Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001470.1 Hibiscus syriacus cultivar Beakdansim tig00002847_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: 1178067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:958118 original size:85 final size:85
Alignment explanation
Indices: 958028--958290 Score: 359
Period size: 85 Copynumber: 3.1 Consensus size: 85
958018 AAAATCAAGA
* *
958028 AACCCCTACATATCACGATGGTCCTCAAGCTTTTCATCAAGAAACCCCTACATATCATGATGGTT
1 AACCCCTACATATCACGATGGTCCTCAAGCTTTTCATCAACAAACCCCTACATATCACGATGGTT
958093 TCTCAAGCTTGTCATCAAAG
66 TCTCAAGCTTGTCATCAAAG
* * * * *
958113 AACCCCTACATATCATGATAGTCCCTCAAGCTTTTTATCAATAAA-CCCTATATATCACGATGGT
1 AACCCCTACATATCACGATGGT-CCTCAAGCTTTTCATCAACAAACCCCTACATATCACGATGGT
*
958177 TTCTTAAGCTTGTCATCAAAG
65 TTCTCAAGCTTGTCATCAAAG
* * *
958198 AACCCCTACATATCACGATGGTCCTTCAAACTTGTCCTCAACAAACCCCTACATATCACGATGGT
1 AACCCCTACATATCACGATGGTCC-TCAAGCTTTTCATCAACAAACCCCTACATATCACGATGGT
* * *
958263 CTCTCAAGCTTTTCTTC-AAG
65 TTCTCAAGCTTGTCATCAAAG
958283 AAACCCCT
1 -AACCCCT
958291 GAAAATCAGG
Statistics
Matches: 155, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
84 2 0.01
85 95 0.61
86 58 0.37
ACGTcount: A:0.30, C:0.29, G:0.11, T:0.29
Consensus pattern (85 bp):
AACCCCTACATATCACGATGGTCCTCAAGCTTTTCATCAACAAACCCCTACATATCACGATGGTT
TCTCAAGCTTGTCATCAAAG
Found at i:958186 original size:128 final size:128
Alignment explanation
Indices: 958021--958288 Score: 348
Period size: 128 Copynumber: 2.1 Consensus size: 128
958011 GGACTTAAAA
*
958021 ATCAAGAAACCCCTACATATCACGATGGTCCTCAAGCTTTTCATC-AAGAAACCCCTACATATCA
1 ATCAAGAAA-CCCTACATATCACGATGGTCCTCAAGCTTGTCATCAAAG-AACCCCTACATATCA
* * * *
958085 TGATGGT-TTCTCAAGCTTGTCATCAA-AGAACCCCTACATATCATGATAGTCCCTCAAGCTTTT
64 CGATGGTCCT-TCAAACTTGTCATCAACA-AACCCCTACATATCACGATAGTCCCTCAAGCTTTT
958148 -T
127 CT
* * * *
958149 ATCAATAAACCCTATATATCACGATGGTTTCTTAAGCTTGTCATCAAAGAACCCCTACATATCAC
1 ATCAAGAAACCCTACATATCACGATGG-TCCTCAAGCTTGTCATCAAAGAACCCCTACATATCAC
* * *
958214 GATGGTCCTTCAAACTTGTCCTCAACAAACCCCTACATATCACGATGGTCTCTCAAGCTTTTCT
65 GATGGTCCTTCAAACTTGTCATCAACAAACCCCTACATATCACGATAGTCCCTCAAGCTTTTCT
958278 -TCAAGAAACCC
1 ATCAAGAAACCC
958289 CTGAAAATCA
Statistics
Matches: 122, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
127 17 0.14
128 99 0.81
129 6 0.05
ACGTcount: A:0.31, C:0.29, G:0.11, T:0.29
Consensus pattern (128 bp):
ATCAAGAAACCCTACATATCACGATGGTCCTCAAGCTTGTCATCAAAGAACCCCTACATATCACG
ATGGTCCTTCAAACTTGTCATCAACAAACCCCTACATATCACGATAGTCCCTCAAGCTTTTCT
Found at i:958429 original size:40 final size:40
Alignment explanation
Indices: 958343--958594 Score: 443
Period size: 40 Copynumber: 6.3 Consensus size: 40
958333 AACTATCTCA
* **
958343 AGTGAGATAAAATCTTCTGTTTCAA-GTAAAACAATCTCA
1 AGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
*
958382 AGCGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
1 AGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
958422 AGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
1 AGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
958462 AGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
1 AGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
*
958502 AATGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
1 AGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
*
958542 AATGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
1 AGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
958582 AGTGAGATAAAAT
1 AGTGAGATAAAAT
958595 ATTATGTATT
Statistics
Matches: 205, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
39 24 0.12
40 181 0.88
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (40 bp):
AGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
Found at i:964518 original size:29 final size:28
Alignment explanation
Indices: 964465--964525 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
964455 ATTATAACAG
* *
964465 TGACCTAAATAGAAAAACTATAAATTAA
1 TGACCAAAATAGAAAAACTAAAAATTAA
964493 TGACCAAAATAAGAAAAA-TAAAAAATTAA
1 TGACCAAAAT-AGAAAAACT-AAAAATTAA
964522 -GACC
1 TGACC
964526 CCAAGCATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 14 0.48
29 15 0.52
ACGTcount: A:0.61, C:0.11, G:0.08, T:0.20
Consensus pattern (28 bp):
TGACCAAAATAGAAAAACTAAAAATTAA
Found at i:965611 original size:3 final size:3
Alignment explanation
Indices: 965598--965633 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
965588 AAATAAGTAT
*
965598 ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
965634 TTTATAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:967821 original size:22 final size:22
Alignment explanation
Indices: 967793--967835 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
967783 AGTTTTATTG
967793 AAGTTTTCTC-TTTTTACTTTTC
1 AAGTTTT-TCATTTTTACTTTTC
*
967815 AAGTTTTTCATTTTTTCTTTT
1 AAGTTTTTCATTTTTACTTTT
967836 ATTTTCAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.14, C:0.14, G:0.05, T:0.67
Consensus pattern (22 bp):
AAGTTTTTCATTTTTACTTTTC
Found at i:972694 original size:23 final size:23
Alignment explanation
Indices: 972668--972712 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
972658 GACACGAAAG
*
972668 AAAAAAATGGAAAACAAAAAAAC
1 AAAAAAATGAAAAACAAAAAAAC
** *
972691 AAAAGTATGAAAAAGAAAAAAA
1 AAAAAAATGAAAAACAAAAAAA
972713 TGCATTTCGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.78, C:0.04, G:0.11, T:0.07
Consensus pattern (23 bp):
AAAAAAATGAAAAACAAAAAAAC
Found at i:977221 original size:55 final size:54
Alignment explanation
Indices: 977179--977880 Score: 613
Period size: 55 Copynumber: 12.7 Consensus size: 54
977169 CCCACTACCA
* * * *
977179 ATACGAAAATTAATAAACTTATTATGAATTTCTTAGTTTTGCACATATAGTGCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCC
* *
977233 TATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTACACACACTGTGCCC
1 -ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTG-CC
*
977289 ATACGGAAATTCATAAACTTATTCTGAATTTCTTAGTTTTGCACACACAGTGTCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTG-CC
* * *
977344 ATATGTAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGACTT
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTG-C-C
* * * * * ** ** * * **
977400 ATTA-TGAATTTC-TTAGC---TT-TGCA-CACAAAG---TGCTCATAC-G-GAA
1 A-TACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCC
* ** * * * **
977443 ATTCATAAACTT-ATTATGAATTTCTTAGTTTGTACGCATAGTGTTATTCGGTAAT-CACACACA
1 ATACGGAAA-TTCA-TA--AA---CTTA---T-TATG-A-A-T-TTCTT-AGTTTTGCACACACA
*
977506 ATGCC
50 GTGCC
* * * *
977511 TATACGGAAATCCATAAACTTATTATAAATTTCTTAGTTTTGCACACATAGTACC
1 -ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCC
*
977566 TATACGGAAATTCATAAACTTATTATGAATTTCTAAGTTTTGCACACACAGTGCCC
1 -ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTG-CC
* * *
977622 ATACAGAAATTCATAAACTTATTCTGAATTTTTTAGTTTTGCACACACAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTG-CC
*
977677 ATACAGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTG-CC
* *
977732 ATATGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAATGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTG-CC
* *
977787 ATAAGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCATACACAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTG-CC
* * *
977842 AAACGAAAATTCATAAATTTATTATGAATTTCTTAGTTT
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTT
977881 GCATGCATAG
Statistics
Matches: 530, Mismatches: 82, Indels: 70
0.78 0.12 0.10
Matches are distributed among these distances:
42 1 0.00
43 3 0.01
44 2 0.00
45 2 0.00
46 1 0.00
47 8 0.02
50 4 0.01
51 3 0.01
52 2 0.00
54 3 0.01
55 455 0.86
56 12 0.02
57 4 0.01
58 2 0.00
59 2 0.00
60 2 0.00
63 4 0.01
64 1 0.00
66 7 0.01
67 1 0.00
68 4 0.01
69 7 0.01
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (54 bp):
ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCC
Found at i:977378 original size:165 final size:164
Alignment explanation
Indices: 977179--977880 Score: 678
Period size: 165 Copynumber: 4.2 Consensus size: 164
977169 CCCACTACCA
* * *
977179 ATACGAAAATTAATAAACTTATTATGAATTTCTTAGTTTTGCACATATAGTGCCTATACGGAAAT
1 ATACG-AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCTATACGGAAAT
* *
977244 TCATAAACTTATTATGAATTTCTTAGTTTTACACACACTGTGCCCATACGGAAATTCATAAACTT
65 TCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGGAAATTCATAAACTT
*
977309 ATTCTGAATTTCTTAGTTTTGCACACACAGTGTCC
130 ATTCTGAATTTCTTAGTTTTGCACACACAGTGCCC
* * *
977344 ATATGTAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGACTTATTA-TGAA
1 ATACG-AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTG-CCTA-TACGGAA
* * * * ** ** * * ** * **
977408 TTTC-TTAGC---TT-TGCA-CACAAAG---TGCTCATAC-G-G-AAATTCATAAACTT-ATTAT
63 ATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGGAAA-TTCA-TA-
* * * ** * *
977460 GAATTTCTTAGTTTGTACGCATAGTGTTATTCGGTAAT-CACACACAATGCCT
125 -AA---CTTA--TTCT--G-A-A-T-TTCTT-AGTTTTGCACACACAGTGCCC
* * * *
977512 ATACGGAAATCCATAAACTTATTATAAATTTCTTAGTTTTGCACACATAGTACCTATACGGAAAT
1 ATAC-GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCTATACGGAAAT
* *
977577 TCATAAACTTATTATGAATTTCTAAGTTTTGCACACACAGTGCCCATACAGAAATTCATAAACTT
65 TCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGGAAATTCATAAACTT
*
977642 ATTCTGAATTTTTTAGTTTTGCACACACAGTGCCC
130 ATTCTGAATTTCTTAGTTTTGCACACACAGTGCCC
* *
977677 ATACAGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATATGGAAAT
1 ATAC-GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCTATACGGAAAT
* *
977742 TCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAATGCCCATAAGGAAATTCATAAACTT
65 TCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGGAAATTCATAAACTT
* *
977807 ATTATGAATTTCTTAGTTTTGCATACACAGTGCCC
130 ATTCTGAATTTCTTAGTTTTGCACACACAGTGCCC
* *
977842 AAACGAAAATTCATAAATTTATTATGAATTTCTTAGTTT
1 ATACG-AAATTCATAAACTTATTATGAATTTCTTAGTTT
977881 GCATGCATAG
Statistics
Matches: 428, Mismatches: 74, Indels: 70
0.75 0.13 0.12
Matches are distributed among these distances:
154 7 0.02
155 5 0.01
156 1 0.00
157 8 0.02
160 7 0.02
161 3 0.01
162 5 0.01
164 5 0.01
165 253 0.59
166 13 0.03
167 13 0.03
168 64 0.15
169 5 0.01
171 5 0.01
172 3 0.01
173 8 0.02
176 9 0.02
177 1 0.00
178 5 0.01
179 8 0.02
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (164 bp):
ATACGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCTATACGGAAATT
CATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGGAAATTCATAAACTTA
TTCTGAATTTCTTAGTTTTGCACACACAGTGCCC
Found at i:977407 original size:36 final size:36
Alignment explanation
Indices: 977360--977431 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
977350 AAATTCATAA
* *
977360 ACTTATTATGAATTTCTTAGTTTTGCACACACAGTG
1 ACTTATTATGAATTTCTTAGCTTTGCACACAAAGTG
977396 ACTTATTATGAATTTCTTAGCTTTGCACACAAAGTG
1 ACTTATTATGAATTTCTTAGCTTTGCACACAAAGTG
977432 CTCATACGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (36 bp):
ACTTATTATGAATTTCTTAGCTTTGCACACAAAGTG
Found at i:977460 original size:91 final size:91
Alignment explanation
Indices: 977305--977473 Score: 277
Period size: 91 Copynumber: 1.9 Consensus size: 91
977295 AAATTCATAA
* * * * *
977305 ACTTATTCTGAATTTCTTAGTTTTGCACACACAGTGTCCATATGTAAATTCATAAACTTATTATG
1 ACTTATTATGAATTTCTTAGCTTTGCACACAAAGTGTCCATACGGAAATTCATAAACTTATTATG
977370 AATTTCTTAGTTTTGCACACACAGTG
66 AATTTCTTAGTTTTGCACACACAGTG
977396 ACTTATTATGAATTTCTTAGCTTTGCACACAAAGTG-CTCATACGGAAATTCATAAACTTATTAT
1 ACTTATTATGAATTTCTTAGCTTTGCACACAAAGTGTC-CATACGGAAATTCATAAACTTATTAT
977460 GAATTTCTTAGTTT
65 GAATTTCTTAGTTT
977474 GTACGCATAG
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
90 1 0.01
91 71 0.99
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.41
Consensus pattern (91 bp):
ACTTATTATGAATTTCTTAGCTTTGCACACAAAGTGTCCATACGGAAATTCATAAACTTATTATG
AATTTCTTAGTTTTGCACACACAGTG
Found at i:981967 original size:3 final size:3
Alignment explanation
Indices: 981959--982019 Score: 104
Period size: 3 Copynumber: 20.3 Consensus size: 3
981949 TAATGAGTAA
* *
981959 AAT AAT AAT AAT AGT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
982007 AAT AAT AAT AAT A
1 AAT AAT AAT AAT A
982020 GAGCTTGAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:984879 original size:32 final size:36
Alignment explanation
Indices: 984808--984884 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 36
984798 GTATGTGATA
*
984808 TATAT-ATATATATGTTTTGTGATATGAATTATATG
1 TATATGATATATATGTTGTGTGATATGAATTATATG
*
984843 -ATATGATATATATG-TGTGTTA-ATG-ATTAT-TG
1 TATATGATATATATGTTGTGTGATATGAATTATATG
*
984874 TATATGTTATA
1 TATATGATATA
984885 AGATATATGA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
31 2 0.05
32 14 0.38
33 3 0.08
34 9 0.24
35 9 0.24
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.51
Consensus pattern (36 bp):
TATATGATATATATGTTGTGTGATATGAATTATATG
Found at i:990586 original size:10 final size:10
Alignment explanation
Indices: 990571--990595 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
990561 ATAATTTTAT
990571 TGAAATAAAC
1 TGAAATAAAC
990581 TGAAATAAAC
1 TGAAATAAAC
990591 TGAAA
1 TGAAA
990596 CAAAGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.08, G:0.12, T:0.20
Consensus pattern (10 bp):
TGAAATAAAC
Found at i:990718 original size:15 final size:16
Alignment explanation
Indices: 990698--990732 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
990688 CTAATGAAAA
990698 TAAAATA-CAAACTCT
1 TAAAATATCAAACTCT
990713 TAAAATATTCAAACTCT
1 TAAAATA-TCAAACTCT
990730 TAA
1 TAA
990733 TTCTAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
17 11 0.61
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.31
Consensus pattern (16 bp):
TAAAATATCAAACTCT
Found at i:991368 original size:19 final size:19
Alignment explanation
Indices: 991323--991368 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
991313 TTTCTTCATG
*
991323 CATATTCATATCTTACATC
1 CATATTCGTATCTTACATC
991342 CATATTCGTATCTTACATC
1 CATATTCGTATCTTACATC
991361 CATATTCG
1 CATATTCG
991369 AGTATGAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.28, C:0.26, G:0.04, T:0.41
Consensus pattern (19 bp):
CATATTCGTATCTTACATC
Found at i:996259 original size:18 final size:18
Alignment explanation
Indices: 996229--996266 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
996219 AAATGGAGTC
*
996229 CTTTCTTTCTTTTCTTTT
1 CTTTCTTTCTTTTATTTT
996247 CTTT-TTTCTTTTTATTTT
1 CTTTCTTTC-TTTTATTTT
996265 CT
1 CT
996267 ATCTATTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (18 bp):
CTTTCTTTCTTTTATTTT
Found at i:996264 original size:11 final size:11
Alignment explanation
Indices: 996238--996281 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
996228 CCTTTCTTTC
*
996238 TTTTCTTTTCTT
1 TTTTCTTTT-TA
996250 TTTTCTTTTTA
1 TTTTCTTTTTA
* *
996261 TTTTCTATCTA
1 TTTTCTTTTTA
996272 TTTTCTTTTT
1 TTTTCTTTTT
996282 TAAATCCCTC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTCTTTTTA
Found at i:996669 original size:12 final size:12
Alignment explanation
Indices: 996637--996671 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
996627 CAACAATGGG
*
996637 TGTTTTGCCCTC
1 TGTTTTGCTCTC
996649 TGTTTTGCTCTC
1 TGTTTTGCTCTC
996661 TGTTTTGCTCT
1 TGTTTTGCTCT
996672 GTCCTTTGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.26, G:0.17, T:0.57
Consensus pattern (12 bp):
TGTTTTGCTCTC
Found at i:1001879 original size:18 final size:17
Alignment explanation
Indices: 1001852--1001906 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
1001842 ATATATATTA
*
1001852 TATACTTATTTCCAAAAT
1 TATACATATTT-CAAAAT
1001870 TATACATATTT-AAAA-
1 TATACATATTTCAAAAT
1001885 TATA-ATATTTTCAAAAT
1 TATACATA-TTTCAAAAT
1001902 CTATA
1 -TATA
1001907 TATAATATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
14 3 0.09
15 7 0.22
16 8 0.25
18 14 0.44
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.44
Consensus pattern (17 bp):
TATACATATTTCAAAAT
Found at i:1001900 original size:16 final size:17
Alignment explanation
Indices: 1001851--1001901 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
1001841 AATATATATT
* *
1001851 ATATACTTATTTCCAAA
1 ATATACATATTTTCAAA
1001868 ATTATACATA-TTT-AAA
1 A-TATACATATTTTCAAA
1001884 ATATA-ATATTTTCAAA
1 ATATACATATTTTCAAA
1001900 AT
1 AT
1001902 CTATATATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 3 0.10
15 7 0.24
16 9 0.31
17 3 0.10
18 7 0.24
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATACATATTTTCAAA
Found at i:1001907 original size:29 final size:28
Alignment explanation
Indices: 1001883--1001978 Score: 90
Period size: 29 Copynumber: 3.4 Consensus size: 28
1001873 ACATATTTAA
1001883 AATATAATATTTTCAAAATCTATA-TAT
1 AATATAATATTTTCAAAATCTATATTAT
* * *
1001910 AATAT-ATTTTTTCAAAATTTTATAAATAT
1 AATATAATATTTTCAAAA-TCTAT-ATTAT
*
1001939 AATATACTATTTTCAAAA-CTATATATAT
1 AATATAATATTTTCAAAATCTATAT-TAT
1001967 ATATATATATAT
1 A-ATATA-ATAT
1001979 ATGCTATTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
26 11 0.20
27 10 0.18
28 8 0.15
29 13 0.24
30 13 0.24
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (28 bp):
AATATAATATTTTCAAAATCTATATTAT
Found at i:1001937 original size:24 final size:25
Alignment explanation
Indices: 1001878--1001939 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 25
1001868 ATTATACATA
1001878 TTTA-AAATATAATATTTTCAAAATC
1 TTTATAAATAT-ATATTTTCAAAATC
* *
1001903 TATATATAATATATTTTTTCAAAAT-
1 TTTATA-AATATATATTTTCAAAATC
1001928 TTTATAAATATA
1 TTTATAAATATA
1001940 ATATACTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
24 6 0.19
25 8 0.25
26 13 0.41
27 5 0.16
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (25 bp):
TTTATAAATATATATTTTCAAAATC
Found at i:1001998 original size:28 final size:28
Alignment explanation
Indices: 1001966--1002027 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
1001956 ACTATATATA
1001966 TATATATA-TA-TATATGCTATTTTAAAAC
1 TATATATACTACTATATGC--TTTTAAAAC
*
1001994 TATATGTACTACTATATGCTTTTAAAAC
1 TATATATACTACTATATGCTTTTAAAAC
1002022 TATATA
1 TATATA
1002028 AAATATTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 21 0.70
29 2 0.07
30 7 0.23
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (28 bp):
TATATATACTACTATATGCTTTTAAAAC
Found at i:1002010 original size:36 final size:36
Alignment explanation
Indices: 1001903--1001998 Score: 109
Period size: 36 Copynumber: 2.9 Consensus size: 36
1001893 TTTCAAAATC
*
1001903 TATATATAATATA-TTTTTTCAAAA-T-T-T-TATA
1 TATATATAATATACTATTTTCAAAACTATATATATA
1001934 -A-ATATAATATACTATTTTCAAAACTATATATATA
1 TATATATAATATACTATTTTCAAAACTATATATATA
*
1001968 TATATATATATATGCTATTTT-AAAACTATAT
1 TATATATA-ATATACTATTTTCAAAACTATAT
1001999 GTACTACTAT
Statistics
Matches: 55, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
29 10 0.18
30 11 0.20
31 1 0.02
32 1 0.02
33 1 0.02
34 4 0.07
35 1 0.02
36 15 0.27
37 11 0.20
ACGTcount: A:0.45, C:0.06, G:0.01, T:0.48
Consensus pattern (36 bp):
TATATATAATATACTATTTTCAAAACTATATATATA
Found at i:1002037 original size:28 final size:29
Alignment explanation
Indices: 1001962--1002038 Score: 75
Period size: 28 Copynumber: 2.6 Consensus size: 29
1001952 CAAAACTATA
*
1001962 TATATATATATATATATATGCTATTTTAAAAC
1 TATATA-AAATAT-TATATGC-ATTTTAAAAC
** * *
1001994 TATATGTACTACTATATGC-TTTTAAAAC
1 TATATAAAATATTATATGCATTTTAAAAC
1002022 TATATAAAATATTATAT
1 TATATAAAATATTATAT
1002039 ACAAATTATA
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
28 22 0.61
30 7 0.19
31 2 0.06
32 5 0.14
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (29 bp):
TATATAAAATATTATATGCATTTTAAAAC
Found at i:1014019 original size:24 final size:20
Alignment explanation
Indices: 1013967--1014004 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1013957 GAGACAGTAG
1013967 GTGAACTAACATTCAGGTCT
1 GTGAACTAACATTCAGGTCT
1013987 GTGAACTAACATTCAGGT
1 GTGAACTAACATTCAGGT
1014005 GCTATTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (20 bp):
GTGAACTAACATTCAGGTCT
Found at i:1014509 original size:18 final size:18
Alignment explanation
Indices: 1014486--1014532 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
1014476 GGTTTACCAG
*
1014486 CTAACTGTATGCTAACAA
1 CTAACTGCATGCTAACAA
1014504 CTAACTGCATGCTAACAA
1 CTAACTGCATGCTAACAA
1014522 CTAACTGCATG
1 CTAACTGCATG
1014533 AATACAAGCA
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:0.36, C:0.26, G:0.13, T:0.26
Consensus pattern (18 bp):
CTAACTGCATGCTAACAA
Found at i:1019206 original size:18 final size:18
Alignment explanation
Indices: 1019185--1019223 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1019175 AGCTAACTGT
*
1019185 ATGCTAACAACTAATTAC
1 ATGCTAACAACTAACTAC
1019203 ATGCTAACAACTAACTAC
1 ATGCTAACAACTAACTAC
1019221 ATG
1 ATG
1019224 TATACGAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.23, G:0.08, T:0.26
Consensus pattern (18 bp):
ATGCTAACAACTAACTAC
Found at i:1032052 original size:29 final size:27
Alignment explanation
Indices: 1031995--1032063 Score: 93
Period size: 29 Copynumber: 2.5 Consensus size: 27
1031985 TTGTTAAAGG
*
1031995 TTCAATATTATAATTAAAAAATTAAAA
1 TTCAATATTATAATTAAAAAATAAAAA
*
1032022 TTTAATATTATAATTAAAAAAATAAAAAA
1 TTCAATATTATAATT-AAAAAAT-AAAAA
*
1032051 TTCAATAATATAA
1 TTCAATATTATAA
1032064 ATAGTATATC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
27 14 0.39
28 7 0.19
29 15 0.42
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (27 bp):
TTCAATATTATAATTAAAAAATAAAAA
Found at i:1032868 original size:20 final size:20
Alignment explanation
Indices: 1032845--1032907 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
1032835 ATTTAACATG
1032845 ATATTTAAGTGACATATATC
1 ATATTTAAGTGACATATATC
* * * *
1032865 ATATTATAAAT-TC-T-CATG
1 ATATT-TAAGTGACATATATC
1032883 ATATTTAAGTGACATATATC
1 ATATTTAAGTGACATATATC
1032903 ATATT
1 ATATT
1032908 ATAAATTCTT
Statistics
Matches: 31, Mismatches: 8, Indels: 8
0.66 0.17 0.17
Matches are distributed among these distances:
17 4 0.13
18 8 0.26
19 2 0.06
20 13 0.42
21 4 0.13
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.43
Consensus pattern (20 bp):
ATATTTAAGTGACATATATC
Found at i:1032884 original size:38 final size:38
Alignment explanation
Indices: 1032841--1032916 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
1032831 AAATATTTAA
1032841 CATGATATTTAAGTGACATATATCATATTATAAATTCT
1 CATGATATTTAAGTGACATATATCATATTATAAATTCT
1032879 CATGATATTTAAGTGACATATATCATATTATAAATTCT
1 CATGATATTTAAGTGACATATATCATATTATAAATTCT
1032917 TCAATCTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (38 bp):
CATGATATTTAAGTGACATATATCATATTATAAATTCT
Found at i:1034044 original size:24 final size:23
Alignment explanation
Indices: 1033986--1034045 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 23
1033976 TTTTATAATA
*
1033986 TTTTTAAA-ATCATTTTTGAAAAC
1 TTTTTAAATAT-AGTTTTGAAAAC
* *
1034009 TATATAATATATAGTTTTGAAAAC
1 TTTTTAA-ATATAGTTTTGAAAAC
1034033 GTTTTTAAATATA
1 -TTTTTAAATATA
1034046 ATATATAGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
23 5 0.17
24 17 0.59
25 7 0.24
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (23 bp):
TTTTTAAATATAGTTTTGAAAAC
Found at i:1034069 original size:31 final size:31
Alignment explanation
Indices: 1034010--1034069 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
1034000 TTTGAAAACT
** *
1034010 ATATAATATATAGTTTTGAAAACGTTTTTAA
1 ATATAATATATAGTTTAAAAAACATTTTTAA
*
1034041 ATATAATATATAGTTTAAAAAATATTTTT
1 ATATAATATATAGTTTAAAAAACATTTTT
1034070 TTTTGAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.47
Consensus pattern (31 bp):
ATATAATATATAGTTTAAAAAACATTTTTAA
Found at i:1034645 original size:21 final size:23
Alignment explanation
Indices: 1034621--1034668 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 23
1034611 ACAACAGAGC
*
1034621 AACCAAACACA-AAAC-CAACCA
1 AACCAAACACATAAACACAACAA
* *
1034642 AACCGAACTCATAAACACAACAA
1 AACCAAACACATAAACACAACAA
1034665 AACC
1 AACC
1034669 GACTCCAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 9 0.41
22 4 0.18
23 9 0.41
ACGTcount: A:0.58, C:0.35, G:0.02, T:0.04
Consensus pattern (23 bp):
AACCAAACACATAAACACAACAA
Found at i:1035264 original size:2 final size:2
Alignment explanation
Indices: 1035257--1035294 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1035247 TTATTATCAG
1035257 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1035295 GTGTGTGTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1039893 original size:84 final size:84
Alignment explanation
Indices: 1039653--1040910 Score: 1273
Period size: 84 Copynumber: 15.2 Consensus size: 84
1039643 GCTCAAGACA
* * * *
1039653 AGAAGGGTTATTTGCCAACCAAATACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATT
1 AGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
1039718 TGCAGCATAGCTTAAGTCG
66 TGCAGCATAACTTAAGTCG
* * *
1039737 AGAAGGGCTATCTG----CCAAAGACCCTCGAGTTCGATTA----CA-C-CCGAGGGCACATCAT
1 AGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCC-AAGGCACATCAT
*
1039792 TTGCAGCATAACATAAGTCG
65 TTGCAGCATAACTTAAGTCG
* * *
1039812 AGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
1 AGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
1039877 TGCAGCATAGCTTAAGTCG
66 TGCAGCATAACTTAAGTCG
** *
1039896 AGAAGGGCTATCTG----CCAAATTCCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCATT
1 AGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * * *
1039957 TACAGCATAACTCAAGGCT
66 TGCAGCATAACTTAAGTCG
* * * * * *
1039976 AAAAGGGTTATCTGTC-ACCAATGACATTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
1 AGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
1040040 TGTAGCATAACTTAAGTCA
66 TGCAGCATAACTTAAGTCG
* * * *
1040059 AGAAGGGTTATCTGTCAA-CAAAGACCTTCGCGTTCGACTACGCTCAACTCCAAGGCACATCATT
1 AGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
1040123 TGCAGCATAGCTTAAGTCG
66 TGCAGCATAACTTAAGTCG
* * * *
1040142 AGAAGGGCTATCTG----CCAAAGACAC-TCGAGTTCGATTACACTCAGCATCGAGGGCACATCA
1 AGAAGGGCTATCTGCCAACCAAAGAC-CTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCA
* * *
1040202 TTTGCAGCATAACTCAAGGCT
64 TTTGCAGCATAACTTAAGTCG
* * * *
1040223 AGAAGAGTTATCTGCCAACCGAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATT
1 AGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
1040288 TGTAGTATAACTTAAGTCG
66 TGCAGCATAACTTAAGTCG
* *
1040307 AGAAGGGCTATCTGTC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
1 AGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * *
1040371 TGCAACACAACTTAAGTCT
66 TGCAGCATAACTTAAGTCG
* * * * *
1040390 AGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTTAGCT-CAACGGCACATCAT
1 AGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCAT
*
1040454 TTGCAGCATAGCTTAAGTCG
65 TTGCAGCATAACTTAAGTCG
* * ** * * * * * *
1040474 ATAAGGGCTATCT----TCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGAATATCAT
1 AGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCAT
* * * * *
1040535 TTACAACATAACTCAAGGCT
65 TTGCAGCATAACTTAAGTCG
* * * *
1040555 AGAAGGGTTATCTGTC-ACCAATA-ACCTTTGAGTTCGACTACGCTCAGCT-CAACAGCACATCA
1 AGAAGGGCTATCTGCCAACCAA-AGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCA
*
1040617 TTTGCAGCATATCTTAAGTCG
64 TTTGCAGCATAACTTAAGTCG
* * * *
1040638 AGAAGGGCTATCTGCCAACCAAAGACCTTCCAGTTTGACTACGCTCAGCTCCAAGACATATCATT
1 AGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
1040703 TGCAGCATAACTTAGGTCG
66 TGCAGCATAACTTAAGTCG
* * * *
1040722 AGAAAGGGTTATCTGCTAACCAAAGACCTTCGAGTTCGACCACGCTCAACTCCAAGGCACATCAT
1 AG-AAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
* * *
1040787 CTGCAGTATAGCTTAAGTCG
65 TTGCAGCATAACTTAAGTCG
* * * * * * * *
1040807 AGAAGAGCTATTTGCCAACCAAGGACCTTTGAGTTCGATTACACTCAACT-CATAGGCAAATCAA
1 AGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCA-AGGCACATC--
* * * * *
1040871 ATTTACAGCATAGCTCAAGACA
63 ATTTGCAGCATAACTTAAGTCG
*
1040893 AGAAGAGCTATCTGCCAA
1 AGAAGGGCTATCTGCCAA
1040911 TAAATTTGTC
Statistics
Matches: 961, Mismatches: 174, Indels: 76
0.79 0.14 0.06
Matches are distributed among these distances:
74 1 0.00
75 43 0.04
76 2 0.00
79 20 0.02
80 136 0.14
81 76 0.08
82 2 0.00
83 256 0.27
84 288 0.30
85 104 0.11
86 33 0.03
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (84 bp):
AGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
TGCAGCATAACTTAAGTCG
Found at i:1040322 original size:331 final size:326
Alignment explanation
Indices: 1039670--1040853 Score: 1422
Period size: 331 Copynumber: 3.6 Consensus size: 326
1039660 TTATTTGCCA
* * * *
1039670 ACCAAATACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGT
* * * *
1039735 CGAGAAGGGCTATCTGC--CAAAGACCCTCGAGTTCGATTA----C-AC-CCGAGGGCACATCAT
66 CGAGAAGGGTTATCTGCAACAAAGACCTTCGAGTTCGACTACGCTCAACTCC-AAGGCACATCAT
* * * * * *
1039792 TTGCAGCATAACATAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCT
130 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACC-TCGAGTTCGATTACACT
* * * * * * * **
1039857 CAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCA--AATTCCT
190 CAGCTCGAGGGCATATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAACCT
* * * * * *
1039920 TCGAGTTCGACTACGCTCAGCT-TCAAGGCACATCATTTACAGCATAACTCAAGGCTAAAAGGGT
255 TCGAGTTCGACTACGCTCAGCTCT-AAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGC
1039984 TATCTGTC
319 TATCTGTC
* * *
1039992 ACCAATGACATTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGTAGCATAACTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGT
* *
1040057 CAAGAAGGGTTATCTGTCAACAAAGACCTTCGCGTTCGACTACGCTCAACTCCAAGGCACATCAT
66 CGAGAAGGGTTATCTG-CAACAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCAT
1040122 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACACTCGAGTTCGATTACACTCAGC
130 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC-CTCGAGTTCGATTACACTCAGC
* * *
1040187 ATCGAGGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGAGTTATCTGCCAACCGAAGACCTT
194 -TCGAGGGCATATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCC-ACC-AAAACCTT
* *
1040252 CGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGTAGTATAACTTAAGTCGAGAAGGGCTA
256 CGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTA
1040317 TCTGTC
321 TCTGTC
* *
1040323 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACACAACTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGT
* * * * *
1040388 CTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTTAGCT-CAACGGCACATC
66 CGAGAAGGGTTATCTG-CAAC-AAAGACCTTCGAGTTCGACTACGCTCAACTCCAA-GGCACATC
* * *
1040452 ATTTGCAGCATAGCTTAAGTCGATAAGGGCTATCTTCCAAAGACCCCCGAGTTCGATTACACTCA
128 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA-CCTCGAGTTCGATTACACTCA
* * * *
1040517 GCTTCGAGGGAATATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAATAACCT
192 GC-TCGAGGGCATATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAA-AACCT
* * *
1040582 TTGAGTTCGACTACGCTCAGCTC-AACAGCACATCATTTGCAGCATATCTTAAGTCGAGAAGGGC
255 TCGAGTTCGACTACGCTCAGCTCTAA-GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGC
*
1040646 TATCTGCC
319 TATCTGTC
* * * *
1040654 AACCAAAGACCTTCCAGTTTGACTACGCTCAGCTCCAAGACATATCATTTGCAGCATAACTTAGG
1 -ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAG
*
1040719 TCGAGAAAGGGTTATCTGCTAACCAAAGACCTTCGAGTTCGACCACGCTCAACTCCAAGGCACAT
65 TCGAG-AAGGGTTATCTGC-AA-CAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACAT
* * * * *
1040784 CATCTGCAGTATAGCTTAAGTCGAGAAGAGCTATTTGCCAACCAAGGACCTTTGAGTTCGATTAC
127 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC-A--AA-GACC-TCGAGTTCGATTAC
1040849 ACTCA
187 ACTCA
1040854 ACTCATAGGC
Statistics
Matches: 744, Mismatches: 87, Indels: 47
0.85 0.10 0.05
Matches are distributed among these distances:
322 72 0.10
323 1 0.00
325 19 0.03
326 26 0.03
327 43 0.06
328 1 0.00
329 1 0.00
330 48 0.06
331 220 0.30
332 205 0.28
333 80 0.11
334 5 0.01
336 4 0.01
337 19 0.03
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (326 bp):
ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGT
CGAGAAGGGTTATCTGCAACAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATT
TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTCGAGTTCGATTACACTCAGCTC
GAGGGCATATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAACCTTCGAGT
TCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGT
C
Found at i:1040344 original size:248 final size:244
Alignment explanation
Indices: 1039671--1040910 Score: 1286
Period size: 248 Copynumber: 5.0 Consensus size: 244
1039661 TATTTGCCAA
* * * *
1039671 CCAAATACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTC-AAGGCACATCATTTGCAGCATAACTCAAGGC
* * * *
1039736 GAGAAGGGCTATCTGCCA--AAGACCCTCGAGTTCGATTA----CA-C-CCGAGGGCACATCATT
65 GAGAAGGGTTATCTGCCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCC-AAGGCACATCATT
* *
1039793 TGCAGCATAACATAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTC
129 TGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTC-ACCAAAGACCTTTGAGTTCGACTACGCTC
*
1039858 AGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
193 AGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
** *
1039910 CCAAATTCCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTTACAGCATAACTCAAGGC
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCAAGGCACATCATTTGCAGCATAACTCAAGGC
* * * * *
1039975 TAAAAGGGTTATCTGTCACCAATGACATTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
65 GAGAAGGGTTATCTGCCACCAA-GACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * * * *
1040040 TGTAGCATAACTTAAGTCAAGAAGGGTTATCTGTCAACAAAGACCTTCGCGTTCGACTACGCTCA
129 TGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCGACTACGCTCA
*
1040105 ACTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
194 GCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
* * *
1040156 CCAAAGACAC-TCGAGTTCGATTACACTCAGCATCGAGGGCACATCATTTGCAGCATAACTCAAG
1 CCAAAGAC-CTTCGAGTTCGACTACGCTCAGC-TC-AAGGCACATCATTTGCAGCATAACTCAAG
* * *
1040220 GCTAGAAGAGTTATCTGCCAACCGAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATC
63 GCGAGAAGGGTTATCTGCC-ACC-AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* * * *
1040285 ATTTGTAGTATAACTTAAGTCGAGAAGGGCTATCTGTCACCAAAGACCTTCGAGTTCGACTACGC
126 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCGACTACGC
* * * * * * *
1040350 TCAGCTCCAAGGCATATCATTTGCAACACAACTTAAGTCTAGAAGGGTTGTCTG
191 TCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
* * * *
1040404 CCAACAAAAGACCTTTGAGTTCGACTACGCTTAGCTCAACGGCACATCATTTGCAGCATAGCTTA
1 -C--C-AAAGACCTTCGAGTTCGACTACGCTCAGCTCAA-GGCACATCATTTGCAGCATAACTCA
* * * * ** * * * * * *
1040469 AGTCGATAAGGGCTATCTTCCA--AAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGAATAT
61 AGGCGAGAAGGGTTATCTGCCACCAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACAT
* * * * *
1040532 CATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAATA-ACCTTTGAGTTCGACTAC
125 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCACCAA-AGACCTTTGAGTTCGACTAC
* *
1040596 GCTCAGCT-CAACAGCACATCATTTGCAGCATATCTTAAGTCGAGAAGGGCTATCTG
189 GCTCAGCTCCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
* * * * *
1040652 CCAACCAAAGACCTTCCAGTTTGACTACGCTCAGCTCCAAGACATATCATTTGCAGCATAACT-T
1 ----CCAAAGACCTTCGAGTTCGACTACGCTCAGCT-CAAGGCACATCATTTGCAGCATAACTCA
* * *
1040716 AGGTCGAGAAAGGGTTATCTGCTAACCAAAGACCTTCGAGTTCGACCACGCTCAACTCCAAGGCA
61 AGG-CGAG-AAGGGTTATCTGC-CACC-AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA
* * * * * * * * *
1040781 CATCATCTGCAGTATAGCTTAAGTCGAGAAGAGCTATTTGCCAACCAAGGACCTTTGAGTTCGAT
122 CATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTC-ACCAAAGACCTTTGAGTTCGAC
* * * * * * * *
1040846 TACACTCAACT-CATAGGCAAATCAAATTTACAGCATAGCTCAAGACAAGAAGAGCTATCTG
186 TACGCTCAGCTCCA-AGGCACATC--ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
1040907 CCAA
1 CCAA
1040911 TAAATTTGTC
Statistics
Matches: 828, Mismatches: 135, Indels: 64
0.81 0.13 0.06
Matches are distributed among these distances:
239 71 0.09
240 2 0.00
241 2 0.00
242 15 0.02
246 105 0.13
247 116 0.14
248 301 0.36
249 19 0.02
250 3 0.00
251 47 0.06
252 58 0.07
253 58 0.07
254 1 0.00
255 30 0.04
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (244 bp):
CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAGGCACATCATTTGCAGCATAACTCAAGGCG
AGAAGGGTTATCTGCCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
CAGCATAACTTAAGTCGAGAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCGACTACGCTCAGC
TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
Found at i:1041594 original size:39 final size:35
Alignment explanation
Indices: 1041533--1041787 Score: 172
Period size: 35 Copynumber: 7.1 Consensus size: 35
1041523 CAAAAAATAT
* *
1041533 ATTTTGGAAA-TATATATTATATAGTTTTTAAAAC
1 ATTTTGAAAATTATATAATATATAGTTTTTAAAAC
1041567 ATTTTTGAAAACTTATATACAATATATAAG-TTTTAAAAC
1 A-TTTTGAAAA-TTATAT--AATATAT-AGTTTTTAAAAC
* * *
1041606 ATTTTGAAAATTATATAGTATATAGTTTTGAAATC
1 ATTTTGAAAATTATATAATATATAGTTTTTAAAAC
*
1041641 ATTTTG-AAA--ATATAATATATAGTTTTAACAAAAAAC
1 ATTTTGAAAATTATATAATATATAGTTTT----TAAAAC
*
1041677 ATTTTTGGAAAATTGATATAATATATAGATTTTTTAAAAA
1 A-TTTT-GAAAATT-ATATAATATATAG--TTTTTAAAAC
* **
1041717 AATTTG-AAA--AGCT-ATA-ATA-TTTTTAAAATC
1 ATTTTGAAAATTATATAATATATAGTTTTTAAAA-C
* *
1041747 ATTTTTGAAAACTATATAATATATAGTTTTGAAAAC
1 A-TTTTGAAAATTATATAATATATAGTTTTTAAAAC
*
1041783 GTTTT
1 ATTTT
1041788 TAAATATAAT
Statistics
Matches: 175, Mismatches: 19, Indels: 53
0.71 0.08 0.21
Matches are distributed among these distances:
29 9 0.05
30 1 0.01
31 4 0.02
32 22 0.13
33 3 0.02
34 10 0.06
35 34 0.19
36 9 0.05
37 26 0.15
38 11 0.06
39 22 0.13
40 7 0.04
42 13 0.07
44 4 0.02
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.43
Consensus pattern (35 bp):
ATTTTGAAAATTATATAATATATAGTTTTTAAAAC
Found at i:1041794 original size:24 final size:23
Alignment explanation
Indices: 1041736--1041795 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 23
1041726 AGCTATAATA
*
1041736 TTTTTAAA-ATCATTTTTGAAAAC
1 TTTTTAAATAT-AGTTTTGAAAAC
* *
1041759 TATATAATATATAGTTTTGAAAAC
1 TTTTTAA-ATATAGTTTTGAAAAC
1041783 GTTTTTAAATATA
1 -TTTTTAAATATA
1041796 ATATTTATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
23 5 0.17
24 17 0.59
25 7 0.24
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (23 bp):
TTTTTAAATATAGTTTTGAAAAC
Found at i:1041816 original size:29 final size:31
Alignment explanation
Indices: 1041760--1041817 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1041750 TTTGAAAACT
**
1041760 ATATAATATATAGTTTTGAAAACGTTTTTAA
1 ATATAATATATAGTTTTGAAAAAATTTTTAA
*
1041791 ATATAATATTTA-TTTT-AAAAAATTTTT
1 ATATAATATATAGTTTTGAAAAAATTTTT
1041818 TTTTTGAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.38
30 4 0.17
31 11 0.46
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (31 bp):
ATATAATATATAGTTTTGAAAAAATTTTTAA
Found at i:1045415 original size:28 final size:29
Alignment explanation
Indices: 1045365--1045423 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
1045355 AAAATATGTC
* * *
1045365 ATGATATGCTTTATTTTATTAATATTTTT
1 ATGATAAGATTTATTTTATTAATACTTTT
1045394 ATGATAAGATTTATTTTA-TAATACTTTT
1 ATGATAAGATTTATTTTATTAATACTTTT
1045422 AT
1 AT
1045424 CACGAGGATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 11 0.41
29 16 0.59
ACGTcount: A:0.32, C:0.03, G:0.07, T:0.58
Consensus pattern (29 bp):
ATGATAAGATTTATTTTATTAATACTTTT
Found at i:1045433 original size:29 final size:29
Alignment explanation
Indices: 1045374--1045435 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
1045364 CATGATATGC
* * *
1045374 TTTATTTTATTAATATTTTTATGATAAGA
1 TTTATTTTATTAATACTTTTATCAGAAGA
*
1045403 TTTATTTTA-TAATACTTTTATCACGAGGA
1 TTTATTTTATTAATACTTTTATCA-GAAGA
1045432 TTTA
1 TTTA
1045436 AAGTAAAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (29 bp):
TTTATTTTATTAATACTTTTATCAGAAGA
Found at i:1046108 original size:27 final size:27
Alignment explanation
Indices: 1046071--1046129 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
1046061 TTCTAATTAA
* *
1046071 AAAAAATTATAAATATA-TCACTCAGTT
1 AAAATATTATAAATA-AGTCACTCAATT
1046098 AAAATATTATAAATAAGTCACTCAATT
1 AAAATATTATAAATAAGTCACTCAATT
1046125 AAAAT
1 AAAAT
1046130 GTTGTTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 1 0.03
27 28 0.97
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.32
Consensus pattern (27 bp):
AAAATATTATAAATAAGTCACTCAATT
Found at i:1047416 original size:13 final size:13
Alignment explanation
Indices: 1047387--1047421 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1047377 ATAACTAATA
*
1047387 ATATTAAAT-ATT
1 ATATTAAATAAAT
1047399 ATATTAAATAAAT
1 ATATTAAATAAAT
1047412 ATATTAAATA
1 ATATTAAATA
1047422 TATTTATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTAAATAAAT
Found at i:1050603 original size:33 final size:31
Alignment explanation
Indices: 1050561--1050638 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 31
1050551 TTAATAATTC
* * *
1050561 TAAATAAATAATAATTATATAATATTATTTTAA
1 TAAAAAAATAATAATTACATAA-A-TATATTAA
*
1050594 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTACATAAATATATTAA
1050625 TATAAAAAATAATA
1 TA-AAAAAATAATA
1050639 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
31 9 0.22
32 12 0.30
33 19 0.47
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (31 bp):
TAAAAAAATAATAATTACATAAATATATTAA
Found at i:1050659 original size:33 final size:34
Alignment explanation
Indices: 1050595--1050670 Score: 93
Period size: 33 Copynumber: 2.2 Consensus size: 34
1050585 TTATTTTAAT
* *
1050595 AAAAAAATAATATTTACATAAATATATTAATATA
1 AAAAAAATAATATTTACATAAAAATACTAATATA
*
1050629 AAAAATAATACTATTTA-A-AAAAATACTAATATA
1 AAAAA-AATAATATTTACATAAAAATACTAATATA
1050662 AAAATAAAT
1 AAAA-AAAT
1050671 TCTTACCACT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
33 20 0.54
34 7 0.19
35 10 0.27
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (34 bp):
AAAAAAATAATATTTACATAAAAATACTAATATA
Found at i:1050670 original size:18 final size:17
Alignment explanation
Indices: 1050622--1050670 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
1050612 ATAAATATAT
1050622 TAATATAAAAAATAATAC
1 TAATATAAAAAA-AATAC
*
1050640 T-AT-TTAAAAAAATAC
1 TAATATAAAAAAAATAC
1050655 TAATATAAAAATAAAT
1 TAATATAAAAA-AAAT
1050671 TCTTACCACT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 6 0.23
16 8 0.31
17 7 0.27
18 5 0.19
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (17 bp):
TAATATAAAAAAAATAC
Found at i:1053799 original size:15 final size:15
Alignment explanation
Indices: 1053779--1053808 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1053769 TATATTCCTT
1053779 AGCTGCATTCGAGTG
1 AGCTGCATTCGAGTG
1053794 AGCTGCATTCGAGTG
1 AGCTGCATTCGAGTG
1053809 CTCCAAGTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.33, T:0.27
Consensus pattern (15 bp):
AGCTGCATTCGAGTG
Found at i:1058193 original size:6 final size:6
Alignment explanation
Indices: 1058160--1058235 Score: 57
Period size: 6 Copynumber: 12.7 Consensus size: 6
1058150 AAAAGAAGAA
* * * *
1058160 AAAAAT ATAAATAT AAAAAT GAAGAT AAAAAT AAGAAT AAGAAT AAAAAT
1 AAAAAT A-AAA-AT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
* * *
1058210 GAAACT -AAAAT -AAAAT AAGAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1058236 CAAAGAAAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
5 9 0.16
6 38 0.68
7 6 0.11
8 3 0.05
ACGTcount: A:0.72, C:0.01, G:0.08, T:0.18
Consensus pattern (6 bp):
AAAAAT
Found at i:1058193 original size:18 final size:18
Alignment explanation
Indices: 1058149--1058235 Score: 65
Period size: 18 Copynumber: 4.9 Consensus size: 18
1058139 AAAGAAGGAA
*
1058149 AAAAAGAAGAA-AAAAAT
1 AAAAATAAGAATAAAAAT
* * *
1058166 ATAAATATAAAAATGAAGAT
1 A-AAA-ATAAGAATAAAAAT
*
1058186 AAAAATAAGAATAAGAAT
1 AAAAATAAGAATAAAAAT
*
1058204 AAAAATGAA-ACT-AAAAT
1 AAAAAT-AAGAATAAAAAT
1058221 -AAAATAAGAATAAAA
1 AAAAATAAGAATAAAA
1058236 CAAAGAAAAA
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
15 2 0.04
16 7 0.13
17 8 0.15
18 21 0.40
19 10 0.19
20 5 0.09
ACGTcount: A:0.74, C:0.01, G:0.09, T:0.16
Consensus pattern (18 bp):
AAAAATAAGAATAAAAAT
Found at i:1058227 original size:22 final size:21
Alignment explanation
Indices: 1058195--1058250 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
1058185 TAAAAATAAG
*
1058195 AATAAGAATAAAAATGAAACTAA
1 AATAA-AATAAAAATAAAAC-AA
*
1058218 AATAAAATAAGAATAAAACAA
1 AATAAAATAAAAATAAAACAA
*
1058239 AGAAAAAATAAA
1 A-ATAAAATAAA
1058251 GAAAATAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 3 0.11
22 20 0.71
23 5 0.18
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.14
Consensus pattern (21 bp):
AATAAAATAAAAATAAAACAA
Found at i:1058311 original size:13 final size:13
Alignment explanation
Indices: 1058282--1058315 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1058272 ATATGGTATC
1058282 TAAATAAT-AAGA
1 TAAATAATAAAGA
*
1058294 AAAATAATAAAGA
1 TAAATAATAAAGA
1058307 TAAATAATA
1 TAAATAATA
1058316 TGTAAAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (13 bp):
TAAATAATAAAGA
Found at i:1064685 original size:16 final size:17
Alignment explanation
Indices: 1064651--1064723 Score: 51
Period size: 17 Copynumber: 4.2 Consensus size: 17
1064641 TGTTAGAGGG
*
1064651 AAAAATGAATAAATGAA
1 AAAAATGAATAAATAAA
*
1064668 AAAAATGAA-GAATAAA
1 AAAAATGAATAAATAAA
* *
1064684 AATAAGTAAAATAAATAAAA
1 AA-AAAT-GAATAAAT-AAA
*
1064704 ATAAAAGGAA-AAATAAA
1 A-AAAATGAATAAATAAA
1064721 AAA
1 AAA
1064724 TAAATAAATA
Statistics
Matches: 43, Mismatches: 8, Indels: 11
0.69 0.13 0.18
Matches are distributed among these distances:
16 9 0.21
17 16 0.37
18 6 0.14
19 5 0.12
20 6 0.14
21 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.10, T:0.15
Consensus pattern (17 bp):
AAAAATGAATAAATAAA
Found at i:1064727 original size:29 final size:29
Alignment explanation
Indices: 1064681--1064788 Score: 92
Period size: 29 Copynumber: 3.5 Consensus size: 29
1064671 AATGAAGAAT
1064681 AAAAATAAGTAAAATAAATAAAAATAAAAGG
1 AAAAATAA--AAAATAAATAAAAATAAAAGG
*
1064712 AAAAATAAAAAATAAATAAATAAT-AAATG
1 AAAAATAAAAAATAAATAAA-AATAAAAGG
* * *
1064741 AAATATTAAAAAATAATATATATATAAAATGAG
1 AAA-AATAAAAAATAA-ATAAAAATAAAA-G-G
* *
1064774 TAAAATAGAAAATAA
1 AAAAATAAAAAATAA
1064789 TAATCATAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
29 19 0.30
30 16 0.25
31 15 0.24
32 10 0.16
33 3 0.05
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.22
Consensus pattern (29 bp):
AAAAATAAAAAATAAATAAAAATAAAAGG
Found at i:1064750 original size:12 final size:11
Alignment explanation
Indices: 1064692--1064758 Score: 59
Period size: 11 Copynumber: 6.1 Consensus size: 11
1064682 AAAATAAGTA
1064692 AAATAAATAA-
1 AAATAAATAAT
*
1064702 AAATAAA-AGGAA
1 AAATAAATA--AT
*
1064714 AAATAAAAAAT
1 AAATAAATAAT
1064725 AAATAAATAAT
1 AAATAAATAAT
*
1064736 AAATGAAATATT
1 AAAT-AAATAAT
1064748 AAA-AAATAAT
1 AAATAAATAAT
1064758 A
1 A
1064759 TATATATAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
9 1 0.02
10 14 0.29
11 16 0.33
12 16 0.33
13 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:1064875 original size:20 final size:19
Alignment explanation
Indices: 1064823--1064877 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
1064813 GAAAATATAA
1064823 ATAAAACAAATAAAAAACT
1 ATAAAACAAATAAAAAACT
1064842 A-AAAACAAAAATAAAAAA-T
1 ATAAAAC--AAATAAAAAACT
1064861 ATAAAATCAATATAAAA
1 ATAAAA-CAA-ATAAAA
1064878 GATACATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
18 5 0.16
19 5 0.16
20 20 0.65
21 1 0.03
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.16
Consensus pattern (19 bp):
ATAAAACAAATAAAAAACT
Found at i:1070160 original size:2 final size:2
Alignment explanation
Indices: 1070153--1070202 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
1070143 AGAAATATGA
1070153 AT AT AT AT AT A- AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1070193 AT AT AT AT AT
1 AT AT AT AT AT
1070203 CTGACTTGGA
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1070968 original size:75 final size:75
Alignment explanation
Indices: 1070887--1071036 Score: 300
Period size: 75 Copynumber: 2.0 Consensus size: 75
1070877 GCGATCTCCG
1070887 GTATCGCAAGTCAGTTTCCAGATTCGCAACGCTATTTTGACTATCGCATTGCGATTTCCCAAATT
1 GTATCGCAAGTCAGTTTCCAGATTCGCAACGCTATTTTGACTATCGCATTGCGATTTCCCAAATT
1070952 CGTGTTGCGA
66 CGTGTTGCGA
1070962 GTATCGCAAGTCAGTTTCCAGATTCGCAACGCTATTTTGACTATCGCATTGCGATTTCCCAAATT
1 GTATCGCAAGTCAGTTTCCAGATTCGCAACGCTATTTTGACTATCGCATTGCGATTTCCCAAATT
1071027 CGTGTTGCGA
66 CGTGTTGCGA
1071037 TTTCCTAAAT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (75 bp):
GTATCGCAAGTCAGTTTCCAGATTCGCAACGCTATTTTGACTATCGCATTGCGATTTCCCAAATT
CGTGTTGCGA
Found at i:1071065 original size:22 final size:21
Alignment explanation
Indices: 1071005--1071066 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
1070995 ATTTTGACTA
*
1071005 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCTAAAT
**
1071026 TCGTGTTGCGATTTCCTAAAT
1 TCGCATTGCGATTTCCTAAAT
*
1071047 TCGCATTACGATTTTCCTAA
1 TCGCATTGCGA-TTTCCTAA
1071067 TTTGGAATGC
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 26 0.76
22 8 0.24
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTCCTAAAT
Found at i:1071103 original size:20 final size:20
Alignment explanation
Indices: 1071072--1071140 Score: 120
Period size: 20 Copynumber: 3.5 Consensus size: 20
1071062 CCTAATTTGG
1071072 AATGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGC
* *
1071092 AACGCGATTACGTAAATCGC
1 AATGCGAATACGTAAATCGC
1071112 AATGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGC
1071132 AATGCGAAT
1 AATGCGAAT
1071141 CTGACTATCG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (20 bp):
AATGCGAATACGTAAATCGC
Found at i:1071755 original size:21 final size:21
Alignment explanation
Indices: 1071694--1071772 Score: 94
Period size: 20 Copynumber: 3.9 Consensus size: 21
1071684 TTCTAAACTT
1071694 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
1071714 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
1071734 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
1071755 AAAATCGCAACGAGAGAA
1 AAAATCGCAACGAGAGAA
1071773 TCGCAATGCG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 30 0.58
21 22 0.42
ACGTcount: A:0.52, C:0.18, G:0.19, T:0.11
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:1071776 original size:14 final size:14
Alignment explanation
Indices: 1071754--1071818 Score: 58
Period size: 14 Copynumber: 4.3 Consensus size: 14
1071744 CGAGAGAAAT
1071754 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
1071768 GAGAATCGCAATGCGAAA
1 GAAAATCGCAA--CG--A
1071786 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
* *
1071801 GATAATCGCAACGC
1 GAAAATCGCAACGA
1071815 GAAA
1 GAAA
1071819 CCAAACCGTA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
14 25 0.61
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 10 0.24
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:1071788 original size:33 final size:33
Alignment explanation
Indices: 1071749--1071818 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
1071739 CGCAACGAGA
*
1071749 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
1071782 GAAATGAAAATCGCAACGAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1071815 GAAA
1 GAAA
1071819 CCAAACCGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1071865 original size:14 final size:14
Alignment explanation
Indices: 1071846--1071901 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
1071836 TTTCATTTCG
1071846 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1071860 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1071879 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1071893 CGTTGCGAT
1 CGTTGCGAT
1071902 AGTCATTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1071871 original size:33 final size:33
Alignment explanation
Indices: 1071829--1071922 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
1071819 CCAAACCGTA
1071829 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1071862 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
1071895 TTGCGATAGTCATTTCCGCGTTGCGATT
1 TTGCGATTTTCATTT-CGCGTTGCGATT
1071923 TTCATTCTCT
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 46 0.79
34 12 0.21
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1071927 original size:20 final size:19
Alignment explanation
Indices: 1071829--1071950 Score: 102
Period size: 20 Copynumber: 6.8 Consensus size: 19
1071819 CCAAACCGTA
1071829 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
1071848 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
1071862 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
1071881 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
**
1071895 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
*
1071915 TTGCGATTTTCATTCTCTCG
1 TTGCGATTTTCATT-TCGCG
*
1071935 TTGCGCTTTTCATTTC
1 TTGCGATTTTCATTTC
1071951 AACCAAAAGA
Statistics
Matches: 82, Mismatches: 9, Indels: 24
0.71 0.08 0.21
Matches are distributed among these distances:
14 20 0.24
16 5 0.06
17 6 0.07
19 19 0.23
20 31 0.38
21 1 0.01
ACGTcount: A:0.10, C:0.25, G:0.20, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:1073713 original size:93 final size:92
Alignment explanation
Indices: 1073534--1073832 Score: 469
Period size: 93 Copynumber: 3.2 Consensus size: 92
1073524 AGGTTCATAC
* *
1073534 TTTTGTCTTTTGGTTGAAGTAATTTATTCGGTTGCTGCCAATTCTGCTAAAATGTGTATTCTTTA
1 TTTTGTCTTTTGGTTGAAGTAATTTGTTCGTTTGCTGCCAATTCTGCTAAAATGTGTATTCTTTA
*
1073599 ACATTGTGAAGTTAGTATTTGTCTTTG
66 ACACTGTGAAGTTAGTATTTGTCTTTG
*
1073626 TTTTGTC-TTTGGTTGAACGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTT
1 TTTTGTCTTTTGGTTGAA-GT-AATTTGTTCGTTTGCTGCCAATTCTGCTAAAATGTGTATTCTT
1073690 TAACACTGTGAAGTTAGTATTTGTCTTTG
64 TAACACTGTGAAGTTAGTATTTGTCTTTG
* * *
1073719 TTTTGTCTTTTGATTGAAAGTAATTTGTTCATTTGCTGCCAATTCTGCTAAATTGTGTATTCTTT
1 TTTTGTCTTTTGGTTG-AAGTAATTTGTTCGTTTGCTGCCAATTCTGCTAAAATGTGTATTCTTT
* *
1073784 -ATACTCTGAAGTTAGTATTTGTCTTTG
65 AACACTGTGAAGTTAGTATTTGTCTTTG
1073811 TTTTGTC-TTTGGTTGAAGTAAT
1 TTTTGTCTTTTGGTTGAAGTAAT
1073833 GCAATCCATT
Statistics
Matches: 193, Mismatches: 10, Indels: 10
0.91 0.05 0.05
Matches are distributed among these distances:
90 7 0.04
91 17 0.09
92 41 0.21
93 117 0.61
94 9 0.05
95 2 0.01
ACGTcount: A:0.20, C:0.12, G:0.19, T:0.49
Consensus pattern (92 bp):
TTTTGTCTTTTGGTTGAAGTAATTTGTTCGTTTGCTGCCAATTCTGCTAAAATGTGTATTCTTTA
ACACTGTGAAGTTAGTATTTGTCTTTG
Found at i:1074021 original size:20 final size:19
Alignment explanation
Indices: 1073920--1074035 Score: 134
Period size: 19 Copynumber: 6.3 Consensus size: 19
1073910 TCTTTTGGTT
* *
1073920 GAAATGAAAATCGCAACGA
1 GAAACGAAAATCGCAACGC
*
1073939 GAGAATGAAAATCGCAACGC
1 GA-AACGAAAATCGCAACGC
1073959 GAAACGAAAATCGCAACGC
1 GAAACGAAAATCGCAACGC
*
1073978 GAAATGAAAATCGCAA--C
1 GAAACGAAAATCGCAACGC
1073995 G--AC-AAAATCGCAACGC
1 GAAACGAAAATCGCAACGC
*
1074011 GAAACCAAAAATCGCAACGC
1 GAAA-CGAAAATCGCAACGC
1074031 GAAAC
1 GAAAC
1074036 TATAATCGCG
Statistics
Matches: 86, Mismatches: 4, Indels: 14
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 35 0.41
20 35 0.41
ACGTcount: A:0.49, C:0.23, G:0.20, T:0.08
Consensus pattern (19 bp):
GAAACGAAAATCGCAACGC
Found at i:1074069 original size:18 final size:19
Alignment explanation
Indices: 1074041--1074143 Score: 94
Period size: 18 Copynumber: 5.7 Consensus size: 19
1074031 GAAACTATAA
1074041 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1074060 T-GCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1074073 TCTCGTTGCGATTTT-ATT
1 TCGCGTTGCGATTTTCATT
*
1074091 TCGCGTTGCGATTTTCGTT
1 TCGCGTTGCGATTTTCATT
**
1074110 TCGCGTTGCGATAGTCATTT
1 TCGCGTTGCGATTTTCA-TT
*
1074130 TCACGTTGCGATTT
1 TCGCGTTGCGATTT
1074144 AAGTTCCAGA
Statistics
Matches: 65, Mismatches: 11, Indels: 15
0.71 0.12 0.16
Matches are distributed among these distances:
13 1 0.02
14 7 0.11
16 5 0.08
18 22 0.34
19 17 0.26
20 13 0.20
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1074614 original size:42 final size:42
Alignment explanation
Indices: 1074534--1074626 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
1074524 GCCCGACTCG
* * * *
1074534 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAATCCACTCCCACCGTTCAAGAGGCC
* * *
1074576 CCTATCATTCCTCGAGAATCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAATCCACTCCCACCGTTCAAGAGGCC
*
1074618 ACTATCATC
1 CCTATCATC
1074627 GTTGAAGAGG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.24, C:0.39, G:0.14, T:0.24
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAATCCACTCCCACCGTTCAAGAGGCC
Found at i:1074655 original size:21 final size:20
Alignment explanation
Indices: 1074596--1074656 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
1074586 CTCGAGAATC
1074596 CCCTCCCACCGTTCAAGAGG
1 CCCTCCCACCGTTCAAGAGG
** * *
1074616 CCACTATCATCGTTGAAGAGG
1 CC-CTCCCACCGTTCAAGAGG
*
1074637 TCCCTCCCACCATTCAAGAG
1 -CCCTCCCACCGTTCAAGAG
1074657 CCCGATTCAC
Statistics
Matches: 30, Mismatches: 9, Indels: 3
0.71 0.21 0.07
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.25, C:0.38, G:0.18, T:0.20
Consensus pattern (20 bp):
CCCTCCCACCGTTCAAGAGG
Found at i:1076022 original size:14 final size:14
Alignment explanation
Indices: 1076003--1076038 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1075993 ATTGTTTAAT
1076003 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1076017 TGATTTGAAAAAGT
1 TGATTTGTAAAAGA
1076031 TGATTTGT
1 TGATTTGT
1076039 TTAATTGATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1076230 original size:19 final size:19
Alignment explanation
Indices: 1076145--1076239 Score: 78
Period size: 19 Copynumber: 5.3 Consensus size: 19
1076135 AAAAATGACT
*
1076145 ATCGCAATGCGAAA-TGAAA
1 ATCGCAACGCGAAACT-AAA
1076164 ATCGCAACGCGAAA-TGAAA
1 ATCGCAACGCGAAACT-AAA
**
1076183 ATCATAA--CG--AC-AAA
1 ATCGCAACGCGAAACTAAA
*
1076197 ATCGCAACACGAAACTAAA
1 ATCGCAACGCGAAACTAAA
1076216 ATCGCAACGCGAAACTAAA
1 ATCGCAACGCGAAACTAAA
*
1076235 TTCGC
1 ATCGC
1076240 GTTGCGATTT
Statistics
Matches: 63, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
14 8 0.13
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 48 0.76
ACGTcount: A:0.47, C:0.23, G:0.16, T:0.14
Consensus pattern (19 bp):
ATCGCAACGCGAAACTAAA
Found at i:1076257 original size:19 final size:19
Alignment explanation
Indices: 1076235--1076385 Score: 89
Period size: 19 Copynumber: 8.7 Consensus size: 19
1076225 CGAAACTAAA
1076235 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1076254 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1076269 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1076287 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1076302 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
1076320 TTCGCATTGTGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1076335 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
1076353 TTCGCATTGCGATAGTCATT
1 TTCGCGTTGCGATTTTCA-T
1076373 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
1076386 AGACATTAAG
Statistics
Matches: 96, Mismatches: 20, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 25 0.26
16 9 0.09
17 9 0.09
19 40 0.42
20 13 0.14
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1076281 original size:33 final size:33
Alignment explanation
Indices: 1076239--1076365 Score: 227
Period size: 33 Copynumber: 3.8 Consensus size: 33
1076229 ACTAAATTCG
* *
1076239 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1076272 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
1076305 CGTTGCGATTTTCATTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1076338 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1076366 AGTCATTTTC
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:1076312 original size:14 final size:14
Alignment explanation
Indices: 1076260--1076347 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
1076250 TCATTTCGCT
*
1076260 TTGCGATTCCCTCG
1 TTGCGATTCTCTCG
*
1076274 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
1076291 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
1076307 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
*
1076324 CATTGTGATTCTCTCG
1 --TTGCGATTCTCTCG
1076340 TTGCGATT
1 TTGCGATT
1076348 TTCATTTCGC
Statistics
Matches: 57, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
14 19 0.33
16 14 0.25
17 13 0.23
19 11 0.19
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:1076377 original size:20 final size:20
Alignment explanation
Indices: 1076352--1076392 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1076342 GCGATTTTCA
*
1076352 TTTCGCATTGCGATAGTCAT
1 TTTCGCATTGCGATAGACAT
*
1076372 TTTCGCGTTGCGATAGACAT
1 TTTCGCATTGCGATAGACAT
1076392 T
1 T
1076393 AAGATGATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.39
Consensus pattern (20 bp):
TTTCGCATTGCGATAGACAT
Found at i:1076431 original size:20 final size:20
Alignment explanation
Indices: 1076359--1076431 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
1076349 TCATTTCGCA
* *
1076359 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTACGTG
* *
1076379 TTGCGATAGACA-TTAAGATG
1 TTGCGATAGTCATTTACG-TG
*
1076399 ATTGCGA-ACGTCATTTCCGTG
1 -TTGCGATA-GTCATTTACGTG
1076420 TTGCGATAGTCA
1 TTGCGATAGTCA
1076432 AATGAATGCC
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
19 3 0.07
20 23 0.56
21 12 0.29
22 3 0.07
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (20 bp):
TTGCGATAGTCATTTACGTG
Found at i:1079206 original size:23 final size:23
Alignment explanation
Indices: 1079180--1079224 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1079170 CACCACAGCT
*
1079180 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
1079203 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1079225 ATATAATGAT
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:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:1079367 original size:25 final size:26
Alignment explanation
Indices: 1079332--1079382 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
1079322 CAAAGAATAT
1079332 ATATATATCCCGAAGGACCGCGTAGA
1 ATATATATCCCGAAGGACCGCGTAGA
1079358 ATAT-TATCCCGAAGGACCGCGTAGA
1 ATATATATCCCGAAGGACCGCGTAGA
1079383 CCCTCTACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.20
Consensus pattern (26 bp):
ATATATATCCCGAAGGACCGCGTAGA
Found at i:1084330 original size:23 final size:23
Alignment explanation
Indices: 1084304--1084348 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1084294 CACCACAGCT
*
1084304 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
1084327 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1084349 ATATAATGAT
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:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:1086172 original size:21 final size:21
Alignment explanation
Indices: 1086130--1086174 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1086120 ATTTGTTCGT
* * *
1086130 TTGAAGGGGTATCGGTTTCCC
1 TTGAAGGGGTACCGATTCCCC
*
1086151 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1086172 TTG
1 TTG
1086175 CCCAAAATCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1087270 original size:24 final size:24
Alignment explanation
Indices: 1087236--1087289 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1087226 CTGAAAAATC
1087236 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1087260 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1087284 ATCAAA
1 ATCAAA
1087290 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1087303 original size:24 final size:24
Alignment explanation
Indices: 1087236--1087303 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1087226 CTGAAAAATC
* * *
1087236 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
1087260 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1087284 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1087304 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1087979 original size:22 final size:21
Alignment explanation
Indices: 1087936--1087979 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
1087926 TGCCGGATGG
** *
1087936 GGAAGGATGTCGTTGGATATA
1 GGAAGGATGTCGCCGGAGATA
1087957 GGAACGGATGTCGCCGGAGATA
1 GGAA-GGATGTCGCCGGAGATA
1087979 G
1 G
1087980 TGATAGATGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.27, C:0.11, G:0.41, T:0.20
Consensus pattern (21 bp):
GGAAGGATGTCGCCGGAGATA
Found at i:1088163 original size:20 final size:20
Alignment explanation
Indices: 1088147--1088332 Score: 275
Period size: 20 Copynumber: 9.2 Consensus size: 20
1088137 CAGAATCTCG
1088147 TTGCGATTTAC-TAAATCGCA
1 TTGCGATTTACGT-AATCGCA
1088167 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
*
1088187 TTGTGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
1088207 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
*
1088227 TTGTGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
* *
1088247 TTGCGATTTTCCTAATTCGCA
1 TTGCGATTTACGTAA-TCGCA
1088268 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
* *
1088288 TTGCGATTTTCCTAATTCGCA
1 TTGCGATTTACGTAA-TCGCA
*
1088309 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTAATCGCA
1088329 TTGC
1 TTGC
1088333 AAATTAGGAA
Statistics
Matches: 150, Mismatches: 13, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
20 114 0.76
21 36 0.24
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACGTAATCGCA
Found at i:1088358 original size:21 final size:21
Alignment explanation
Indices: 1088336--1088376 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1088326 GCATTGCAAA
1088336 TTAGGAAAGTCGCAACGCGAAT
1 TTAGGAAA-TCGCAACGCGAAT
* *
1088358 TTGGGAAATCGCAATGCGA
1 TTAGGAAATCGCAACGCGA
1088377 TAGTCAGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.20
Consensus pattern (21 bp):
TTAGGAAATCGCAACGCGAAT
Found at i:1088744 original size:21 final size:21
Alignment explanation
Indices: 1088693--1088745 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1088683 ATTATGACTA
1088693 TCGCAATGCGATTTTACAATT
1 TCGCAATGCGATTTTACAATT
** *
1088714 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-ACAATT
1088735 TCGCAATGCGA
1 TCGCAATGCGA
1088746 ATAAGTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTACAATT
Found at i:1088778 original size:21 final size:20
Alignment explanation
Indices: 1088735--1088783 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
1088725 TTTTCCCAAT
*
1088735 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
**
1088755 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
1088776 TCGCAATG
1 TCGCAATG
1088784 TGATACTGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:1088808 original size:20 final size:20
Alignment explanation
Indices: 1088775--1088843 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
1088765 AATTTGGAAA
* *
1088775 ATCGCAATGTGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1088795 ATCGTAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1088815 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
1088835 TTCGCAACG
1 ATCGCAACG
1088844 AGATTCTGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1088848 original size:20 final size:20
Alignment explanation
Indices: 1088789--1088852 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
1088779 CAATGTGATA
* * *
1088789 CTGACTATCGTAACGCGATA
1 CTGACTTTCGCAACGCGATT
1088809 CTGACTTTCGCAACGCGATT
1 CTGACTTTCGCAACGCGATT
*
1088829 CTGACTTTCGCAACGAGATT
1 CTGACTTTCGCAACGCGATT
1088849 CTGA
1 CTGA
1088853 AAATCGCAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (20 bp):
CTGACTTTCGCAACGCGATT
Found at i:1088859 original size:20 final size:20
Alignment explanation
Indices: 1088816--1088861 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1088806 ATACTGACTT
* ***
1088816 TCGCAACGCGATTCTGACTT
1 TCGCAACGAGATTCTGAAAA
1088836 TCGCAACGAGATTCTGAAAA
1 TCGCAACGAGATTCTGAAAA
1088856 TCGCAA
1 TCGCAA
1088862 TCATCTTCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (20 bp):
TCGCAACGAGATTCTGAAAA
Found at i:1088860 original size:40 final size:40
Alignment explanation
Indices: 1088771--1088861 Score: 92
Period size: 40 Copynumber: 2.3 Consensus size: 40
1088761 TGCGAATTTG
* * * *
1088771 GAAAATCGCAATGTGATACTGACTATCGTAACGCGATACT
1 GAAAATCGCAACGCGATACTGACTATCGCAACGAGATACT
*** * * *
1088811 GACTTTCGCAACGCGATTCTGACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGCGATACTGACTATCGCAACGAGATACT
1088851 GAAAATCGCAA
1 GAAAATCGCAA
1088862 TCATCTTCAA
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (40 bp):
GAAAATCGCAACGCGATACTGACTATCGCAACGAGATACT
Found at i:1089100 original size:20 final size:20
Alignment explanation
Indices: 1089075--1089130 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
1089065 CAACGGGGAA
1089075 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
1089095 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGACT
*
1089115 ATCGCAACGAGAAAAT
1 ATCGCAACGCGAAAAT
1089131 CGCAATGCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.41, C:0.23, G:0.21, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1089182 original size:34 final size:34
Alignment explanation
Indices: 1089136--1089209 Score: 103
Period size: 34 Copynumber: 2.2 Consensus size: 34
1089126 AAAATCGCAA
* * *
1089136 TGCGATTTTCTCGTTGCGATAGCCATTTTCGCGT
1 TGCGATTCTCTCGTTACGATAGCCAGTTTCGCGT
* *
1089170 TGCGATTCTCTCGTTACGATAGTCAGTTTCGTGT
1 TGCGATTCTCTCGTTACGATAGCCAGTTTCGCGT
1089204 TGCGAT
1 TGCGAT
1089210 AGTCTGTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.14, C:0.22, G:0.24, T:0.41
Consensus pattern (34 bp):
TGCGATTCTCTCGTTACGATAGCCAGTTTCGCGT
Found at i:1090804 original size:42 final size:42
Alignment explanation
Indices: 1090758--1090850 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
1090748 CCTCTTCAAC
* * * * * *
1090758 GATGACAGTGGCCTTTTGAACGGTGGGGGGGGACTTTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGAGAGGGGACTCTTGAGG
* *
1090800 GATGATAGGGGCCTCTTGAACGATTAGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGAGAGGGGACTCTTGAGG
1090842 GATGACAGG
1 GATGACAGG
1090851 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.22, C:0.13, G:0.42, T:0.24
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGAGAGGGGACTCTTGAGG
Found at i:1090810 original size:21 final size:21
Alignment explanation
Indices: 1090786--1090846 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1090776 AACGGTGGGG
* *
1090786 GGGGACTTTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* ** *
1090807 GGGGCCTCTTGAACGATTAGA
1 GGGGACTCTTGAGGGATGAGA
1090828 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
1090847 CAGGTGAGTC
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.23, C:0.11, G:0.41, T:0.25
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:1091235 original size:40 final size:40
Alignment explanation
Indices: 1091191--1091276 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 40
1091181 TAGTTTACTT
* *
1091191 TCGCAACAC-GAAACTTACTTTCGCAACGCGAAAATGACTA
1 TCGCAACACGGAAA-TGACTATCGCAACGCGAAAATGACTA
* * * *
1091231 TCGCAACACGGAAATGGCTATCGCAATGCGGAAATGGCTA
1 TCGCAACACGGAAATGACTATCGCAACGCGAAAATGACTA
1091271 TCGCAA
1 TCGCAA
1091277 TGCGAAATGA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 35 0.90
41 4 0.10
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.19
Consensus pattern (40 bp):
TCGCAACACGGAAATGACTATCGCAACGCGAAAATGACTA
Found at i:1091246 original size:20 final size:20
Alignment explanation
Indices: 1091191--1091276 Score: 84
Period size: 20 Copynumber: 4.3 Consensus size: 20
1091181 TAGTTTACTT
* *
1091191 TCGCAACAC-GAAACTTACTT
1 TCGCAACACGGAAA-TGACTA
* *
1091211 TCGCAACGCGAAAATGACTA
1 TCGCAACACGGAAATGACTA
*
1091231 TCGCAACACGGAAATGGCTA
1 TCGCAACACGGAAATGACTA
** *
1091251 TCGCAATGCGGAAATGGCTA
1 TCGCAACACGGAAATGACTA
1091271 TCGCAA
1 TCGCAA
1091277 TGCGAAATGA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 53 0.95
21 3 0.05
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAACACGGAAATGACTA
Found at i:1091277 original size:20 final size:20
Alignment explanation
Indices: 1091211--1091285 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
1091201 AAACTTACTT
* *
1091211 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGGAAATGGCTA
*
1091231 TCGCAACACGGAAATGGCTA
1 TCGCAACGCGGAAATGGCTA
*
1091251 TCGCAATGCGGAAATGGCTA
1 TCGCAACGCGGAAATGGCTA
*
1091271 TCGCAATGC-GAAATG
1 TCGCAACGCGGAAATG
1091286 AAAATCGCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 6 0.12
20 44 0.88
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.17
Consensus pattern (20 bp):
TCGCAACGCGGAAATGGCTA
Found at i:1091292 original size:19 final size:19
Alignment explanation
Indices: 1091250--1091330 Score: 91
Period size: 19 Copynumber: 4.5 Consensus size: 19
1091240 GGAAATGGCT
***
1091250 ATCGCAATGCGGAAATGGCT
1 ATCGCAATGC-GAAATGAAA
1091270 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1091289 ATCGCAA--CG-AA--AAA
1 ATCGCAATGCGAAATGAAA
1091303 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1091322 ATCGCAATG
1 ATCGCAATG
1091331 ATAAAATCGC
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
14 10 0.19
16 4 0.08
17 4 0.08
19 25 0.47
20 10 0.19
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1091305 original size:14 final size:14
Alignment explanation
Indices: 1091286--1091344 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
1091276 ATGCGAAATG
1091286 AAAATCGCAACGAA
1 AAAATCGCAACGAA
1091300 AAAATCGCAATGCGAAA
1 AAAATCGCAA--CG-AA
* *
1091317 TGAAAATCGCAATGAT
1 --AAAATCGCAACGAA
1091333 AAAATCGCAACG
1 AAAATCGCAACG
1091345 CGAAACACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 21 0.57
16 3 0.08
17 3 0.08
19 10 0.27
ACGTcount: A:0.51, C:0.19, G:0.17, T:0.14
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:1091312 original size:33 final size:33
Alignment explanation
Indices: 1091270--1091349 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
1091260 GGAAATGGCT
1091270 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
* *
1091303 ATCGCAATGCGAAATGAAAATCGCAATGATAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
*
1091336 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
1091350 CACAAATTGC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.49, C:0.19, G:0.19, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
Found at i:1091383 original size:19 final size:19
Alignment explanation
Indices: 1091358--1091458 Score: 113
Period size: 19 Copynumber: 5.5 Consensus size: 19
1091348 AACACAAATT
1091358 GCATTGCGATTTTCATTTC
1 GCATTGCGATTTTCATTTC
*
1091377 GCGTTGCGATTTTCATTTC
1 GCATTGCGATTTTCATTTC
*
1091396 GCATTGCGA-TTT--TGTC
1 GCATTGCGATTTTCATTTC
1091412 G--TTGCGATTTTCATTTC
1 GCATTGCGATTTTCATTTC
***
1091429 GCATTGCGATAGCCATTTCC
1 GCATTGCGATTTTCATTT-C
1091449 GCATTGCGAT
1 GCATTGCGAT
1091459 AGTCATTTTC
Statistics
Matches: 69, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
14 6 0.09
15 3 0.04
16 4 0.06
17 4 0.06
18 3 0.04
19 38 0.55
20 11 0.16
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.43
Consensus pattern (19 bp):
GCATTGCGATTTTCATTTC
Found at i:1091453 original size:20 final size:19
Alignment explanation
Indices: 1091423--1091466 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
1091413 TTGCGATTTT
1091423 CATTTCGCATTGCGATAGC
1 CATTTCGCATTGCGATAGC
*
1091442 CATTTCCGCATTGCGATAGT
1 CATTT-CGCATTGCGATAGC
1091462 CATTT
1 CATTT
1091467 TCATGTTACG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:1092012 original size:18 final size:18
Alignment explanation
Indices: 1091989--1092036 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1091979 CGGGTCGATC
1091989 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
1092007 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
1092025 AGGTGATGGCTC
1 AGGTGATGGCTC
1092037 CTGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:1093390 original size:20 final size:20
Alignment explanation
Indices: 1093342--1093400 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1093332 AATAGTTTCT
* *
1093342 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
1093362 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
1093382 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
1093401 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:1093688 original size:22 final size:22
Alignment explanation
Indices: 1093663--1093706 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1093653 GATGTAGATA
1093663 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1093685 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1093707 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1093958 original size:41 final size:41
Alignment explanation
Indices: 1093913--1093990 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
1093903 CGAAAGTCAG
*
1093913 TATCGCGTTGCAAAAGTCAGTATCGTGTTGCGATTTTGTAT
1 TATCGCGTTGCAAAAGTCAGTATCGCGTTGCGATTTTGTAT
* *
1093954 TATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTT
1 TATCGCGTTGCAAAAGTCAGTATCGCGTTGCGATTTT
1093991 CCAAATATCG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (41 bp):
TATCGCGTTGCAAAAGTCAGTATCGCGTTGCGATTTTGTAT
Found at i:1093987 original size:20 final size:20
Alignment explanation
Indices: 1093893--1093987 Score: 102
Period size: 20 Copynumber: 4.7 Consensus size: 20
1093883 GATTATGTAT
* *
1093893 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
1093913 TATCGCGTTGCAAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
1093933 TATCGTGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
1093954 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
1093974 TATCGCGTTGCGAT
1 TATCGCGTTGCGAT
1093988 TTTCCAAATA
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.71
21 13 0.21
22 2 0.03
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:1094002 original size:22 final size:22
Alignment explanation
Indices: 1093974--1094032 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
1093964 CGATAGTCAG
1093974 TATCGCGTTGCGATTTTCCAAA
1 TATCGCGTTGCGATTTTCCAAA
1093996 TATCGCGTTGCGATTTTCCAAA
1 TATCGCGTTGCGATTTTCCAAA
* *
1094018 T-TCACATTGCGATTT
1 TATCGCGTTGCGATTT
1094033 ACTTATTCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
21 12 0.34
22 23 0.66
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (22 bp):
TATCGCGTTGCGATTTTCCAAA
Found at i:1094091 original size:21 final size:22
Alignment explanation
Indices: 1094039--1094091 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
1094029 ATTTACTTAT
1094039 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
1094060 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
1094081 TCGCATTGCGA
1 TCGCATTGCGA
1094092 TAATCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:1097994 original size:12 final size:10
Alignment explanation
Indices: 1097963--1098013 Score: 75
Period size: 10 Copynumber: 5.1 Consensus size: 10
1097953 TTTCATCACA
1097963 TCAAATTCTC
1 TCAAATTCTC
1097973 TCAAATTCTC
1 TCAAATTCTC
1097983 TCAAATTCTC
1 TCAAATTCTC
* *
1097993 TCAACTTCTG
1 TCAAATTCTC
*
1098003 TCAAATACTC
1 TCAAATTCTC
1098013 T
1 T
1098014 TATAATCCCT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 36 1.00
ACGTcount: A:0.29, C:0.29, G:0.02, T:0.39
Consensus pattern (10 bp):
TCAAATTCTC
Found at i:1098061 original size:15 final size:16
Alignment explanation
Indices: 1098041--1098081 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1098031 ATATATTTTA
1098041 TTATATTTTAA-TATT
1 TTATATTTTAATTATT
1098056 TTATA-TTTAATTTATT
1 TTATATTTTAA-TTATT
*
1098072 TAATATTTTA
1 TTATATTTTA
1098082 CTTAATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 5 0.23
15 5 0.23
16 8 0.36
17 4 0.18
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATATTTTAATTATT
Found at i:1098077 original size:23 final size:25
Alignment explanation
Indices: 1098032--1098081 Score: 77
Period size: 23 Copynumber: 2.1 Consensus size: 25
1098022 CTGTCTAAGA
*
1098032 TATATTTTATTATATTTTAATATTT
1 TATATTTAATTATATTTTAATATTT
1098057 TATATTTAATT-TA-TTTAATATTT
1 TATATTTAATTATATTTTAATATTT
1098080 TA
1 TA
1098082 CTTAATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 12 0.50
24 2 0.08
25 10 0.42
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (25 bp):
TATATTTAATTATATTTTAATATTT
Found at i:1098088 original size:21 final size:23
Alignment explanation
Indices: 1098047--1098093 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
1098037 TTTATTATAT
* *
1098047 TTTAATATTTTATATTTAATTTA
1 TTTAATATTTTATACTTAATTAA
1098070 TTTAATA-TTT-TACTTAATTAA
1 TTTAATATTTTATACTTAATTAA
1098091 TTT
1 TTT
1098094 TTTTGCAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 12 0.55
22 3 0.14
23 7 0.32
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTAATATTTTATACTTAATTAA
Found at i:1099823 original size:33 final size:33
Alignment explanation
Indices: 1099778--1099841 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
1099768 CAGATGCCGC
* *
1099778 CGCCGCCGCCTTCACCTG-GTTTTATGACCCCGT
1 CGCCGCCACCTTCA-CAGAGTTTTATGACCCCGT
1099811 CGCCGCCACCTTCACAGAGTTTTATGACCCC
1 CGCCGCCACCTTCACAGAGTTTTATGACCCC
1099842 TCCTTGAGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 2 0.07
33 26 0.93
ACGTcount: A:0.14, C:0.42, G:0.19, T:0.25
Consensus pattern (33 bp):
CGCCGCCACCTTCACAGAGTTTTATGACCCCGT
Found at i:1100306 original size:13 final size:13
Alignment explanation
Indices: 1100265--1100308 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
1100255 TATTTAGTAC
*
1100265 TTTTTATTGTAGT
1 TTTTTATTGTAAT
* * *
1100278 TGTTTATTGGACT
1 TTTTTATTGTAAT
1100291 TTTTTATTGTAAT
1 TTTTTATTGTAAT
1100304 TTTTT
1 TTTTT
1100309 TATTATTTAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.16, C:0.02, G:0.14, T:0.68
Consensus pattern (13 bp):
TTTTTATTGTAAT
Done.