAGGATTTAGAATATTATATTATTTTTTAG
17457 GTATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTAGAATATTATATTATTTTTTAG
1 GTATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTAGAATATTATATTATTTTTTAG
*
17521 GTATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGGATTTA
1 GTATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTA
17564 AGATGTTTTA
Statistics
Matches: 105, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
63 4 0.04
64 101 0.96
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.54
Consensus pattern (64 bp):
GTATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTAGAATATTATATTATTTTTTAG
Found at i:17677 original size:12 final size:12
Alignment explanation
Indices: 17660--17689 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
17650 TACAATCTTC
17660 TCTTTCTCTCTA
1 TCTTTCTCTCTA
17672 TCTTTCTCTCTA
1 TCTTTCTCTCTA
*
17684 TTTTTC
1 TCTTTC
17690 GCATACTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.30, G:0.00, T:0.63
Consensus pattern (12 bp):
TCTTTCTCTCTA
Found at i:18179 original size:18 final size:18
Alignment explanation
Indices: 18156--18198 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
18146 CTTTAATTTG
*
18156 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
18174 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
18192 TTTATTT
1 TTTATTT
18199 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:18280 original size:16 final size:17
Alignment explanation
Indices: 18234--18283 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
18224 CCTTTTATAT
*
18234 TTATTAGTATTAATATTTA
1 TTATTA-TATT-ATTTTTA
18253 TTATTATATTATTTTTA
1 TTATTATATTATTTTTA
*
18270 TT-TTATTTTATTTT
1 TTATTATATTATTTT
18284 AATATATCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 11 0.38
17 8 0.28
18 4 0.14
19 6 0.21
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (17 bp):
TTATTATATTATTTTTA
Found at i:26957 original size:14 final size:15
Alignment explanation
Indices: 26938--26966 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
26928 CATTATCTTG
26938 TTTCTTTATT-ATTT
1 TTTCTTTATTGATTT
26952 TTTCTTTATTGATTT
1 TTTCTTTATTGATTT
26967 ATTCGATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.14, C:0.07, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTCTTTATTGATTT
Found at i:28308 original size:21 final size:21
Alignment explanation
Indices: 28284--28326 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
28274 GCTTCACTAC
* *
28284 AAGATTTTATGGCCTCGACAA
1 AAGATTTCATGGCCTCAACAA
*
28305 AAGATTTCATGGCTTCAACAA
1 AAGATTTCATGGCCTCAACAA
28326 A
1 A
28327 GGTCTTAATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (21 bp):
AAGATTTCATGGCCTCAACAA
Found at i:35629 original size:20 final size:20
Alignment explanation
Indices: 35493--35620 Score: 238
Period size: 20 Copynumber: 6.4 Consensus size: 20
35483 GTTTCTAAAT
35493 TCGCAACGCGAATATGTGAA
1 TCGCAACGCGAATATGTGAA
35513 TCGCAACGCGAATATGTGAA
1 TCGCAACGCGAATATGTGAA
35533 TCGCAACGCGAATATGTGAA
1 TCGCAACGCGAATATGTGAA
35553 TCGCAACGCGAATATGTGAA
1 TCGCAACGCGAATATGTGAA
*
35573 TCGCAACGCGAATTTGTGAA
1 TCGCAACGCGAATATGTGAA
*
35593 TCGCAACGCGAATTTGTGAA
1 TCGCAACGCGAATATGTGAA
35613 TCGCAACG
1 TCGCAACG
35621 TAAATTTGTA
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
20 107 1.00
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAATATGTGAA
Found at i:35653 original size:20 final size:20
Alignment explanation
Indices: 35630--35671 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
35620 GTAAATTTGT
*
35630 AATTCACAACACATAAGTCA
1 AATTCACAACACAGAAGTCA
*
35650 AATTCGCAACACAGAAGTCA
1 AATTCACAACACAGAAGTCA
35670 AA
1 AA
35672 GCGCGTTTAT
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:0.50, C:0.24, G:0.10, T:0.17
Consensus pattern (20 bp):
AATTCACAACACAGAAGTCA
Found at i:36185 original size:20 final size:20
Alignment explanation
Indices: 36162--36203 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
36152 TTGAAACTTA
* *
36162 GATTTTTATTTTCGCGTTGC
1 GATTTTCATTTTCGCATTGC
36182 GATTTTCATTTTCGCATTGC
1 GATTTTCATTTTCGCATTGC
36202 GA
1 GA
36204 ATTTAAGTTT
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:0.14, C:0.17, G:0.19, T:0.50
Consensus pattern (20 bp):
GATTTTCATTTTCGCATTGC
Found at i:36214 original size:20 final size:20
Alignment explanation
Indices: 36171--36214 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
36161 AGATTTTTAT
* * * *
36171 TTTCGCGTTGCGATTTTCAT
1 TTTCGCATTGCGAATTTAAG
36191 TTTCGCATTGCGAATTTAAG
1 TTTCGCATTGCGAATTTAAG
36211 TTTC
1 TTTC
36215 AGAAACTACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.48
Consensus pattern (20 bp):
TTTCGCATTGCGAATTTAAG
Found at i:38393 original size:42 final size:42
Alignment explanation
Indices: 38341--38459 Score: 157
Period size: 42 Copynumber: 2.8 Consensus size: 42
38331 GATGTACCTA
* * * *
38341 TCATCATTCAAGAGGCGCCTCCTATCATTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTCCCACCATTCAAGAGGCCCCTC
* * *
38383 TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCTTG
1 TCATCGTTCAAGAGGCCCCTCCCACCATTCAAGAGGCCCCTC
* *
38425 TCATCGTTCAAGAGGTCCCTCCCACCGTTCAAGAG
1 TCATCGTTCAAGAGGCCCCTCCCACCATTCAAGAG
38460 CCCGATTCAC
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (42 bp):
TCATCGTTCAAGAGGCCCCTCCCACCATTCAAGAGGCCCCTC
Found at i:38432 original size:21 final size:21
Alignment explanation
Indices: 38341--38459 Score: 116
Period size: 21 Copynumber: 5.7 Consensus size: 21
38331 GATGTACCTA
* *
38341 TCATCATTCAAGAGGCGCCTCC
1 TCATCGTTCAAGAGGC-CCTTC
* *
38363 T-ATCATTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCTTC
*
38383 TCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCTTC
* * *
38404 CCACCGTTCAAGAGGCCCTTG
1 TCATCGTTCAAGAGGCCCTTC
38425 TCATCGTTCAAGAGGTCCC-TC
1 TCATCGTTCAAGAGG-CCCTTC
* *
38446 CCACCGTTCAAGAG
1 TCATCGTTCAAGAG
38460 CCCGATTCAC
Statistics
Matches: 83, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
20 4 0.05
21 75 0.90
22 4 0.05
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCTTC
Found at i:39440 original size:45 final size:46
Alignment explanation
Indices: 39352--39442 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 46
39342 TTAAAAAAGC
* *
39352 CTGAGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
*
39398 CTGAGTGCATTGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
39443 TTCGATGTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 22 0.52
46 20 0.48
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
Found at i:39490 original size:20 final size:20
Alignment explanation
Indices: 39462--39500 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39452 CAAGAAATTA
39462 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
39482 ATTGGTGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
39501 CCCTTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:42018 original size:21 final size:20
Alignment explanation
Indices: 41932--42089 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
41922 AAATGACCAA
**
41932 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
41951 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
41971 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
41991 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
42012 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
42033 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
42053 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
42074 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
42090 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:42118 original size:20 final size:20
Alignment explanation
Indices: 42056--42249 Score: 203
Period size: 20 Copynumber: 9.7 Consensus size: 20
42046 CGATTTTCCA
* ** *
42056 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
42076 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
42096 AAATCGCAACTCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
42116 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
42136 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
* *
42156 AAATCTCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
42176 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
42196 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
42216 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
42237 AAATCGCAACGCG
1 AAATCGCAACGCG
42250 ATATTTAAAG
Statistics
Matches: 142, Mismatches: 27, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
19 2 0.01
20 122 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:42140 original size:60 final size:60
Alignment explanation
Indices: 42056--42249 Score: 228
Period size: 60 Copynumber: 3.2 Consensus size: 60
42046 CGATTTTCCA
* ** * *
42056 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACTCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACTCGTATCCGT
* * *** *
42116 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCTCAA-TGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACT-CGTATCCGT
* ** *
42176 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACTCGTATCCGT
42237 AAATCGCAACGCG
1 AAATCGCAACGCG
42250 ATATTTAAAG
Statistics
Matches: 109, Mismatches: 22, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
59 1 0.01
60 79 0.72
61 29 0.27
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACTCGTATCCGT
Found at i:42667 original size:32 final size:32
Alignment explanation
Indices: 42629--42697 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
42619 ATTTCACTTA
*
42629 GATTTCATTTCGCGTTACGATTCTGTCGTTGC
1 GATTTCATTTCGCGTTACGATTCTCTCGTTGC
* *
42661 GATTTCATTTCGCGTTGCTATTCTCTCGTTGC
1 GATTTCATTTCGCGTTACGATTCTCTCGTTGC
42693 GATTT
1 GATTT
42698 TCAAGTTAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (32 bp):
GATTTCATTTCGCGTTACGATTCTCTCGTTGC
Found at i:42678 original size:18 final size:18
Alignment explanation
Indices: 42629--42678 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
42619 ATTTCACTTA
*
42629 GATTTCATTTCGCGTTAC
1 GATTTCATTTCGCGTTGC
*
42647 GA-TTC-TGT--CGTTGC
1 GATTTCATTTCGCGTTGC
42661 GATTTCATTTCGCGTTGC
1 GATTTCATTTCGCGTTGC
42679 TATTCTCTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 8
0.69 0.08 0.22
Matches are distributed among these distances:
14 7 0.28
15 3 0.12
16 4 0.16
17 3 0.12
18 8 0.32
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (18 bp):
GATTTCATTTCGCGTTGC
Found at i:42837 original size:41 final size:41
Alignment explanation
Indices: 42779--42856 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
42769 TTGCAGAAGA
*
42779 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
42820 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
42857 CGCAACGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:42853 original size:21 final size:21
Alignment explanation
Indices: 42780--42855 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
42770 TGCAGAAGAG
*
42780 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
***
42801 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGAAAA
42821 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
42842 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
42856 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.46, C:0.17, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:42859 original size:14 final size:14
Alignment explanation
Indices: 42840--42896 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
42830 GAGAAATGAA
42840 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
42854 AATCGCAACGCGATATGAA
1 AATCGCAA--CG--A-GAG
42873 AATCGCAACGAGAG
1 AATCGCAACGAGAG
42887 AATCGCAACG
1 AATCGCAACG
42897 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:42875 original size:33 final size:33
Alignment explanation
Indices: 42835--42899 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
42825 AACGAGAGAA
42835 ATGAAAATCGCAACGAGAGAATCGCAACGCGAT
1 ATGAAAATCGCAACGAGAGAATCGCAACGCGAT
42868 ATGAAAATCGCAACGAGAGAATCGCAACGCGA
1 ATGAAAATCGCAACGAGAGAATCGCAACGCGA
42900 AACCAAAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.11
Consensus pattern (33 bp):
ATGAAAATCGCAACGAGAGAATCGCAACGCGAT
Found at i:42908 original size:33 final size:33
Alignment explanation
Indices: 42838--42912 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
42828 GAGAGAAATG
* **
42838 AAAATCGCAACGAGAGAATCGCAACGCGATATG
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
42871 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
42904 AAAATCGCA
1 AAAATCGCA
42913 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.45, C:0.24, G:0.21, T:0.09
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:42930 original size:19 final size:19
Alignment explanation
Indices: 42908--43005 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
42898 GAAACCAAAA
*
42908 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
42927 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
42941 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
42960 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
42974 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
42993 TCGCGTTGCGATT
1 TCGCGTTGCGATT
43006 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:42949 original size:14 final size:14
Alignment explanation
Indices: 42930--43019 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
42920 TTTCATTTCG
42930 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
42944 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
42963 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
42977 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
42996 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
43010 CGTTGCGATT
1 CGTTGCGATT
43020 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:42955 original size:33 final size:33
Alignment explanation
Indices: 42913--43027 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
42903 CAAAATCGCA
42913 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
42946 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
42979 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
43012 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
43028 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:45199 original size:93 final size:93
Alignment explanation
Indices: 44722--45740 Score: 1948
Period size: 93 Copynumber: 11.1 Consensus size: 93
44712 TAGATTGCTT
*
44722 AGTAAA-TTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
44786 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
44813 AGTAAA-TTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
44877 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
44904 AGTAAATTTG-TCGGTTGCTGCC-ATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
44967 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
44995 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTC-TTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
45059 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
45087 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
45152 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
45180 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACATTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
45245 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
45273 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
45338 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
45366 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
45431 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
45459 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
45524 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
45552 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACATTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
45617 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
45645 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
45710 TTTGTCTTTGTTTTGTC-TTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
45736 AGTAA
1 AGTAA
45741 TGCAATCCAT
Statistics
Matches: 917, Mismatches: 5, Indels: 12
0.98 0.01 0.01
Matches are distributed among these distances:
90 57 0.06
91 134 0.15
92 115 0.13
93 611 0.67
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:45828 original size:19 final size:19
Alignment explanation
Indices: 45788--45916 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
45778 TAGTTTACTT
* *
45788 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
45808 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
45827 TCGCAACGCGAAATAAAAA
1 TCGCAACGCGAAACCAAAA
*
45846 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
45860 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
45879 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
45893 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
45912 TCGCA
1 TCGCA
45917 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:45862 original size:33 final size:32
Alignment explanation
Indices: 45824--45916 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
45814 CGCGAAACCA
**
45824 AAATCGCAACGCGAAATAAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
45856 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
45889 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
45917 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:45914 original size:52 final size:52
Alignment explanation
Indices: 45788--45916 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 52
45778 TAGTTTACTT
* **
45788 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACGCGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
*** *
45840 TAAAAATCGC--AACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAA-CGCGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
45893 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACGCGAAACACAAAATCGCA
45917 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
51 3 0.05
52 47 0.78
53 7 0.12
54 3 0.05
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (52 bp):
TCGCAACGCGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:45934 original size:19 final size:19
Alignment explanation
Indices: 45912--46032 Score: 135
Period size: 19 Copynumber: 6.6 Consensus size: 19
45902 GAAACCAAAA
*
45912 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
45931 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
45950 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
45966 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
45983 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
46002 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
46022 TCGTGTTGCGA
1 TCGCGTTGCGA
46033 AAGTAAACTA
Statistics
Matches: 86, Mismatches: 10, Indels: 11
0.80 0.09 0.10
Matches are distributed among these distances:
14 7 0.08
16 5 0.06
17 5 0.06
19 57 0.66
20 12 0.14
ACGTcount: A:0.12, C:0.19, G:0.24, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:47961 original size:14 final size:14
Alignment explanation
Indices: 47942--47977 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
47932 ATTGTTTAAT
47942 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
47956 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
47970 TGATTTGT
1 TGATTTGT
47978 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:48100 original size:19 final size:19
Alignment explanation
Indices: 48084--48128 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
48074 AAAAATGACT
48084 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
48103 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
48122 ATCGCAA
1 ATCGCAA
48129 CGAGAGAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:48190 original size:33 final size:33
Alignment explanation
Indices: 48153--48304 Score: 152
Period size: 33 Copynumber: 4.5 Consensus size: 33
48143 TGCGTTTATA
48153 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
48186 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * *
48226 -TTT-GCGATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGC-A-TTGCGATTCTCTCGTTGCGATTTTC
48257 ATTTCGCA-TGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
48289 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
48305 TTCATTTCGC
Statistics
Matches: 97, Mismatches: 8, Indels: 28
0.73 0.06 0.21
Matches are distributed among these distances:
30 2 0.02
31 5 0.05
32 27 0.28
33 31 0.32
35 5 0.05
36 4 0.04
37 2 0.02
38 10 0.10
39 6 0.06
40 5 0.05
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:48193 original size:52 final size:52
Alignment explanation
Indices: 48153--48460 Score: 457
Period size: 52 Copynumber: 5.9 Consensus size: 52
48143 TGCGTTTATA
48153 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
48205 ATTTCGCATTGCGATTCTCTCTTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
48257 ATTTCGCA-TGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
48308 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* * * * *
48360 ATTTCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGTTGCGA-TTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
* *
48411 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATTTCGCATTGCGATT
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTCATTTCGCATTGCGATT
48461 CTCTCGTTGC
Statistics
Matches: 233, Mismatches: 13, Indels: 19
0.88 0.05 0.07
Matches are distributed among these distances:
50 9 0.04
51 63 0.27
52 148 0.64
53 6 0.03
54 6 0.03
55 1 0.00
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:48199 original size:19 final size:19
Alignment explanation
Indices: 48175--48460 Score: 320
Period size: 19 Copynumber: 16.4 Consensus size: 19
48165 GATTCTCTCG
48175 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
48194 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
48213 TTGCGA--TTC---TCTCT
1 TTGCGATTTTCATTTCGCA
48227 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
48246 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
48265 -TGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
48278 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
48297 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
48316 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
48330 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
48349 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
48368 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
48387 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
48401 TTGCGA-TTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
48420 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
48434 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
48453 TTGCGATT
1 TTGCGATT
48461 CTCTCGTTGC
Statistics
Matches: 228, Mismatches: 12, Indels: 54
0.78 0.04 0.18
Matches are distributed among these distances:
14 37 0.16
15 7 0.03
16 24 0.11
17 20 0.09
18 6 0.03
19 129 0.57
20 5 0.02
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:48253 original size:71 final size:67
Alignment explanation
Indices: 48153--48474 Score: 278
Period size: 71 Copynumber: 4.8 Consensus size: 67
48143 TGCGTTTATA
* *
48153 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC-TCTCG--TTGCGATTTTCATTTCGCA
48213 TTGCG
63 TTGCG
* * * * * *
48218 ATTCTCTCTTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATGCGATTCTCTCGTTGCG
1 ATT-TCGCATTGCGATTTTCATTTCGCATTGCGATTTTC-TCTCG-TTGCGATT-T-TCATTTCG
*
48283 -ATTTTC-
61 CA-TTGCG
48289 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTCTCTCGTTGCGATTTTCATTTCGCATTG
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTCTCGTTGCGATTTTCATTTCGCATTG
48352 CG
66 CG
48354 ATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTCTCTCGTTGCGA-TTTCATTTC
1 ------ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTCTCGTTGCGATTTTCATTT-
48416 CGCATTGCG
59 CGCATTGCG
* *
48425 ATTT-TCATGTTGGGATTTTCATTTCGCATTGCGA--TTCTCTCGTTGCGATT
1 ATTTCGCA--TTGCGATTTTCATTTCGCATTGCGATTTTCTCTCGTTGCGATT
48475 GTAATTTCCG
Statistics
Matches: 219, Mismatches: 17, Indels: 40
0.79 0.06 0.14
Matches are distributed among these distances:
64 11 0.05
65 9 0.04
66 54 0.25
67 5 0.02
68 6 0.03
69 4 0.02
70 43 0.20
71 78 0.36
72 9 0.04
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (67 bp):
ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTCTCGTTGCGATTTTCATTTCGCATTG
CG
Found at i:48482 original size:33 final size:33
Alignment explanation
Indices: 48194--48474 Score: 302
Period size: 33 Copynumber: 8.2 Consensus size: 33
48184 TCATTTCGCA
*
48194 TTGCGATTTTCATTTCGCATTGCGATTCTCTCT
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
48227 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * * *
48263 CATGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 -TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
48297 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
48330 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
48366 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
48401 TTGCGA-TTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
48434 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
48467 TTGCGATT
1 TTGCGATT
48475 GTAATTTCCG
Statistics
Matches: 208, Mismatches: 21, Indels: 38
0.78 0.08 0.14
Matches are distributed among these distances:
31 9 0.04
32 14 0.07
33 108 0.52
34 11 0.05
35 10 0.05
36 12 0.06
37 7 0.03
38 28 0.13
39 9 0.04
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:50763 original size:12 final size:12
Alignment explanation
Indices: 50746--50770 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
50736 TCTTCGGGGA
50746 CTTTTTCTTCTT
1 CTTTTTCTTCTT
50758 CTTTTTCTTCTT
1 CTTTTTCTTCTT
50770 C
1 C
50771 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:51699 original size:20 final size:20
Alignment explanation
Indices: 51671--51900 Score: 219
Period size: 20 Copynumber: 11.5 Consensus size: 20
51661 AAATTTCAGT
* * *
51671 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
51691 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
51711 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
51731 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
51751 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
51771 GTTGCGATATACGGATAGGC
1 GTTGCGATTTACGGATTCGC
* ** *
51791 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
51811 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
51831 GTTGCGATTTACGGATACGA
1 GTTGCGATTTACGGATTCGC
*
51851 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
51871 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
51891 GTTGCGATTT
1 GTTGCGATTT
51901 TGGAAAATCG
Statistics
Matches: 178, Mismatches: 30, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
20 177 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:51917 original size:21 final size:21
Alignment explanation
Indices: 51887--51969 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
51877 ATTTTCATAT
*
51887 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
51908 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
51929 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
51950 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
51970 CTGATTTCCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:51960 original size:42 final size:43
Alignment explanation
Indices: 51867--51965 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
51857 ATTTATGTGT
* *
51867 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
51908 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
51950 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
51966 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:56007 original size:47 final size:45
Alignment explanation
Indices: 55913--56038 Score: 173
Period size: 47 Copynumber: 2.8 Consensus size: 45
55903 GTAACCATGC
* * *
55913 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATTGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGAA
* *
55957 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATTGGAA
*
56004 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
56039 AGATTTTATA
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
44 22 0.30
45 11 0.15
46 1 0.01
47 39 0.53
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGAA
Found at i:59480 original size:19 final size:20
Alignment explanation
Indices: 59442--59481 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
59432 GAGTTTATTT
*
59442 TCATTTTTCAATTTTGAAACA
1 TCATTTTT-AATTTTAAAACA
59463 TCATTTTT-ATTTTAAAACA
1 TCATTTTTAATTTTAAAACA
59482 ATTTCTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
21 8 0.44
ACGTcount: A:0.35, C:0.12, G:0.03, T:0.50
Consensus pattern (20 bp):
TCATTTTTAATTTTAAAACA
Found at i:62997 original size:64 final size:65
Alignment explanation
Indices: 62888--63037 Score: 216
Period size: 64 Copynumber: 2.3 Consensus size: 65
62878 TTAATTGAAT
* * *
62888 TTTACATTGA-TTATAAATGTTGATTTGTTTAATTGATGAGGAAATAATAATTA-TTTTTTACTT
1 TTTA-ATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTTACTT
62951 G
65 G
* *
62952 TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGAT-ATGTAAATAAGAATTATTTTTTTTCTT
1 TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGA-GGAAATAAGAATTATTTTTTTACTT
63016 G
65 G
63017 TTTAATTGATTTGTAAAAGTT
1 TTTAATTGATTTGTAAAAGTT
63038 TATTGTTGTT
Statistics
Matches: 78, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
63 6 0.08
64 41 0.53
65 31 0.40
ACGTcount: A:0.32, C:0.02, G:0.14, T:0.52
Consensus pattern (65 bp):
TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTTACTTG
Found at i:63208 original size:20 final size:20
Alignment explanation
Indices: 63180--63218 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
63170 GATAATCACA
63180 TTGCAAATTTGACTTTCGCG
1 TTGCAAATTTGACTTTCGCG
*
63200 TTGCGAATTTGACTTTCGC
1 TTGCAAATTTGACTTTCGC
63219 ATCAATCACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.41
Consensus pattern (20 bp):
TTGCAAATTTGACTTTCGCG
Found at i:65689 original size:24 final size:24
Alignment explanation
Indices: 65655--65708 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
65645 CTGAAACATC
65655 ATCAAAATCCGAGTATTGACAAAG
1 ATCAAAATCCGAGTATTGACAAAG
* * *
65679 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACAAAG
65703 ATCAAA
1 ATCAAA
65709 TTTCTAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACAAAG
Found at i:66465 original size:13 final size:13
Alignment explanation
Indices: 66447--66471 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
66437 AATCATTGAA
66447 AAATTATATAAAT
1 AAATTATATAAAT
66460 AAATTATATAAA
1 AAATTATATAAA
66472 AAAAATTAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATTATATAAAT
Found at i:66696 original size:19 final size:19
Alignment explanation
Indices: 66655--66717 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
66645 TTAAATTTGT
* *
66655 GTTGCGAATTCGAAAATCGA
1 GTTGCGAATTTGAAATTC-A
*
66675 GTTGCGAATTTGAAATTTA
1 GTTGCGAATTTGAAATTCA
66694 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
66713 GTTGC
1 GTTGC
66718 AAAATTGGCA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 24 0.62
20 15 0.38
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:69313 original size:19 final size:20
Alignment explanation
Indices: 69276--69323 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
69266 TTATACATTT
*
69276 TTTTAAAAAAACACATAAA-
1 TTTTAAAATAACACATAAAC
* *
69295 TTTTAAAATAACCCCTAAAC
1 TTTTAAAATAACACATAAAC
*
69315 TTTGAAAAT
1 TTTTAAAAT
69324 CTTCATTTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.52, C:0.15, G:0.02, T:0.31
Consensus pattern (20 bp):
TTTTAAAATAACACATAAAC
Done.