Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007766.1 Hibiscus syriacus cultivar Beakdansim tig00110038_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: 442891
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:202738 original size:20 final size:20
Alignment explanation
Indices: 202715--202756 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
202705 TGTAATTCGA
202715 AACACAGAAGTCAAATTCAC
1 AACACAGAAGTCAAATTCAC
*
202735 AACACATAAGTCAAATTCAC
1 AACACAGAAGTCAAATTCAC
202755 AA
1 AA
202757 AGCGTGTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.07, T:0.17
Consensus pattern (20 bp):
AACACAGAAGTCAAATTCAC
Found at i:202929 original size:22 final size:22
Alignment explanation
Indices: 202904--202953 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
202894 TCACTCTCTA
* *
202904 CGGCGATATCCGTCCCCATCTC
1 CGGCGAAATCCGTCCCCATATC
* *
202926 CGGCAAAATCCGTTCCCATATC
1 CGGCGAAATCCGTCCCCATATC
202948 CGGCGA
1 CGGCGA
202954 CCCCCCTCTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.40, G:0.20, T:0.20
Consensus pattern (22 bp):
CGGCGAAATCCGTCCCCATATC
Found at i:203365 original size:20 final size:20
Alignment explanation
Indices: 203319--203370 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
203309 GAAAATGAAA
*
203319 TTCGCGTTGTGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
** *
203339 TAAGCGTTGCGATTTTCTTT
1 TTCGCGTTGCGATTTTCATT
203359 TTCGCGTTGCGA
1 TTCGCGTTGCGA
203371 ATTTAAGTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.12, C:0.17, G:0.23, T:0.48
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCATT
Found at i:205011 original size:21 final size:21
Alignment explanation
Indices: 204987--205036 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
204977 GTTAGGGGAG
*
204987 TTACGTGATGAGGTCAGTGCT
1 TTACGTGATGAGGTCAGTACT
*
205008 TTACGTGATGAGGTCGGTACT
1 TTACGTGATGAGGTCAGTACT
205029 TTACGTGA
1 TTACGTGA
205037 CGACAATAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.20, C:0.14, G:0.32, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:205474 original size:21 final size:21
Alignment explanation
Indices: 205450--205565 Score: 105
Period size: 21 Copynumber: 5.6 Consensus size: 21
205440 CCTTTCATCG
205450 TTCAAGAGGCCCCTCCTATCA
1 TTCAAGAGGCCCCTCCTATCA
* **
205471 TTCAAGAGGCCTCT-CTCATTG
1 TTCAAGAGGCCCCTCCT-ATCA
*
205492 TTCAAGAGGCCCCTCCCATCA
1 TTCAAGAGGCCCCTCCTATCA
**
205513 TTCAAGAGGCCCCT-CTCATTG
1 TTCAAGAGGCCCCTCCT-ATCA
* *
205534 TTCAAGAGGTCCCTCCCA-CA
1 TTCAAGAGGCCCCTCCTATCA
205554 GTTCAAG-GGCCC
1 -TTCAAGAGGCCC
205566 GATTCACATG
Statistics
Matches: 75, Mismatches: 15, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
20 7 0.09
21 66 0.88
22 2 0.03
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.24
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCCTATCA
Found at i:205513 original size:42 final size:42
Alignment explanation
Indices: 205444--205565 Score: 185
Period size: 42 Copynumber: 2.9 Consensus size: 42
205434 GATTCACCTT
* * *
205444 TCATCGTTCAAGAGGCCCCTCCTATCATTCAAGAGGCCTCTC
1 TCATTGTTCAAGAGGCCCCTCCCATCATTCAAGAGGCCCCTC
205486 TCATTGTTCAAGAGGCCCCTCCCATCATTCAAGAGGCCCCTC
1 TCATTGTTCAAGAGGCCCCTCCCATCATTCAAGAGGCCCCTC
*
205528 TCATTGTTCAAGAGGTCCCTCCCA-CAGTTCAAG-GGCCC
1 TCATTGTTCAAGAGGCCCCTCCCATCA-TTCAAGAGGCCC
205566 GATTCACATG
Statistics
Matches: 75, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
41 7 0.09
42 68 0.91
ACGTcount: A:0.21, C:0.36, G:0.18, T:0.25
Consensus pattern (42 bp):
TCATTGTTCAAGAGGCCCCTCCCATCATTCAAGAGGCCCCTC
Found at i:205558 original size:63 final size:62
Alignment explanation
Indices: 205445--205565 Score: 147
Period size: 63 Copynumber: 1.9 Consensus size: 62
205435 ATTCACCTTT
* * **
205445 CATCGTTCAAGAGGCCCCTCCTATCATTCAAGAGGCCTCTCTCATTGTTCAAGAGGCCCCTCC
1 CATCATTCAAGAGGCCCCTCCTATCATTCAAGAGGCCTCTCCCACAGTTCAAG-GGCCCCTCC
**
205508 CATCATTCAAGAGGCCCCT-CTCATTGTTCAAGAGGTCC-CTCCCACAGTTCAAGGGCCC
1 CATCATTCAAGAGGCCCCTCCT-ATCATTCAAGAGG-CCTCTCCCACAGTTCAAGGGCCC
205566 GATTCACATG
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
62 7 0.14
63 41 0.82
64 2 0.04
ACGTcount: A:0.21, C:0.36, G:0.18, T:0.24
Consensus pattern (62 bp):
CATCATTCAAGAGGCCCCTCCTATCATTCAAGAGGCCTCTCCCACAGTTCAAGGGCCCCTCC
Found at i:207166 original size:20 final size:20
Alignment explanation
Indices: 207143--207194 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
207133 TGCGTTGTGG
* *
207143 ATTTGATTTTCGCATTGCGA
1 ATTTGACTTTCGCATTGCAA
*
207163 ATTTGACTTTCGCGTTGCAA
1 ATTTGACTTTCGCATTGCAA
*
207183 ATTTGTCTTTCG
1 ATTTGACTTTCG
207195 TAACAATCGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.17, C:0.17, G:0.19, T:0.46
Consensus pattern (20 bp):
ATTTGACTTTCGCATTGCAA
Found at i:207214 original size:29 final size:29
Alignment explanation
Indices: 207179--207241 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
207169 CTTTCGCGTT
* *
207179 GCAAATTTGTCTTTCGTAACAATCGCAAC
1 GCAAATTTGACTTTCGCAACAATCGCAAC
*
207208 GCAAATTTGACTTTCGCAACAATCGCAAT
1 GCAAATTTGACTTTCGCAACAATCGCAAC
207237 GCAAA
1 GCAAA
207242 AAATCGCAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (29 bp):
GCAAATTTGACTTTCGCAACAATCGCAAC
Found at i:207277 original size:20 final size:20
Alignment explanation
Indices: 207244--207303 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
207234 AATGCAAAAA
*
207244 ATCGCAACGTGAATTTGACT
1 ATCGCAACGCGAATTTGACT
* *
207264 TTCGCGTA-GCGAATTTGACT
1 ATCGC-AACGCGAATTTGACT
207284 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
207304 CAAGTTACTA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 1 0.03
20 31 0.94
21 1 0.03
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:210073 original size:12 final size:12
Alignment explanation
Indices: 210052--210086 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
210042 GGTTGTGGGT
*
210052 TTTGAGATTGTG
1 TTTGATATTGTG
210064 TTTGATATTGTG
1 TTTGATATTGTG
*
210076 TTTGGTATTGT
1 TTTGATATTGT
210087 AAATTTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.29, T:0.57
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:210897 original size:20 final size:20
Alignment explanation
Indices: 210872--210935 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
210862 AAATAAAATC
210872 TGTTGCGAAATTAAAATTCG
1 TGTTGCGAAATTAAAATTCG
*
210892 TGTTGCGAATTTGAAAA-TCG
1 TGTTGCGAAATT-AAAATTCG
* **
210912 AGTTGCGAAAAAAAAATTCG
1 TGTTGCGAAATTAAAATTCG
210932 TGTT
1 TGTT
210936 ACGATTTAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 4 0.11
20 28 0.78
21 4 0.11
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (20 bp):
TGTTGCGAAATTAAAATTCG
Found at i:210920 original size:40 final size:40
Alignment explanation
Indices: 210873--211081 Score: 137
Period size: 40 Copynumber: 5.2 Consensus size: 40
210863 AATAAAATCT
210873 GTTGCGAAATTAAAATTCGTGTTGCGAATTTGAAAATCGA
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTTGAAAATCGA
** * ***
210913 GTTGCGAAAAAAAAATTCGTGTTACG-ATTTAGAAAATATT
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTT-GAAAATCGA
* ** * *
210953 GTTGTGAAAAGGAAACTT-GTGTTGCGAA-TTCAGAAATCGA
1 GTTGCG-AAATTAAAATTCGTGTTGCGAATTTGA-AAATCGA
* * *
210993 GTTGC-TAATTGAAATTCTGTGTTGCGAATTTGGAAAATCGT
1 GTTGCGAAATTAAAATTC-GTGTTGCGAATTT-GAAAATCGA
* *
211034 GTTGCGAGAA--AGAAATTCGCGTTGCG-A-TTGCAGAAATTGA
1 GTTGCGA-AATTA-AAATTCGTGTTGCGAATTTG-A-AAATCGA
211074 GTTGCGAA
1 GTTGCGAA
211082 TTTGGAAACT
Statistics
Matches: 128, Mismatches: 28, Indels: 27
0.70 0.15 0.15
Matches are distributed among these distances:
38 7 0.05
39 9 0.07
40 74 0.58
41 29 0.23
42 7 0.05
43 2 0.02
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.31
Consensus pattern (40 bp):
GTTGCGAAATTAAAATTCGTGTTGCGAATTTGAAAATCGA
Found at i:211089 original size:20 final size:20
Alignment explanation
Indices: 211066--211125 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
211056 TGCGATTGCA
211066 GAAATTGAGTTGCGAATTTG
1 GAAATTGAGTTGCGAATTTG
* * *
211086 GAAACTGTGTTGCGAAATTG
1 GAAATTGAGTTGCGAATTTG
* *
211106 G-AGTTCGCGTTGCGAATTTG
1 GAAATT-GAGTTGCGAATTTG
211126 TTGGCCATTT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.25, C:0.10, G:0.32, T:0.33
Consensus pattern (20 bp):
GAAATTGAGTTGCGAATTTG
Found at i:211118 original size:121 final size:119
Alignment explanation
Indices: 210873--211101 Score: 275
Period size: 121 Copynumber: 1.9 Consensus size: 119
210863 AATAAAATCT
*
210873 GTTGCGAAATTAAAATTCGTGTTGCGAATTTGAAAATCGAGTTGCGAAAAAAAAATTCGTGTTAC
1 GTTGCG-AATTAAAATTCGTGTTGCGAATTTGAAAATCGAGTTGCGAAAAAAAAATTCGCGTTAC
* * *
210938 GATTTAGAAAATATTGTTGTGAAAAGGAAACTTGTGTTGCGAATTCAGAAATCGA
65 GATTCAGAAAATATAGTTGCGAAAAGGAAACTTGTGTTGCGAATTCAGAAATCGA
* * * * * *
210993 GTTGCTAATTGAAATTCTGTGTTGCGAATTTGGAAAATCGTGTTGCGAGAAAGAAATTCGCGTTG
1 GTTGCGAATTAAAATTC-GTGTTGCGAATTT-GAAAATCGAGTTGCGAAAAAAAAATTCGCGTTA
**
211058 CGATTGCAG-AAAT-TGAGTTGCGAATTTGGAAAC-TGTGTTGCGAA
64 CGATT-CAGAAAATAT-AGTTGCGAA-AAGGAAACTTGTGTTGCGAA
211102 ATTGGAGTTC
Statistics
Matches: 92, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
119 10 0.11
120 19 0.21
121 55 0.60
122 8 0.09
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.31
Consensus pattern (119 bp):
GTTGCGAATTAAAATTCGTGTTGCGAATTTGAAAATCGAGTTGCGAAAAAAAAATTCGCGTTACG
ATTCAGAAAATATAGTTGCGAAAAGGAAACTTGTGTTGCGAATTCAGAAATCGA
Found at i:216276 original size:42 final size:42
Alignment explanation
Indices: 216217--216299 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
216207 CCGAAATCAT
* ***
216217 GTGTTTGTTTCATGTAATTCGTTTTTTGGAAAATGTTTTCTC
1 GTGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTTTCTC
216259 GTGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTTTCT
1 GTGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTTTCT
216300 AGTATTTGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.52
Consensus pattern (42 bp):
GTGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTTTCTC
Found at i:216537 original size:11 final size:11
Alignment explanation
Indices: 216521--216556 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
216511 AATTATTAAA
216521 ATATTTAAAAT
1 ATATTTAAAAT
216532 ATATTTAAAAT
1 ATATTTAAAAT
216543 AT-TTTAATAAT
1 ATATTTAA-AAT
216554 ATA
1 ATA
216557 ATATTATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.22
11 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATATTTAAAAT
Found at i:216541 original size:20 final size:22
Alignment explanation
Indices: 216516--216556 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
216506 ATATTAATTA
216516 TTAAAATA-TTTAA-AATATAT
1 TTAAAATATTTTAATAATATAT
216536 TTAAAATATTTTAATAATATA
1 TTAAAATATTTTAATAATATA
216557 ATATTATATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
21 5 0.26
22 6 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TTAAAATATTTTAATAATATAT
Found at i:216570 original size:22 final size:21
Alignment explanation
Indices: 216541--216581 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
216531 TATATTTAAA
216541 ATATTTTAATAATATAATATT
1 ATATTTTAATAATATAATATT
*
216562 ATATCTTTAATATTATAATA
1 ATAT-TTTAATAATATAATA
216582 AAATAATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
ATATTTTAATAATATAATATT
Found at i:216664 original size:27 final size:28
Alignment explanation
Indices: 216634--216698 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
216624 TATTTTCATA
216634 AATATATAATAACT-TT-TTTATATATTT
1 AATATATAATAA-TATTATTTATATATTT
216661 AATA-ATGAATAATATTATTTATATATTT
1 AATATAT-AATAATATTATTTATATATTT
216689 AATAT-TAATA
1 AATATATAATA
216699 TAATAATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
26 3 0.09
27 15 0.44
28 16 0.47
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (28 bp):
AATATATAATAATATTATTTATATATTT
Found at i:216681 original size:28 final size:29
Alignment explanation
Indices: 216554--216723 Score: 95
Period size: 30 Copynumber: 5.8 Consensus size: 29
216544 TTTTAATAAT
* *
216554 ATAATA-TTATATCTTTAATATTATAATAAA
1 ATAATATTTATATATTTAATA--ATAATATA
* *
216584 ATAATCAATTATAT-TATAATAAT-ATA-A
1 ATAAT-ATTTATATATTTAATAATAATATA
* *
216611 GATATTATATTTTTAT-TTTCATAA-ATATATA
1 -ATA--ATATTTATATATTTAATAATA-ATATA
* *
216642 ATAACTTTTTTATATATTTAATAATGA-ATA
1 ATAA--TATTTATATATTTAATAATAATATA
* *
216672 ATATTATTTATATATTTAATATTAATATA
1 ATAATATTTATATATTTAATAATAATATA
216701 ATAATA-TTATAATATTTTAATAA
1 ATAATATTTAT-ATA-TTTAATAA
216724 AGATATTTAA
Statistics
Matches: 110, Mismatches: 15, Indels: 30
0.71 0.10 0.19
Matches are distributed among these distances:
27 1 0.01
28 29 0.26
29 25 0.23
30 33 0.30
31 16 0.15
32 6 0.05
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.49
Consensus pattern (29 bp):
ATAATATTTATATATTTAATAATAATATA
Found at i:216744 original size:23 final size:23
Alignment explanation
Indices: 216718--216762 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
216708 TATAATATTT
216718 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
216741 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
216763 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:217090 original size:13 final size:13
Alignment explanation
Indices: 217072--217108 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
217062 TTTGGTAATC
217072 CCCGCCCCGATTA
1 CCCGCCCCGATTA
217085 CCCGCCCCGATTA
1 CCCGCCCCGATTA
*
217098 ACCGCCCCGAT
1 CCCGCCCCGAT
217109 ACTCGACCCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.16, C:0.54, G:0.16, T:0.14
Consensus pattern (13 bp):
CCCGCCCCGATTA
Found at i:217189 original size:24 final size:26
Alignment explanation
Indices: 217144--217222 Score: 69
Period size: 24 Copynumber: 3.2 Consensus size: 26
217134 AATTATTTAT
* * * *
217144 ATATATATATATATATATATAATATTA
1 ATATATATTTA-ATTTAAATAATATAA
217171 ATA-A-ATTTAATTTAAATAA-A-AA
1 ATATATATTTAATTTAAATAATATAA
*
217193 ATATATATTTAATTTAAAT-ATATAT
1 ATATATATTTAATTTAAATAATATAA
217218 ATATA
1 ATATA
217223 CCCGACCCGA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
22 4 0.09
23 3 0.07
24 22 0.51
25 10 0.23
26 1 0.02
27 3 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
ATATATATTTAATTTAAATAATATAA
Found at i:217204 original size:19 final size:19
Alignment explanation
Indices: 217180--217219 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
217170 AATAAATTTA
217180 ATTTAAATAAAAAATATAT
1 ATTTAAATAAAAAATATAT
* * *
217199 ATTTAATTTAAATATATAT
1 ATTTAAATAAAAAATATAT
217218 AT
1 AT
217220 ATACCCGACC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAAATATAT
Found at i:217264 original size:12 final size:12
Alignment explanation
Indices: 217220--217285 Score: 80
Period size: 12 Copynumber: 5.6 Consensus size: 12
217210 ATATATATAT
*
217220 ATACCCGACCCG
1 ATACCCGACCCA
* *
217232 ATTCCCGGCCCA
1 ATACCCGACCCA
217244 ATA-CCGACCCA
1 ATACCCGACCCA
217255 ATACCCGACCCA
1 ATACCCGACCCA
**
217267 ATACCCGGTCCA
1 ATACCCGACCCA
217279 ATACCCG
1 ATACCCG
217286 TTTAAATAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
11 10 0.22
12 36 0.78
ACGTcount: A:0.27, C:0.47, G:0.14, T:0.12
Consensus pattern (12 bp):
ATACCCGACCCA
Found at i:217284 original size:24 final size:23
Alignment explanation
Indices: 217224--217285 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
217214 ATATATATAC
* * *
217224 CCGACCCGATTCCCGGCCCAATA
1 CCGACCCAATACCCGACCCAATA
217247 CCGACCCAATACCCGACCCAATA
1 CCGACCCAATACCCGACCCAATA
**
217270 CCCGGTCCAATACCCG
1 -CCGACCCAATACCCG
217286 TTTAAATAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
23 20 0.61
24 13 0.39
ACGTcount: A:0.26, C:0.48, G:0.15, T:0.11
Consensus pattern (23 bp):
CCGACCCAATACCCGACCCAATA
Found at i:217617 original size:14 final size:14
Alignment explanation
Indices: 217598--217631 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
217588 AAATGTAATT
217598 CATTTTACGGAAAA
1 CATTTTACGGAAAA
*
217612 CATTTTCCGGAAAA
1 CATTTTACGGAAAA
*
217626 CGTTTT
1 CATTTT
217632 TCAGAAATGT
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:0.18, G:0.15, T:0.35
Consensus pattern (14 bp):
CATTTTACGGAAAA
Found at i:217692 original size:30 final size:29
Alignment explanation
Indices: 217641--217716 Score: 125
Period size: 30 Copynumber: 2.6 Consensus size: 29
217631 TTCAGAAATG
*
217641 TAATTCATTTTCCAGAATTCAAATTTCAA
1 TAATTCATTTTCCAGAATTCAAATTCCAA
*
217670 TAATTCATTTTCCAGTAATTCAAATTCCAG
1 TAATTCATTTTCCAG-AATTCAAATTCCAA
217700 TAATTCATTTTCCAGAA
1 TAATTCATTTTCCAGAA
217717 AACCAATTAC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 17 0.39
30 27 0.61
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (29 bp):
TAATTCATTTTCCAGAATTCAAATTCCAA
Found at i:217712 original size:15 final size:15
Alignment explanation
Indices: 217640--217714 Score: 91
Period size: 15 Copynumber: 5.1 Consensus size: 15
217630 TTTCAGAAAT
217640 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
*
217655 G-AATTCAAATTT-CA
1 GTAATTC-ATTTTCCA
*
217669 ATAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
217684 GTAATTCAAATTCCA
1 GTAATTCATTTTCCA
217699 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
217714 G
1 G
217715 AAAACCAATT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
14 11 0.22
15 38 0.78
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:219041 original size:15 final size:15
Alignment explanation
Indices: 219021--219049 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
219011 TGGCCGATCG
219021 AACCGAATTAACCAT
1 AACCGAATTAACCAT
219036 AACCGAATTAACCA
1 AACCGAATTAACCA
219050 AACTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.28, G:0.07, T:0.17
Consensus pattern (15 bp):
AACCGAATTAACCAT
Found at i:219479 original size:183 final size:184
Alignment explanation
Indices: 219163--219551 Score: 619
Period size: 183 Copynumber: 2.1 Consensus size: 184
219153 AATTTTCTAA
* *
219163 TTTATATA-AAAAT-TA-AATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATA
1 TTTATATATAATATATATAATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATA
**
219225 TAATTATAAAATAAAATTTTTAGATAAATATTTTAATTAATTAATATTGATTTAAGTTTAAAAGT
66 TAATTATAAAATAAAAAATTTAGATAAATATTTTAATTAATTAATATTGATTTAAGTTTAAAAGT
*
219290 TATTGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGACTT-AGCCCATAT
131 TATTGGATCTTAAATTATTAATTGGGTTTTAAATGATTTGG-CTTGAGCCCATAT
*
219344 TTTATATATAATATATATAATATTTTTTAATT-AGAAAACAGTTTACAATTAATTTAAATAATAT
1 TTTATATATAATATATATAATATTTTTTAATTCA-AAAAAAGTTTACAATTAATTTAAATAATAT
* *
219408 ATAATTATAAAATAAAAAATTTATAT-AATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAG
65 ATAATTATAAAATAAAAAATTTAGATAAATATTTTAATTAATTAATATTGATTTAAGTTTAAAAG
*
219472 TTATTGGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATAT
130 TTATTGGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGCTTGAGCCCATAT
* *
219527 GTTATATATAATATATTTAATATTT
1 TTTATATATAATATATATAATATTT
219552 AAAATTTAAT
Statistics
Matches: 192, Mismatches: 11, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
181 8 0.04
182 6 0.03
183 113 0.59
184 65 0.34
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.46
Consensus pattern (184 bp):
TTTATATATAATATATATAATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATA
TAATTATAAAATAAAAAATTTAGATAAATATTTTAATTAATTAATATTGATTTAAGTTTAAAAGT
TATTGGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGCTTGAGCCCATAT
Found at i:219576 original size:9 final size:9
Alignment explanation
Indices: 219557--219590 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
219547 TATTTAAAAT
219557 TTAATTTCGG
1 TTAA-TTCGG
219567 TTAATTCGG
1 TTAATTCGG
219576 TTAATTCGG
1 TTAATTCGG
219585 TTAATT
1 TTAATT
219591 AACCGAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 20 0.83
10 4 0.17
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.50
Consensus pattern (9 bp):
TTAATTCGG
Found at i:222705 original size:21 final size:22
Alignment explanation
Indices: 222681--222725 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
222671 ATAGTCATAC
*
222681 CAAAGACGA-GAAGA-CCCTTCA
1 CAAAGAC-ATGAAGATCACTTCA
222702 CAAAGACATGAAGATCACTTCA
1 CAAAGACATGAAGATCACTTCA
222724 CA
1 CA
222726 TTGGAAATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 1 0.05
21 12 0.57
22 8 0.38
ACGTcount: A:0.44, C:0.27, G:0.16, T:0.13
Consensus pattern (22 bp):
CAAAGACATGAAGATCACTTCA
Found at i:226546 original size:16 final size:16
Alignment explanation
Indices: 226525--226559 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
226515 CAAGATTGAA
*
226525 ACCCGATAAAATAAGG
1 ACCCGATAAAACAAGG
226541 ACCCGATAAAACAAGG
1 ACCCGATAAAACAAGG
226557 ACC
1 ACC
226560 TTGACCTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.49, C:0.26, G:0.17, T:0.09
Consensus pattern (16 bp):
ACCCGATAAAACAAGG
Found at i:228815 original size:54 final size:54
Alignment explanation
Indices: 228733--228838 Score: 187
Period size: 54 Copynumber: 2.0 Consensus size: 54
228723 TCACTGATTG
*
228733 AAAATCTGAGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTATT
1 AAAATCTGAGCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTATT
228787 AAAATCTG-GACAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTA
1 AAAATCTGAG-CAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTA
228839 CGAACCAATG
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
53 1 0.02
54 49 0.98
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.26
Consensus pattern (54 bp):
AAAATCTGAGCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTATT
Found at i:230780 original size:136 final size:135
Alignment explanation
Indices: 230276--230891 Score: 846
Period size: 136 Copynumber: 4.6 Consensus size: 135
230266 AATGTTTTCA
* * * *
230276 ACATTTCCAATGGATAGTTCATAATGAGAAGAACTCATCTGACAGAGGGAGAAGAAGTTCATAAT
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATC-CAAAGAGGGAGAAAAAGTTCATAAT
* * *
230341 GAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACAATTCGAATCAGTGACGCATCGCTTGAG
65 GAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACGCCTCACTTGAG
*
230406 GGATTA
130 GGATTG
* * * * * *
230412 ACATTTCAAATGTAGAGTTCATAATAAGAAAAACTCACCCAAAGAGGGAGAATAAGTTCATAATG
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGGAGAAAAAGTTCATAATG
* *
230477 AGAAGAGCTTGTTCGACCTATCACTCGATTCACGATATTTCGAATAAGTGACGCCTCACTTGAGG
66 AGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACGCCTCACTTGAGG
230542 GATT-
131 GATTG
* * * *
230546 ACATTTCCAATGGAGAGATCATAATGAAAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATG
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGGAGAAAAAGTTCATAATG
* * ** *
230611 AGAAGAGCTTGTTCAACCTATCACGCGATTCACGGTATTTCGAATCAGTGACGTCTCACTTGAGG
66 AGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACGCCTCACTTGAGG
230676 GATTG
131 GATTG
* * * *
230681 ACATTTCCAATTGAGAGTTCATAACGAGAAGAACTCATTCGATAGAGGGAGAAAAAGTTCATAAT
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCA-TCCAAAGAGGGAGAAAAAGTTCATAAT
* * * *
230746 GAGAAGAGTTTGTTCGACCTATCACTCAAATCACGACATTTCGAATCAGTGACGCCTCGCTTGAG
65 GAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACGCCTCACTTGAG
230811 GGATTG
130 GGATTG
* * *
230817 ACATTTCTAATGGAGAGTTCATAATGAGAAGAACTCGTCCTAA-AGGG-G--AAAGTTCATAATG
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGGAGAAAAAGTTCATAATG
*
230878 AGAAGAACTTGTTC
66 AGAAGAGCTTGTTC
230892 CTTTCAAATT
Statistics
Matches: 424, Mismatches: 54, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
131 25 0.06
133 1 0.00
134 124 0.29
135 123 0.29
136 151 0.36
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (135 bp):
ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGGAGAAAAAGTTCATAATG
AGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACGCCTCACTTGAGG
GATTG
Found at i:230789 original size:270 final size:269
Alignment explanation
Indices: 230276--230891 Score: 859
Period size: 270 Copynumber: 2.3 Consensus size: 269
230266 AATGTTTTCA
* * *
230276 ACATTTCCAATGGATAGTTCATAATGAGAAGAACTCATCTGACAGAGGGAGAAGAAGTTCATAAT
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATC-CAAAGA-GGAGAAGAAGTTCATAAT
* * *
230341 GAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACAATTCGAATCAGTGACGCATCGCTTGAG
64 GAGAAGAGCTTGTTCAACCTATCACGCGATTCACGACAATTCGAATCAGTGACGCATCACTTGAG
* *
230406 GGATTAACATTTCAAATGTAGAGTTCATAATAAGAAAAACTCACCCAAAGAGGGAGAATAAGTTC
129 GGATTAACATTTCAAATGTAGAGTTCATAACAAGAAAAACTCACCCAAAGAGGGAGAAAAAGTTC
* * *
230471 ATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGATATTTCGAATAAGTGACGCCTCAC
194 ATAATGAGAAGAGCTTGTTCGACCTATCACTCAAATCACGACATTTCGAATAAGTGACGCCTCAC
230536 TTGAGGGATT-
259 TTGAGGGATTG
* *
230546 ACATTTCCAATGGAGAGATCATAATGAAAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATG
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAGAGG-AGAAGAAGTTCATAATG
** *
230611 AGAAGAGCTTGTTCAACCTATCACGCGATTCACGGTATTTCGAATCAGTGACGTC-TCACTTGAG
65 AGAAGAGCTTGTTCAACCTATCACGCGATTCACGACAATTCGAATCAGTGACG-CATCACTTGAG
* * * * * * *
230675 GGATTGACATTTCCAAT-TGAGAGTTCATAACGAGAAGAACTCATTCGATAGAGGGAGAAAAAGT
129 GGATTAACATTTCAAATGT-AGAGTTCATAACAAGAAAAACTCA-CCCAAAGAGGGAGAAAAAGT
* *
230739 TCATAATGAGAAGAGTTTGTTCGACCTATCACTCAAATCACGACATTTCGAATCAGTGACGCCTC
192 TCATAATGAGAAGAGCTTGTTCGACCTATCACTCAAATCACGACATTTCGAATAAGTGACGCCTC
*
230804 GCTTGAGGGATTG
257 ACTTGAGGGATTG
* *
230817 ACATTTCTAATGGAGAGTTCATAATGAGAAGAACTCGTCCTAAAG-GG-G-A-AAGTTCATAATG
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCC-AAAGAGGAGAAGAAGTTCATAATG
*
230878 AGAAGAACTTGTTC
65 AGAAGAGCTTGTTC
230892 CTTTCAAATT
Statistics
Matches: 309, Mismatches: 31, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
267 25 0.08
268 4 0.01
269 114 0.37
270 124 0.40
271 38 0.12
272 4 0.01
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (269 bp):
ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAGAAGAAGTTCATAATGA
GAAGAGCTTGTTCAACCTATCACGCGATTCACGACAATTCGAATCAGTGACGCATCACTTGAGGG
ATTAACATTTCAAATGTAGAGTTCATAACAAGAAAAACTCACCCAAAGAGGGAGAAAAAGTTCAT
AATGAGAAGAGCTTGTTCGACCTATCACTCAAATCACGACATTTCGAATAAGTGACGCCTCACTT
GAGGGATTG
Found at i:231000 original size:70 final size:71
Alignment explanation
Indices: 230867--231028 Score: 211
Period size: 70 Copynumber: 2.3 Consensus size: 71
230857 TAAAGGGGAA
* *
230867 AGTTCATAATGAGAAGAACTTGTTCCTTTCAAATTCACCACAAAAGGAGCTGAACCAGCATTTCC
1 AGTTCATAATGAGAAGAACTTGTTCCTTTCAAATCCACCACAAAAGAAGCTGAACCAGCATTTCC
230932 AA-AAG
66 AAGAAG
* * * * * *
230937 AGTTCATAATGAGAAGAACTTGTTCCTTTCAAGTCCATCACAGAATGAAG-TGGATCAGTATTTC
1 AGTTCATAATGAGAAGAACTTGTTCCTTTCAAATCCACCACA-AAAGAAGCTGAACCAGCATTTC
231001 CAATGAAG
65 CAA-GAAG
*
231009 AGTTGATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
231029 GATCCAAAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
70 53 0.66
71 5 0.06
72 22 0.28
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.27
Consensus pattern (71 bp):
AGTTCATAATGAGAAGAACTTGTTCCTTTCAAATCCACCACAAAAGAAGCTGAACCAGCATTTCC
AAGAAG
Found at i:233701 original size:29 final size:28
Alignment explanation
Indices: 233648--233702 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
233638 CTTAAATTGT
*
233648 AAAATAATAAAACTATAGTCTCTAATTC
1 AAAATAATAAAACTATAGTCACTAATTC
*
233676 AAAATATTATAAACTATAAGT-ACTAAT
1 AAAATAATA-AAACTAT-AGTCACTAAT
233703 AATATAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 8 0.35
29 12 0.52
30 3 0.13
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.33
Consensus pattern (28 bp):
AAAATAATAAAACTATAGTCACTAATTC
Found at i:234461 original size:21 final size:20
Alignment explanation
Indices: 234432--234490 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
234422 TGTTCATCGT
234432 TCTTCGTTGCTTGATGTGTC
1 TCTTCGTTGCTTGATGTGTC
* *
234452 TCTGTCGTTG-TTCAT-TAT-
1 TCT-TCGTTGCTTGATGTGTC
*
234470 TCTTCGTTGCTTGCTGTGTC
1 TCTTCGTTGCTTGATGTGTC
234490 T
1 T
234491 TTGTTTCTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
17 6 0.20
18 6 0.20
19 4 0.13
20 8 0.27
21 6 0.20
ACGTcount: A:0.05, C:0.20, G:0.22, T:0.53
Consensus pattern (20 bp):
TCTTCGTTGCTTGATGTGTC
Found at i:234488 original size:38 final size:38
Alignment explanation
Indices: 234375--234490 Score: 142
Period size: 38 Copynumber: 3.1 Consensus size: 38
234365 TTTGTGTCTC
* * * * **
234375 CTCTATCGTTGTTCGTCGTTCTTCGTTGGTTGTTGCAT
1 CTCTGTCGTTGTTCATCGTTCTTCGTTGCTTGATGTGT
*
234413 CTCTGTCATTGTTCATCGTTCTTCGTTGCTTGATGTGT
1 CTCTGTCGTTGTTCATCGTTCTTCGTTGCTTGATGTGT
** *
234451 CTCTGTCGTTGTTCATTATTCTTCGTTGCTTGCTGTGT
1 CTCTGTCGTTGTTCATCGTTCTTCGTTGCTTGATGTGT
234489 CT
1 CT
234491 TTGTTTCTTG
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 67 1.00
ACGTcount: A:0.06, C:0.22, G:0.22, T:0.51
Consensus pattern (38 bp):
CTCTGTCGTTGTTCATCGTTCTTCGTTGCTTGATGTGT
Found at i:234990 original size:7 final size:7
Alignment explanation
Indices: 234951--235001 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
234941 TCGGGTCTTG
234951 TAATA-A
1 TAATATA
234957 TAATA-A
1 TAATATA
234963 T-ATATA
1 TAATATA
234969 TAATAATA
1 TAAT-ATA
*
234977 TAGTATA
1 TAATATA
*
234984 TTATATA
1 TAATATA
234991 TAATATA
1 TAATATA
234998 TAAT
1 TAAT
235002 GAAACCGTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
5 3 0.08
6 9 0.24
7 20 0.53
8 6 0.16
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (7 bp):
TAATATA
Found at i:238872 original size:21 final size:21
Alignment explanation
Indices: 238842--238891 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
238832 TCATGAAATA
*
238842 ATGTTACCATATCCCTTTGAT
1 ATGTTGCCATATCCCTTTGAT
238863 ATGTTGCCATATCCCTTTGAT
1 ATGTTGCCATATCCCTTTGAT
238884 ATGTTGCC
1 ATGTTGCC
238892 CCTGTATTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.42
Consensus pattern (21 bp):
ATGTTGCCATATCCCTTTGAT
Found at i:248156 original size:17 final size:17
Alignment explanation
Indices: 248134--248186 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
248124 AATTAAGAGT
248134 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
248151 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
*
248168 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
248185 TA
1 TA
248187 CTTCCCTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:252538 original size:18 final size:18
Alignment explanation
Indices: 252489--252559 Score: 88
Period size: 18 Copynumber: 3.9 Consensus size: 18
252479 ACTGAATATT
252489 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* * *
252507 TGTTCCAAATGACCACTA
1 TGTCCCGAAGGACCACTA
* *
252525 TGTCTCGAAGGACCACTT
1 TGTCCCGAAGGACCACTA
*
252543 TATCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
252560 GTTAATCCCT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:254048 original size:20 final size:20
Alignment explanation
Indices: 254023--254067 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
254013 AAAATTTCCA
254023 TGCATCGATGCCTACCGGTG
1 TGCATCGATGCCTACCGGTG
* *
254043 TGCATCGATTCCTATCGGTG
1 TGCATCGATGCCTACCGGTG
254063 TGCAT
1 TGCAT
254068 TGATACACCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.31
Consensus pattern (20 bp):
TGCATCGATGCCTACCGGTG
Found at i:259211 original size:21 final size:21
Alignment explanation
Indices: 259187--259226 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
259177 TAAGACTTTT
259187 TTTCAAAATAAAAAAATGATG
1 TTTCAAAATAAAAAAATGATG
**
259208 TTTCAAAATTGAAAAATGA
1 TTTCAAAATAAAAAAATGA
259227 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.05, G:0.10, T:0.30
Consensus pattern (21 bp):
TTTCAAAATAAAAAAATGATG
Found at i:262358 original size:13 final size:15
Alignment explanation
Indices: 262339--262375 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
262329 CGTATATAGA
262339 TTTTTCAAACATT-G
1 TTTTTCAAACATTAG
262353 -TTTTCAAA-ATTAG
1 TTTTTCAAACATTAG
262366 TTTTTCAAAC
1 TTTTTCAAAC
262376 TTGCCCATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.15
13 9 0.45
14 8 0.40
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.49
Consensus pattern (15 bp):
TTTTTCAAACATTAG
Found at i:263890 original size:2 final size:2
Alignment explanation
Indices: 263883--263925 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
263873 CTTAAATGTT
263883 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
263925 T
1 T
263926 GTTTGCTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:267849 original size:20 final size:19
Alignment explanation
Indices: 267826--267865 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
267816 AAGTTGGAGT
*
267826 AGAAGACTAGTATTAAGACA
1 AGAAGAATAG-ATTAAGACA
*
267846 AGAAGAATAGGTTAAGACA
1 AGAAGAATAGATTAAGACA
267865 A
1 A
267866 TAAAATAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.53, C:0.07, G:0.23, T:0.17
Consensus pattern (19 bp):
AGAAGAATAGATTAAGACA
Found at i:273206 original size:18 final size:18
Alignment explanation
Indices: 273182--273222 Score: 59
Period size: 16 Copynumber: 2.3 Consensus size: 18
273172 TAGTATTTTA
273182 ATATATTTTATATCATTAT
1 ATATATTTT-TATCATTAT
273201 -TATA-TTTTATCATTAT
1 ATATATTTTTATCATTAT
273217 ATATAT
1 ATATAT
273223 ATATACACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
16 9 0.45
17 7 0.35
18 4 0.20
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (18 bp):
ATATATTTTTATCATTAT
Found at i:273267 original size:2 final size:2
Alignment explanation
Indices: 273260--273292 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
273250 TGTTTATCAC
*
273260 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
273293 TTGATTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:273707 original size:15 final size:15
Alignment explanation
Indices: 273629--273729 Score: 100
Period size: 15 Copynumber: 6.6 Consensus size: 15
273619 TTTTCTTTGT
273629 TTTTTATTCTTTTGTT-
1 TTTTTATT-TTTT-TTA
*
273645 TTTTTCTTATTTTTT-
1 TTTTTATT-TTTTTTA
*
273660 TTTTTTTTTTTTTTA
1 TTTTTATTTTTTTTA
*
273675 TTTTT-TTTTTTTTT
1 TTTTTATTTTTTTTA
273689 TTTTTATTTTTTTTA
1 TTTTTATTTTTTTTA
273704 TTTTTACTTTTTTTATA
1 TTTTTA-TTTTTTT-TA
*
273721 TCTTTATTT
1 TTTTTATTT
273730 ATATTACCAT
Statistics
Matches: 75, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
14 19 0.25
15 28 0.37
16 21 0.28
17 7 0.09
ACGTcount: A:0.09, C:0.04, G:0.01, T:0.86
Consensus pattern (15 bp):
TTTTTATTTTTTTTA
Found at i:273707 original size:17 final size:17
Alignment explanation
Indices: 273628--273729 Score: 88
Period size: 17 Copynumber: 6.1 Consensus size: 17
273618 TTTTTCTTTG
273628 TTTTTTATTCTTTTGT-TT
1 TTTTTTATT-TTTT-TATT
273646 TTTTCTTATTTTTTT-TT
1 TTTT-TTATTTTTTTATT
*
273663 TTTTTT-TTTTTATTTTT
1 TTTTTTATTTTT-TTATT
*
273680 TTTTTTTTTTTTTTATT
1 TTTTTTATTTTTTTATT
*
273697 TTTTTTA--TTTTTACT
1 TTTTTTATTTTTTTATT
* *
273712 TTTTTTATATCTTTATT
1 TTTTTTATTTTTTTATT
273729 T
1 T
273730 ATATTACCAT
Statistics
Matches: 73, Mismatches: 5, Indels: 13
0.80 0.05 0.14
Matches are distributed among these distances:
15 19 0.26
16 4 0.05
17 32 0.44
18 13 0.18
19 5 0.07
ACGTcount: A:0.09, C:0.04, G:0.01, T:0.86
Consensus pattern (17 bp):
TTTTTTATTTTTTTATT
Found at i:273714 original size:7 final size:6
Alignment explanation
Indices: 273629--273734 Score: 66
Period size: 6 Copynumber: 18.3 Consensus size: 6
273619 TTTTCTTTGT
273629 TTTTTA TTCTTT- TGTTTT- TTTCTTA TTTTT- TTTTT- TTTTT- TTTTTA
1 TTTTTA TT-TTTA T-TTTTA TTT-TTA TTTTTA TTTTTA TTTTTA TTTTTA
* * * *
273675 TTTTT- TTTTT- TTTTTT TTTATTT TTTTTA TTTTTA CTTTT- TTTATA
1 TTTTTA TTTTTA TTTTTA TTT-TTA TTTTTA TTTTTA TTTTTA TTTTTA
* *
273721 TCTTTA TTTATA TT
1 TTTTTA TTTTTA TT
273735 ACCATTGTAC
Statistics
Matches: 84, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
5 30 0.36
6 41 0.49
7 13 0.15
ACGTcount: A:0.10, C:0.04, G:0.01, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:273714 original size:21 final size:20
Alignment explanation
Indices: 273613--273708 Score: 113
Period size: 20 Copynumber: 4.7 Consensus size: 20
273603 TTCTCTGGTG
*
273613 TTTTGTTTTTCTTTGTTTTTTA
1 TTTT-TTTTT-TTTTTTTTTTA
* * *
273635 -TTCTTTTGTTTTTTTCTTA
1 TTTTTTTTTTTTTTTTTTTA
273654 TTTTTTTTTTTTTTTTTTTTA
1 -TTTTTTTTTTTTTTTTTTTA
273675 TTTTTTTTTTTTTTTTTTTA
1 TTTTTTTTTTTTTTTTTTTA
273695 TTTTTTTTATTTTT
1 TTTTTTTT-TTTTT
273709 ACTTTTTTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
19 9 0.14
20 32 0.50
21 23 0.36
ACGTcount: A:0.05, C:0.03, G:0.03, T:0.89
Consensus pattern (20 bp):
TTTTTTTTTTTTTTTTTTTA
Found at i:273716 original size:9 final size:8
Alignment explanation
Indices: 273628--273729 Score: 81
Period size: 7 Copynumber: 13.2 Consensus size: 8
273618 TTTTTCTTTG
273628 TTTTTTAT
1 TTTTTTAT
* *
273636 TCTTTTGT
1 TTTTTTAT
*
273644 TTTTTTCT
1 TTTTTTAT
273652 TATTTTT-T
1 T-TTTTTAT
273660 TTTTTT-T
1 TTTTTTAT
273667 TTTTTT-T
1 TTTTTTAT
*
273674 ATTTTT-T
1 TTTTTTAT
273681 TTTTTT-T
1 TTTTTTAT
273688 TTTTTTAT
1 TTTTTTAT
273696 TTTTTT-T
1 TTTTTTAT
*
273703 ATTTTTACT
1 TTTTTTA-T
273712 TTTTTTAT
1 TTTTTTAT
* *
273720 ATCTTTAT
1 TTTTTTAT
273728 TT
1 TT
273730 ATATTACCAT
Statistics
Matches: 79, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
7 37 0.47
8 30 0.38
9 12 0.15
ACGTcount: A:0.09, C:0.04, G:0.01, T:0.86
Consensus pattern (8 bp):
TTTTTTAT
Found at i:273717 original size:1 final size:1
Alignment explanation
Indices: 273613--273708 Score: 93
Period size: 1 Copynumber: 96.0 Consensus size: 1
273603 TTCTCTGGTG
* * * * * * * * *
273613 TTTTGTTTTTCTTTGTTTTTTATTCTTTTGTTTTTTTCTTATTTTTTTTTTTTTTTTTTTTATTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
273678 TTTTTTTTTTTTTTTTATTTTTTTTATTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
273709 ACTTTTTTTA
Statistics
Matches: 73, Mismatches: 22, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 73 1.00
ACGTcount: A:0.05, C:0.03, G:0.03, T:0.89
Consensus pattern (1 bp):
T
Found at i:273736 original size:26 final size:26
Alignment explanation
Indices: 273685--273736 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
273675 TTTTTTTTTT
* * *
273685 TTTTTTTTTATTTTTTTTATTTTTAC
1 TTTTTTTATATTTTATTTATTATTAC
273711 TTTTTTTATATCTTTATTTA-TATTAC
1 TTTTTTTATAT-TTTATTTATTATTAC
273737 CATTGTACCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (26 bp):
TTTTTTTATATTTTATTTATTATTAC
Found at i:284210 original size:7 final size:7
Alignment explanation
Indices: 284198--284231 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
284188 GCCCTAAATT
284198 GAAAAAA
1 GAAAAAA
284205 GAAAAAA
1 GAAAAAA
*
284212 GAGAAAA
1 GAAAAAA
*
284219 GAGAAAA
1 GAAAAAA
284226 GAAAAA
1 GAAAAA
284232 TAAGGTGGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:285241 original size:43 final size:41
Alignment explanation
Indices: 285179--285287 Score: 146
Period size: 43 Copynumber: 2.6 Consensus size: 41
285169 ACGAAGGGGC
*
285179 CATCCACAATTTCAACTCCACGACGGAGGATATCGTACCCA
1 CATCCACAATTTCAACTCCACGACGGAGGATATCATACCCA
* *
285220 CGGATCCACAATTTCAACTCCACAACGGAGGATATCATGCCCA
1 C--ATCCACAATTTCAACTCCACGACGGAGGATATCATACCCA
** *
285263 CATCCACGGTTTCAACTTCACGACG
1 CATCCACAATTTCAACTCCACGACG
285288 AAATATATCG
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
41 21 0.36
43 38 0.64
ACGTcount: A:0.30, C:0.34, G:0.16, T:0.20
Consensus pattern (41 bp):
CATCCACAATTTCAACTCCACGACGGAGGATATCATACCCA
Found at i:285296 original size:41 final size:43
Alignment explanation
Indices: 285251--285333 Score: 100
Period size: 44 Copynumber: 2.0 Consensus size: 43
285241 ACAACGGAGG
*
285251 ATATCATGCCCACATC-CA-CGG-TTTCAACTTCACGACGAAAT
1 ATATCATGCCAAC-TCACATCGGATTTCAACTTCACGACGAAAT
* *
285292 ATATCGTGCCAACTCTACATTGGATTTCAACTTCACGACGAA
1 ATATCATGCCAACTC-ACATCGGATTTCAACTTCACGACGAA
285334 GGATATCTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
40 2 0.06
41 11 0.31
42 2 0.06
43 2 0.06
44 18 0.51
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (43 bp):
ATATCATGCCAACTCACATCGGATTTCAACTTCACGACGAAAT
Found at i:286564 original size:18 final size:18
Alignment explanation
Indices: 286539--286580 Score: 61
Period size: 16 Copynumber: 2.4 Consensus size: 18
286529 TCTATATATG
286539 TATATATTTTATATCATTA
1 TATATATTTT-TATCATTA
286558 T-TATA-TTTTATCATTA
1 TATATATTTTTATCATTA
286574 TATATAT
1 TATATAT
286581 ATACACACGT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 9 0.43
17 7 0.33
18 4 0.19
19 1 0.05
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (18 bp):
TATATATTTTTATCATTA
Found at i:286764 original size:18 final size:18
Alignment explanation
Indices: 286741--286775 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
286731 TACTATTTTA
286741 TTATT-ATTTCTATTATTT
1 TTATTAATTT-TATTATTT
286759 TTATTAATTTTATTATT
1 TTATTAATTTTATTATT
286776 CCTGGTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATTAATTTTATTATTT
Found at i:286979 original size:14 final size:13
Alignment explanation
Indices: 286962--287005 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
286952 CTTTTTGTTA
286962 TTTATCTGGTTTTT
1 TTTAT-TGGTTTTT
*
286976 TTTATTTGTTTTT
1 TTTATTGGTTTTT
*
286989 TTTCTTGTGTTTTT
1 TTTATTG-GTTTTT
287003 TTT
1 TTT
287006 CTTATTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 12 0.46
14 14 0.54
ACGTcount: A:0.05, C:0.05, G:0.11, T:0.80
Consensus pattern (13 bp):
TTTATTGGTTTTT
Found at i:286983 original size:25 final size:27
Alignment explanation
Indices: 286955--287005 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
286945 CTATTTTCTT
286955 TTTGTTATTTATC-TG-GTTTTTTTTA
1 TTTGTTATTTATCTTGTGTTTTTTTTA
* *
286980 TTTGTTTTTTTTCTTGTGTTTTTTTT
1 TTTGTTATTTATCTTGTGTTTTTTTT
287006 CTTATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 11 0.50
26 2 0.09
27 9 0.41
ACGTcount: A:0.06, C:0.04, G:0.12, T:0.78
Consensus pattern (27 bp):
TTTGTTATTTATCTTGTGTTTTTTTTA
Found at i:287006 original size:14 final size:13
Alignment explanation
Indices: 286970--287008 Score: 60
Period size: 14 Copynumber: 2.9 Consensus size: 13
286960 TATTTATCTG
*
286970 GTTTTTTTTATTT
1 GTTTTTTTTCTTT
286983 GTTTTTTTTCTTGT
1 GTTTTTTTTCTT-T
286997 GTTTTTTTTCTT
1 GTTTTTTTTCTT
287009 ATTTTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.03, C:0.05, G:0.10, T:0.82
Consensus pattern (13 bp):
GTTTTTTTTCTTT
Found at i:287018 original size:6 final size:6
Alignment explanation
Indices: 286998--287073 Score: 59
Period size: 6 Copynumber: 12.8 Consensus size: 6
286988 TTTTCTTGTG
* * * *
286998 TTTTT- TTTCTTA TTTTTA TTTTGA TTTTGA TTTTTA TATTTA TATTTA
1 TTTTTA TTT-TTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
* *
287046 -TTTTA TTGTT- TTTCTA TTTTTA CTTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA -TTTTT
287074 TATATCTTTA
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
5 10 0.17
6 40 0.69
7 8 0.14
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.76
Consensus pattern (6 bp):
TTTTTA
Found at i:287019 original size:14 final size:14
Alignment explanation
Indices: 286970--287019 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
286960 TATTTATCTG
*
286970 GTTTTTTTTATT-T
1 GTTTTTTTTCTTAT
*
286983 GTTTTTTTTCTTGT
1 GTTTTTTTTCTTAT
286997 GTTTTTTTTCTTAT
1 GTTTTTTTTCTTAT
287011 -TTTTATTTT
1 GTTTT-TTTT
287020 GATTTTGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
13 15 0.45
14 18 0.55
ACGTcount: A:0.06, C:0.04, G:0.08, T:0.82
Consensus pattern (14 bp):
GTTTTTTTTCTTAT
Found at i:287019 original size:18 final size:17
Alignment explanation
Indices: 286974--287074 Score: 62
Period size: 18 Copynumber: 5.7 Consensus size: 17
286964 TATCTGGTTT
286974 TTTTTATTTGTTTTTTT-
1 TTTTTATTT-TTTTTTTA
* *
286991 TCTTGTGTTTTTTTTCTTA
1 T-TTTTATTTTTTTT-TTA
* *
287010 TTTTTATTTTGATTTTGA
1 TTTTTATTTT-TTTTTTA
* *
287028 TTTTTATATTTATATTTA
1 TTTTTAT-TTTTTTTTTA
* *
287046 -TTTTATTGTTTTTCTA
1 TTTTTATTTTTTTTTTA
287062 TTTTTACTTTTTT
1 TTTTTA-TTTTTT
287075 ATATCTTTAT
Statistics
Matches: 64, Mismatches: 13, Indels: 13
0.71 0.14 0.14
Matches are distributed among these distances:
16 6 0.09
17 17 0.27
18 34 0.53
19 7 0.11
ACGTcount: A:0.13, C:0.04, G:0.06, T:0.77
Consensus pattern (17 bp):
TTTTTATTTTTTTTTTA
Found at i:287024 original size:12 final size:11
Alignment explanation
Indices: 287011--287086 Score: 57
Period size: 11 Copynumber: 6.7 Consensus size: 11
287001 TTTTTCTTAT
*
287011 TTTTATTTTGA
1 TTTTATTTTTA
287022 TTTTGATTTTTA
1 TTTT-ATTTTTA
*
287034 TATTTATATTTA
1 T-TTTATTTTTA
287046 TTTTATTGTTT-
1 TTTTATT-TTTA
*
287057 TTCTATTTTTA
1 TTTTATTTTTA
* *
287068 CTTT-TTTATA
1 TTTTATTTTTA
287078 TCTTTATTT
1 T-TTTATTT
287087 ATGTTACCAT
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
10 8 0.16
11 20 0.39
12 20 0.39
13 3 0.06
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.74
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:291322 original size:20 final size:20
Alignment explanation
Indices: 291297--291334 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
291287 GGTTAATACC
291297 ATTTGATGAAA-AGATTTGAT
1 ATTTGAT-AAAGAGATTTGAT
291317 ATTTGATAAAGAGATTTG
1 ATTTGATAAAGAGATTTG
291335 TTGAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (20 bp):
ATTTGATAAAGAGATTTGAT
Found at i:293025 original size:13 final size:14
Alignment explanation
Indices: 293002--293030 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
292992 TTATTCTTAA
293002 TATTTATATATTTT
1 TATTTATATATTTT
293016 TATTTA-ATATTTT
1 TATTTATATATTTT
293029 TA
1 TA
293031 ACCAATAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TATTTATATATTTT
Found at i:293492 original size:24 final size:24
Alignment explanation
Indices: 293462--293568 Score: 142
Period size: 24 Copynumber: 4.5 Consensus size: 24
293452 CTGTTCGATA
* * *
293462 TCGTAGATGTCTATCACCTATGTG
1 TCGTAGATCTCCATCACCTATGCG
* *
293486 TCATAGATCTCCTTCACCTATGCG
1 TCGTAGATCTCCATCACCTATGCG
*
293510 TCGTAGATCTCCATCACGTATGCG
1 TCGTAGATCTCCATCACCTATGCG
* *
293534 TCGTAGATCTCCATCACCTTTGCA
1 TCGTAGATCTCCATCACCTATGCG
293558 TCGTAGATCTC
1 TCGTAGATCTC
293569 GTTCGCCAGT
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 72 1.00
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.34
Consensus pattern (24 bp):
TCGTAGATCTCCATCACCTATGCG
Found at i:295000 original size:7 final size:7
Alignment explanation
Indices: 294990--295041 Score: 54
Period size: 7 Copynumber: 7.7 Consensus size: 7
294980 TATATATATA
294990 ATATTTT
1 ATATTTT
294997 ATATTTT
1 ATATTTT
*
295004 -TATATT
1 ATATTTT
*
295010 A-ATTAT
1 ATATTTT
* *
295016 ATATATA
1 ATATTTT
295023 ATATTTT
1 ATATTTT
295030 ATATTTT
1 ATATTTT
295037 ATATT
1 ATATT
295042 AATTATATAT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
6 9 0.26
7 26 0.74
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (7 bp):
ATATTTT
Found at i:295037 original size:32 final size:33
Alignment explanation
Indices: 294980--295061 Score: 148
Period size: 32 Copynumber: 2.5 Consensus size: 33
294970 ATTATATATA
294980 TATATATATAATATTTTATATTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTATATTAAT
295013 TATATATATAATATTTTATA-TTTTATATTAAT
1 TATATATATAATATTTTATATTTTTATATTAAT
*
295045 TATATATAAAATATTTT
1 TATATATATAATATTTT
295062 CAGGTTCGGG
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 28 0.58
33 20 0.42
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (33 bp):
TATATATATAATATTTTATATTTTTATATTAAT
Found at i:297548 original size:23 final size:24
Alignment explanation
Indices: 297509--297558 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
297499 AACTGTAAAA
*
297509 TATATAATTTTTATATTTGT-AGT
1 TATATAATTTTTATATTTCTAAGT
*
297532 TATAT-ATTTTCTTTATTTCTAAGT
1 TATATAATTTT-TATATTTCTAAGT
297556 TAT
1 TAT
297559 GTAAAATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 5 0.22
23 12 0.52
24 6 0.26
ACGTcount: A:0.28, C:0.04, G:0.06, T:0.62
Consensus pattern (24 bp):
TATATAATTTTTATATTTCTAAGT
Found at i:297904 original size:20 final size:20
Alignment explanation
Indices: 297879--297920 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
297869 ATCCGTAGCT
*
297879 CCGCAACAGCGACA-CCGCAA
1 CCGCAACACCG-CATCCGCAA
297899 CCGCAACACCGCATCCGCAA
1 CCGCAACACCGCATCCGCAA
297919 CC
1 CC
297921 TCAATTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.31, C:0.50, G:0.17, T:0.02
Consensus pattern (20 bp):
CCGCAACACCGCATCCGCAA
Found at i:297916 original size:14 final size:14
Alignment explanation
Indices: 297879--297919 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
297869 ATCCGTAGCT
* *
297879 CCGCAACAGCGACA
1 CCGCAACCGCAACA
297893 CCGCAACCGCAACA
1 CCGCAACCGCAACA
*
297907 CCGCATCCGCAAC
1 CCGCAACCGCAAC
297920 CTCAATTTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.32, C:0.49, G:0.17, T:0.02
Consensus pattern (14 bp):
CCGCAACCGCAACA
Found at i:302586 original size:16 final size:17
Alignment explanation
Indices: 302554--302587 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
302544 TTACTTTATG
*
302554 TATCCGAAATTTTCGGA
1 TATCCGAAATATTCGGA
302571 TATCCGAAA-ATTCGGA
1 TATCCGAAATATTCGGA
302587 T
1 T
302588 CGAATAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (17 bp):
TATCCGAAATATTCGGA
Found at i:306690 original size:18 final size:18
Alignment explanation
Indices: 306669--306707 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
306659 TTGCTTCATT
*
306669 TCCCTCTCATCCTTCCTC
1 TCCCTCACATCCTTCCTC
*
306687 TCCCTCACATTCTTCCTC
1 TCCCTCACATCCTTCCTC
306705 TCC
1 TCC
306708 AAGTGCTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.08, C:0.54, G:0.00, T:0.38
Consensus pattern (18 bp):
TCCCTCACATCCTTCCTC
Found at i:309977 original size:31 final size:29
Alignment explanation
Indices: 309918--309978 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 29
309908 GTTACCGAAT
*
309918 TGGTCCCCAACTTTTCAAAAATTATAGAA
1 TGGTCCCCAAATTTTCAAAAATTATAGAA
* *
309947 TGGTCCCCAAAATTTTCTAAGACTTATAGAA
1 TGGTCCCC-AAATTTTC-AAAAATTATAGAA
309978 T
1 T
309979 ACTTCCTACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 8 0.30
30 7 0.26
31 12 0.44
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (29 bp):
TGGTCCCCAAATTTTCAAAAATTATAGAA
Found at i:327243 original size:19 final size:20
Alignment explanation
Indices: 327219--327269 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
327209 TCAACGACTA
327219 GTCAACGGTCAATTA-CTGG
1 GTCAACGGTCAATTAGCTGG
*
327238 GTCAACGGTCAA-TAGCTGT
1 GTCAACGGTCAATTAGCTGG
*
327257 GTCAACAGTCAAT
1 GTCAACGGTCAAT
327270 GGCTCACCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 2 0.07
19 26 0.93
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (20 bp):
GTCAACGGTCAATTAGCTGG
Found at i:334605 original size:13 final size:13
Alignment explanation
Indices: 334587--334629 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
334577 CTTGAATTTG
334587 ATTATTTGAATCA
1 ATTATTTGAATCA
334600 ATTATTTG-----
1 ATTATTTGAATCA
334608 ATTATTTGAATCA
1 ATTATTTGAATCA
334621 ATTATTTGA
1 ATTATTTGA
334630 TTAGAATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
8 8 0.32
13 17 0.68
ACGTcount: A:0.35, C:0.05, G:0.09, T:0.51
Consensus pattern (13 bp):
ATTATTTGAATCA
Found at i:334606 original size:21 final size:21
Alignment explanation
Indices: 334582--334632 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
334572 ATTGACTTGA
334582 ATTTGATTATTTGAATCAATT
1 ATTTGATTATTTGAATCAATT
334603 ATTTGATTATTTGAATCAATT
1 ATTTGATTATTTGAATCAATT
334624 ATTTGATTA
1 ATTTGATTA
334633 GAATTCAGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.53
Consensus pattern (21 bp):
ATTTGATTATTTGAATCAATT
Found at i:335780 original size:3 final size:3
Alignment explanation
Indices: 335766--335881 Score: 159
Period size: 3 Copynumber: 39.3 Consensus size: 3
335756 CAACAGCCAT
*
335766 ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
335814 ATA ATA ATA ATA AT- ATA ATA ATA ATA AT- ATA AT- ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
335859 TATA GTA TTA ATA A-A TATA ATA A
1 -ATA ATA ATA ATA ATA -ATA ATA A
335882 ATATAGTAAT
Statistics
Matches: 102, Mismatches: 5, Indels: 12
0.86 0.04 0.10
Matches are distributed among these distances:
2 7 0.07
3 91 0.89
4 4 0.04
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:335882 original size:9 final size:8
Alignment explanation
Indices: 335764--335902 Score: 119
Period size: 9 Copynumber: 16.9 Consensus size: 8
335754 ATCAACAGCC
*
335764 ATATAATG
1 ATATAATA
335772 ATAATAATA
1 AT-ATAATA
335781 ATAATAATA
1 AT-ATAATA
335790 ATAATAATA
1 AT-ATAATA
335799 ATAATAATA
1 AT-ATAATA
335808 ATAATAATA
1 AT-ATAATA
335817 ATAATAATA
1 AT-ATAATA
335826 ATATAAT-
1 ATATAATA
335833 A-ATAATA
1 ATATAATA
335840 ATATAAT-
1 ATATAATA
335847 ATAATAATA
1 AT-ATAATA
335856 ATAT-ATA
1 ATATAATA
*
335863 GTATTAATAA
1 ATA-TAAT-A
335873 ATATAATAA
1 ATATAAT-A
*
335882 ATATAGTA
1 ATATAATA
335890 ATA-AATA
1 ATATAATA
335897 A-ATAAT
1 ATATAAT
335903 GTCTCGAATA
Statistics
Matches: 117, Mismatches: 5, Indels: 19
0.83 0.04 0.13
Matches are distributed among these distances:
6 6 0.05
7 16 0.14
8 24 0.21
9 68 0.58
10 3 0.03
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (8 bp):
ATATAATA
Found at i:338844 original size:22 final size:19
Alignment explanation
Indices: 338813--338855 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 19
338803 AAAAATCGGG
338813 AAAAATATTAATTAATAAAAT
1 AAAAATATTAA-TAA-AAAAT
338834 AAAAATAATTAATAAAAAAT
1 AAAAAT-ATTAATAAAAAAT
338854 AA
1 AA
338856 TATGTTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.33
21 9 0.43
22 5 0.24
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAAATATTAATAAAAAAT
Found at i:338923 original size:38 final size:39
Alignment explanation
Indices: 338855--339163 Score: 186
Period size: 38 Copynumber: 8.4 Consensus size: 39
338845 ATAAAAAATA
*
338855 ATATGTTTTCAAAAAAATCT-TTTTTAAAACTATAT-ATGAT
1 ATATGTTTTC--AAAAAT-TGTTTTTAAAACTATATAATTAT
* * *
338895 ATATGCTTTCAAAAATTATTTTTGAAACTATATAA-TAT
1 ATATGTTTTCAAAAATTGTTTTTAAAACTATATAATTAT
*
338933 ATGTGTTTTCAAAAATTGTTTTTCAAAAGCTATATAATATAT
1 ATATGTTTTCAAAAATTGTTTTT-AAAA-CTATATAAT-TAT
*
338975 ATATGTTTTC-AAAA-TGTTTTCAAAACTATAT-ATTAT
1 ATATGTTTTCAAAAATTGTTTTTAAAACTATATAATTAT
* *
339011 ATAAATGTTTTCAAAAA------CT---A-TATATTA-TAT
1 AT--ATGTTTTCAAAAATTGTTTTTAAAACTATATAATTAT
** * * * * *
339041 ATAT-TTTCAAAATATTTTTA-AAAA-CTATATATTATAT
1 ATATGTTTTCAAAAATTGTTTTTAAAACTATATAAT-TAT
* *
339078 ATAT-TTTTCAAAAA-CGTTTTCAAAACTATAT-ATTAT
1 ATATGTTTTCAAAAATTGTTTTTAAAACTATATAATTAT
*
339114 ATA--TTTTCAAAAA-TGTTTTCAAAACTATAT-ATTAT
1 ATATGTTTTCAAAAATTGTTTTTAAAACTATATAATTAT
339149 ATATGTTTTCAAAAA
1 ATATGTTTTCAAAAA
339164 ACTATATATA
Statistics
Matches: 217, Mismatches: 26, Indels: 55
0.73 0.09 0.18
Matches are distributed among these distances:
27 7 0.03
28 2 0.01
30 10 0.05
31 2 0.01
35 39 0.18
36 13 0.06
37 31 0.14
38 62 0.29
39 12 0.06
40 23 0.11
41 4 0.02
42 12 0.06
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (39 bp):
ATATGTTTTCAAAAATTGTTTTTAAAACTATATAATTAT
Found at i:338966 original size:78 final size:78
Alignment explanation
Indices: 338852--339027 Score: 187
Period size: 78 Copynumber: 2.2 Consensus size: 78
338842 TTAATAAAAA
*
338852 ATAATATGTTTTCAAAAAAATCTTTTTTAAAACTATAT-AT-GATATATGCTTTCAAAAATTATT
1 ATAA-ATGTTTTC-AAAAAATCTTTTTCAAAACTATATAATAGATATATGCTTTC-AAAA-TATT
**
338915 TTTGAAACTATATA-AT
62 TTCAAAACTATATATAT
** * * * * *
338931 ATATGTGTTTTCAAAAATTGTTTTTCAAAAGCTATATAATATATATATGTTTTCAAAATGTTTTC
1 ATAAATGTTTTCAAAAAATCTTTTTCAAAA-CTATATAATAGATATATGCTTTCAAAATATTTTC
338996 AAAACTATATATTAT
65 AAAACTATATA-TAT
339011 ATAAATGTTTTCAAAAA
1 ATAAATGTTTTCAAAAA
339028 CTATATATTA
Statistics
Matches: 80, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
77 15 0.19
78 28 0.35
79 9 0.11
80 28 0.35
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.44
Consensus pattern (78 bp):
ATAAATGTTTTCAAAAAATCTTTTTCAAAACTATATAATAGATATATGCTTTCAAAATATTTTCA
AAACTATATATAT
Found at i:339039 original size:26 final size:28
Alignment explanation
Indices: 338986--339041 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
338976 TATGTTTTCA
338986 AAATGTTTTC-AAAACTATATATTATAT
1 AAATGTTTTCAAAAACTATATATTATAT
339013 AAATGTTTTCAAAAACTATATATTATAT
1 AAATGTTTTCAAAAACTATATATTATAT
339041 A
1 A
339042 TATTTTCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 10 0.36
28 18 0.64
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (28 bp):
AAATGTTTTCAAAAACTATATATTATAT
Found at i:339047 original size:26 final size:27
Alignment explanation
Indices: 338991--339052 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 27
338981 TTTCAAAATG
*
338991 TTTTC-AAAACTATATATTATATAAATG
1 TTTTCAAAAACTATATATTATAT-AATA
339018 TTTTCAAAAACTATATATTATAT-ATA
1 TTTTCAAAAACTATATATTATATAATA
339044 TTTTCAAAA
1 TTTTCAAAA
339053 TATTTTTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
26 11 0.33
27 5 0.15
28 17 0.52
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (27 bp):
TTTTCAAAAACTATATATTATATAATA
Found at i:339064 original size:37 final size:36
Alignment explanation
Indices: 339013--339163 Score: 198
Period size: 37 Copynumber: 4.1 Consensus size: 36
339003 TATATTATAT
339013 AAATGTTTTCAAAAACTATATATTATATATATTTTCAA
1 AAAT-TTTT-AAAAACTATATATTATATATATTTTCAA
339051 AATATTTTTAAAAACTATATATTATATATATTTTTCAA
1 AA-ATTTTTAAAAACTATATATTATATATA-TTTTCAA
* *
339089 AAACGTTTTCAAAACTATATA-T-TATATATTTTCAA
1 AAA-TTTTTAAAAACTATATATTATATATATTTTCAA
* *
339124 AAATGTTTTCAAAACTATATATTATATATGTTTTCAA
1 AAAT-TTTTAAAAACTATATATTATATATATTTTCAA
339161 AAA
1 AAA
339164 ACTATATATA
Statistics
Matches: 103, Mismatches: 4, Indels: 13
0.86 0.03 0.11
Matches are distributed among these distances:
35 26 0.25
36 7 0.07
37 38 0.37
38 30 0.29
39 2 0.02
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (36 bp):
AAATTTTTAAAAACTATATATTATATATATTTTCAA
Found at i:339086 original size:64 final size:65
Alignment explanation
Indices: 338951--339189 Score: 272
Period size: 73 Copynumber: 3.6 Consensus size: 65
338941 TCAAAAATTG
* * * *
338951 TTTTTCAAAAGCTATATAATATATATATGTTTTCAAAAT-GTTTTCAAAACTATATATTATATAA
1 TTTTTCAAAAACTATAT-ATATATATATATTTTCAAAATATTTTTCAAAACTATATATTATATAT
339015 A
65 A
*
339016 TGTTTTCAAAAACTATATAT-TATATATATTTTCAAAATATTTTTAAAAACTATATATTATATAT
1 T-TTTTCAAAAACTATATATATATATATATTTTCAAAATATTTTTCAAAACTATATATTATATAT
339080 A
65 A
*
339081 TTTTTCAAAAACGTTTTCAAAACTATATATTATATATTTTCAAAA-ATGTTTTCAAAACTATATA
1 TTTTTCAAAAAC----T--ATA-TATATA-TATATATTTTCAAAATAT-TTTTCAAAACTATATA
339145 TTATATAT-
57 TTATATATA
*
339153 GTTTTCAAAAAACTATATATA-ATATATATTTTCAAAA
1 TTTTTC-AAAAACTATATATATATATATATTTTCAAAA
339190 ACCCATTTTT
Statistics
Matches: 152, Mismatches: 9, Indels: 27
0.81 0.05 0.14
Matches are distributed among these distances:
64 43 0.28
65 28 0.18
66 19 0.12
67 2 0.01
68 1 0.01
69 1 0.01
70 2 0.01
71 3 0.02
72 9 0.06
73 44 0.29
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (65 bp):
TTTTTCAAAAACTATATATATATATATATTTTCAAAATATTTTTCAAAACTATATATTATATATA
Found at i:339150 original size:33 final size:33
Alignment explanation
Indices: 339073--339150 Score: 115
Period size: 35 Copynumber: 2.4 Consensus size: 33
339063 AACTATATAT
339073 TATATA-TAT-TTTTCAAAAACGTTTTCAAAAC
1 TATATATTATATTTTCAAAAACGTTTTCAAAAC
*
339104 TATATATTATATATTTTCAAAAATGTTTTCAAAAC
1 TATATA-T-TATATTTTCAAAAACGTTTTCAAAAC
339139 TATATATTATAT
1 TATATATTATAT
339151 ATGTTTTCAA
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
31 6 0.14
33 5 0.12
34 4 0.10
35 27 0.64
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.46
Consensus pattern (33 bp):
TATATATTATATTTTCAAAAACGTTTTCAAAAC
Found at i:339172 original size:27 final size:27
Alignment explanation
Indices: 339126--339190 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
339116 ATTTTCAAAA
*
339126 ATGTTTTC--AAAACTATATATTATAT
1 ATGTTTTCAAAAAACTATATATAATAT
339151 ATGTTTTCAAAAAACTATATATAATAT
1 ATGTTTTCAAAAAACTATATATAATAT
*
339178 ATATTTTCAAAAA
1 ATGTTTTCAAAAA
339191 CCCATTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 8 0.22
27 28 0.78
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (27 bp):
ATGTTTTCAAAAAACTATATATAATAT
Found at i:340838 original size:17 final size:17
Alignment explanation
Indices: 340816--340865 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
340806 TGAATACAGT
340816 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
340833 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
*
340850 TAGTTCATTTATTAAA
1 TAGTTCATTAATTAAA
340866 GTAACTCTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:349282 original size:100 final size:99
Alignment explanation
Indices: 349109--349299 Score: 301
Period size: 100 Copynumber: 1.9 Consensus size: 99
349099 TTGTAATTTG
* *
349109 CCTTTATCAGGCTAGCTGAATCTTATCCATAAAGTTGGGGCATTTAACCAATTTCTCTAAAGGGA
1 CCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCTGGGGCATTTAACCAATTGCTCTAAAGGGA
* *
349174 CAACTCAAGCTTTTATTGTATATATATTATAATCA
66 CAACTCAAGC-TTTATTATATACATATTATAATCA
* * *
349209 CCTTTATCAGGCTAGTTGAATCTTATCCATAAAGCTGGGGCATTTAATCAATTGCTCTAGAGGGA
1 CCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCTGGGGCATTTAACCAATTGCTCTAAAGGGA
*
349274 CAGCTCAAGCTTTATTATATACATAT
66 CAACTCAAGCTTTATTATATACATAT
349300 AATATTATAA
Statistics
Matches: 83, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
99 14 0.17
100 69 0.83
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (99 bp):
CCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCTGGGGCATTTAACCAATTGCTCTAAAGGGA
CAACTCAAGCTTTATTATATACATATTATAATCA
Found at i:355098 original size:36 final size:37
Alignment explanation
Indices: 354925--355232 Score: 292
Period size: 36 Copynumber: 8.5 Consensus size: 37
354915 AATCATTTTT
* ** *
354925 AAAACTATATATGATATATGCTTTCAAAATTTATTTCA
1 AAAACTATATATTATATATATTTTCAAAATGT-TTTCA
* *
354963 AAAA-TATA-A-TATATATGTTTCCAAAAAATGTTTTTTCA
1 AAAACTATATATTATATATATTTTC--AAAATG--TTTTCA
*
355001 AAAACTATATATATATATATATATATATTCGAAATG-TTTCA
1 AAAAC--TATATAT-TATATATAT-T-TTCAAAATGTTTTCA
355042 AAAACTATATA-TATAT-TATTTTC-AAATGTTTTCA
1 AAAACTATATATTATATATATTTTCAAAATGTTTTCA
355076 AAAACTATATATTATATATA-TTTCAAAATGTTTTCA
1 AAAACTATATATTATATATATTTTCAAAATGTTTTCA
*
355112 AAAACTATATA-TATATATAGTTTTC-AAACGTTTTCA
1 AAAACTATATATTATATATA-TTTTCAAAATGTTTTCA
*
355148 AAAAC--TATATCATATATA-TTTCAAAAT-TTTT--
1 AAAACTATATATTATATATATTTTCAAAATGTTTTCA
355179 AAAACTATATATTATTATATATTTTCAAAAATGTTTTC-
1 AAAACTATATATTA-TATATATTTTC-AAAATGTTTTCA
355217 AAAACTATATA-TATAT
1 AAAACTATATATTATAT
355233 TTCAAAAAAA
Statistics
Matches: 232, Mismatches: 11, Indels: 56
0.78 0.04 0.19
Matches are distributed among these distances:
31 5 0.02
33 19 0.08
34 32 0.14
35 39 0.17
36 51 0.22
37 24 0.10
38 24 0.10
39 7 0.03
41 14 0.06
42 1 0.00
44 13 0.06
45 1 0.00
46 2 0.01
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.44
Consensus pattern (37 bp):
AAAACTATATATTATATATATTTTCAAAATGTTTTCA
Found at i:355122 original size:70 final size:71
Alignment explanation
Indices: 355010--355232 Score: 293
Period size: 70 Copynumber: 3.2 Consensus size: 71
355000 AAAAACTATA
*
355010 TATATATATATATATATATTCGAAATG-TTTCAAAAACTATATATATAT-TATTTTCAAATGTTT
1 TATATAT-TATATATAT-TTCAAAATGTTTTCAAAAACTATATATATATATATTTTCAAATGTTT
355073 TCAAAAAC
64 TCAAAAAC
*
355081 TATATATTATATATATTTCAAAATGTTTTCAAAAACTATATATATATATAGTTTTCAAACGTTTT
1 TATATATTATATATATTTCAAAATGTTTTCAAAAACTATATATATATATA-TTTTCAAATGTTTT
355146 CAAAAAC
65 CAAAAAC
*
355153 --TATATCATATATATTTCAAAAT-TTTT--AAAACTATATATTATTATATATTTTCAAAAATGT
1 TATATATTATATATATTTCAAAATGTTTTCAAAAACTATATA-TA-TATATATTTTC--AAATGT
355213 TTTC-AAAAC
62 TTTCAAAAAC
355222 TATATA-TATAT
1 TATATATTATAT
355233 TTCAAAAAAA
Statistics
Matches: 138, Mismatches: 5, Indels: 19
0.85 0.03 0.12
Matches are distributed among these distances:
67 11 0.08
68 7 0.05
69 23 0.17
70 64 0.46
71 13 0.09
72 20 0.14
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (71 bp):
TATATATTATATATATTTCAAAATGTTTTCAAAAACTATATATATATATATTTTCAAATGTTTTC
AAAAAC
Found at i:358243 original size:22 final size:23
Alignment explanation
Indices: 358216--358270 Score: 85
Period size: 22 Copynumber: 2.4 Consensus size: 23
358206 TCCATCATTA
*
358216 AAAAGAGAATCTATCAT-TTTTG
1 AAAAGAGAATCTATCATCTCTTG
358238 AAAAGAGAATCTATCATCTCTTG
1 AAAAGAGAATCTATCATCTCTTG
*
358261 ACAAGAGAAT
1 AAAAGAGAAT
358271 ATATGTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 17 0.57
23 13 0.43
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.29
Consensus pattern (23 bp):
AAAAGAGAATCTATCATCTCTTG
Found at i:367574 original size:31 final size:30
Alignment explanation
Indices: 367523--367634 Score: 129
Period size: 31 Copynumber: 3.7 Consensus size: 30
367513 CTTTTAAAAC
** *
367523 TTTCAATATCATCCCCCAACATTTAGTT-TG
1 TTTCAATATGGTCCCTCAACATTTA-TTCTG
367553 TTGTCAATATGGTCCCTCAACATTTATTCTG
1 TT-TCAATATGGTCCCTCAACATTTATTCTG
*
367584 TTTTTAATATGGTCCCTCAACATTTATTCTG
1 -TTTCAATATGGTCCCTCAACATTTATTCTG
*
367615 TTTATAATATGGTCCC-CAAC
1 TTT-CAATATGGTCCCTCAAC
367635 GTAACTTTTG
Statistics
Matches: 74, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
30 11 0.15
31 61 0.82
32 2 0.03
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (30 bp):
TTTCAATATGGTCCCTCAACATTTATTCTG
Found at i:369857 original size:13 final size:13
Alignment explanation
Indices: 369838--369871 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
369828 ATTCGAGCGC
369838 ACCTCTCTCTCTTT
1 ACCTCTC-CTCTTT
369852 -CCTCTCCTCTTT
1 ACCTCTCCTCTTT
369864 ACCTCTCC
1 ACCTCTCC
369872 AACAATGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.06, C:0.50, G:0.00, T:0.44
Consensus pattern (13 bp):
ACCTCTCCTCTTT
Found at i:370625 original size:31 final size:31
Alignment explanation
Indices: 370585--370651 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
370575 TGCAATATAA
* *
370585 TCCCCCAACATTTAGTCTT-TTTGTAATATGG
1 TCCCTCAACATTTAGT-TTGTCTGTAATATGG
370616 TCCCTCAACATTTAGTTTGTCTGTAATATGG
1 TCCCTCAACATTTAGTTTGTCTGTAATATGG
370647 TCCCT
1 TCCCT
370652 GATGTAATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 2 0.06
31 31 0.94
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.42
Consensus pattern (31 bp):
TCCCTCAACATTTAGTTTGTCTGTAATATGG
Found at i:373840 original size:23 final size:23
Alignment explanation
Indices: 373813--373907 Score: 79
Period size: 23 Copynumber: 4.2 Consensus size: 23
373803 CATTGAACCA
* *
373813 TTAATGCATACTATTCTCATTTT
1 TTAATGCATAATATTCTCATCTT
** *
373836 TTAATTTATAATATTCTCATCGT
1 TTAATGCATAATATTCTCATCTT
* *
373859 TTAATGAATAATATAT-T-ATCTA
1 TTAATGCATAATAT-TCTCATCTT
* *
373881 TTAATCCATAATA-TCTCATTTT
1 TTAATGCATAATATTCTCATCTT
373903 TTAAT
1 TTAAT
373908 TAAGTTAACA
Statistics
Matches: 56, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 22 0.39
23 31 0.55
24 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.03, T:0.51
Consensus pattern (23 bp):
TTAATGCATAATATTCTCATCTT
Found at i:378400 original size:45 final size:45
Alignment explanation
Indices: 378344--378563 Score: 363
Period size: 45 Copynumber: 4.9 Consensus size: 45
378334 TATAAAATTT
* *
378344 CTTATCATTTA-TCCTATAAGCTCGTAAGCTTATTCTACCAATATA
1 CTTACCATTTATTCC-ATAAGCTCGTAAGCTTATTTTACCAATATA
*
378389 CTTACCATTTATTCCATAAGCTTGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
378434 CTTATCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
378479 CTTACCATTTATTCCATAAGCTCGTAAGCTTATCTTA-CATATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA-ATATA
378524 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
378564 TTATTATATA
Statistics
Matches: 164, Mismatches: 8, Indels: 5
0.93 0.05 0.03
Matches are distributed among these distances:
44 2 0.01
45 157 0.96
46 5 0.03
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:378575 original size:32 final size:33
Alignment explanation
Indices: 378525--378591 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 33
378515 ACATATATAC
*
378525 TTACCATTTATTCCATAAGCTCGTAAGCTTATT
1 TTACCATTTATTACATAAGCTCGTAAGCTTATT
*
378558 TTACCA-TTATTATATAAGCTCGTAAGCTTATT
1 TTACCATTTATTACATAAGCTCGTAAGCTTATT
378590 TT
1 TT
378592 CATGTTTACC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 26 0.81
33 6 0.19
ACGTcount: A:0.28, C:0.18, G:0.09, T:0.45
Consensus pattern (33 bp):
TTACCATTTATTACATAAGCTCGTAAGCTTATT
Found at i:383237 original size:8 final size:8
Alignment explanation
Indices: 383224--383314 Score: 62
Period size: 8 Copynumber: 11.1 Consensus size: 8
383214 AGGCGATAAC
383224 AGAAAAAA
1 AGAAAAAA
383232 AGAAAAAA
1 AGAAAAAA
383240 AG-AAAAA
1 AGAAAAAA
* *
383247 ATAAAGAA
1 AGAAAAAA
383255 AGAAAAAA
1 AGAAAAAA
*
383263 TGAAAAAA
1 AGAAAAAA
383271 TA-AAGAGAAA
1 -AGAA-A-AAA
*
383281 AGAGAAAA
1 AGAAAAAA
* *
383289 A-TAAGAA
1 AGAAAAAA
383296 AGAAAAATA
1 AGAAAAA-A
383305 AGAAAGAAA
1 AGAAA-AAA
383314 A
1 A
383315 TGGATCAACT
Statistics
Matches: 63, Mismatches: 12, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
7 10 0.16
8 36 0.57
9 11 0.17
10 6 0.10
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (8 bp):
AGAAAAAA
Found at i:383239 original size:7 final size:7
Alignment explanation
Indices: 383227--383302 Score: 57
Period size: 7 Copynumber: 10.7 Consensus size: 7
383217 CGATAACAGA
383227 AAAAAAG
1 AAAAAAG
383234 AAAAAAAG
1 -AAAAAAG
*
383242 AAAAAAT
1 AAAAAAG
383249 AAAGAAAG
1 AAA-AAAG
383257 AAAAAATG
1 AAAAAA-G
383265 AAAAAA-
1 AAAAAAG
* *
383271 TAAAGAG
1 AAAAAAG
*
383278 AAAAGAG
1 AAAAAAG
*
383285 -AAAAAT
1 AAAAAAG
*
383291 AAGAAAG
1 AAAAAAG
383298 AAAAA
1 AAAAA
383303 TAAGAAAGAA
Statistics
Matches: 54, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
6 8 0.15
7 26 0.48
8 20 0.37
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.05
Consensus pattern (7 bp):
AAAAAAG
Found at i:383252 original size:11 final size:10
Alignment explanation
Indices: 383226--383302 Score: 54
Period size: 11 Copynumber: 7.6 Consensus size: 10
383216 GCGATAACAG
383226 AAAAAAAG--
1 AAAAAAAGAA
383234 AAAAAAAGAA
1 AAAAAAAGAA
383244 AAAATAAAGAA
1 AAAA-AAAGAA
383255 AGAAAAAATGAA
1 A-AAAAAA-GAA
383267 AAAATAAAG-A
1 AAAA-AAAGAA
* *
383277 GAAAAGAG-A
1 AAAAAAAGAA
*
383286 AAAATAAGAA
1 AAAAAAAGAA
383296 AGAAAAA
1 A-AAAAA
383303 TAAGAAAGAA
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
8 8 0.15
9 9 0.16
10 10 0.18
11 18 0.33
12 10 0.18
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:383254 original size:19 final size:20
Alignment explanation
Indices: 383226--383302 Score: 79
Period size: 19 Copynumber: 3.8 Consensus size: 20
383216 GCGATAACAG
383226 AAAA-AAAGA-AAAAAAGAA
1 AAAATAAAGAGAAAAAAGAA
383244 AAAATAAAGAAAGAAAAAATGAA
1 AAAATAAAG--AGAAAAAA-GAA
*
383267 AAAATAAAGAGAAAAGAG-A
1 AAAATAAAGAGAAAAAAGAA
*
383286 AAAATAAGAAAGAAAAA
1 AAAATAA-AGAGAAAAA
383303 TAAGAAAGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
18 4 0.08
19 12 0.24
20 8 0.16
21 8 0.16
22 6 0.12
23 12 0.24
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (20 bp):
AAAATAAAGAGAAAAAAGAA
Found at i:383260 original size:13 final size:12
Alignment explanation
Indices: 383226--383314 Score: 76
Period size: 13 Copynumber: 7.1 Consensus size: 12
383216 GCGATAACAG
383226 AAAA-AAAGAAA
1 AAAAGAAAGAAA
383237 AAAAGAAA-AAA
1 AAAAGAAAGAAA
*
383248 TAAAGAAAGAAA
1 AAAAGAAAGAAA
*
383260 AAATGAAA-AAA
1 AAAAGAAAGAAA
383271 TAAAGAGAAAAGAGAAA
1 -AAA-AG--AA-AGAAA
383288 AATAAGAAAGAAA
1 AA-AAGAAAGAAA
383301 AATAAGAAAGAAA
1 AA-AAGAAAGAAA
383314 A
1 A
383315 TGGATCAACT
Statistics
Matches: 65, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
11 17 0.26
12 15 0.23
13 20 0.31
14 2 0.03
15 2 0.03
16 5 0.08
17 4 0.06
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.06
Consensus pattern (12 bp):
AAAAGAAAGAAA
Found at i:390948 original size:94 final size:98
Alignment explanation
Indices: 390845--391024 Score: 244
Period size: 94 Copynumber: 1.8 Consensus size: 98
390835 TTTGAGATTG
390845 TTTCTCTCAAAACAAATTTCGTCTCGCTTGAGACAAATTT-C-C-AC-AAATTTTGAAATTTGTT
1 TTTCTCTCAAAACAAATTTCGTCTCGCTTGAGACAAATTTCCTCAACAAAATTTTGAAA-TTGTT
390906 TCACTTAAAACAAAATTGTCACCTTTGAAATAGT
65 TCACTTAAAACAAAATTGTCACCTTTGAAATAGT
* * *
390940 TTTC-CTCAAAACAAATTTTGTCTCGCTTGAGATAATTTTCCCTCAAAACAAAAATTTTGAAATT
1 TTTCTCTCAAAACAAATTTCGTCTCGCTTGAGACAAATTT-CCTC--AAC-AAAATTTTGAAATT
*
391004 GTTTCACTTGAAACAAAATTG
62 GTTTCACTTAAAACAAAATTG
391025 ATCTCACTTG
Statistics
Matches: 73, Mismatches: 4, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
94 32 0.44
95 4 0.05
96 1 0.01
97 1 0.01
100 2 0.03
101 22 0.30
102 11 0.15
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (98 bp):
TTTCTCTCAAAACAAATTTCGTCTCGCTTGAGACAAATTTCCTCAACAAAATTTTGAAATTGTTT
CACTTAAAACAAAATTGTCACCTTTGAAATAGT
Found at i:390961 original size:36 final size:36
Alignment explanation
Indices: 390912--390992 Score: 94
Period size: 36 Copynumber: 2.2 Consensus size: 36
390902 TGTTTCACTT
*
390912 AAAACAAAATTGTCAC-CTTTGAAATAGTTTT-CCTC
1 AAAACAAAATTGTCACGC-TTGAAATAATTTTCCCTC
* * *
390947 AAAACAAATTTTGTCTCGCTTGAGATAATTTTCCCTC
1 AAAACAAA-ATTGTCACGCTTGAAATAATTTTCCCTC
390984 AAAACAAAA
1 AAAACAAAA
390993 ATTTTGAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
35 8 0.21
36 17 0.45
37 13 0.34
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.32
Consensus pattern (36 bp):
AAAACAAAATTGTCACGCTTGAAATAATTTTCCCTC
Found at i:391520 original size:140 final size:140
Alignment explanation
Indices: 391266--391523 Score: 329
Period size: 140 Copynumber: 1.8 Consensus size: 140
391256 TGCAACTATG
* * * * *
391266 ACTAGATCTTCTCAACACGAAGGAACAATGTTGTCCACTGATCAAATCTCCTCAATACGAAGGAG
1 ACTAGATCTCCTCAACACGAAGGAACAATGTTGTCCACCGACCAAATCTCCTCAACACGAACGAG
* * *
391331 AAATATCATACTCAGATAATCAAACTTCTTCAACGTGAATGAACCGTGTTGTCTCCAAAATTATC
66 AAATATCATACTCAGATAATCAAACTTCCTCAACGTGAAGGAAACGTGTTGTCTCCAAAATTATC
391396 TCCAAATACA
131 TCCAAATACA
* * * * *
391406 ACTAGATGTCCTCAACACGAAGGAACAATGTTTTCCTCCGACCAGATCTCCTCAACGCGAACGA-
1 ACTAGATCTCCTCAACACGAAGGAACAATGTTGTCCACCGACCAAATCTCCTCAACACGAACGAG
* * * * * *
391470 ACAGTGTCATCCTCAGATAATTAGACTTCCTCAACGTGAAGGAAATGTGTTGTC
66 A-AATATCATACTCAGATAATCAAACTTCCTCAACGTGAAGGAAACGTGTTGTC
391524 ACTATCAAGG
Statistics
Matches: 98, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
139 1 0.01
140 97 0.99
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.26
Consensus pattern (140 bp):
ACTAGATCTCCTCAACACGAAGGAACAATGTTGTCCACCGACCAAATCTCCTCAACACGAACGAG
AAATATCATACTCAGATAATCAAACTTCCTCAACGTGAAGGAAACGTGTTGTCTCCAAAATTATC
TCCAAATACA
Found at i:392082 original size:19 final size:18
Alignment explanation
Indices: 392042--392083 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
392032 TTAACACTAA
*
392042 CATTTTATTTTTTTATTG
1 CATTTTATTTTCTTATTG
*
392060 CATTTTATTTTCCTTATTT
1 CATTTTATTTT-CTTATTG
392079 CATTT
1 CATTT
392084 CATGCACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.17, C:0.12, G:0.02, T:0.69
Consensus pattern (18 bp):
CATTTTATTTTCTTATTG
Found at i:392359 original size:16 final size:16
Alignment explanation
Indices: 392340--392385 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
392330 TTATTTATTT
392340 ATGTATATATTATATC
1 ATGTATATATTATATC
*
392356 ATGT-TATA-GATATAC
1 ATGTATATATTATAT-C
392371 ATGTATATATT-TATC
1 ATGTATATATTATATC
392386 TAATATTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
14 4 0.16
15 10 0.40
16 11 0.44
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (16 bp):
ATGTATATATTATATC
Found at i:393817 original size:20 final size:20
Alignment explanation
Indices: 393792--393838 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
393782 CTTACAGTAT
393792 CGATACTGCATGAACAATAC
1 CGATACTGCATGAACAATAC
393812 CGATACTGCATGAACAATAC
1 CGATACTGCATGAACAATAC
393832 CGATACT
1 CGATACT
393839 ATTCACGTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.26, G:0.15, T:0.21
Consensus pattern (20 bp):
CGATACTGCATGAACAATAC
Found at i:393969 original size:18 final size:18
Alignment explanation
Indices: 393946--393992 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
393936 ATGCAAAATA
393946 GGTACTGATACCCAAAGG
1 GGTACTGATACCCAAAGG
393964 GGTACTGATACCCAAAGG
1 GGTACTGATACCCAAAGG
*
393982 GGTACCGATAC
1 GGTACTGATAC
393993 TACTTTACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.32, C:0.23, G:0.28, T:0.17
Consensus pattern (18 bp):
GGTACTGATACCCAAAGG
Done.