Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold446
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: 3567220
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 22
Found at i:2539581 original size:51 final size:50
Alignment explanation
Indices: 2539462--2539588 Score: 155
Period size: 51 Copynumber: 2.5 Consensus size: 50
2539452 TGCATATATG
* * *
2539462 GATACATTGAATAATGTATCGATACATCTAGGTAAAATCCAGAATGTATC
1 GATACAATGAATAATGTATCGATACATCTAGATAAAACCCAGAATGTATC
** * * * *
2539512 GATACACCGAAGAATGTATTGATACATCTCGATAAAAACCCAGAATGTATT
1 GATACAATGAATAATGTATCGATACATCTAGAT-AAAACCCAGAATGTATC
*
2539563 GATACAATGAATATTGTATCGATACA
1 GATACAATGAATAATGTATCGATACA
2539589 AATAGTAAAA
Statistics
Matches: 63, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
50 27 0.43
51 36 0.57
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (50 bp):
GATACAATGAATAATGTATCGATACATCTAGATAAAACCCAGAATGTATC
Found at i:2542533 original size:20 final size:20
Alignment explanation
Indices: 2542510--2542555 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
2542500 CTAGGTCGCG
*
2542510 ACCGGTATACCCAGGTCACA
1 ACCGGTACACCCAGGTCACA
2542530 ACCGGTACACCCAGGTCACA
1 ACCGGTACACCCAGGTCACA
2542550 ACCGGT
1 ACCGGT
2542556 CAGCTCCCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.37, G:0.22, T:0.13
Consensus pattern (20 bp):
ACCGGTACACCCAGGTCACA
Found at i:2544037 original size:20 final size:20
Alignment explanation
Indices: 2543989--2544038 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
2543979 TTGGAAACAA
*
2543989 AAAGGGTGAGAGATATTTTTT
1 AAAGGG-GAGAGAAATTTTTT
*
2544010 AAATGGGA-AGAAATTTTATT
1 AAAGGGGAGAGAAATTTT-TT
2544030 AAAGGGGAG
1 AAAGGGGAG
2544039 TTATAATTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 8 0.33
20 11 0.46
21 5 0.21
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.30
Consensus pattern (20 bp):
AAAGGGGAGAGAAATTTTTT
Found at i:2546412 original size:15 final size:15
Alignment explanation
Indices: 2546392--2546429 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
2546382 TCAAAAACCT
2546392 AGATTCATTTTTACA
1 AGATTCATTTTTACA
2546407 AGATTCATTTTTACA
1 AGATTCATTTTTACA
2546422 AGATTCAT
1 AGATTCAT
2546430 GTATTTGAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (15 bp):
AGATTCATTTTTACA
Found at i:2547625 original size:21 final size:20
Alignment explanation
Indices: 2547601--2547651 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
2547591 TTACCAAAAT
2547601 GTATTGATACATTA-GGCTAAG
1 GTATTGATACATTATGGC--AG
* *
2547622 GTATTGATTCATTATGGCAT
1 GTATTGATACATTATGGCAG
2547642 GTATTGATAC
1 GTATTGATAC
2547652 CTCGACATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 10 0.38
21 13 0.50
22 3 0.12
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (20 bp):
GTATTGATACATTATGGCAG
Found at i:2554433 original size:20 final size:20
Alignment explanation
Indices: 2554408--2554493 Score: 93
Period size: 20 Copynumber: 4.3 Consensus size: 20
2554398 GGAAGGAAAT
2554408 TGTATCGATACATTTTTCAA
1 TGTATCGATACATTTTTCAA
* ****
2554428 TGTATCGACACA-TAAGAAA
1 TGTATCGATACATTTTTCAA
*
2554447 TTGTATCGATACATTTTTCAT
1 -TGTATCGATACATTTTTCAA
2554468 TGTATCGATACATTTTTCAA
1 TGTATCGATACATTTTTCAA
*
2554488 AGTATC
1 TGTATC
2554494 AATATATCCA
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
19 3 0.06
20 46 0.90
21 2 0.04
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATTTTTCAA
Found at i:2554454 original size:40 final size:40
Alignment explanation
Indices: 2554403--2554480 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
2554393 ATTTTGGAAG
2554403 GAAATTGTATCGATACATTTTTCAATGTATCGACACATAA
1 GAAATTGTATCGATACATTTTTCAATGTATCGACACATAA
* *
2554443 GAAATTGTATCGATACATTTTTCATTGTATCGATACAT
1 GAAATTGTATCGATACATTTTTCAATGTATCGACACAT
2554481 TTTTCAAAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (40 bp):
GAAATTGTATCGATACATTTTTCAATGTATCGACACATAA
Found at i:2554696 original size:14 final size:14
Alignment explanation
Indices: 2554677--2554706 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2554667 TTGAATTGTC
2554677 ACATTTTCATCATT
1 ACATTTTCATCATT
*
2554691 ACATTTTCTTCATT
1 ACATTTTCATCATT
2554705 AC
1 AC
2554707 CACACTCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (14 bp):
ACATTTTCATCATT
Found at i:2555408 original size:20 final size:21
Alignment explanation
Indices: 2555383--2555422 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2555373 TCTAAACAGC
2555383 CCATGTT-CATGCATTTTAAG
1 CCATGTTCCATGCATTTTAAG
2555403 CCATGTTCCATGCATTTTAA
1 CCATGTTCCATGCATTTTAA
2555423 AATGTCCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (21 bp):
CCATGTTCCATGCATTTTAAG
Found at i:2560675 original size:29 final size:29
Alignment explanation
Indices: 2560642--2560731 Score: 96
Period size: 29 Copynumber: 3.2 Consensus size: 29
2560632 AATTAATGCA
2560642 AGAAACATAAATAATCAACAAGTATCCTG
1 AGAAACATAAATAATCAACAAGTATCCTG
* * * * * *
2560671 AGAAAGAGAAATAAT--GCAATTAATGC-A
1 AGAAACATAAATAATCAACAAGT-ATCCTG
2560698 AGAAACATAAATAATCAACAAGTATCCTG
1 AGAAACATAAATAATCAACAAGTATCCTG
2560727 AGAAA
1 AGAAA
2560732 GAGAACATTT
Statistics
Matches: 45, Mismatches: 12, Indels: 8
0.69 0.18 0.12
Matches are distributed among these distances:
27 17 0.38
28 6 0.13
29 22 0.49
ACGTcount: A:0.54, C:0.13, G:0.13, T:0.19
Consensus pattern (29 bp):
AGAAACATAAATAATCAACAAGTATCCTG
Found at i:2560709 original size:27 final size:27
Alignment explanation
Indices: 2560626--2560712 Score: 86
Period size: 27 Copynumber: 3.1 Consensus size: 27
2560616 CATAGCCCCG
2560626 TAATGCAATTAATGCAAGAAACATAAA
1 TAATGCAATTAATGCAAGAAACATAAA
** * * * *
2560653 TAAT-CAACAAGTATCCTGAGAAAGAGAAA
1 TAATGCAATTA--ATGC-AAGAAACATAAA
2560682 TAATGCAATTAATGCAAGAAACATAAA
1 TAATGCAATTAATGCAAGAAACATAAA
2560709 TAAT
1 TAAT
2560713 CAACAAGTAT
Statistics
Matches: 44, Mismatches: 12, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
26 4 0.09
27 17 0.39
28 6 0.14
29 13 0.30
30 4 0.09
ACGTcount: A:0.54, C:0.11, G:0.13, T:0.22
Consensus pattern (27 bp):
TAATGCAATTAATGCAAGAAACATAAA
Found at i:2560712 original size:56 final size:56
Alignment explanation
Indices: 2560626--2560736 Score: 222
Period size: 56 Copynumber: 2.0 Consensus size: 56
2560616 CATAGCCCCG
2560626 TAATGCAATTAATGCAAGAAACATAAATAATCAACAAGTATCCTGAGAAAGAGAAA
1 TAATGCAATTAATGCAAGAAACATAAATAATCAACAAGTATCCTGAGAAAGAGAAA
2560682 TAATGCAATTAATGCAAGAAACATAAATAATCAACAAGTATCCTGAGAAAGAGAA
1 TAATGCAATTAATGCAAGAAACATAAATAATCAACAAGTATCCTGAGAAAGAGAA
2560737 CATTTTAAGC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.53, C:0.13, G:0.14, T:0.20
Consensus pattern (56 bp):
TAATGCAATTAATGCAAGAAACATAAATAATCAACAAGTATCCTGAGAAAGAGAAA
Found at i:2564068 original size:13 final size:13
Alignment explanation
Indices: 2564050--2564078 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2564040 CAATTCTTCA
2564050 TGTATCGATACAT
1 TGTATCGATACAT
2564063 TGTATCGATACAT
1 TGTATCGATACAT
2564076 TGT
1 TGT
2564079 TCCATGTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2564072 original size:33 final size:33
Alignment explanation
Indices: 2564030--2564094 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
2564020 TTTGAGGTAA
2564030 TGTATCGATACAATTCTT-CATGTATCGATACAT
1 TGTATCGATAC-ATTCTTCCATGTATCGATACAT
*
2564063 TGTATCGATACATTGTTCCATGTATCGATACA
1 TGTATCGATACATTCTTCCATGTATCGATACA
2564095 AATAGTGGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 5 0.17
33 25 0.83
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.38
Consensus pattern (33 bp):
TGTATCGATACATTCTTCCATGTATCGATACAT
Found at i:2564147 original size:20 final size:20
Alignment explanation
Indices: 2564122--2564178 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
2564112 TACTGCCAGT
2564122 TTCATGTATCGATACATTTG
1 TTCATGTATCGATACATTTG
* *
2564142 TTCATGTATCAATACA-ATG
1 TTCATGTATCGATACATTTG
**
2564161 AACATGTATCGATACATT
1 TTCATGTATCGATACATT
2564179 GTATCGATAC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (20 bp):
TTCATGTATCGATACATTTG
Found at i:2564183 original size:13 final size:13
Alignment explanation
Indices: 2564165--2564202 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
2564155 ACAATGAACA
2564165 TGTATCGATACAT
1 TGTATCGATACAT
2564178 TGTATCGATACAT
1 TGTATCGATACAT
*
2564191 TGTATCGGTACA
1 TGTATCGATACA
2564203 AAGCATAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2570828 original size:141 final size:139
Alignment explanation
Indices: 2570614--2571252 Score: 544
Period size: 141 Copynumber: 4.5 Consensus size: 139
2570604 ACTTTTCACC
* * *
2570614 TTTTTGGTCCTCAAAGAGTAGGATGCCTTTTCTTCTTCTTTCTCAAAGCTTACACAAGCTAGTGG
1 TTTTTAGTCCTCAAAGAGTAGGATG-CTTTT-TTC-T-TTT-T-AAAGCTCACACAAGCTGGTGG
* * *
2570679 CACCTTTTATCCATTTTT-GTTCTCAAAGAGCATGACACCTTTTTCTTTTTAAAGCTCACACAAA
60 CACCTTTTAT-C-TTTTTAGTTCTCAAAGAGCAGGACACCTTTTTCTTTTTAAAGCCCACACAAG
2570743 CT-GTGGCACCCTTCACAT
123 CTGGTGGCACCCTT-AC-T
* * *
2570761 TTTTTAGTCCTCAAAGAGCAAGATGCTTTTTTCTTTTTAAAGTTCACACAAGCTGGTGGCACCTT
1 TTTTTAGTCCTCAAAGAGTAGGATGCTTTTTTCTTTTTAAAGCTCACACAAGCTGGTGGCACCTT
* ** * *
2570826 TTATCTTTTTTAGTCCTCAAAGAATAGGACACCTTTTTCTTTTTAAAGCCCACATAAGTTGGTGG
66 TTATC-TTTTTAGTTCTCAAAGAGCAGGACACCTTTTTCTTTTTAAAGCCCACACAAGCTGGTGG
**
2570891 CACATTTTA-T
130 CAC-CCTTACT
* * * *
2570901 CTTTTTAGTCCTCAAAGAATAGGACGC-CTTTTCTTTTTAAAGCTCACACAAGCTAGTGGCACCC
1 -TTTTTAGTCCTCAAAGAGTAGGATGCTTTTTTCTTTTTAAAGCTCACACAAGCTGGTGGCA-CC
* * ** *
2570965 TTTCTATCCTTTTTA-ATCTTCAAAGAGTAGGATGCCTTTTT-TCTTTTAAAGTCCACACAAGCT
64 TTT-TAT-CTTTTTAGTTC-TCAAAGAGCAGGACACCTTTTTCT-TTTTAAAGCCCACACAAGCT
* **
2571028 GGTGGCA-TCTTTTT
125 GGTGGCACCCTTACT
* * * *
2571042 TCTCTTTTGTCCTCAAAGAGTAGGATGC-CTTTTCTTTTTCAAAGC-CTGCACATGCTGGTGGCA
1 T-T-TTTAGTCCTCAAAGAGTAGGATGCTTTTTTCTTTTT-AAAGCTC-ACACAAGCTGGTGGCA
* ** *
2571105 CCTTTTATCTTTTTAGTACTCAAAGAGCAGGATGTTTTTCTTTTTTCTTTTTCAAAGCCCACACA
62 CCTTTTATCTTTTTAGTTCTCAAAGAGCAGGA-----CACCTTTTTCTTTTT-AAAGCCCACACA
* *
2571170 AGTTGGTGGAACCCTTATCT
121 AGCTGGTGGCACCCTTA-CT
* * * * *
2571190 TTTCTAGT-TTCAAAGAGTAAGATGCTTTTTT-TTTCTTAAAGCCCACACAAGTTGGTGGCACCT
1 TTTTTAGTCCTCAAAGAGTAGGATGCTTTTTTCTTT-TTAAAGCTCACACAAGCTGGTGGCACCT
2571253 GTCTATTTCA
Statistics
Matches: 406, Mismatches: 59, Indels: 56
0.78 0.11 0.11
Matches are distributed among these distances:
140 61 0.15
141 103 0.25
142 99 0.24
143 24 0.06
144 1 0.00
145 53 0.13
146 37 0.09
147 26 0.06
148 2 0.00
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (139 bp):
TTTTTAGTCCTCAAAGAGTAGGATGCTTTTTTCTTTTTAAAGCTCACACAAGCTGGTGGCACCTT
TTATCTTTTTAGTTCTCAAAGAGCAGGACACCTTTTTCTTTTTAAAGCCCACACAAGCTGGTGGC
ACCCTTACT
Found at i:2571012 original size:142 final size:138
Alignment explanation
Indices: 2570613--2571252 Score: 558
Period size: 142 Copynumber: 4.5 Consensus size: 138
2570603 AACTTTTCAC
* * * *
2570613 CTTTTTGGTCCTCAAAGAGTAGGATGCCTTTTCTTCTTCTTTCTCAAAGCTTACACAAGCTAGTG
1 CTTTTTAGTCCTCAAAGAGTAAGATGCC--TT-TTC-T-TTT-T-AAAGCTCACACAAGCTGGTG
* *
2570678 GCACCTTTTATCCATTTTT-GTTCTCAAAGAGCATGACACCTTTTTCTTTTTAAAGCTCACACAA
59 GCACCTTTTATCC-TTTTTAG-TCTCAAAGAGCAGGACACCTTTTTCTTTTTAAAGCCCACACAA
* *
2570742 ACT-GTGGCACCCTTCA-
122 GCTGGTGGCA-CCTTTAT
* * *
2570758 CATTTTTTAGTCCTCAAAGAGCAAGATGCTTTTTTCTTTTTAAAGTTCACACAAGCTGGTGGCAC
1 C--TTTTTAGTCCTCAAAGAGTAAGATGC-CTTTTCTTTTTAAAGCTCACACAAGCTGGTGGCAC
* ** * *
2570823 CTTTTATCTTTTTTAGTCCTCAAAGAATAGGACACCTTTTTCTTTTTAAAGCCCACATAAGTTGG
63 CTTTTATCCTTTTTAGT-CTCAAAGAGCAGGACACCTTTTTCTTTTTAAAGCCCACACAAGCTGG
*
2570888 TGGCACATTTTAT
127 TGGCAC-CTTTAT
* * * *
2570901 CTTTTTAGTCCTCAAAGAATAGGACGCCTTTTCTTTTTAAAGCTCACACAAGCTAGTGGCACCCT
1 CTTTTTAGTCCTCAAAGAGTAAGATGCCTTTTCTTTTTAAAGCTCACACAAGCTGGTGGCA-CCT
* * ** *
2570966 TTCTATCCTTTTTAATCTTCAAAGAGTAGGATGCCTTTTT-TCTTTTAAAGTCCACACAAGCTGG
65 TT-TATCCTTTTTAGTC-TCAAAGAGCAGGACACCTTTTTCT-TTTTAAAGCCCACACAAGCTGG
* *
2571030 TGGCATCTTTTTT
127 TGGCA-CCTTTAT
* * *
2571043 CTCTTTT-GTCCTCAAAGAGTAGGATGCCTTTTCTTTTTCAAAGC-CTGCACATGCTGGTGGCAC
1 CT-TTTTAGTCCTCAAAGAGTAAGATGCCTTTTCTTTTT-AAAGCTC-ACACAAGCTGGTGGCAC
** *
2571106 CTTTTAT-CTTTTTAGTACTCAAAGAGCAGGATGTTTTTCTTTTTTCTTTTTCAAAGCCCACACA
63 CTTTTATCCTTTTTAGT-CTCAAAGAGCAGGA-----CACCTTTTTCTTTTT-AAAGCCCACACA
* * *
2571170 AGTTGGTGGAACCCTTAT
121 AGCTGGTGGCACCTTTAT
* * * * *
2571188 CTTTTCTAGT-TTCAAAGAGTAAGATGCTTTTTTTTTCTTAAAGCCCACACAAGTTGGTGGCACC
1 CTTTT-TAGTCCTCAAAGAGTAAGATGCCTTTTCTTT-TTAAAGCTCACACAAGCTGGTGGCACC
2571252 T
64 T
2571253 GTCTATTTCA
Statistics
Matches: 412, Mismatches: 55, Indels: 56
0.79 0.11 0.11
Matches are distributed among these distances:
140 57 0.14
141 102 0.25
142 106 0.26
143 27 0.07
144 4 0.01
145 65 0.16
146 28 0.07
147 23 0.06
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (138 bp):
CTTTTTAGTCCTCAAAGAGTAAGATGCCTTTTCTTTTTAAAGCTCACACAAGCTGGTGGCACCTT
TTATCCTTTTTAGTCTCAAAGAGCAGGACACCTTTTTCTTTTTAAAGCCCACACAAGCTGGTGGC
ACCTTTAT
Found at i:2571099 original size:70 final size:69
Alignment explanation
Indices: 2570649--2571252 Score: 481
Period size: 70 Copynumber: 8.5 Consensus size: 69
2570639 CCTTTTCTTC
* * * * * *
2570649 TTCTTTCTCAAAGCTTACACAAGCTAGTGGCACCTTTTATCCATTTTT-GTTCTCAAAGAGCATG
1 TTCTTT-TTAAAGCCTACACAAGCTGGTGGCACCTTTTAT-C-TTTTTAGTCCTCAAAGAGTAGG
**
2570713 ACACCTTT
63 ATGCC-TT
* * * * *
2570721 TTCTTTTTAAAG-CTCACACAAACT-GTGGCACCCTTCA-CATTTTTTAGTCCTCAAAGAGCAAG
1 TTCTTTTTAAAGCCT-ACACAAGCTGGTGGCACCTTTTATC--TTTTTAGTCCTCAAAGAGTAGG
*
2570783 ATGCTTTT
63 ATGC-CTT
* *
2570791 TTCTTTTTAAAG-TTCACACAAGCTGGTGGCACCTTTTATCTTTTTTAGTCCTCAAAGAATAGGA
1 TTCTTTTTAAAGCCT-ACACAAGCTGGTGGCACCTTTTATC-TTTTTAGTCCTCAAAGAGTAGGA
**
2570855 CACCTTT
64 TGCC-TT
* * * * * *
2570862 TTCTTTTTAAAGCCCACATAAGTTGGTGGCACATTTTATCTTTTTAGTCCTCAAAGAATAGGACG
1 TTCTTTTTAAAGCCTACACAAGCTGGTGGCACCTTTTATCTTTTTAGTCCTCAAAGAGTAGGATG
2570927 CCTT
66 CCTT
* * *
2570931 TTCTTTTTAAAG-CTCACACAAGCTAGTGGCACCCTTTCTATCCTTTTTAATCTTCAAAGAGTAG
1 TTCTTTTTAAAGCCT-ACACAAGCTGGTGGCA-CCTTT-TAT-CTTTTTAGTCCTCAAAGAGTAG
2570995 GATGCCTT
62 GATGCCTT
* * *
2571003 TTTTCTTTTAAAGTCC-ACACAAGCTGGTGGCATCTTTTTTCTCTTTT-GTCCTCAAAGAGTAGG
1 TTCT-TTTTAAAG-CCTACACAAGCTGGTGGCACCTTTTATCT-TTTTAGTCCTCAAAGAGTAGG
2571066 ATGCCTT
63 ATGCCTT
* * * *
2571073 TTCTTTTTCAAAGCCTGCACATGCTGGTGGCACCTTTTATCTTTTTAGTACTCAAAGAGCAGGAT
1 TTCTTTTT-AAAGCCTACACAAGCTGGTGGCACCTTTTATCTTTTTAGTCCTCAAAGAGTAGGAT
*
2571138 GTTTTTCTTTT
65 G-----C-CTT
* * * * * *
2571149 TTCTTTTTCAAAGCCCACACAAGTTGGTGGAACC-CTTATCTTTTCTAGT-TTCAAAGAGTAAGA
1 TTCTTTTT-AAAGCCTACACAAGCTGGTGGCACCTTTTATCTTTT-TAGTCCTCAAAGAGTAGGA
*
2571212 TGCTTT
64 TGCCTT
* * *
2571218 TTTTTTCTTAAAGCCCACACAAGTTGGTGGCACCT
1 TTCTTT-TTAAAGCCTACACAAGCTGGTGGCACCT
2571253 GTCTATTTCA
Statistics
Matches: 443, Mismatches: 61, Indels: 58
0.79 0.11 0.10
Matches are distributed among these distances:
68 2 0.00
69 74 0.17
70 154 0.35
71 91 0.21
72 40 0.09
73 23 0.05
75 24 0.05
76 35 0.08
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (69 bp):
TTCTTTTTAAAGCCTACACAAGCTGGTGGCACCTTTTATCTTTTTAGTCCTCAAAGAGTAGGATG
CCTT
Found at i:2574508 original size:86 final size:87
Alignment explanation
Indices: 2574412--2574577 Score: 223
Period size: 87 Copynumber: 1.9 Consensus size: 87
2574402 CGAGTTTGGA
* * *
2574412 AAACTCCATCCCCACTCT-TCTGAGG-GGACACTCT-AACCCCGCTCTTCATAAATTAAATTGTC
1 AAACTCCATCCCCACTATCT-TAAGGAGGACACT-TGAACCCCGCTCTTCATAAATCAAATT-TC
2574474 -CTTTGTATAATTTTATCCTTGGGG
63 TCTTTGTATAATTTTATCCTTGGGG
** *
2574498 AAACTCCATCCCCACTATCTTAAGGAGGACACTTGAACCTTGCTTTTCATAAATCAAATTTCTCT
1 AAACTCCATCCCCACTATCTTAAGGAGGACACTTGAACCCCGCTCTTCATAAATCAAATTTCTCT
2574563 TTGTATAATTTTATC
66 TTGTATAATTTTATC
2574578 TCTAGGGGTA
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
86 24 0.34
87 46 0.66
ACGTcount: A:0.27, C:0.26, G:0.11, T:0.36
Consensus pattern (87 bp):
AAACTCCATCCCCACTATCTTAAGGAGGACACTTGAACCCCGCTCTTCATAAATCAAATTTCTCT
TTGTATAATTTTATCCTTGGGG
Found at i:2574784 original size:79 final size:78
Alignment explanation
Indices: 2574569--2574793 Score: 254
Period size: 81 Copynumber: 2.8 Consensus size: 78
2574559 CTCTTTGTAT
* * * *
2574569 AATTTTATCTCTAGGGGTAC-CCTAACCCTACCATCTCCGATGGGATATTCCAATCCCATTTTTT
1 AATTTTATCTCTA-GGGTACTCC-AACCCCACCATCTCCGAGGGGATATTCCAACCCCATTTTTA
* *
2574633 CTTTCAAAACACTAA
64 CTTCCAAAACACCAA
* * * * *
2574648 ATTTTTTCATCTCTAGAAGTACTCCAACCCCACCATCTCCGAGGGAAAACTCCAACCCCATTTTT
1 A-ATTTT-ATCTCTAG-GGTACTCCAACCCCACCATCTCCGAGGGGATATTCCAACCCCATTTTT
2574713 ACTTCCAAAACACCAA
63 ACTTCCAAAACACCAA
** * *
2574729 AATTTTAATCTCTAGGGTACTCCAACCCCACCATCTATGAGGGGATATTCTAACCCTATTTTTAC
1 AATTTT-ATCTCTAGGGTACTCCAACCCCACCATCTCCGAGGGGATATTCCAACCCCATTTTTAC
2574794 ATTAAAATTT
Statistics
Matches: 121, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
79 43 0.36
80 17 0.14
81 59 0.49
82 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.10, T:0.31
Consensus pattern (78 bp):
AATTTTATCTCTAGGGTACTCCAACCCCACCATCTCCGAGGGGATATTCCAACCCCATTTTTACT
TCCAAAACACCAA
Found at i:2578367 original size:13 final size:13
Alignment explanation
Indices: 2578349--2578375 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2578339 ACATTATGCT
2578349 TTGTATCGATACA
1 TTGTATCGATACA
2578362 TTGTATCGATACA
1 TTGTATCGATACA
2578375 T
1 T
2578376 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2578405 original size:20 final size:19
Alignment explanation
Indices: 2578359--2578415 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
2578349 TTGTATCGAT
*
2578359 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
* *
2578378 TCATTGTATCAATACATGG
1 ACATTGTATCGATACATGG
2578397 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
2578416 AAACTGGCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:2579685 original size:20 final size:20
Alignment explanation
Indices: 2579660--2579712 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
2579650 CTTACAAGCT
2579660 ATGTATCGATACATT-T-CTTC
1 ATGTATCGATACATTGTAC--C
2579680 ATGTATCGATACATTGTACC
1 ATGTATCGATACATTGTACC
2579700 ATGTATCGATACA
1 ATGTATCGATACA
2579713 AATAGTGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 29 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTGTACC
Found at i:2579768 original size:21 final size:19
Alignment explanation
Indices: 2579742--2579815 Score: 85
Period size: 19 Copynumber: 3.7 Consensus size: 19
2579732 CTGCCAGTTT
**
2579742 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAA--TGAA
2579763 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
* *
2579782 CATGTATCGATACAAAGCAG
1 CATGTATCGATACAATG-AA
2579802 CATGTATCGATACA
1 CATGTATCGATACA
2579816 TCTGGGTGTG
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
19 18 0.38
20 15 0.31
21 15 0.31
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.28
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:2588458 original size:21 final size:21
Alignment explanation
Indices: 2588411--2588465 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
2588401 CTACCACTGT
2588411 TTGTATCGATACATGGCATAA
1 TTGTATCGATACATGGCATAA
2588432 -TGTATCGATACAT-G-ATGGAA
1 TTGTATCGATACATGGCAT--AA
2588452 TTGTATCGATACAT
1 TTGTATCGATACAT
2588466 TGCTTGTAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
18 2 0.06
19 1 0.03
20 15 0.48
21 13 0.42
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.35
Consensus pattern (21 bp):
TTGTATCGATACATGGCATAA
Found at i:2592347 original size:32 final size:33
Alignment explanation
Indices: 2592291--2592352 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
2592281 ACCCCAAATG
*
2592291 TATCGATACATATTGCTTAGTATCGATACATTA
1 TATCAATACATATTGCTTAGTATCGATACATTA
* *
2592324 TATCAATACATGTT-CTTTGTATCGATACA
1 TATCAATACATATTGCTTAGTATCGATACA
2592353 CCATAAAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 14 0.54
33 12 0.46
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.40
Consensus pattern (33 bp):
TATCAATACATATTGCTTAGTATCGATACATTA
Found at i:2592486 original size:52 final size:52
Alignment explanation
Indices: 2592399--2592507 Score: 139
Period size: 52 Copynumber: 2.1 Consensus size: 52
2592389 TACCCTAAGT
* * *
2592399 GAATTGTATCGATACATGGTAAATTGTATCGATACATT-AAGCCCAATGGCTA
1 GAATTGTATCGATACATGATAAATTGTATCAATACATTGAA-CCCAATGACTA
* * * *
2592451 TAATTGTATCGATACATTATGAATTTTATCAATACATTGAACCCAATGACTA
1 GAATTGTATCGATACATGATAAATTGTATCAATACATTGAACCCAATGACTA
2592503 GAATT
1 GAATT
2592508 TCAAATGCAT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
52 46 0.96
53 2 0.04
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (52 bp):
GAATTGTATCGATACATGATAAATTGTATCAATACATTGAACCCAATGACTA
Found at i:2592967 original size:35 final size:33
Alignment explanation
Indices: 2592928--2593055 Score: 138
Period size: 34 Copynumber: 3.9 Consensus size: 33
2592918 AGTGATTGAG
2592928 AGGTTCTATCTTAGCCTTTGAAAAGATAGAGAGAA
1 AGGTTCTATCTTAGCCTTTGAAAAGATAG-G-GAA
*
2592963 AGGTTCTATCTTAG-CTTGTGAAAAAATAGGGGAA
1 AGGTTCTATCTTAGCCTT-TGAAAAGATA-GGGAA
* * *
2592997 AAGTTCTATCTTTGCCTGTGAAAAGATAGGG--
1 AGGTTCTATCTTAGCCTTTGAAAAGATAGGGAA
* *
2593028 AGGTTCTATCTTAGAC-TTCAAAAGATAG
1 AGGTTCTATCTTAGCCTTTGAAAAGATAG
2593056 TGTTGTAAGG
Statistics
Matches: 80, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
30 10 0.12
31 13 0.16
33 3 0.04
34 27 0.34
35 26 0.32
36 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.30
Consensus pattern (33 bp):
AGGTTCTATCTTAGCCTTTGAAAAGATAGGGAA
Found at i:2593550 original size:28 final size:28
Alignment explanation
Indices: 2593518--2593666 Score: 113
Period size: 28 Copynumber: 5.3 Consensus size: 28
2593508 TACTATGGAC
* *
2593518 ATTGTCTTGTTAAGACAACCTTACCCAT
1 ATTGTCTTATTAAGACAACCTTATCCAT
* *
2593546 ATTGTCTTATTAAGATAAGCTTATCCAT
1 ATTGTCTTATTAAGACAACCTTATCCAT
* ** * * * *
2593574 TTTGTCTTAACACATGTCTACCTTA--GAC
1 ATTGTCTTATTA-A-GACAACCTTATCCAT
*
2593602 ATTGTCTTGTTAAGACAACCTTATCCAT
1 ATTGTCTTATTAAGACAACCTTATCCAT
* ***
2593630 ATTCTCTTATTAAGACAGGTTTATCCAT
1 ATTGTCTTATTAAGACAACCTTATCCAT
*
2593658 TTTGTCTTA
1 ATTGTCTTA
2593667 ACACATGTCT
Statistics
Matches: 89, Mismatches: 28, Indels: 8
0.71 0.22 0.06
Matches are distributed among these distances:
26 8 0.09
27 1 0.01
28 73 0.82
29 1 0.01
30 6 0.07
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.42
Consensus pattern (28 bp):
ATTGTCTTATTAAGACAACCTTATCCAT
Found at i:2593559 original size:110 final size:110
Alignment explanation
Indices: 2593371--2593582 Score: 248
Period size: 110 Copynumber: 1.9 Consensus size: 110
2593361 TATTATCTTC
* * * * * * *** *
2593371 TTAAGATAACTTATCTTAAGAGATGTCTACTTTAGACATTGTTTTGTTTAAATATGTTTATCAAT
1 TTAAGAAAACTTATCTTAAAACATGTCTACTATAGACATTGTCTTGTTTAAACAACCTTACCAAT
*
2593436 ATTGACTTGTTAAGACTAA-CTTAACCATTTTATCTTATTAATACA
66 ATTGACTTATTAAGA-TAAGCTTAACCATTTTATCTTATTAATACA
* *
2593481 TTAAGAAAACTTATCTTAAAACATGTCTACTATGGACATTGTCTTG-TTAAGACAACCTTACCCA
1 TTAAGAAAACTTATCTTAAAACATGTCTACTATAGACATTGTCTTGTTTAA-ACAACCTTACCAA
* * *
2593545 TATTGTCTTATTAAGATAAGCTTATCCATTTTGTCTTA
65 TATTGACTTATTAAGATAAGCTTAACCATTTTATCTTA
2593583 ACACATGTCT
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
109 7 0.08
110 77 0.92
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (110 bp):
TTAAGAAAACTTATCTTAAAACATGTCTACTATAGACATTGTCTTGTTTAAACAACCTTACCAAT
ATTGACTTATTAAGATAAGCTTAACCATTTTATCTTATTAATACA
Found at i:2593603 original size:84 final size:84
Alignment explanation
Indices: 2593494--2593750 Score: 322
Period size: 84 Copynumber: 3.1 Consensus size: 84
2593484 AGAAAACTTA
*
2593494 TCTTAAAACATGTCTA-CTATGGACATTGTCTTGTTAAGACAACCTTACCCATATTGTCTTATTA
1 TCTTAACACATGTCTACCT-TGGACATTGTCTTGTTAAGACAACCTTACCCATATTGTCTTATTA
*
2593558 AGATAAGCTTATCCATTTTG
65 AGATAAGTTTATCCATTTTG
* * *
2593578 TCTTAACACATGTCTACCTTAGACATTGTCTTGTTAAGACAACCTTATCCATATTCTCTTATTAA
1 TCTTAACACATGTCTACCTTGGACATTGTCTTGTTAAGACAACCTTACCCATATTGTCTTATTAA
* *
2593643 GACAGGTTTATCCATTTTG
66 GATAAGTTTATCCATTTTG
* * * * * * *
2593662 TCTTAACACATGTCTACTTTGGACATTATTTTATTAAGACAACCTTTTCTGC-T-TTGTCTTATA
1 TCTTAACACATGTCTACCTTGGACATTGTCTTGTTAAGACAACC-TTAC-CCATATTGTCTTATT
**
2593725 AAGATAAGTTTATCCACATTG
64 AAGATAAGTTTATCCATTTTG
2593746 TCTTA
1 TCTTA
2593751 TTAAGAAATC
Statistics
Matches: 149, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
84 143 0.96
85 5 0.03
86 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.41
Consensus pattern (84 bp):
TCTTAACACATGTCTACCTTGGACATTGTCTTGTTAAGACAACCTTACCCATATTGTCTTATTAA
GATAAGTTTATCCATTTTG
Found at i:2593829 original size:15 final size:15
Alignment explanation
Indices: 2593791--2593823 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2593781 CCAAATTGTC
*
2593791 TTAAAATTTTCTTAA
1 TTAAACTTTTCTTAA
2593806 TTAAACTTTTC-TAA
1 TTAAACTTTTCTTAA
2593820 TTAA
1 TTAA
2593824 GTCTTTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (15 bp):
TTAAACTTTTCTTAA
Found at i:2594737 original size:13 final size:13
Alignment explanation
Indices: 2594719--2594744 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2594709 TACACAAAGT
2594719 ATGTATCGATACA
1 ATGTATCGATACA
2594732 ATGTATCGATACA
1 ATGTATCGATACA
2594745 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2594742 original size:32 final size:33
Alignment explanation
Indices: 2594701--2594764 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
2594691 TAGCCAAACT
**
2594701 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
2594733 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
2594765 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:2596968 original size:84 final size:84
Alignment explanation
Indices: 2596795--2596955 Score: 209
Period size: 84 Copynumber: 1.9 Consensus size: 84
2596785 ACTCAAAGAA
* * * * *
2596795 GAAAATAAATCAATAAGTGTAGAGAATGATTTTCTTGAAAAGAAATTAAGTGAATTAGAGAAGAA
1 GAAAATAAATCAATAAGTGTAGAAAATAATTTTCTTAAAAAGAAAATAAATGAATTAGAGAAGAA
*
2596860 TATGAAAGAGTTACAAAAT
66 TAAGAAAGAGTTACAAAAT
* * *
2596879 GAAAATAAATCAATGAGTTTAGAAAATAATTCTT-TTAAAAAGAAAATAAATGAATTAGAGGAGA
1 GAAAATAAATCAATAAGTGTAGAAAATAATT-TTCTTAAAAAGAAAATAAATGAATTAGAGAAGA
2596943 A-AAGAAATGAGTT
65 ATAAGAAA-GAGTT
2596956 GCAAGTGGAA
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
83 5 0.08
84 59 0.89
85 2 0.03
ACGTcount: A:0.53, C:0.03, G:0.18, T:0.26
Consensus pattern (84 bp):
GAAAATAAATCAATAAGTGTAGAAAATAATTTTCTTAAAAAGAAAATAAATGAATTAGAGAAGAA
TAAGAAAGAGTTACAAAAT
Found at i:2600249 original size:13 final size:13
Alignment explanation
Indices: 2600231--2600289 Score: 55
Period size: 13 Copynumber: 4.0 Consensus size: 13
2600221 TACACAAAGT
2600231 ATGTATCGATACA
1 ATGTATCGATACA
2600244 ATGTATCGATACACAAAAA
1 ATGTATCGAT--AC----A
2600263 ATTGTATCGATACA
1 A-TGTATCGATACA
2600277 ATGTATCGATACA
1 ATGTATCGATACA
2600290 CAAAAAATTG
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 22 0.56
14 2 0.05
15 2 0.05
18 2 0.05
19 2 0.05
20 9 0.23
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2600270 original size:20 final size:20
Alignment explanation
Indices: 2600245--2600309 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
2600235 ATCGATACAA
2600245 TGTATCGATACACAAAAAAT
1 TGTATCGATACACAAAAAAT
2600265 TGTATCGAT--AC----AA-
1 TGTATCGATACACAAAAAAT
2600278 TGTATCGATACACAAAAAAT
1 TGTATCGATACACAAAAAAT
2600298 TGTATCGATACA
1 TGTATCGATACA
2600310 TTGGCTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 9 0.24
14 2 0.05
15 2 0.05
18 2 0.05
19 2 0.05
20 21 0.55
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (20 bp):
TGTATCGATACACAAAAAAT
Found at i:2600274 original size:33 final size:33
Alignment explanation
Indices: 2600213--2600309 Score: 169
Period size: 33 Copynumber: 3.0 Consensus size: 33
2600203 TAGCCAAACT
**
2600213 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
2600245 TGTATCGATACACAAAAAATTGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
2600278 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
2600310 TTGGCTTGTA
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 17 0.27
33 45 0.73
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:2603167 original size:164 final size:163
Alignment explanation
Indices: 2602896--2603224 Score: 586
Period size: 164 Copynumber: 2.0 Consensus size: 163
2602886 GAATATTGCA
* *
2602896 TTGGTTACTAATGTTGTTATTTGTATTGTTTCTTATATAACTATAGGGGGATTATTTTTGAATAT
1 TTGGTTACTAATGCTGTTATTTGTATTCTTTCTTATATAACTATAGGGGGATTATTTTTGAATAT
* *
2602961 CAAGTTTTAGAATGAGAAATTGTTGGTTTCCTTGACACACAAAGAGCACTTGGGTATACTTAGAC
66 CAAGTTTTAGAATAAGAAATTGTTAGTTTCCTTGACACACAAAGAGCACTTGGGTATACTT-GAC
*
2603026 TTTTTGCCAAATTATTAGAGATAGCATAGGTAAC
130 TCTTTGCCAAATTATTAGAGATAGCATAGGTAAC
2603060 TTGGTTACTAATGCTGTTATTTGTATTCTTTCTTATATAACTATAGGGGGATTATTTTTGAATAT
1 TTGGTTACTAATGCTGTTATTTGTATTCTTTCTTATATAACTATAGGGGGATTATTTTTGAATAT
2603125 CAAGTTTTAGAATAAGAAATTGTTAGTTTCCTTGACACACAAAGAGCACTTGGGTATACTTGACT
66 CAAGTTTTAGAATAAGAAATTGTTAGTTTCCTTGACACACAAAGAGCACTTGGGTATACTTGACT
* *
2603190 CTTTGCCAAATTATTGGAGATAGCATAGGTTAC
131 CTTTGCCAAATTATTAGAGATAGCATAGGTAAC
2603223 TT
1 TT
2603225 AAGTTTAGGT
Statistics
Matches: 158, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
163 36 0.23
164 122 0.77
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.40
Consensus pattern (163 bp):
TTGGTTACTAATGCTGTTATTTGTATTCTTTCTTATATAACTATAGGGGGATTATTTTTGAATAT
CAAGTTTTAGAATAAGAAATTGTTAGTTTCCTTGACACACAAAGAGCACTTGGGTATACTTGACT
CTTTGCCAAATTATTAGAGATAGCATAGGTAAC
Found at i:2606597 original size:76 final size:77
Alignment explanation
Indices: 2606511--2606697 Score: 182
Period size: 77 Copynumber: 2.4 Consensus size: 77
2606501 ACAATGACCT
* * * *
2606511 TAATGGATATGTTTCAACATGAAGGTTCTCACTTGATCCT-A-GA-TTCAGTTTTAAGGTACTTT
1 TAATAGATATGTTTCAACATGAAGGTTCCCACATAATCCTAATGACTT--GTTTTAAGGTACTTT
2606573 CACCTAAATAACCC
64 CACCTAAATAACCC
** * ** *
2606587 TAATAGATATGTTTTTACACGAAGGTTCCCACATAATCCTAATGACTTGTTTTAAGGTGTTTTTA
1 TAATAGATATGTTTCAACATGAAGGTTCCCACATAATCCTAATGACTTGTTTTAAGGTACTTTCA
* ***
2606652 TCTAAATGGTCC
66 CCTAAATAACCC
* * *
2606664 TAATAGACATGTTTCAATATGAAGGTTCCTACAT
1 TAATAGATATGTTTCAACATGAAGGTTCCCACAT
2606698 GATCTTAAGG
Statistics
Matches: 88, Mismatches: 20, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
76 33 0.38
77 51 0.58
78 2 0.02
79 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.37
Consensus pattern (77 bp):
TAATAGATATGTTTCAACATGAAGGTTCCCACATAATCCTAATGACTTGTTTTAAGGTACTTTCA
CCTAAATAACCC
Found at i:2607510 original size:37 final size:37
Alignment explanation
Indices: 2607468--2607543 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
2607458 GGAAAAAAGT
*
2607468 TTGTTGAACATGGGTTGAATGAAAACTCCATTTGGTA
1 TTGTTGAACATAGGTTGAATGAAAACTCCATTTGGTA
* * *
2607505 TTGTTGAACATATGTTGTATGAAAACTCCATTTGTTA
1 TTGTTGAACATAGGTTGAATGAAAACTCCATTTGGTA
2607542 TT
1 TT
2607544 AGTCACTCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.41
Consensus pattern (37 bp):
TTGTTGAACATAGGTTGAATGAAAACTCCATTTGGTA
Found at i:2608565 original size:17 final size:18
Alignment explanation
Indices: 2608543--2608581 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
2608533 AATTTTATAA
2608543 TATTAGAT-AAT-TATATT
1 TATTAGATGAATAT-TATT
2608560 TATTAGATGAATATTATT
1 TATTAGATGAATATTATT
2608578 TATT
1 TATT
2608582 GAAAATAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.40
18 11 0.55
19 1 0.05
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (18 bp):
TATTAGATGAATATTATT
Found at i:2608579 original size:18 final size:17
Alignment explanation
Indices: 2608543--2608581 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
2608533 AATTTTATAA
2608543 TATTAGATAATTATATT
1 TATTAGATAATTATATT
2608560 TATTAGATGAA-TATTATT
1 TATTAGAT-AATTA-TATT
2608578 TATT
1 TATT
2608582 GAAAATAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (17 bp):
TATTAGATAATTATATT
Found at i:2610629 original size:26 final size:26
Alignment explanation
Indices: 2610600--2610659 Score: 120
Period size: 26 Copynumber: 2.3 Consensus size: 26
2610590 ACAACTCACC
2610600 TAAGCCTTGTTTGCAAGTAATCTCCT
1 TAAGCCTTGTTTGCAAGTAATCTCCT
2610626 TAAGCCTTGTTTGCAAGTAATCTCCT
1 TAAGCCTTGTTTGCAAGTAATCTCCT
2610652 TAAGCCTT
1 TAAGCCTT
2610660 AGATGTTTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (26 bp):
TAAGCCTTGTTTGCAAGTAATCTCCT
Found at i:2611597 original size:29 final size:30
Alignment explanation
Indices: 2611544--2611601 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
2611534 AGCCAATGTA
*
2611544 TCGATACATTTTGGGATGTATCGATACAAG
1 TCGATACATCTTGGGATGTATCGATACAAG
*
2611574 TCGATACATCTTGTG-TGTATCGATACAA
1 TCGATACATCTTGGGATGTATCGATACAA
2611602 ACAGTTAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (30 bp):
TCGATACATCTTGGGATGTATCGATACAAG
Found at i:2613689 original size:20 final size:22
Alignment explanation
Indices: 2613650--2613694 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
2613640 GCTGCTAGTG
*
2613650 TGGGGGCTGCCCGGTTGCGACC
1 TGGGGGCTGCCCGGTCGCGACC
2613672 TGGGGG-TG-CCGGTCGCGACC
1 TGGGGGCTGCCCGGTCGCGACC
2613692 TGG
1 TGG
2613695 TGAGTGCTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.64
21 2 0.09
22 6 0.27
ACGTcount: A:0.04, C:0.29, G:0.49, T:0.18
Consensus pattern (22 bp):
TGGGGGCTGCCCGGTCGCGACC
Found at i:2614154 original size:13 final size:13
Alignment explanation
Indices: 2614136--2614160 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2614126 ATAAACCCTT
2614136 TGTATCGATACAA
1 TGTATCGATACAA
2614149 TGTATCGATACA
1 TGTATCGATACA
2614161 GAGAATGCTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2620448 original size:20 final size:21
Alignment explanation
Indices: 2620394--2620449 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 21
2620384 ACGTTTGGTC
*
2620394 ATGTATCGATAC-TGTGCAAT
1 ATGTATCGATACATTTGCAAT
2620414 ATGTATCGATACATTTG-AAT
1 ATGTATCGATACATTTGCAAT
*
2620434 GTGTATCGATACATTT
1 ATGTATCGATACATTT
2620450 CAGGGTTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 30 0.91
21 3 0.09
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (21 bp):
ATGTATCGATACATTTGCAAT
Found at i:2624024 original size:133 final size:133
Alignment explanation
Indices: 2623757--2624022 Score: 310
Period size: 133 Copynumber: 2.0 Consensus size: 133
2623747 AAAAAGGCAT
* * * *
2623757 ATTTTAGATAAAAATTTTTTGGCAAAAATAAATTCATAGGAAATAAATTTTATTTTTAACCAAAA
1 ATTTTAGATAAAAATGTTTTGGCAAAAATAAATCCATAGGAAATAAAATTTACTTTTAACCAAAA
** * * * *
2623822 TTAGTTATTTTTGATAGAATTTTTGTCAAAAATAAAGAATGACATTTTTCCATAAAAATTTCGTC
66 TTAGTTATTTTTGATAGAATTTTCATAAAAAATAAAGAATGACACTTTTCAACAAAAATTTCGTC
2623887 AAA
131 AAA
* * * *
2623890 ATTTT-GATGAAAATGTTTTGTCAAAAAATAAATCCATAGGAAATAAAATTTGCTTTTGA-CAAC
1 ATTTTAGATAAAAATGTTTTGGC-AAAAATAAATCCATAGGAAATAAAATTTACTTTTAACCAA-
*
2623953 AATTCA-TTATTTTTGATGGAATTTTCATAAAAAATAAAGCAA-GAC-CTTTTCAACAAAAACTT
64 AATT-AGTTATTTTTGATAGAATTTTCATAAAAAATAAAG-AATGACACTTTTCAACAAAAA-TT
2624015 T-GTCAAA
126 TCGTCAAA
2624022 A
1 A
2624023 ATGAAATAAT
Statistics
Matches: 113, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
132 35 0.31
133 75 0.66
134 3 0.03
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37
Consensus pattern (133 bp):
ATTTTAGATAAAAATGTTTTGGCAAAAATAAATCCATAGGAAATAAAATTTACTTTTAACCAAAA
TTAGTTATTTTTGATAGAATTTTCATAAAAAATAAAGAATGACACTTTTCAACAAAAATTTCGTC
AAA
Found at i:2624566 original size:23 final size:23
Alignment explanation
Indices: 2624539--2624582 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2624529 CGTTTTAAGG
*
2624539 TATTTTTTAAAATATTTTGTTAT
1 TATTTTTCAAAATATTTTGTTAT
* *
2624562 TATTTTTCACAATGTTTTGTT
1 TATTTTTCAAAATATTTTGTT
2624583 TTAACTTATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.64
Consensus pattern (23 bp):
TATTTTTCAAAATATTTTGTTAT
Found at i:2626952 original size:236 final size:235
Alignment explanation
Indices: 2626507--2626979 Score: 514
Period size: 236 Copynumber: 2.0 Consensus size: 235
2626497 TAAAATTTAC
* * *
2626507 TGTTAGGATCTTGGTTTTGATATAACAAAGATTGAATAAAATCGAAAATTATTTTGAAAACTGTA
1 TGTTAGGATCTCGGTTTTAATATAACAAAGATTGAATAAAATCGAAAA-TAGTTTGAAAACTGTA
* * * *
2626572 ATAAGTTTTATTCATTCAAAAATACTCTAAAAACCTTGTTCTAAGTGATTTTCAATATCAATAAT
65 ACAAGTTTTATTCACTCAAAAATACTCTAAAAACCATGTTCTAAGTAATTTTC-ATATCAATAAT
* ** ** * * *
2626637 GTTTTATAGTTTCTTATTAATGTTTTCAAGTCTTAAATCAAATGTTCTCAAGTAAGAATAATCCA
129 GTTTTAGAGTTTCAAACAAATGTTTTCAAGCCTTAAATCAAATGTTCTCAAGCAAAAATAATCCA
* *
2626702 AAAGCATAGATACATAGGTATTTGTATTGATACGTTAAGGTT
194 AAAGCATAGATACATAGGTATTTGTATCGATACATTAAGGTT
*
2626744 TGTTAGGATCTCGGTTTTAATATAAC-AAGGTTGAATAAAATCGAAAA-ACGTTTGAAAAACTGT
1 TGTTAGGATCTCGGTTTTAATATAACAAAGATTGAATAAAATCGAAAATA-GTTTG-AAAACTGT
*
2626807 AAACAAGTTTTATTCACTCAAAAACT-CTCTAAAAA-CATGTTCTAAGTAATTTTC-TATTAATG
64 -AACAAGTTTTATTCACTCAAAAA-TACTCTAAAAACCATGTTCTAAGTAATTTTCATATCAAT-
* * * * *
2626869 GAA-GTTTTTAGAGTTAT-AAACAAATGTTTTTGAA-CCTTAATTTAAATGTTTTTAAGGCAAAA
126 -AATG-TTTTAGAGTT-TCAAACAAATG-TTTTCAAGCCTTAAATCAAATGTTCTCAA-GCAAAA
* * * * *
2626931 ATACTTC-AAAGTATCGATACATAGGTATTTGTATCGATACATTATGGTT
186 ATAATCCAAAAGCATAGATACATAGGTATTTGTATCGATACATTAAGGTT
2626980 GACTTAGGCT
Statistics
Matches: 197, Mismatches: 29, Indels: 21
0.80 0.12 0.09
Matches are distributed among these distances:
234 7 0.04
235 5 0.03
236 114 0.58
237 70 0.36
238 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (235 bp):
TGTTAGGATCTCGGTTTTAATATAACAAAGATTGAATAAAATCGAAAATAGTTTGAAAACTGTAA
CAAGTTTTATTCACTCAAAAATACTCTAAAAACCATGTTCTAAGTAATTTTCATATCAATAATGT
TTTAGAGTTTCAAACAAATGTTTTCAAGCCTTAAATCAAATGTTCTCAAGCAAAAATAATCCAAA
AGCATAGATACATAGGTATTTGTATCGATACATTAAGGTT
Found at i:2627155 original size:33 final size:33
Alignment explanation
Indices: 2627113--2627179 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
2627103 CTATCACTAT
*
2627113 TTGTATCGATACATGGT-ACAATGTATCGATACA
1 TTGTATCGATACATGATGA-AATGTATCGATACA
*
2627146 TTGTATCGATGCATGATGAAATGTATCGATACA
1 TTGTATCGATACATGATGAAATGTATCGATACA
2627179 T
1 T
2627180 AGCTTGTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACATGATGAAATGTATCGATACA
Found at i:2629431 original size:13 final size:13
Alignment explanation
Indices: 2629413--2629437 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2629403 ATGTTGCACA
2629413 GTATCGATACATT
1 GTATCGATACATT
2629426 GTATCGATACAT
1 GTATCGATACAT
2629438 GTTGCATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:2629432 original size:33 final size:33
Alignment explanation
Indices: 2629390--2629455 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
2629380 TACACATTTA
2629390 ATTGTATCGATACATGTTGCACAGTATCGATAC
1 ATTGTATCGATACATGTTGCACAGTATCGATAC
**
2629423 ATTGTATCGATACATGTTGCATTGTATCGATAC
1 ATTGTATCGATACATGTTGCACAGTATCGATAC
2629456 TTGAAAAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (33 bp):
ATTGTATCGATACATGTTGCACAGTATCGATAC
Found at i:2635876 original size:32 final size:33
Alignment explanation
Indices: 2635813--2635877 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
2635803 CACACCCAGA
* *
2635813 TGTATTGATACATATTGCATTTTATCGATACAT
1 TGTATCGATACATATTGCATTGTATCGATACAT
*
2635846 TGTATCGATACATGTT-CATTGTATCGATACAT
1 TGTATCGATACATATTGCATTGTATCGATACAT
2635878 GGACAATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATATTGCATTGTATCGATACAT
Found at i:2635888 original size:20 final size:19
Alignment explanation
Indices: 2635842--2635898 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
2635832 TTTTATCGAT
*
2635842 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
2635861 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
2635880 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
2635899 AGATTGGTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:2635961 original size:13 final size:13
Alignment explanation
Indices: 2635943--2635972 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2635933 CGATACATGG
*
2635943 TACAATGTATCGA
1 TACAATGTAACGA
2635956 TACAATGTAACGA
1 TACAATGTAACGA
2635969 TACA
1 TACA
2635973 TGCTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (13 bp):
TACAATGTAACGA
Found at i:2644081 original size:33 final size:33
Alignment explanation
Indices: 2644037--2644136 Score: 146
Period size: 33 Copynumber: 3.0 Consensus size: 33
2644027 GGACAATTTT
* * *
2644037 TTTTTAAGAAATTCCTTGATTATGGGAGAGAAAA
1 TTTTT-AGAAATTCTTTGATTAAGGGGGAGAAAA
2644071 TTTTTAGAAATTCTTTGATTAAGGGGGAGAAAA
1 TTTTTAGAAATTCTTTGATTAAGGGGGAGAAAA
* *
2644104 TTTTTAGAAAATCTTTAATTAAGGGGGAGAAAA
1 TTTTTAGAAATTCTTTGATTAAGGGGGAGAAAA
2644137 ATGAAAACTT
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
33 56 0.92
34 5 0.08
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (33 bp):
TTTTTAGAAATTCTTTGATTAAGGGGGAGAAAA
Found at i:2651940 original size:19 final size:19
Alignment explanation
Indices: 2651916--2651971 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
2651906 TGTATCTATA
*
2651916 CATTGTATCGATACATGCT
1 CATTGTATCGATACATGCC
* *
2651935 CATTGTATTGATACATACC
1 CATTGTATCGATACATGCC
*
2651954 CAATTATATCGATACATG
1 C-ATTGTATCGATACATG
2651972 AAACTAGCAG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (19 bp):
CATTGTATCGATACATGCC
Found at i:2652025 original size:20 final size:20
Alignment explanation
Indices: 2652000--2652052 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
2651990 CTAAGTGAAA
2652000 TGTATCGATACATG-GGACAT
1 TGTATCGATACATGAGGA-AT
2652020 TGTATCGATACATGAGGAAT
1 TGTATCGATACATGAGGAAT
*
2652040 TGTGTCGATACAT
1 TGTATCGATACAT
2652053 TATGCCCAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 28 0.90
21 3 0.10
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (20 bp):
TGTATCGATACATGAGGAAT
Found at i:2658227 original size:13 final size:13
Alignment explanation
Indices: 2658209--2658248 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
2658199 ACAAGGTTCT
2658209 TTGTATCGATACA
1 TTGTATCGATACA
2658222 TTGTATCGATACA
1 TTGTATCGATACA
** *
2658235 AAGTATCTATACA
1 TTGTATCGATACA
2658248 T
1 T
2658249 GGGTTACTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2660197 original size:19 final size:19
Alignment explanation
Indices: 2660173--2660228 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
2660163 TGTATCGTTA
* *
2660173 CATTGTATCGATACATGCT
1 CATTGTATTGATACATGCC
*
2660192 CATTGTATTGATACATACC
1 CATTGTATTGATACATGCC
2660211 CAATTGTATTGATACATG
1 C-ATTGTATTGATACATG
2660229 AAACTGGCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (19 bp):
CATTGTATTGATACATGCC
Found at i:2660282 original size:20 final size:20
Alignment explanation
Indices: 2660257--2660309 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
2660247 CTAAGTGAAA
*
2660257 TGTATCGATACATG-GGACAT
1 TGTATCGATACATGAAGA-AT
2660277 TGTATCGATACATGAAGAAT
1 TGTATCGATACATGAAGAAT
2660297 TGTATCGATACAT
1 TGTATCGATACAT
2660310 TATGCCCAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 29 0.94
21 2 0.06
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (20 bp):
TGTATCGATACATGAAGAAT
Found at i:2663606 original size:24 final size:24
Alignment explanation
Indices: 2663579--2663654 Score: 81
Period size: 24 Copynumber: 3.3 Consensus size: 24
2663569 TGAAGTAATA
2663579 CAAATGCAAAGGTTGTCAATGATG
1 CAAATGCAAAGGTTGTCAATGATG
* **
2663603 CAAATGC-ATGTGAAG-CAAT-A--
1 CAAATGCAAAG-GTTGTCAATGATG
2663623 CAAATGCAAAGGTTGTCAATGATG
1 CAAATGCAAAGGTTGTCAATGATG
2663647 CAAATGCA
1 CAAATGCA
2663655 TTTAAAATGA
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
20 9 0.22
21 6 0.15
22 2 0.05
23 6 0.15
24 17 0.43
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.22
Consensus pattern (24 bp):
CAAATGCAAAGGTTGTCAATGATG
Found at i:2663614 original size:44 final size:44
Alignment explanation
Indices: 2663550--2663655 Score: 176
Period size: 44 Copynumber: 2.4 Consensus size: 44
2663540 AGTACAAACT
* * * *
2663550 TCAATAATGTAAACGCATGTGAAGTAATACAAATGCAAAGGTTG
1 TCAATGATGCAAATGCATGTGAAGCAATACAAATGCAAAGGTTG
2663594 TCAATGATGCAAATGCATGTGAAGCAATACAAATGCAAAGGTTG
1 TCAATGATGCAAATGCATGTGAAGCAATACAAATGCAAAGGTTG
2663638 TCAATGATGCAAATGCAT
1 TCAATGATGCAAATGCAT
2663656 TTAAAATGAT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 58 1.00
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.25
Consensus pattern (44 bp):
TCAATGATGCAAATGCATGTGAAGCAATACAAATGCAAAGGTTG
Found at i:2664906 original size:14 final size:14
Alignment explanation
Indices: 2664887--2664913 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2664877 ATATCCTTAC
2664887 TTTTTTCTTTTTCA
1 TTTTTTCTTTTTCA
2664901 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
2664914 TTTGCTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTTCTTTTTCA
Found at i:2664924 original size:20 final size:20
Alignment explanation
Indices: 2664888--2664925 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2664878 TATCCTTACT
*
2664888 TTTTTCTTTTTCATTTTTTC
1 TTTTTCTTTCTCATTTTTTC
2664908 TTTTTCTTTGCTC-TTTTT
1 TTTTTCTTT-CTCATTTTT
2664926 AAGCTTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.79
Consensus pattern (20 bp):
TTTTTCTTTCTCATTTTTTC
Found at i:2667319 original size:163 final size:163
Alignment explanation
Indices: 2667049--2667367 Score: 620
Period size: 163 Copynumber: 2.0 Consensus size: 163
2667039 TTGAAAGTTC
*
2667049 TTTTGTATTCCTTGTGCTTATACTTTCATAAACACCAACCTACCTAGAGGCAATTTTTGTTTATC
1 TTTTGTATTCATTGTGCTTATACTTTCATAAACACCAACCTACCTAGAGGCAATTTTTGTTTATC
*
2667114 AAATTTCTTTGTGTTGTAAAAGGTTTTATTCAACCTTGGTGTACGATCTCTTAAGAATTTGGGGT
66 AAATTTCTTTGTGTTGTAAAAGGTTATATTCAACCTTGGTGTACGATCTCTTAAGAATTTGGGGT
2667179 ATAATTCTTGAAGAGATTGAAATGTTTATCAAT
131 ATAATTCTTGAAGAGATTGAAATGTTTATCAAT
2667212 TTTTGTATTCATTGTGCTTATACTTTCATAAACACCAACCTACCTAGAGGCAATTTTTGTTTATC
1 TTTTGTATTCATTGTGCTTATACTTTCATAAACACCAACCTACCTAGAGGCAATTTTTGTTTATC
2667277 AAATTTCTTTGTGTTGTAAAAGGTTATATTCAACCTTGGTGTACGATCTCTTAAGAATTTGGGGT
66 AAATTTCTTTGTGTTGTAAAAGGTTATATTCAACCTTGGTGTACGATCTCTTAAGAATTTGGGGT
2667342 ATAATTCTTGAAGAGATTGAAATGTT
131 ATAATTCTTGAAGAGATTGAAATGTT
2667368 CTTATCTTAG
Statistics
Matches: 154, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
163 154 1.00
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (163 bp):
TTTTGTATTCATTGTGCTTATACTTTCATAAACACCAACCTACCTAGAGGCAATTTTTGTTTATC
AAATTTCTTTGTGTTGTAAAAGGTTATATTCAACCTTGGTGTACGATCTCTTAAGAATTTGGGGT
ATAATTCTTGAAGAGATTGAAATGTTTATCAAT
Found at i:2673140 original size:22 final size:22
Alignment explanation
Indices: 2673115--2673168 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
2673105 AAATCTTTTT
2673115 AAAATTTCATCTATTTAACATC
1 AAAATTTCATCTATTTAACATC
**
2673137 AAAA-TT-ATCTATTTTTCATC
1 AAAATTTCATCTATTTAACATC
2673157 AAAATCTTCATC
1 AAAAT-TTCATC
2673169 AAAAACGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 16 0.59
21 2 0.07
22 6 0.22
23 3 0.11
ACGTcount: A:0.39, C:0.19, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAATTTCATCTATTTAACATC
Found at i:2675816 original size:13 final size:13
Alignment explanation
Indices: 2675780--2675816 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
2675770 ACTCACTCAA
*
2675780 TATCGATACAGTG
1 TATCGATACATTG
*
2675793 TATCCATACATTG
1 TATCGATACATTG
2675806 TATCGATACAT
1 TATCGATACAT
2675817 AGTCAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:2679995 original size:31 final size:30
Alignment explanation
Indices: 2679958--2680015 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
2679948 GAGAAACATT
*
2679958 AAAGAAAAT-TACAAAGAAGAAGAAAAAAAAG
1 AAAGAAAATGAACAAA-AA-AAGAAAAAAAAG
2679989 AAAGAAAATGAACAAAAAAAGAAAAAA
1 AAAGAAAATGAACAAAAAAAGAAAAAA
2680016 TGATAATGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 9 0.36
31 11 0.44
32 5 0.20
ACGTcount: A:0.78, C:0.03, G:0.14, T:0.05
Consensus pattern (30 bp):
AAAGAAAATGAACAAAAAAAGAAAAAAAAG
Found at i:2684520 original size:15 final size:14
Alignment explanation
Indices: 2684485--2684520 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 14
2684475 TTAATACTAC
2684485 TTTTATTTATATTT
1 TTTTATTTATATTT
2684499 TTCTTATTTATATTT
1 TT-TTATTTATATTT
2684514 ATTTTAT
1 -TTTTAT
2684521 GAATATTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 2 0.10
15 16 0.80
16 2 0.10
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTATTTATATTT
Found at i:2686813 original size:20 final size:21
Alignment explanation
Indices: 2686767--2686813 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
2686757 ATAATTTGTG
*
2686767 TTGATACAATAAGTTAATGTA
1 TTGATACAATAAGTGAATGTA
* *
2686788 TCGATAC-ATAAGTGAATTTA
1 TTGATACAATAAGTGAATGTA
2686808 TTGATA
1 TTGATA
2686814 TGCTTGTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.38
Consensus pattern (21 bp):
TTGATACAATAAGTGAATGTA
Found at i:2686943 original size:20 final size:20
Alignment explanation
Indices: 2686871--2686945 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
2686861 TTCTAAAAAA
*
2686871 ATTGTATCGATACATTCACTT
1 ATTGTATCGATACA-TCACTC
**
2686892 A-TGTAT-GATACATGCAAGC
1 ATTGTATCGATACAT-CACTC
* **
2686911 AATGTATTAATACATCACTC
1 ATTGTATCGATACATCACTC
2686931 ATTGTATCGATACAT
1 ATTGTATCGATACAT
2686946 TCTGGGTTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
18 1 0.02
19 9 0.21
20 25 0.60
21 7 0.17
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (20 bp):
ATTGTATCGATACATCACTC
Found at i:2689391 original size:79 final size:80
Alignment explanation
Indices: 2689244--2689418 Score: 203
Period size: 79 Copynumber: 2.2 Consensus size: 80
2689234 AAAACATCAA
* * * *
2689244 GAGGGG-TACTCCAACCTCATTTTTACTTCTAAAACACCAAAATTTTCATTTCTAGAGATACTCT
1 GAGGGGATACTCCAACCCCATTTTTACTTCAAAAACACCAAAATTTTCATCTCTAGAGATACTCC
2689308 AACCCCACCATCTCT
66 AACCCCACCATCTCT
* ****
2689323 GAGGGGATACTCTAACCCCATTTTTACTTCAAAAACA-TTGCATTTTCATCTCTACG-GATACTC
1 GAGGGGATACTCCAACCCCATTTTTACTTCAAAAACACCAAAATTTTCATCTCTA-GAGATACTC
* *
2689386 CAACCCTATCATCTCT
65 CAACCCCACCATCTCT
* *
2689402 AAGGGTATACTCCAACC
1 GAGGGGATACTCCAACC
2689419 TTGGTTTTCA
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
79 52 0.65
80 28 0.35
ACGTcount: A:0.30, C:0.29, G:0.10, T:0.31
Consensus pattern (80 bp):
GAGGGGATACTCCAACCCCATTTTTACTTCAAAAACACCAAAATTTTCATCTCTAGAGATACTCC
AACCCCACCATCTCT
Found at i:2700981 original size:33 final size:32
Alignment explanation
Indices: 2700915--2701102 Score: 193
Period size: 31 Copynumber: 5.8 Consensus size: 32
2700905 GGCATCTTTT
* * * *
2700915 TTCTTCAAAGCCTACACAAATTGGTAGCAACCC
1 TTCTT-AAAGCCCACACAAGTCGGTGGCAACCC
* *
2700948 TTCTTTAAAGCCCACACAAGTCAGTGGCTACCC
1 TTC-TTAAAGCCCACACAAGTCGGTGGCAACCC
* * * *
2700981 TTCTCTAAAGCTCACACAAGTCGATGGTAACCA
1 TTCT-TAAAGCCCACACAAGTCGGTGGCAACCC
* *
2701014 TTC-TAAAGCCTACACAAGTCGGTGGCAACCA
1 TTCTTAAAGCCCACACAAGTCGGTGGCAACCC
*
2701045 TTC-TAAAGCCCATACAAGTCGGTGGCAACCC
1 TTCTTAAAGCCCACACAAGTCGGTGGCAACCC
*
2701076 -TCTCAAAAGCCCACACAAGTCGGTGGC
1 TTCT-TAAAGCCCACACAAGTCGGTGGC
2701103 CTCTTTTTCT
Statistics
Matches: 130, Mismatches: 21, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
30 2 0.02
31 52 0.40
32 22 0.17
33 52 0.40
34 2 0.02
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (32 bp):
TTCTTAAAGCCCACACAAGTCGGTGGCAACCC
Found at i:2701029 original size:64 final size:63
Alignment explanation
Indices: 2700953--2701102 Score: 185
Period size: 63 Copynumber: 2.4 Consensus size: 63
2700943 AACCCTTCTT
* * * * *
2700953 TAAAGCCCACACAAGTCAGTGGCTACCCTTCTCTAAAGCTCACACAAGTCGATGGTAACCAT-TC
1 TAAAGCCCACACAAGTCGGTGGC-AACCAT-TCTAAAGCCCACACAAGTCGATGGCAACCATCTC
* * * *
2701017 TAAAGCCTACACAAGTCGGTGGCAACCATTCTAAAGCCCATACAAGTCGGTGGCAACCCTCTC
1 TAAAGCCCACACAAGTCGGTGGCAACCATTCTAAAGCCCACACAAGTCGATGGCAACCATCTC
*
2701080 AAAAGCCCACACAAGTCGGTGGC
1 TAAAGCCCACACAAGTCGGTGGC
2701103 CTCTTTTTCT
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
62 26 0.35
63 27 0.36
64 21 0.28
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (63 bp):
TAAAGCCCACACAAGTCGGTGGCAACCATTCTAAAGCCCACACAAGTCGATGGCAACCATCTC
Found at i:2702033 original size:13 final size:13
Alignment explanation
Indices: 2702015--2702040 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2702005 TACACAAAGT
2702015 ATGTATCGATACA
1 ATGTATCGATACA
2702028 ATGTATCGATACA
1 ATGTATCGATACA
2702041 GAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2702038 original size:32 final size:33
Alignment explanation
Indices: 2701997--2702060 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2701987 TAGCCAAACT
**
2701997 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
*
2702029 TGTATCGATACAGAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
2702061 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:2702123 original size:20 final size:21
Alignment explanation
Indices: 2702094--2702132 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
2702084 GCTATATTTT
2702094 AAAATATGTATCGATACATCA
1 AAAATATGTATCGATACATCA
2702115 AAAAT-TGTATCGATACAT
1 AAAATATGTATCGATACAT
2702133 TCACACGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31
Consensus pattern (21 bp):
AAAATATGTATCGATACATCA
Found at i:2702564 original size:34 final size:35
Alignment explanation
Indices: 2702501--2702567 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
2702491 CTAAGTGATT
2702501 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
2702537 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
2702568 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:2704250 original size:84 final size:84
Alignment explanation
Indices: 2704090--2704250 Score: 186
Period size: 84 Copynumber: 1.9 Consensus size: 84
2704080 ACTCAAAGAA
* * * *
2704090 GAAAATAAATCAATAAGTGTAGAGAATCATATTCTTGAAAAGAAATTAAGTGAATTAGAGAAGAG
1 GAAAATAAATCAATAAGTGTAGAAAATCATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAG
* *
2704155 TATGAAAGAGTTACAAAAT
66 AAAGAAAGAGTTACAAAAT
* *
2704174 GAAAATAAATCAATGAGTTTAGAAAAT-A-ATTCTTTTAAAAAGAAAATAAATGAATT--AGAAG
1 GAAAATAAATCAATAAGTGTAGAAAATCATATTC--TTAAAAAGAAAATAAATGAATTAGAGAAG
2704235 AGAAAAGAAATGAGTT
64 AG-AAAGAAA-GAGTT
2704251 GCAAGTCGAA
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
82 11 0.17
83 6 0.09
84 48 0.74
ACGTcount: A:0.53, C:0.04, G:0.17, T:0.25
Consensus pattern (84 bp):
GAAAATAAATCAATAAGTGTAGAAAATCATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAG
AAAGAAAGAGTTACAAAAT
Found at i:2705790 original size:13 final size:13
Alignment explanation
Indices: 2705772--2705796 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2705762 TTTTCCAGAT
2705772 TGTATCGATACAA
1 TGTATCGATACAA
2705785 TGTATCGATACA
1 TGTATCGATACA
2705797 TTACTTCAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2706647 original size:30 final size:32
Alignment explanation
Indices: 2706611--2706678 Score: 104
Period size: 30 Copynumber: 2.2 Consensus size: 32
2706601 GGGTGACAAC
* *
2706611 GTATTAAGGGGGAGAGTTTGTATAAA-TTTT-
1 GTATTAAGGGGGAGAGCTTGCATAAACTTTTG
2706641 GTATTAAGGGGGAGAGCTTGCATAAACTTTTG
1 GTATTAAGGGGGAGAGCTTGCATAAACTTTTG
2706673 GTATTA
1 GTATTA
2706679 GTTGCATGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 24 0.71
31 4 0.12
32 6 0.18
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.37
Consensus pattern (32 bp):
GTATTAAGGGGGAGAGCTTGCATAAACTTTTG
Found at i:2707812 original size:13 final size:13
Alignment explanation
Indices: 2707794--2707819 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2707784 TACACAAAGT
2707794 ATGTATCGATACA
1 ATGTATCGATACA
2707807 ATGTATCGATACA
1 ATGTATCGATACA
2707820 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2707817 original size:32 final size:33
Alignment explanation
Indices: 2707776--2707839 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
2707766 TAGCCAAACT
**
2707776 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
2707808 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
2707840 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:2710173 original size:13 final size:13
Alignment explanation
Indices: 2710155--2710180 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2710145 TACACAAAGT
2710155 ATGTATCGATACA
1 ATGTATCGATACA
2710168 ATGTATCGATACA
1 ATGTATCGATACA
2710181 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2710178 original size:32 final size:33
Alignment explanation
Indices: 2710137--2710200 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
2710127 TAGCCAAACT
**
2710137 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
2710169 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
2710201 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:2714267 original size:15 final size:15
Alignment explanation
Indices: 2714247--2714277 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2714237 TAAAAATGTC
*
2714247 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2714262 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
2714277 C
1 C
2714278 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:2718924 original size:13 final size:13
Alignment explanation
Indices: 2718906--2718931 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2718896 TACACAAAGT
2718906 ATGTATCGATACA
1 ATGTATCGATACA
2718919 ATGTATCGATACA
1 ATGTATCGATACA
2718932 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2718929 original size:32 final size:33
Alignment explanation
Indices: 2718888--2718951 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
2718878 TAGCCAAACT
**
2718888 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
2718920 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
2718952 TTAGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:2724359 original size:12 final size:12
Alignment explanation
Indices: 2724342--2724367 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2724332 TTTCAAGATG
2724342 AGTTTAAAAATT
1 AGTTTAAAAATT
2724354 AGTTTAAAAATT
1 AGTTTAAAAATT
2724366 AG
1 AG
2724368 AAACGATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (12 bp):
AGTTTAAAAATT
Found at i:2724819 original size:19 final size:19
Alignment explanation
Indices: 2724795--2724850 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
2724785 TGTATCGATA
*
2724795 CATTATATCGATACATGTT
1 CATTATATCGATACATGCT
*
2724814 CATTATATCGATACATACT
1 CATTATATCGATACATGCT
*
2724833 CAATTGTATCGATACATG
1 C-ATTATATCGATACATG
2724851 AAACTAGCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.38
Consensus pattern (19 bp):
CATTATATCGATACATGCT
Found at i:2727115 original size:32 final size:32
Alignment explanation
Indices: 2727079--2727145 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
2727069 AATACCCCTC
* *
2727079 AACTAAATATTCC-AAGCCCGTCAAAACAAATA
1 AACTAAATA-CCCTAAGCCCATCAAAACAAATA
* *
2727111 AACTAATTACCCTAAGCCCATCAAAACATATA
1 AACTAAATACCCTAAGCCCATCAAAACAAATA
2727143 AAC
1 AAC
2727146 CCAATATTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 2 0.07
32 28 0.93
ACGTcount: A:0.49, C:0.27, G:0.04, T:0.19
Consensus pattern (32 bp):
AACTAAATACCCTAAGCCCATCAAAACAAATA
Found at i:2728043 original size:6 final size:6
Alignment explanation
Indices: 2728032--2728072 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
2728022 ATTTATGTTC
2728032 AGAATT AGAATT AGAATT AGAATT AGAATT AGAATT AGAAT
1 AGAATT AGAATT AGAATT AGAATT AGAATT AGAATT AGAAT
2728073 CCATGGCATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.17, T:0.32
Consensus pattern (6 bp):
AGAATT
Found at i:2730251 original size:19 final size:19
Alignment explanation
Indices: 2730229--2730266 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2730219 TGTTGTTTGT
*
2730229 TGTTTGCTATTGGTATTGC
1 TGTTTGCTATTGCTATTGC
*
2730248 TGTTTGCTGTTGCTATTGC
1 TGTTTGCTATTGCTATTGC
2730267 ATTTGTGACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.08, C:0.13, G:0.26, T:0.53
Consensus pattern (19 bp):
TGTTTGCTATTGCTATTGC
Found at i:2733255 original size:16 final size:16
Alignment explanation
Indices: 2733234--2733324 Score: 69
Period size: 16 Copynumber: 5.6 Consensus size: 16
2733224 TTGAAATATT
2733234 ATTCAAAATAATTTAA
1 ATTCAAAATAATTTAA
*
2733250 ATTCAAAACT-ATTTGA
1 ATTCAAAA-TAATTTAA
*
2733266 ATTTAAAA-ATATTTAA
1 ATTCAAAATA-ATTTAA
** *
2733282 AGCCCAAAAAAATTTAA
1 A-TTCAAAATAATTTAA
* *
2733299 ATTTAAAATAATCTAA
1 ATTCAAAATAATTTAA
*
2733315 ATTAAAAATA
1 ATTCAAAATA
2733325 TAGTAAAACA
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
16 45 0.78
17 12 0.21
18 1 0.02
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.34
Consensus pattern (16 bp):
ATTCAAAATAATTTAA
Found at i:2733275 original size:33 final size:32
Alignment explanation
Indices: 2733238--2733322 Score: 84
Period size: 33 Copynumber: 2.7 Consensus size: 32
2733228 AATATTATTC
** *
2733238 AAAATAATTTAAATTCAAAACTATTTGAATTT
1 AAAATAATTTAAATTCAAAAAAATTTAAATTT
**
2733270 AAAA-ATATTTAAAGCCCAAAAAAATTTAAATTT
1 AAAATA-ATTTAAA-TTCAAAAAAATTTAAATTT
*
2733303 AAAATAATCTAAATT-AAAAA
1 AAAATAATTTAAATTCAAAAA
2733323 TATAGTAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
31 6 0.14
32 11 0.26
33 24 0.57
34 1 0.02
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (32 bp):
AAAATAATTTAAATTCAAAAAAATTTAAATTT
Found at i:2733595 original size:34 final size:34
Alignment explanation
Indices: 2733527--2733750 Score: 265
Period size: 34 Copynumber: 6.6 Consensus size: 34
2733517 AAGGTTGAAG
* **
2733527 TTGTTGATTAAAT-GGTGATTTAGTAATTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* * *
2733560 TTGTTGATTAAATGGGTGATTTGGTGGTTTGCCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* *
2733594 TTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* ** *
2733628 TTGTTGATTAAATGAGAAATTTAGTAGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* *
2733662 TTATTGATTAAATGGGTGATTTGGTGGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* * *
2733696 TTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCCA
1 TTGTTGATTAAATGGGT-GATTTGGTAGCTTACCA
2733730 TTGTTGATTAAAT-GGTGATTT
1 TTGTTGATTAAATGGGTGATTT
2733751 TTACCAAACC
Statistics
Matches: 164, Mismatches: 25, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
33 21 0.13
34 143 0.87
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.42
Consensus pattern (34 bp):
TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
Found at i:2733661 original size:102 final size:101
Alignment explanation
Indices: 2733527--2733744 Score: 337
Period size: 102 Copynumber: 2.1 Consensus size: 101
2733517 AAGGTTGAAG
** * * * *
2733527 TTGTTGATTAAATGGTGATTTAGTAATTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGC
1 TTGTTGATTAAATGGAAATTTAGTAACTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
2733592 CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
66 CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
*
2733628 TTGTTGATTAAATGAGAAATTTAGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
1 TTGTTGATTAAATG-GAAATTTAGTAACTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
* * *
2733693 CCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCCA
65 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
2733730 TTGTTGATTAAATGG
1 TTGTTGATTAAATGG
2733745 TGATTTTTAC
Statistics
Matches: 106, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 15 0.14
102 91 0.86
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.41
Consensus pattern (101 bp):
TTGTTGATTAAATGGAAATTTAGTAACTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
Found at i:2738210 original size:34 final size:34
Alignment explanation
Indices: 2738153--2738371 Score: 280
Period size: 34 Copynumber: 6.5 Consensus size: 34
2738143 AAGTGGGAGA
*
2738153 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
2738186 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
2738220 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
2738254 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
2738288 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * * *
2738322 ATTGTTGACTAAA-AGGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
2738356 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2738372 TGGTTTTTAC
Statistics
Matches: 160, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
33 17 0.11
34 142 0.89
35 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:2738296 original size:102 final size:101
Alignment explanation
Indices: 2738153--2738371 Score: 339
Period size: 102 Copynumber: 2.2 Consensus size: 101
2738143 AAGTGGGAGA
** * * * *
2738153 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
*
2738218 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAAAGGGAGATTTGGTAGCTTACC
2738254 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
* * *
2738319 ACCATTGTTGACTAAAAGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAAAGGGAGATTTGGTAGCTTACC
2738356 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2738372 TGGTTTTTAC
Statistics
Matches: 107, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 16 0.15
102 91 0.85
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAAAGGGAGATTTGGTAGCTTACC
Found at i:2739896 original size:20 final size:18
Alignment explanation
Indices: 2739864--2739901 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 18
2739854 TTTGTCCTAC
2739864 TTTTTTTCTTTTCTTTTT
1 TTTTTTTCTTTTCTTTTT
2739882 TTTTTTTCTGGTTTCTTTTT
1 TTTTTTTCT--TTTCTTTTT
2739902 GTGCGGTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
20 9 0.50
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (18 bp):
TTTTTTTCTTTTCTTTTT
Found at i:2741442 original size:32 final size:33
Alignment explanation
Indices: 2741396--2741460 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
2741386 AGATATGATA
2741396 CAAAAAATATAAATATAACATATTTAATAAATT
1 CAAAAAATATAAATATAACATATTTAATAAATT
* *
2741429 CAAAAAATA-AAATATGATATATTTAATAAATT
1 CAAAAAATATAAATATAACATATTTAATAAATT
2741461 TATTGTATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 21 0.70
33 9 0.30
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.34
Consensus pattern (33 bp):
CAAAAAATATAAATATAACATATTTAATAAATT
Found at i:2742742 original size:149 final size:149
Alignment explanation
Indices: 2742571--2742875 Score: 592
Period size: 149 Copynumber: 2.0 Consensus size: 149
2742561 CGAAAACCAT
2742571 CTTGGGAGATCACATAAAAAAAATTAAAATGTTTGATCTTATGGTAATGATTACTACTGAATCAT
1 CTTGGGAGATCACATAAAAAAAATTAAAATGTTTGATCTTATGGTAATGATTACTACTGAATCAT
2742636 ACATCTTTGGATTTTGGGCTTACAGGCATTTAGAAGACACAGTATGTTTAATATTTTGGCTCATG
66 ACATCTTTGGATTTTGGGCTTACAGGCATTTAGAAGACACAGTATGTTTAATATTTTGGCTCATG
2742701 ATAAGAAATTAATGGGTTA
131 ATAAGAAATTAATGGGTTA
2742720 CTTGGGAGATCACATAAAAAAAATTAAAATGTTTGATCTTATGGTAATGATTACTACTGAATCAT
1 CTTGGGAGATCACATAAAAAAAATTAAAATGTTTGATCTTATGGTAATGATTACTACTGAATCAT
*
2742785 ACATCTTTGGATTTTGGGCTTACAGGCATTTAGAAGACACAGTATGTTTAATATTTTGGCTCTTG
66 ACATCTTTGGATTTTGGGCTTACAGGCATTTAGAAGACACAGTATGTTTAATATTTTGGCTCATG
2742850 ATAAGAAATTAATGGGTTA
131 ATAAGAAATTAATGGGTTA
*
2742869 CTGGGGA
1 CTTGGGA
2742876 ATGTTGGTTT
Statistics
Matches: 154, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (149 bp):
CTTGGGAGATCACATAAAAAAAATTAAAATGTTTGATCTTATGGTAATGATTACTACTGAATCAT
ACATCTTTGGATTTTGGGCTTACAGGCATTTAGAAGACACAGTATGTTTAATATTTTGGCTCATG
ATAAGAAATTAATGGGTTA
Found at i:2750121 original size:12 final size:12
Alignment explanation
Indices: 2750101--2750132 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2750091 TCAACCTAAA
2750101 CCCAAGCCGAAG
1 CCCAAGCCGAAG
*
2750113 CCGAAGCCGAAG
1 CCCAAGCCGAAG
2750125 CCCAAGCC
1 CCCAAGCC
2750133 CGAGGCTCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.31, C:0.44, G:0.25, T:0.00
Consensus pattern (12 bp):
CCCAAGCCGAAG
Found at i:2751776 original size:70 final size:70
Alignment explanation
Indices: 2751663--2751808 Score: 222
Period size: 70 Copynumber: 2.1 Consensus size: 70
2751653 AGTGGGGTTA
* * *
2751663 GAGTACCCCCGATGATAATAACTTAGGCAAAAATAAGATTTGAATCTTGACAAGTTTAAAAGCGG
1 GAGTATCCCCGATGACAATAACCTAGGCAAAAATAAGATTTGAATCTTGACAAGTTTAAAAGC-G
2751728 GGC-TG
65 GGCTTG
** *
2751733 GAGTATCCCCGATGACAATAACCTAGGCAAAAATAAGATTTGAATCTTGGTAGGTTTAAAAGCGG
1 GAGTATCCCCGATGACAATAACCTAGGCAAAAATAAGATTTGAATCTTGACAAGTTTAAAAGCGG
2751798 GCTTG
66 GCTTG
2751803 GAGTAT
1 GAGTAT
2751809 TCCCTCGGAA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
69 4 0.06
70 65 0.94
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (70 bp):
GAGTATCCCCGATGACAATAACCTAGGCAAAAATAAGATTTGAATCTTGACAAGTTTAAAAGCGG
GCTTG
Found at i:2753185 original size:24 final size:24
Alignment explanation
Indices: 2753151--2753205 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
2753141 GCATGGGCTG
*
2753151 TCAAGATGATGGAGATGAACAACA
1 TCAAGACGATGGAGATGAACAACA
*
2753175 TCAAGACGATGGAGATGAACAGCA
1 TCAAGACGATGGAGATGAACAACA
2753199 TCAAGAC
1 TCAAGAC
2753206 ATTAAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.44, C:0.16, G:0.25, T:0.15
Consensus pattern (24 bp):
TCAAGACGATGGAGATGAACAACA
Found at i:2754213 original size:20 final size:20
Alignment explanation
Indices: 2754164--2754215 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
2754154 TATTTTAGAC
*
2754164 ATGTATCG-TACATTCACTT
1 ATGTATCGATACATCCACTT
*
2754183 ATGTATTGATACATCCACTT
1 ATGTATCGATACATCCACTT
2754203 ATTGTA-CGATACA
1 A-TGTATCGATACA
2754216 AATTGTTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 7 0.25
20 17 0.61
21 4 0.14
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATCCACTT
Found at i:2755274 original size:32 final size:33
Alignment explanation
Indices: 2755204--2755276 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 33
2755194 CTGAAGATCA
*
2755204 AGGTGAAACCAATAATCTGAAGTTAAAGAACTT
1 AGGTGAAACCAATAATCTGAAGTTAAAGAACCT
* * *
2755237 A-GTGAAGCCAGTAATCTTAAGTTAAAG-ACCT
1 AGGTGAAACCAATAATCTGAAGTTAAAGAACCT
2755268 AGGTGAAAC
1 AGGTGAAAC
2755277 TAGCAGTTGG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 4 0.12
32 29 0.85
33 1 0.03
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (33 bp):
AGGTGAAACCAATAATCTGAAGTTAAAGAACCT
Found at i:2755570 original size:32 final size:32
Alignment explanation
Indices: 2755534--2755604 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
2755524 AGTAGTTTGA
*
2755534 AATTGAAAACTTGAGTGAAA-TAGCTAATCTGG
1 AATTGAAAACTTGAGTGAAACCAG-TAATCTGG
* *
2755566 AATTGAAAACTTGGGTGAAACCAGTAATCTGT
1 AATTGAAAACTTGAGTGAAACCAGTAATCTGG
2755598 AATTGAA
1 AATTGAA
2755605 GACCTATGCA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
32 33 0.94
33 2 0.06
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (32 bp):
AATTGAAAACTTGAGTGAAACCAGTAATCTGG
Found at i:2755776 original size:32 final size:32
Alignment explanation
Indices: 2755723--2755802 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 32
2755713 ACTAGTGATT
* * * *
2755723 TGAAATTGAAAATCTAGGCAAAACCAATAATC
1 TGAAATTGAAGACCTAAGCAAAACCAATAATA
2755755 T-AAAGTTGAAGACCTAAGCAAAACCAATAATA
1 TGAAA-TTGAAGACCTAAGCAAAACCAATAATA
*
2755787 TGAAATTGTAGACCTA
1 TGAAATTGAAGACCTA
2755803 GCCTAAACCA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 3 0.07
32 35 0.85
33 3 0.07
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.23
Consensus pattern (32 bp):
TGAAATTGAAGACCTAAGCAAAACCAATAATA
Found at i:2755811 original size:32 final size:32
Alignment explanation
Indices: 2755740--2755877 Score: 92
Period size: 32 Copynumber: 4.4 Consensus size: 32
2755730 GAAAATCTAG
*
2755740 GCAAAACCAATAATCTAAAGTTGAAGACCTAA
1 GCAAAACCAATAATATAAAGTTGAAGACCTAA
*
2755772 GCAAAACCAATAATATGAAA-TTGTAGACCT-A
1 GCAAAACCAATAATAT-AAAGTTGAAGACCTAA
* * * * *
2755803 GCCTAAACCATTAAT-TAGATGTT--TGA--TAG
1 G-CAAAACCAATAATATA-AAGTTGAAGACCTAA
* * *
2755832 GCAAAACCAGTAATATAAAGTTGAAGACTTGA
1 GCAAAACCAATAATATAAAGTTGAAGACCTAA
**
2755864 GTGAAACCAATAAT
1 GCAAAACCAATAAT
2755878 TTGAACTCAG
Statistics
Matches: 80, Mismatches: 16, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
28 16 0.20
29 3 0.04
30 5 0.06
31 4 0.05
32 49 0.61
33 3 0.04
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (32 bp):
GCAAAACCAATAATATAAAGTTGAAGACCTAA
Found at i:2759381 original size:52 final size:52
Alignment explanation
Indices: 2759233--2759361 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
2759223 CGAAATATGA
*
2759233 AAATTCGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
2759285 AAATTTGCTTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
2759337 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
2759362 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:2759388 original size:13 final size:13
Alignment explanation
Indices: 2759370--2759394 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2759360 CAAAGATCAG
2759370 TGTATCGATACAA
1 TGTATCGATACAA
2759383 TGTATCGATACA
1 TGTATCGATACA
2759395 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2761819 original size:13 final size:13
Alignment explanation
Indices: 2761801--2761826 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2761791 CAATTTTTTG
2761801 TGTATCGATACAT
1 TGTATCGATACAT
2761814 TGTATCGATACAT
1 TGTATCGATACAT
2761827 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2761910 original size:20 final size:21
Alignment explanation
Indices: 2761865--2761917 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
2761855 CTGCCAAGAA
* **
2761865 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTGTAAC
2761886 ATGTATCGATACAT-TGTAAC
1 ATGTATCGATACATCTGTAAC
2761906 ATGTATCGATAC
1 ATGTATCGATAC
2761918 TTTGAATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (21 bp):
ATGTATCGATACATCTGTAAC
Found at i:2762565 original size:21 final size:21
Alignment explanation
Indices: 2762524--2762567 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2762514 CTCCCCTTTA
* *
2762524 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
2762545 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
2762566 TC
1 TC
2762568 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:2764383 original size:13 final size:13
Alignment explanation
Indices: 2764365--2764390 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2764355 ATAATCACCC
2764365 TGTATCGATACAA
1 TGTATCGATACAA
2764378 TGTATCGATACAA
1 TGTATCGATACAA
2764391 AGAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Done.