Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007819.1 Hibiscus syriacus cultivar Beakdansim tig00110156_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: 3855360
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2745 characters in sequence are not A, C, G, or T
File 8 of 17
Found at i:1463176 original size:20 final size:20
Alignment explanation
Indices: 1463151--1463190 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1463141 AGCAACAGAA
1463151 TAAAAATGATTC-TATCTAAT
1 TAAAAATGA-TCATATCTAAT
1463171 TAAAAATGATCATATCTAAT
1 TAAAAATGATCATATCTAAT
1463191 AACTAATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCATATCTAAT
Found at i:1463219 original size:53 final size:52
Alignment explanation
Indices: 1463147--1463275 Score: 233
Period size: 53 Copynumber: 2.5 Consensus size: 52
1463137 AATTAGCAAC
1463147 AGAATAAAAA-TGATTCTATCTAATTAAAAATGATCATATCTAATAACTAAT
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCATATCTAATAACTAAT
*
1463198 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAAT-AAAAACTGATTCTATCTAATTAAAAATGATCATATCTAATAACTAAT
1463251 AGAATAAAAACTGATTCTATCTAAT
1 AGAATAAAAACTGATTCTATCTAAT
1463276 ATTTAATTTA
Statistics
Matches: 75, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 5 0.07
52 25 0.33
53 45 0.60
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.33
Consensus pattern (52 bp):
AGAATAAAAACTGATTCTATCTAATTAAAAATGATCATATCTAATAACTAAT
Found at i:1463233 original size:20 final size:21
Alignment explanation
Indices: 1463204--1463243 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1463194 TAATAGAATA
*
1463204 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
1463225 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
1463244 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:1472547 original size:21 final size:21
Alignment explanation
Indices: 1472517--1472568 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1472507 AATGCTAATG
* *
1472517 TGACATTTCACGATA-CTAGCA
1 TGACAATTCACAATATCTA-CA
*
1472538 TGACAATTCACAATATTTACA
1 TGACAATTCACAATATCTACA
1472559 TGACAATTCA
1 TGACAATTCA
1472569 TGTCATGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (21 bp):
TGACAATTCACAATATCTACA
Found at i:1473504 original size:42 final size:39
Alignment explanation
Indices: 1473413--1473569 Score: 147
Period size: 42 Copynumber: 3.9 Consensus size: 39
1473403 AATAACCAAC
* * *
1473413 AAATTCGCAACGCGAA-CTCCAATTTCACAACACAGTTTCT
1 AAATTCGCAACGCGAATTTCTAA-TTCGCAACACAGTTT-T
*
1473453 AAATTCGCAACGCGAATTTCTCAGATTCGCAACTCAGTTTT
1 AAATTCGCAACGCGAATTTCT-A-ATTCGCAACACAGTTTT
* * * *
1473494 GAAATTCGCAACTCGAATTTCT-TTTCCGCAACGCGATTTTT
1 -AAATTCGCAACGCGAATTTCTAATT-CGCAACAC-AGTTTT
*
1473535 CAAATTCGCAACGCGAATTTGTAATTCGCAACACA
1 -AAATTCGCAACGCGAATTTCTAATTCGCAACACA
1473570 TAAGTCAAAT
Statistics
Matches: 97, Mismatches: 13, Indels: 14
0.78 0.10 0.11
Matches are distributed among these distances:
39 2 0.02
40 24 0.25
41 34 0.35
42 36 0.37
43 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.29
Consensus pattern (39 bp):
AAATTCGCAACGCGAATTTCTAATTCGCAACACAGTTTT
Found at i:1473562 original size:20 final size:20
Alignment explanation
Indices: 1473448--1473566 Score: 91
Period size: 20 Copynumber: 5.8 Consensus size: 20
1473438 CACAACACAG
1473448 TTTCTAAATTCGCAACGCGAA
1 TTTCT-AATTCGCAACGCGAA
* *
1473469 TTTCTCAGATTCGCAACTC-AG
1 TTTCT-A-ATTCGCAACGCGAA
*
1473490 TTT-TGAAATTCGCAACTCGAA
1 TTTCT--AATTCGCAACGCGAA
* *
1473511 TTTCT-TTTCCGCAACGCGATT
1 TTTCTAATT-CGCAACGCGA-A
*
1473532 TTTCAAATTCGCAACGCGAA
1 TTTCTAATTCGCAACGCGAA
*
1473552 TTTGTAATTCGCAAC
1 TTTCTAATTCGCAAC
1473567 ACATAAGTCA
Statistics
Matches: 78, Mismatches: 13, Indels: 15
0.74 0.12 0.14
Matches are distributed among these distances:
19 2 0.03
20 34 0.44
21 29 0.37
22 13 0.17
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (20 bp):
TTTCTAATTCGCAACGCGAA
Found at i:1473600 original size:81 final size:83
Alignment explanation
Indices: 1473448--1473614 Score: 189
Period size: 81 Copynumber: 2.0 Consensus size: 83
1473438 CACAACACAG
* ** * **
1473448 TTTCTAAATTCGCAACGCGAATTTCTCAGATTCGCAACTCAGTTTTGAAATTCGCAACTCGAATT
1 TTTCTAAATTCGCAACGCGAATTTCTCAGATTCGCAACACAGTAGTCAAATTCGCAAAGCGAATT
* *
1473513 TCTTTTCCGCAACGCGATT
66 TATTTT-CGCAACGCGAAT
* **
1473532 TTTC-AAATTCGCAACGCGAATTTGT-A-ATTCGCAACACA-TAAGTCAAATTCGCAAAGCGCGT
1 TTTCTAAATTCGCAACGCGAATTTCTCAGATTCGCAACACAGT-AGTCAAATTCGCAAAGCGAAT
1473593 TTATTTTCGCAACGCGAAT
65 TTATTTTCGCAACGCGAAT
1473612 TTT
1 TTT
1473615 ATTTTCGAAT
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
80 15 0.21
81 31 0.44
82 1 0.01
83 20 0.28
84 4 0.06
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (83 bp):
TTTCTAAATTCGCAACGCGAATTTCTCAGATTCGCAACACAGTAGTCAAATTCGCAAAGCGAATT
TATTTTCGCAACGCGAAT
Found at i:1473769 original size:22 final size:22
Alignment explanation
Indices: 1473744--1473791 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
1473734 CTCTTTACGG
*
1473744 CGACATCCGTCCCCATCTCCGA
1 CGACATCCGTCCCCATATCCGA
*
1473766 CGACATCCGTCCCTATATCCGA
1 CGACATCCGTCCCCATATCCGA
1473788 CGAC
1 CGAC
1473792 CCCCCTCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.21, C:0.46, G:0.15, T:0.19
Consensus pattern (22 bp):
CGACATCCGTCCCCATATCCGA
Found at i:1474149 original size:20 final size:20
Alignment explanation
Indices: 1474124--1474161 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1474114 TTTGAAACTT
1474124 AAATTCGCAACACAAAAACG
1 AAATTCGCAACACAAAAACG
1474144 AAATTCGCAACACAAAAA
1 AAATTCGCAACACAAAAA
1474162 TCGCAACGCG
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:0.58, C:0.24, G:0.08, T:0.11
Consensus pattern (20 bp):
AAATTCGCAACACAAAAACG
Found at i:1474217 original size:20 final size:20
Alignment explanation
Indices: 1474192--1474235 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1474182 TCGCAACGCG
1474192 ATTTTAGTTTCGCATTGCGA
1 ATTTTAGTTTCGCATTGCGA
* **
1474212 ATTTTATTTTCGTGTTGCGA
1 ATTTTAGTTTCGCATTGCGA
1474232 ATTT
1 ATTT
1474236 CATTTTTGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.18, C:0.11, G:0.18, T:0.52
Consensus pattern (20 bp):
ATTTTAGTTTCGCATTGCGA
Found at i:1474240 original size:20 final size:20
Alignment explanation
Indices: 1474206--1474255 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1474196 TAGTTTCGCA
*
1474206 TTGCGAATTTTATTTTCGTG
1 TTGCGAATTTCATTTTCGTG
*
1474226 TTGCGAATTTCATTTTTGTG
1 TTGCGAATTTCATTTTCGTG
1474246 TTGCGAATTT
1 TTGCGAATTT
1474256 AAGTTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.16, C:0.10, G:0.20, T:0.54
Consensus pattern (20 bp):
TTGCGAATTTCATTTTCGTG
Found at i:1475809 original size:42 final size:42
Alignment explanation
Indices: 1475750--1475847 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
1475740 CCCCCACTTT
* * * *
1475750 GAGAGCCATCACCTGATCGAGCCGATTTTATAGCTCGACACC
1 GAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACACC
1475792 GAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACACC
1 GAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACACC
*
1475834 GAGAGTCATCACCT
1 GAGAGCCATCACCT
1475848 ATTCCATCAC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.28, C:0.34, G:0.19, T:0.19
Consensus pattern (42 bp):
GAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACACC
Found at i:1476010 original size:21 final size:21
Alignment explanation
Indices: 1475962--1476011 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1475952 GATAAGGGAG
1475962 TTACGTGATGAGGTCAGTGAT
1 TTACGTGATGAGGTCAGTGAT
* * *
1475983 TTGCGTGATGCGGTCGGT-ACT
1 TTACGTGATGAGGTCAGTGA-T
1476004 TTACGTGA
1 TTACGTGA
1476012 CTACGTGGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.18, C:0.14, G:0.34, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTGAT
Found at i:1476076 original size:42 final size:42
Alignment explanation
Indices: 1476013--1476110 Score: 178
Period size: 42 Copynumber: 2.3 Consensus size: 42
1476003 TTTACGTGAC
*
1476013 TACGTGGTGAGGTAGATGTTTTAAGCGATGAAAATTGTGCTT
1 TACGTGGTGAGGTAGAAGTTTTAAGCGATGAAAATTGTGCTT
*
1476055 TACGTGGTGAGGTAGAAGTTTTAAGCGATGACAATTGTGCTT
1 TACGTGGTGAGGTAGAAGTTTTAAGCGATGAAAATTGTGCTT
1476097 TACGTGGTGAGGTA
1 TACGTGGTGAGGTA
1476111 TCTACTTTAC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.26, C:0.08, G:0.33, T:0.34
Consensus pattern (42 bp):
TACGTGGTGAGGTAGAAGTTTTAAGCGATGAAAATTGTGCTT
Found at i:1476453 original size:21 final size:21
Alignment explanation
Indices: 1476424--1476478 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
1476414 ATTCATCTGT
1476424 CATCGTTCAAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
*
1476445 CATCATTCAAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
*
1476466 CACCGTTCAAGAG
1 CATCGTTCAAGAG
1476479 CCCGATTCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.24, C:0.40, G:0.18, T:0.18
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Found at i:1478050 original size:20 final size:20
Alignment explanation
Indices: 1478027--1478082 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
1478017 TTTCACGTGT
* *
1478027 CGAATTCGTTTTTCGTGTTG
1 CGAATTCGATTTTCGCGTTG
*
1478047 CGAATTTGATTTTCGCGTTG
1 CGAATTCGATTTTCGCGTTG
* *
1478067 CGAATTTGACTTTCGC
1 CGAATTCGATTTTCGC
1478083 AACAATCGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.14, C:0.18, G:0.23, T:0.45
Consensus pattern (20 bp):
CGAATTCGATTTTCGCGTTG
Found at i:1480836 original size:12 final size:12
Alignment explanation
Indices: 1480815--1480848 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1480805 GGTTGTGGGT
*
1480815 TTTGAGATTGTG
1 TTTGATATTGTG
1480827 TTTGATATTGTG
1 TTTGATATTGTG
*
1480839 TTTGGTATTG
1 TTTGATATTG
1480849 AAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:1481461 original size:16 final size:15
Alignment explanation
Indices: 1481439--1481477 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1481429 GAAATCATTG
1481439 AAAAATTATATAGAAA
1 AAAAATTATATA-AAA
* *
1481455 TAAAATTATGTAAAA
1 AAAAATTATATAAAA
1481470 AAAAATTA
1 AAAAATTA
1481478 GAGATTGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:1481637 original size:20 final size:20
Alignment explanation
Indices: 1481612--1481676 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
1481602 AAATAAAAGT
1481612 TGTTGCGAAATTAAAATTCG
1 TGTTGCGAAATTAAAATTCG
1481632 TGTTGC-AAATTCGAAAA-TCG
1 TGTTGCGAAATT--AAAATTCG
* **
1481652 AGTTGCGAAAACAAAATTCG
1 TGTTGCGAAATTAAAATTCG
1481672 TGTTG
1 TGTTG
1481677 TGCATTAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 9 0.24
20 21 0.57
21 7 0.19
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (20 bp):
TGTTGCGAAATTAAAATTCG
Found at i:1481688 original size:40 final size:40
Alignment explanation
Indices: 1481613--1481702 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
1481603 AATAAAAGTT
** *
1481613 GTTGCGAAATTAAAATTCGTGTTGCAAATTCGAAAATCGA
1 GTTGCGAAAACAAAATTCGTGTTGCAAATTAGAAAATCGA
*** **
1481653 GTTGCGAAAACAAAATTCGTGTTGTGCATTAGAAAATCTT
1 GTTGCGAAAACAAAATTCGTGTTGCAAATTAGAAAATCGA
1481693 GTTGCGAAAA
1 GTTGCGAAAA
1481703 GGAAACTTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (40 bp):
GTTGCGAAAACAAAATTCGTGTTGCAAATTAGAAAATCGA
Found at i:1481707 original size:20 final size:20
Alignment explanation
Indices: 1481683--1481740 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1481673 GTTGTGCATT
1481683 AGAAAATCT-TGTTGCGAAAA
1 AGAAAAT-TGTGTTGCGAAAA
* *
1481703 GGAAACTTGTGTTGCGAAAA
1 AGAAAATTGTGTTGCGAAAA
* *
1481723 AGAAATTTGCGTTGCGAA
1 AGAAAATTGTGTTGCGAA
1481741 TTCAGAAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 1 0.03
20 31 0.97
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.26
Consensus pattern (20 bp):
AGAAAATTGTGTTGCGAAAA
Found at i:1481790 original size:41 final size:40
Alignment explanation
Indices: 1481724--1481808 Score: 107
Period size: 41 Copynumber: 2.1 Consensus size: 40
1481714 TTGCGAAAAA
*
1481724 GAAATTTGCGTTGCGAATTCAGAAATCGAGTTGCGAATTT
1 GAAATTTGCGTTGCGAATTCAGAAATCGAGTTGCAAATTT
* ** * *
1481764 GAAATTTTGTGTTGCGAATTTGGAAATTGCGTTGCAAATTT
1 GAAA-TTTGCGTTGCGAATTCAGAAATCGAGTTGCAAATTT
1481805 GAAA
1 GAAA
1481809 ATCGCGTTAC
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
40 4 0.11
41 34 0.89
ACGTcount: A:0.31, C:0.09, G:0.25, T:0.35
Consensus pattern (40 bp):
GAAATTTGCGTTGCGAATTCAGAAATCGAGTTGCAAATTT
Found at i:1481803 original size:20 final size:20
Alignment explanation
Indices: 1481724--1481903 Score: 93
Period size: 20 Copynumber: 8.8 Consensus size: 20
1481714 TTGCGAAAAA
**
1481724 GAAATTTGCGTTGCGAATTCA
1 GAAA-TTGCGTTGCGAATTTG
* *
1481745 GAAATCGAGTTGCGAATTT-
1 GAAATTGCGTTGCGAATTTG
*
1481764 GAAATTTTGTGTTGCGAATTTG
1 GAAA--TTGCGTTGCGAATTTG
*
1481786 GAAATTGCGTTGCAAATTTG
1 GAAATTGCGTTGCGAATTTG
* * * **
1481806 AAAATCGCGTTACGAGA--AA
1 GAAATTGCGTTGCGA-ATTTG
1481825 GAAATTCGCGTTGCG-A-TTG
1 GAAATT-GCGTTGCGAATTTG
* *
1481844 CAGAAACTGAGTTGCGAATTTTG
1 --GAAATTGCGTTGCGAA-TTTG
* *
1481867 GAAATTGTGTTGCGAAATTG
1 GAAATTGCGTTGCGAATTTG
*
1481887 G-AGTTCGCGTTGCGAAT
1 GAAATT-GCGTTGCGAAT
1481904 ATTTTGGTTA
Statistics
Matches: 121, Mismatches: 26, Indels: 25
0.70 0.15 0.15
Matches are distributed among these distances:
18 1 0.01
19 11 0.09
20 64 0.53
21 38 0.31
22 4 0.03
23 3 0.02
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (20 bp):
GAAATTGCGTTGCGAATTTG
Found at i:1488086 original size:31 final size:31
Alignment explanation
Indices: 1488048--1488203 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
1488038 CCCGAAGGAC
* * *
1488048 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
1488079 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1488110 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1488141 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1488172 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1488203 C
1 C
1488204 CCTCGACCCT
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 118 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1491636 original size:38 final size:37
Alignment explanation
Indices: 1491591--1491663 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 37
1491581 AACCCGAACC
1491591 CGACCCGACCCGAATACCACACTCAAAAAAACCCGATT
1 CGACCCGACCCGAATACCACACT-AAAAAAACCCGATT
* *
1491629 CGACCCGACCCGAATATCACACTTAAAAAACCCGA
1 CGACCCGACCCGAATACCACACTAAAAAAACCCGA
1491664 CCCGAACAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
37 11 0.33
38 22 0.67
ACGTcount: A:0.40, C:0.38, G:0.11, T:0.11
Consensus pattern (37 bp):
CGACCCGACCCGAATACCACACTAAAAAAACCCGATT
Found at i:1491706 original size:186 final size:183
Alignment explanation
Indices: 1491356--1491725 Score: 584
Period size: 186 Copynumber: 2.0 Consensus size: 183
1491346 TATAAGGTAA
* * * *
1491356 AATTATATATTTTTTTCGGGTTGGTCCGGTTTTTTTTCACCCTAAAGCCGACCCGACCCGAATAT
1 AATTATATATTATTTTCGGGTCGGTCCAGTTTTTTTTCACCCTAAAGCCGACCCGACCCGAATAC
* **
1491421 CACACTTAAAAAAACCCGACACGATTCGACCCGAATATCACACTTAAAAAAACCCGACCCGAACA
66 CACACTCAAAAAAACCCGACACGACCCGACCCGAATATCACACTTAAAAAAACCCGACCCGAACA
1491486 AAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCCGACCCG
131 AAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCCGACCCG
1491539 AATTATATA-TATTTTCGGGTCGGTCCAG-TTTTTTTCACCCTAAACCCGAACCCGACCCGACCC
1 AATTATATATTATTTTCGGGTCGGTCCAGTTTTTTTTCACCCTAAA---G---CCGACCCGACCC
**
1491602 GAATACCACACTCAAAAAAACCCGATTCGACCCGACCCGAATATCACACTT-AAAAAACCCGACC
60 GAATACCACACTCAAAAAAACCCGACACGACCCGACCCGAATATCACACTTAAAAAAACCCGACC
1491666 CGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCCGACCCG
125 CGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCCGACCCG
1491725 A
1 A
1491726 CCCGAAATAA
Statistics
Matches: 172, Mismatches: 9, Indels: 9
0.91 0.05 0.05
Matches are distributed among these distances:
181 16 0.09
182 16 0.09
183 9 0.05
184 1 0.01
186 73 0.42
187 57 0.33
ACGTcount: A:0.35, C:0.30, G:0.13, T:0.22
Consensus pattern (183 bp):
AATTATATATTATTTTCGGGTCGGTCCAGTTTTTTTTCACCCTAAAGCCGACCCGACCCGAATAC
CACACTCAAAAAAACCCGACACGACCCGACCCGAATATCACACTTAAAAAAACCCGACCCGAACA
AAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCCGACCCG
Found at i:1500279 original size:55 final size:54
Alignment explanation
Indices: 1500233--1500486 Score: 295
Period size: 55 Copynumber: 4.7 Consensus size: 54
1500223 CTTCAAATGG
*
1500233 CGGGTCTGCTCCCTATTCTTTCATGGAGTATAAGACTCGAACAATCTTCAGTAAA
1 CGGGTCTGCTCCCTATTCTTTCATGGAGTATAAGACTCGAATAATCTTCAG-AAA
* * *
1500288 CGTGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCGAATAATCTTCAGTAAA
1 CGGGTCTGCTCCCTATTCTTTCATGGAGTATAAGACTCGAATAATCTTCAG-AAA
* *
1500343 CGTGTCTGCTCCCTATTCTTTCATGGAGTATAAGACTCGAATAATCTTCAAAAAA
1 CGGGTCTGCTCCCTATTCTTTCATGGAGTATAAGACTCGAATAATCTTC-AGAAA
* * *
1500398 CGGGTCCGCTCCCTATTCCTTCA-GAGAGTATAAGACTCG----ATCTTCAATAAA
1 CGGGTCTGCTCCCTATTCTTTCATG-GAGTATAAGACTCGAATAATCTTC-AGAAA
* * * *
1500449 CGTGTCCGCTCCCTATTCCTTCA-GAGAGTATAGGACTC
1 CGGGTCTGCTCCCTATTCTTTCATG-GAGTATAAGACTC
1500487 AATCTTCAAC
Statistics
Matches: 184, Mismatches: 13, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
51 47 0.26
54 1 0.01
55 135 0.73
56 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (54 bp):
CGGGTCTGCTCCCTATTCTTTCATGGAGTATAAGACTCGAATAATCTTCAGAAA
Found at i:1500462 original size:51 final size:51
Alignment explanation
Indices: 1500240--1500654 Score: 474
Period size: 51 Copynumber: 7.9 Consensus size: 51
1500230 TGGCGGGTCT
* ** *
1500240 GCTCCCTATTCTTTCATG-GAGTATAAGACTCGAACAATCTTCAGTAAACGTGTCT
1 GCTCCCTATTCCTTCA-GAGAGTATAAGACT----CAATCTTCAACAAACGTGTCC
* * ** *
1500295 GCTCCCTATTCATTCAGGGAGTATAAGACTCGAATAATCTTCAGTAAACGTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTC----AATCTTCAACAAACGTGTCC
* * *
1500350 GCTCCCTATTCTTTCATG-GAGTATAAGACTCGAATAATCTTCAAAAAACGGGTCC
1 GCTCCCTATTCCTTCA-GAGAGTATAAGACTC----AATCTTCAACAAACGTGTCC
* *
1500405 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAATAAACGTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACAAACGTGTCC
* * *
1500456 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACAAACGTGTCC
* * *
1500507 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACAAACGTGTCC
* * *
1500558 GCTCCCTATTCCTTCAGAGAGTATATGACTCAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACAAACGTGTCC
*
1500609 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACG
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACAAACG
1500655 AGTTTGCTTC
Statistics
Matches: 334, Mismatches: 19, Indels: 18
0.90 0.05 0.05
Matches are distributed among these distances:
51 208 0.62
54 2 0.01
55 123 0.37
56 1 0.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (51 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACAAACGTGTCC
Found at i:1502026 original size:9 final size:9
Alignment explanation
Indices: 1502005--1502150 Score: 60
Period size: 8 Copynumber: 17.7 Consensus size: 9
1501995 TGAACCCTCC
1502005 TTTTATTTC-
1 TTTT-TTTCA
1502014 TTTTTTTCA
1 TTTTTTTCA
*
1502023 TTTTTCTC-
1 TTTTTTTCA
1502031 -TTTTTTCA
1 TTTTTTTCA
1502039 --TTTTTC-
1 TTTTTTTCA
1502045 TTTTTTTCA
1 TTTTTTTCA
1502054 --TTTTTC-
1 TTTTTTTCA
1502060 TTTTTTTCA
1 TTTTTTTCA
1502069 --TTTTTCA
1 TTTTTTTCA
1502076 -TTTTTTC-
1 TTTTTTTCA
*
1502083 TTCCCTTTTCCA
1 TT---TTTTTCA
1502095 -TTTTTTC-
1 TTTTTTTCA
1502102 --TTTTT-A
1 TTTTTTTCA
*
1502108 TTTTTTCCA
1 TTTTTTTCA
*
1502117 TCATTTTTC-
1 T-TTTTTTCA
1502126 TTTTTTCTCA
1 TTTTTT-TCA
*
1502136 TTTTTCTCA
1 TTTTTTTCA
1502145 TTTTTT
1 TTTTTT
1502151 CTCTTTTATT
Statistics
Matches: 106, Mismatches: 10, Indels: 42
0.67 0.06 0.27
Matches are distributed among these distances:
6 5 0.05
7 25 0.24
8 36 0.34
9 24 0.23
10 10 0.09
11 6 0.06
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:1502034 original size:15 final size:15
Alignment explanation
Indices: 1502010--1502157 Score: 103
Period size: 15 Copynumber: 9.7 Consensus size: 15
1502000 CCTCCTTTTA
*
1502010 TTTCTTTTTTTCATT
1 TTTCTCTTTTTCATT
1502025 TTTCTCTTTTTTCATT
1 TTTCTC-TTTTTCATT
*
1502041 TTTCTTTTTTTCATT
1 TTTCTCTTTTTCATT
*
1502056 TTTCTTTTTTTCATT
1 TTTCTCTTTTTCATT
1502071 TTTCAT-TTTTTC---
1 TTTC-TCTTTTTCATT
* *
1502083 -TTCCCTTTTCCATT
1 TTTCTCTTTTTCATT
1502097 TTT-TCTTTTT-ATTT
1 TTTCTCTTTTTCA-TT
*
1502111 TTTCCATCATTTTTCTTT
1 TTT-C-TC-TTTTTCATT
1502129 TTTCTCATTTTTCTCATTT
1 TTTCTC--TTTT-TCA-TT
1502148 TTTCTCTTTT
1 TTTCTCTTTT
1502158 ATTTCTTCTT
Statistics
Matches: 108, Mismatches: 9, Indels: 30
0.73 0.06 0.20
Matches are distributed among these distances:
11 8 0.07
13 1 0.01
14 10 0.09
15 41 0.38
16 17 0.16
17 11 0.10
18 12 0.11
19 8 0.07
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTCTCTTTTTCATT
Found at i:1502036 original size:16 final size:15
Alignment explanation
Indices: 1502010--1502142 Score: 142
Period size: 15 Copynumber: 8.3 Consensus size: 15
1502000 CCTCCTTTTA
1502010 TTTCTTTTTTTCATT
1 TTTCTTTTTTTCATT
1502025 TTTCTCTTTTTTCATT
1 TTTCT-TTTTTTCATT
1502041 TTTCTTTTTTTCATT
1 TTTCTTTTTTTCATT
1502056 TTTCTTTTTTTCATT
1 TTTCTTTTTTTCATT
*
1502071 TTTCATTTTTTCTTCCCTT
1 TTTC--TTTTT-TT-CATT
* *
1502090 TTCCATTTTTTC-TT
1 TTTCTTTTTTTCATT
*
1502104 TTTATTTTTTCCATCATT
1 TTTCTTTTTT---TCATT
1502122 TTTCTTTTTTCTCATT
1 TTTCTTTTTT-TCATT
1502138 TTTCT
1 TTTCT
1502143 CATTTTTTCT
Statistics
Matches: 101, Mismatches: 8, Indels: 17
0.80 0.06 0.13
Matches are distributed among these distances:
14 9 0.09
15 35 0.35
16 27 0.27
17 11 0.11
18 13 0.13
19 6 0.06
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTCTTTTTTTCATT
Found at i:1502072 original size:6 final size:7
Alignment explanation
Indices: 1502016--1502080 Score: 67
Period size: 7 Copynumber: 8.7 Consensus size: 7
1502006 TTTATTTCTT
1502016 TTTTTCA
1 TTTTTCA
*
1502023 TTTTTCTCT
1 -TTTT-TCA
1502032 TTTTTCA
1 TTTTTCA
*
1502039 TTTTTCTT
1 TTTTTC-A
1502047 TTTTTCA
1 TTTTTCA
*
1502054 TTTTTCTT
1 TTTTTC-A
1502062 TTTTTCA
1 TTTTTCA
1502069 TTTTTCA
1 TTTTTCA
1502076 TTTTT
1 TTTTT
1502081 TCTTCCCTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
7 26 0.54
8 20 0.42
9 2 0.04
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTTCA
Found at i:1502139 original size:10 final size:10
Alignment explanation
Indices: 1502126--1502163 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
1502116 ATCATTTTTC
1502126 TTTTTTCTCA
1 TTTTTTCTCA
1502136 -TTTTTCTCA
1 TTTTTTCTCA
*
1502145 TTTTTTCTCT
1 TTTTTTCTCA
1502155 TTTATTTCT
1 TTT-TTTCT
1502164 TCTTCAAGCG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
9 9 0.36
10 11 0.44
11 5 0.20
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTTTCTCA
Found at i:1502157 original size:9 final size:9
Alignment explanation
Indices: 1502120--1502157 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
1502110 TTTTCCATCA
1502120 TTTT-TCTT
1 TTTTCTCTT
*
1502128 TTTTCTCAT
1 TTTTCTCTT
1502137 TTTTCTCATT
1 TTTTCTC-TT
1502147 TTTTCTCTT
1 TTTTCTCTT
1502156 TT
1 TT
1502158 ATTTCTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
8 4 0.15
9 14 0.54
10 8 0.31
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTCTCTT
Found at i:1517215 original size:3 final size:3
Alignment explanation
Indices: 1517207--1517231 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1517197 CTGTTGTGTT
1517207 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
1517232 CCTTTTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1519103 original size:2 final size:2
Alignment explanation
Indices: 1519096--1519154 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1519086 ATCTTATAAT
1519096 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1519138 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
1519155 TGTGTGTGTG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1523144 original size:27 final size:27
Alignment explanation
Indices: 1523109--1523163 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
1523099 GTATGGAAAG
*
1523109 ATTGTTAAACCCTTAACTACTATGCTT
1 ATTGCTAAACCCTTAACTACTATGCTT
1523136 ATTGCTAAACCCTTAACTACTATGCTT
1 ATTGCTAAACCCTTAACTACTATGCTT
1523163 A
1 A
1523164 AAAAATATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (27 bp):
ATTGCTAAACCCTTAACTACTATGCTT
Found at i:1526501 original size:50 final size:51
Alignment explanation
Indices: 1526429--1526526 Score: 171
Period size: 50 Copynumber: 1.9 Consensus size: 51
1526419 CATTTGTTCG
*
1526429 AATCCGAAATCTTTAAGTAGAAAAACACTTT-TTTTATTATTAAGATTTGA
1 AATCCGAAATCTTTAAGGAGAAAAACACTTTGTTTTATTATTAAGATTTGA
*
1526479 AATCCGAAATCTTTAAGGAGAAAAATACTTTGTTTTATTATTAAGATT
1 AATCCGAAATCTTTAAGGAGAAAAACACTTTGTTTTATTATTAAGATT
1526527 GTACGATGGG
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
50 29 0.64
51 16 0.36
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (51 bp):
AATCCGAAATCTTTAAGGAGAAAAACACTTTGTTTTATTATTAAGATTTGA
Found at i:1528002 original size:3 final size:3
Alignment explanation
Indices: 1527996--1528037 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1527986 GGAAAGTGAA
1527996 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1528038 ATATTGGCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:1530510 original size:21 final size:21
Alignment explanation
Indices: 1530486--1530526 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1530476 ACATCATTTC
1530486 GTACTTTTTCAAATATCCATT
1 GTACTTTTTCAAATATCCATT
1530507 GTACTTTTTCAAATATCCAT
1 GTACTTTTTCAAATATCCAT
1530527 GGTCGACACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.46
Consensus pattern (21 bp):
GTACTTTTTCAAATATCCATT
Found at i:1535405 original size:19 final size:19
Alignment explanation
Indices: 1535381--1535432 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
1535371 AATGCATTTG
1535381 ATGCATCGATGCACCAACC
1 ATGCATCGATGCACCAACC
* *
1535400 ATGCATCGATGTACCAGCC
1 ATGCATCGATGCACCAACC
1535419 ATGCATCGATGCAC
1 ATGCATCGATGCAC
1535433 TCTTGCTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.29, C:0.33, G:0.19, T:0.19
Consensus pattern (19 bp):
ATGCATCGATGCACCAACC
Found at i:1535421 original size:84 final size:83
Alignment explanation
Indices: 1535315--1535477 Score: 213
Period size: 84 Copynumber: 2.0 Consensus size: 83
1535305 AAATGCATTT
* *
1535315 CATGCATCGATGCACATACCATGCATCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATT
1 CATGCATCGATGCACATACCATGCATCGATGCACTCAGGATATTT-TG-AAACATCGAATGCACT
1535379 TGATGCATCGATGCACCAAC
64 TGATGCATCGATGCACCAAC
* * ** * *
1535399 CATGCATCGATGTACCA-GCCATGCATCGATGCACTCTTGCTATTTTGAAGCATCGAATGCACTT
1 CATGCATCGATGCA-CATACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCACTT
1535463 GATGCATCGATGCAC
65 GATGCATCGATGCAC
1535478 TCTTAGTGCA
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
83 30 0.43
84 34 0.49
85 5 0.07
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (83 bp):
CATGCATCGATGCACATACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCACTTG
ATGCATCGATGCACCAAC
Found at i:1535469 original size:18 final size:17
Alignment explanation
Indices: 1535443--1535478 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1535433 TCTTGCTATT
1535443 TTGAAGCATCGAATGCAC
1 TTGAAGCATCG-ATGCAC
*
1535461 TTGATGCATCGATGCAC
1 TTGAAGCATCGATGCAC
1535478 T
1 T
1535479 CTTAGTGCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (17 bp):
TTGAAGCATCGATGCAC
Found at i:1542050 original size:23 final size:23
Alignment explanation
Indices: 1541986--1542066 Score: 96
Period size: 23 Copynumber: 3.7 Consensus size: 23
1541976 ACACCTAACA
* *
1541986 GTGCAGCGATGCA-TCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
* *
1542008 GTGCATCGAT--ACACCATGAAG
1 GTGCATCGATGCACACCTTGAAT
*
1542029 GTGCACCGATGCACACCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
1542052 GTGCATCGATGCACA
1 GTGCATCGATGCACA
1542067 AGGTCATACA
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
20 1 0.02
21 15 0.31
22 9 0.19
23 23 0.48
ACGTcount: A:0.27, C:0.26, G:0.25, T:0.22
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Found at i:1542057 original size:44 final size:42
Alignment explanation
Indices: 1541967--1542061 Score: 129
Period size: 44 Copynumber: 2.2 Consensus size: 42
1541957 TTGTGCTTAA
* *
1541967 TGCATCGATACACCTAACAGTGCAGCGATGCATCCTTGAATG
1 TGCATCGATACACCTAACAGTGCACCGATGCAACCTTGAATG
*
1542009 TGCATCGATACACCATGAA-GGTGCACCGATGCACACCTTGAATG
1 TGCATCGATACACC-T-AACAGTGCACCGATGCA-ACCTTGAATG
1542053 TGCATCGAT
1 TGCATCGAT
1542062 GCACAAGGTC
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
42 14 0.30
43 13 0.28
44 20 0.43
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.23
Consensus pattern (42 bp):
TGCATCGATACACCTAACAGTGCACCGATGCAACCTTGAATG
Found at i:1544259 original size:2 final size:2
Alignment explanation
Indices: 1544252--1544292 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1544242 CAGCTTAAGC
1544252 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1544293 TTAATCAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1544889 original size:65 final size:64
Alignment explanation
Indices: 1544820--1544945 Score: 173
Period size: 64 Copynumber: 2.0 Consensus size: 64
1544810 CGAATGCATA
* *
1544820 CCATGCATCGATGCACTAAGGAT-TTTATGAAAACATCGAATGCATTTGATGTATCGATGCACCA
1 CCATGCATCGATGCACTAAGGATATTT-TG-AAACATCGAATGCACTTGATGCATCGATGCACCA
1544884 G
64 G
* ** *
1544885 CCATGCATTGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGATGCATCGATGCAC
1 CCATGCATCGATGCACTAAGGATATTTTGAAACATCGAATGCACTTGATGCATCGATGCAC
1544946 TCTTAGTGCA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
64 30 0.56
65 21 0.39
66 3 0.06
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (64 bp):
CCATGCATCGATGCACTAAGGATATTTTGAAACATCGAATGCACTTGATGCATCGATGCACCAG
Found at i:1544945 original size:17 final size:19
Alignment explanation
Indices: 1544917--1544965 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1544907 TATTTTGAAA
1544917 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
1544935 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
1544954 CACCGATGCACT
1 CATCGATGCACT
1544966 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:1546588 original size:21 final size:21
Alignment explanation
Indices: 1546514--1546598 Score: 57
Period size: 21 Copynumber: 4.0 Consensus size: 21
1546504 ATTTATATTT
1546514 CGCAACCATTT-TAGATGCCAC
1 CGCAACCATTTCT-GATGCCAC
** * *
1546535 TACAACCATTTCAGATGGCAC
1 CGCAACCATTTCTGATGCCAC
****
1546556 CGCAGTTGTTTCTGATGCCAC
1 CGCAACCATTTCTGATGCCAC
*
1546577 CGCAATCATTTCAT-ATGCCAC
1 CGCAACCATTTC-TGATGCCAC
1546598 C
1 C
1546599 ACCGCAAGGT
Statistics
Matches: 47, Mismatches: 15, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
21 46 0.98
22 1 0.02
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.27
Consensus pattern (21 bp):
CGCAACCATTTCTGATGCCAC
Found at i:1547361 original size:21 final size:22
Alignment explanation
Indices: 1547324--1547366 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1547314 AAAGTGCTGC
1547324 AACAAAAAGAAAGAAAAGAAAA
1 AACAAAAAGAAAGAAAAGAAAA
1547346 AACAAAAA-AACA-AAAAGAAAA
1 AACAAAAAGAA-AGAAAAGAAAA
1547367 GAAAAGTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.84, C:0.07, G:0.09, T:0.00
Consensus pattern (22 bp):
AACAAAAAGAAAGAAAAGAAAA
Found at i:1547443 original size:23 final size:22
Alignment explanation
Indices: 1547401--1547448 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
1547391 GAGTGCAAAA
*
1547401 GAAATAAAAGGAAAAAAAAAGAT
1 GAAATAAAAAGAAAAAAAAAG-T
* *
1547424 GAAATAAAAAGCAAAGAAAAGT
1 GAAATAAAAAGAAAAAAAAAGT
1547446 GAA
1 GAA
1547449 GCAAGTTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.71, C:0.02, G:0.19, T:0.08
Consensus pattern (22 bp):
GAAATAAAAAGAAAAAAAAAGT
Found at i:1550867 original size:21 final size:21
Alignment explanation
Indices: 1550825--1550867 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1550815 TTTCTGGGTT
* * *
1550825 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
1550846 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
1550867 A
1 A
1550868 ACGAACCAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:1552471 original size:23 final size:23
Alignment explanation
Indices: 1552445--1552507 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
1552435 ATTATTATAT
*
1552445 GGCACTAAGGTGCAATTCTATGC
1 GGCACTACGGTGCAATTCTATGC
* * *
1552468 GGCACTCCGGTACAATTCTATGT
1 GGCACTACGGTGCAATTCTATGC
*
1552491 GGCACTTCGGTGCAATT
1 GGCACTACGGTGCAATT
1552508 ATACGAGCTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTATGC
Found at i:1556027 original size:27 final size:28
Alignment explanation
Indices: 1555986--1556041 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
1555976 ATCATGTAAG
*
1555986 TATTTATTTAATTTTAATCCTTTTAAAA
1 TATTTATTTAATTTTAATCCTTCTAAAA
* *
1556014 TATTT-TTTGATTTTAGTCCTTCTAAAA
1 TATTTATTTAATTTTAATCCTTCTAAAA
1556041 T
1 T
1556042 TATATAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.30, C:0.09, G:0.04, T:0.57
Consensus pattern (28 bp):
TATTTATTTAATTTTAATCCTTCTAAAA
Found at i:1561042 original size:20 final size:21
Alignment explanation
Indices: 1561019--1561058 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1561009 ATTTTTAAAA
1561019 TATTAAAATA-ATTTATTTAT
1 TATTAAAATACATTTATTTAT
*
1561039 TATTAAAATACATTTTTTTA
1 TATTAAAATACATTTATTTA
1561059 ATTTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTAAAATACATTTATTTAT
Found at i:1561180 original size:23 final size:23
Alignment explanation
Indices: 1561153--1561197 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1561143 AGTGTTATAT
1561153 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAAAATATTAATTAG
* *
1561176 TATATTTTAAATATATTTATTA
1 TATATTTTAAAAATATTAATTA
1561198 AAATATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAG
Found at i:1561203 original size:23 final size:23
Alignment explanation
Indices: 1561154--1561204 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1561144 GTGTTATATT
**
1561154 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* *
1561177 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
1561200 ATATT
1 ATATT
1561205 ATTAGATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:1561216 original size:19 final size:19
Alignment explanation
Indices: 1561192--1561256 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
1561182 TTAAATATAT
*
1561192 TTATTAAAATATTATTAGA
1 TTATTAAAATATTATTAAA
* *
1561211 TTATTAAATTAATATTAAA
1 TTATTAAAATATTATTAAA
* *
1561230 TATATAAATAATATTATT-CA
1 T-TATTAA-AATATTATTAAA
1561250 TTATTAA
1 TTATTAA
1561257 TTATTTAATA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
19 22 0.61
20 7 0.19
21 7 0.19
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (19 bp):
TTATTAAAATATTATTAAA
Found at i:1561226 original size:34 final size:34
Alignment explanation
Indices: 1561153--1561219 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
1561143 AGTGTTATAT
*
1561153 TATATTTTAAAAATATTAATTAGTATATTTTAAA
1 TATATTTTAAAAATATTAATTAGTATATATTAAA
*
1561187 TATATTTATTAAAATATT-ATTAG-AT-TATTAAA
1 TATATTT-TAAAAATATTAATTAGTATATATTAAA
1561219 T
1 T
1561220 TAATATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 7 0.23
33 2 0.07
34 12 0.40
35 9 0.30
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (34 bp):
TATATTTTAAAAATATTAATTAGTATATATTAAA
Found at i:1561366 original size:23 final size:23
Alignment explanation
Indices: 1561339--1561392 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
1561329 AAAATAAAAA
*
1561339 TATAATATAATAT-CTTATATTAT
1 TATAATATAAT-TGATTATATTAT
*
1561362 TATAATATAATTGATTATTTTAT
1 TATAATATAATTGATTATATTAT
1561385 TATAATAT
1 TATAATAT
1561393 TAAAGATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 1 0.04
23 27 0.96
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (23 bp):
TATAATATAATTGATTATATTAT
Found at i:1561423 original size:22 final size:22
Alignment explanation
Indices: 1561390--1561433 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1561380 TTTATTATAA
1561390 TATTAAAGATA-TAATATAATAT
1 TATTAAAGATATTAATA-AATAT
1561412 TATTAGAA-ATATTAATAAATAT
1 TATTA-AAGATATTAATAAATAT
1561434 ATTTTAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (22 bp):
TATTAAAGATATTAATAAATAT
Found at i:1561436 original size:21 final size:21
Alignment explanation
Indices: 1561389--1561445 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 21
1561379 TTTTATTATA
1561389 ATATTAAAGATA-TAATATAAT
1 ATATTAAA-ATATTAATATAAT
1561410 ATTATTAGAAATATTAATA-AAT
1 A-TATTA-AAATATTAATATAAT
*
1561432 ATATTTTAAATATT
1 ATA-TTAAAATATT
1561446 CTAATAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
21 10 0.32
22 14 0.45
23 7 0.23
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (21 bp):
ATATTAAAATATTAATATAAT
Found at i:1563198 original size:67 final size:67
Alignment explanation
Indices: 1563072--1563198 Score: 150
Period size: 67 Copynumber: 1.9 Consensus size: 67
1563062 GAATATTTCG
* * * * * *
1563072 AGTTTAAATTTTTTGAGCTCAAGTTGAGCTTCACTTTTTTTTATTTCAAGTCGAGTTAAAAATTT
1 AGTTTAAAATTTTTGAGCTCAAGTCGAACTTCACATTTTTTTATTTCAAGTCAAATTAAAAATTT
1563137 TA
66 TA
* *
1563139 AGTTTACAAATTTTTGAG-TCTAGTCGAACTTCA-ATTTTTTTATTTCAAGTTTAAATTAAA
1 AGTTTA-AAATTTTTGAGCTCAAGTCGAACTTCACATTTTTTTATTTCAAG-TCAAATTAAA
1563199 TTCGATAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
66 15 0.30
67 25 0.50
68 10 0.20
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (67 bp):
AGTTTAAAATTTTTGAGCTCAAGTCGAACTTCACATTTTTTTATTTCAAGTCAAATTAAAAATTT
TA
Found at i:1567813 original size:33 final size:33
Alignment explanation
Indices: 1567776--1567850 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 33
1567766 ACCACCACCC
*
1567776 CCTCCTCCTCCCCCATTGATGTCTGGTGCCCCA
1 CCTCCTCCTCCCCCATTAATGTCTGGTGCCCCA
* * * *
1567809 CCTCCACCACCCCCGTTAATGTCTGGTGCCCCT
1 CCTCCTCCTCCCCCATTAATGTCTGGTGCCCCA
*
1567842 CCACCTCCT
1 CCTCCTCCT
1567851 TCCCTTTCTC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.51, G:0.13, T:0.25
Consensus pattern (33 bp):
CCTCCTCCTCCCCCATTAATGTCTGGTGCCCCA
Found at i:1567882 original size:129 final size:132
Alignment explanation
Indices: 1567673--1567918 Score: 299
Period size: 129 Copynumber: 1.9 Consensus size: 132
1567663 TGAAGTCTAC
* * *
1567673 TGCCCCACCTCCACAACCCACATTGATGTCTGGTTCCCCTCCTCCAACACTTACTCCTTCGCGTG
1 TGCCCCACCTCCACAACCCACATTAATGTCTGGTGCCCCTCCACCAACACTTACTCCTTCGCGTG
* * * *
1567738 GAGTGCCACCTCCT-C-CC-CCGCATCGAGCACCACCACCCCCTCCTCCTCCCCCATTGATGTCT
66 GAGTGCCACCTCCTCCTCCGCCACATCAAGCACCACCACCACCACCTCCTCCCCCATTGATGTCT
1567800 GG
131 GG
* * * * *
1567802 TGCCCCACCTCCACCACCCCCGTTAATGTCTGGTGCCCCTCCACC-TC-CTT-C-CCTTTCTCGT
1 TGCCCCACCTCCACAACCCACATTAATGTCTGGTGCCCCTCCACCAACACTTACTCC-TTCGCGT
1567863 GGAGTGCCACCTCCACCTCCTCCGCCACATCAAGCACCACCACCACCACCTCCTCC
65 GGAGTGCCACCT---CCTCCTCCGCCACATCAAGCACCACCACCACCACCTCCTCC
1567919 TCCACGTGGA
Statistics
Matches: 98, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
125 2 0.02
126 19 0.19
127 3 0.03
128 1 0.01
129 42 0.43
130 1 0.01
131 2 0.02
132 28 0.29
ACGTcount: A:0.15, C:0.50, G:0.13, T:0.22
Consensus pattern (132 bp):
TGCCCCACCTCCACAACCCACATTAATGTCTGGTGCCCCTCCACCAACACTTACTCCTTCGCGTG
GAGTGCCACCTCCTCCTCCGCCACATCAAGCACCACCACCACCACCTCCTCCCCCATTGATGTCT
GG
Found at i:1567906 original size:33 final size:33
Alignment explanation
Indices: 1567869--1567948 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
1567859 TCGTGGAGTG
1567869 CCACCTCCACCTCCTCCGCCACATCAAGCACCA
1 CCACCTCCACCTCCTCCGCCACATCAAGCACCA
* * * **
1567902 CCACCACCACCTCCTCCTCCACGTGGAGCACCA
1 CCACCTCCACCTCCTCCGCCACATCAAGCACCA
*
1567935 CCCCCTCCACCTCC
1 CCACCTCCACCTCC
1567949 ACCTTCCCAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.20, C:0.60, G:0.07, T:0.12
Consensus pattern (33 bp):
CCACCTCCACCTCCTCCGCCACATCAAGCACCA
Found at i:1568013 original size:33 final size:33
Alignment explanation
Indices: 1567976--1568123 Score: 224
Period size: 33 Copynumber: 4.5 Consensus size: 33
1567966 TGGCACCACT
* * *
1567976 CCCACCTCCTGTGCGAGGAGCGCCTGCACCACC
1 CCCACCTCCTATGCGTGGAGCGCCTGCACCGCC
* * **
1568009 CCCACCTCCCATGCGTGGAGTGCCAACACCGCC
1 CCCACCTCCTATGCGTGGAGCGCCTGCACCGCC
*
1568042 TCCACCTCCTATGCGTGGAGCGCCTGCACCGCC
1 CCCACCTCCTATGCGTGGAGCGCCTGCACCGCC
1568075 CCCACCTCCTATGCGTGGAGCGCCTGCACCGCC
1 CCCACCTCCTATGCGTGGAGCGCCTGCACCGCC
1568108 CCCACCTCCTATGCGT
1 CCCACCTCCTATGCGT
1568124 AGTGCTCCTC
Statistics
Matches: 102, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 102 1.00
ACGTcount: A:0.14, C:0.48, G:0.22, T:0.16
Consensus pattern (33 bp):
CCCACCTCCTATGCGTGGAGCGCCTGCACCGCC
Found at i:1568026 original size:99 final size:98
Alignment explanation
Indices: 1567933--1568123 Score: 215
Period size: 99 Copynumber: 1.9 Consensus size: 98
1567923 CGTGGAGCAC
* * *
1567933 CACCCCCTCCACCTCC-ACCTTCCCATGGATC-ACTGGCACCACTCCCACCTCCTGTGCGAGGAG
1 CACCCCCTCCACCTCCTA---T-CCATGGAGCGACT-GCACCACCCCCACCTCCTATGCGAGGAG
1567996 CGCCTGCACCACCCCCACCTCCCATGCGTGGAGTGCCAA
61 CGCCTGCACCACCCCCACCTCCCATGCGTGGAG-GCCAA
* * * * * *
1568035 CACCGCCTCCACCTCCTATGCGTGGAGCGCCTGCACCGCCCCCACCTCCTATGCGTGGAGCGCCT
1 CACCCCCTCCACCTCCTATCCATGGAGCGACTGCACCACCCCCACCTCCTATGCGAGGAGCGCCT
* *
1568100 GCACCGCCCCCACCTCCTATGCGT
66 GCACCACCCCCACCTCCCATGCGT
1568124 AGTGCTCCTC
Statistics
Matches: 76, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
99 57 0.75
100 3 0.04
102 15 0.20
103 1 0.01
ACGTcount: A:0.15, C:0.49, G:0.19, T:0.16
Consensus pattern (98 bp):
CACCCCCTCCACCTCCTATCCATGGAGCGACTGCACCACCCCCACCTCCTATGCGAGGAGCGCCT
GCACCACCCCCACCTCCCATGCGTGGAGGCCAA
Found at i:1569228 original size:54 final size:54
Alignment explanation
Indices: 1569165--1569270 Score: 149
Period size: 54 Copynumber: 2.0 Consensus size: 54
1569155 CCCATAAATC
* * * *
1569165 CCATTCTGAGATCCAAGCTCTAGCCACTAGGAGGTCCTGTTGGGACTAGGTATA
1 CCATTCTGAGATCCAAGCTCTAACCACTACGAAGTCCTATTGGGACTAGGTATA
* * *
1569219 CCATTCTGAGATTCAAGCTCTAACCATTACGAAGTTCTATTGGGACTAGGTA
1 CCATTCTGAGATCCAAGCTCTAACCACTACGAAGTCCTATTGGGACTAGGTA
1569271 CATTCTCCGT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (54 bp):
CCATTCTGAGATCCAAGCTCTAACCACTACGAAGTCCTATTGGGACTAGGTATA
Found at i:1580787 original size:39 final size:39
Alignment explanation
Indices: 1580719--1580831 Score: 140
Period size: 39 Copynumber: 2.9 Consensus size: 39
1580709 AATTTCCAAT
* * *
1580719 AAAATAAATTTATCAATTTGTTTTCTTTTACAAACA-AGG
1 AAAATAAA-TTAACGATTTATTTTCTTTTACAAACATAGG
*
1580758 AAAATAAATCTAACGATTTATTTTATTTTACAAA-ATAGG
1 AAAATAAAT-TAACGATTTATTTTCTTTTACAAACATAGG
*
1580797 AAAATAAATTCAACGATTTATTTCCTTTTACAAAC
1 AAAATAAATT-AACGATTTATTTTCTTTTACAAAC
1580832 CAGAATCATA
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
38 3 0.05
39 61 0.95
ACGTcount: A:0.43, C:0.12, G:0.06, T:0.39
Consensus pattern (39 bp):
AAAATAAATTAACGATTTATTTTCTTTTACAAACATAGG
Found at i:1580977 original size:74 final size:76
Alignment explanation
Indices: 1580855--1580999 Score: 222
Period size: 74 Copynumber: 1.9 Consensus size: 76
1580845 GATTCTTAGT
* * *
1580855 AAATAAATTCAATGATTTATTTTCTTTTACAAAATAGGAAAATAAATTCAACAATTTATTTT-TT
1 AAATAAATTCAATGATTTATTTCCTTTTACAAAACAAGAAAATAAATTCAACAATTTATTTTATT
1580919 ATAAAATAGGA
66 ATAAAATAGGA
* *
1580930 AAATAAGTTCAATGA-TTATTTCCTTTTACAAAACAAGAAAATAAATTCAACGATTTATTTTATT
1 AAATAAATTCAATGATTTATTTCCTTTTACAAAACAAGAAAATAAATTCAACAATTTATTTTATT
*
1580994 TTAAAA
66 ATAAAA
1581000 AACAAAATCA
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
74 42 0.67
75 21 0.33
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.39
Consensus pattern (76 bp):
AAATAAATTCAATGATTTATTTCCTTTTACAAAACAAGAAAATAAATTCAACAATTTATTTTATT
ATAAAATAGGA
Found at i:1581002 original size:39 final size:39
Alignment explanation
Indices: 1580855--1581128 Score: 177
Period size: 39 Copynumber: 6.8 Consensus size: 39
1580845 GATTCTTAGT
* * *
1580855 AAATAAATTCAATGATTTATTTTCTTTTACAAAATAGGA
1 AAATAAATTCAACGATTTATTTTCTTTTACAAAACAAGA
* * * *
1580894 AAATAAATTCAACAATTTA--TT-TTTTATAAAATAGGA
1 AAATAAATTCAACGATTTATTTTCTTTTACAAAACAAGA
* * *
1580930 AAATAAGTTCAATGA-TTATTTCCTTTTACAAAACAAGA
1 AAATAAATTCAACGATTTATTTTCTTTTACAAAACAAGA
* *
1580968 AAATAAATTCAACGATTTATTTTATTTTAAAAAACAA-A
1 AAATAAATTCAACGATTTATTTTCTTTTACAAAACAAGA
* * * *
1581006 ATCATATAAGATTCTTAGGAAACTAAATTCAATGATTT-TTTTACTAAA-TAGA
1 A--A-ATAA-ATTC------AAC--GATT-TAT--TTTCTTTTACAAAACAAGA
* *
1581058 AAA-AAATCCAACGATTTATTTCCTTTTACAAAACAAGA
1 AAATAAATTCAACGATTTATTTTCTTTTACAAAACAAGA
* *
1581096 CAATAAATTCAACGATTTATTTCCTTTTACAAA
1 AAATAAATTCAACGATTTATTTTCTTTTACAAA
1581129 CTTGAATCAT
Statistics
Matches: 184, Mismatches: 28, Indels: 46
0.71 0.11 0.18
Matches are distributed among these distances:
35 3 0.02
36 28 0.15
37 12 0.07
38 34 0.18
39 66 0.36
40 1 0.01
41 7 0.04
42 4 0.02
47 3 0.02
48 5 0.03
49 1 0.01
50 4 0.02
51 3 0.02
52 10 0.05
53 3 0.02
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (39 bp):
AAATAAATTCAACGATTTATTTTCTTTTACAAAACAAGA
Found at i:1581327 original size:57 final size:57
Alignment explanation
Indices: 1581247--1581461 Score: 252
Period size: 58 Copynumber: 3.7 Consensus size: 57
1581237 AAATCCAATT
* * *
1581247 ATTTATTTTTCTTA-TAAGTTTAGAATCATTCAAGATTCTAAGGAAATAAATTAAACA
1 ATTTATTTTCCTTACAAAG-TTAGAATCATTCAAGATTCTAAGGAAATAAATTCAACA
* * *
1581304 ATTTATTTTCCTTACAAAATTAGAATCATCCAAGATTCTTAAGGAAATAAATTCAACT
1 ATTTATTTTCCTTACAAAGTTAGAATCATTCAAGATTC-TAAGGAAATAAATTCAACA
* * * *
1581362 ATTTATTTTCCTTACAAAGTTAGAATCATTTAAGATTTTCAAGGAAATTAATTCAACG
1 ATTTATTTTCCTTACAAAGTTAGAATCATTCAAGATTCT-AAGGAAATAAATTCAACA
* * * * *
1581420 ATTTATTTTTCTTACGAAGTTATAATCAACTCAAAATTCTAA
1 ATTTATTTTCCTTACAAAGTTAGAATC-ATTCAAGATTCTAA
1581462 CAATGAAATA
Statistics
Matches: 135, Mismatches: 19, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
57 32 0.24
58 95 0.70
59 8 0.06
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.40
Consensus pattern (57 bp):
ATTTATTTTCCTTACAAAGTTAGAATCATTCAAGATTCTAAGGAAATAAATTCAACA
Found at i:1581771 original size:45 final size:45
Alignment explanation
Indices: 1581614--1581772 Score: 135
Period size: 46 Copynumber: 3.5 Consensus size: 45
1581604 GAATTAATAC
* * * *
1581614 TTTAATTTTAGCAACTCAATAATAAAAAATGAA-TCAATCCTTTGA-T
1 TTTAATTTTGGCAAC-CAATAAT-CAAAAGGAACT-AATCATTTGATT
*** * * * *
1581660 TTTAATTTCCACAACCAAGTAATCAAAAGTAACTATTCCTTTTATT
1 TTTAATTTTGGCAACCAA-TAATCAAAAGGAACTAATCATTTGATT
1581706 TTTAATTTTGGCAACCCAATAATCAAAAGGAACTAATCATTTGA-T
1 TTTAATTTTGGCAA-CCAATAATCAAAAGGAACTAATCATTTGATT
*
1581751 TTTATTTTTGGCAACACAATAA
1 TTTAATTTTGGCAAC-CAATAA
1581773 AAAAGAATTA
Statistics
Matches: 92, Mismatches: 16, Indels: 11
0.77 0.13 0.09
Matches are distributed among these distances:
44 1 0.01
45 37 0.40
46 50 0.54
47 4 0.04
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.37
Consensus pattern (45 bp):
TTTAATTTTGGCAACCAATAATCAAAAGGAACTAATCATTTGATT
Found at i:1583464 original size:34 final size:34
Alignment explanation
Indices: 1583426--1583531 Score: 130
Period size: 34 Copynumber: 3.2 Consensus size: 34
1583416 GAAAAATCAC
1583426 ATAAATCAATTCAATCTGATTTTTTTAATCCACA
1 ATAAATCAATTCAATCTGATTTTTTTAATCCACA
* * * *
1583460 ATAAATAAATACTAT-T-ATTTTTAATAAAT-CAC-
1 ATAAATCAATTCAATCTGATTTTT--TTAATCCACA
1583492 ATAAATCAATTCAATCTGATTTTTTTAATCCACA
1 ATAAATCAATTCAATCTGATTTTTTTAATCCACA
1583526 ATAAAT
1 ATAAAT
1583532 AAATACTATT
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
32 22 0.38
33 8 0.14
34 28 0.48
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41
Consensus pattern (34 bp):
ATAAATCAATTCAATCTGATTTTTTTAATCCACA
Found at i:1583481 original size:32 final size:32
Alignment explanation
Indices: 1583444--1583547 Score: 122
Period size: 32 Copynumber: 3.2 Consensus size: 32
1583434 ATTCAATCTG
1583444 ATTTTTTTAATCCACAATAAATAAATACTATT
1 ATTTTTTTAATCCACAATAAATAAATACTATT
* * * *
1583476 ATTTTTAATAAAT-CAC-ATAAATCAATTCAATCT
1 ATTTTT--TTAATCCACAATAAATAAATACTAT-T
1583509 GATTTTTTTAATCCACAATAAATAAATACTATT
1 -ATTTTTTTAATCCACAATAAATAAATACTATT
1583542 ATTTTT
1 ATTTTT
1583548 AATACATAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
32 28 0.48
33 8 0.14
34 22 0.38
ACGTcount: A:0.42, C:0.12, G:0.01, T:0.44
Consensus pattern (32 bp):
ATTTTTTTAATCCACAATAAATAAATACTATT
Found at i:1583491 original size:66 final size:66
Alignment explanation
Indices: 1583419--1583551 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
1583409 GATTGATGAA
1583419 AAATCACATAAATCAATTCAATCTGATTTTTTTAATCCACAATAAATAAATACTATTATTTTTAA
1 AAATCACATAAATCAATTCAATCTGATTTTTTTAATCCACAATAAATAAATACTATTATTTTTAA
1583484 T
66 T
1583485 AAATCACATAAATCAATTCAATCTGATTTTTTTAATCCACAATAAATAAATACTATTATTTTTAA
1 AAATCACATAAATCAATTCAATCTGATTTTTTTAATCCACAATAAATAAATACTATTATTTTTAA
1583550 T
66 T
1583551 A
1 A
1583552 CATAAATGTT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.44, C:0.14, G:0.02, T:0.41
Consensus pattern (66 bp):
AAATCACATAAATCAATTCAATCTGATTTTTTTAATCCACAATAAATAAATACTATTATTTTTAA
T
Found at i:1584488 original size:59 final size:59
Alignment explanation
Indices: 1584367--1584493 Score: 129
Period size: 59 Copynumber: 2.1 Consensus size: 59
1584357 TTGGGTGACA
* *
1584367 ATTTTGTAACTTTTGATAATGTAGAAACTCAACAAAGCAACGTCGTATAGTCAGAGATC
1 ATTTTGTAACTTTTGATAATGTAGAAACTCAACAAAGCAACGTCGTATAATCAGAGACC
* *
1584426 ATTTTGTAACTTTT-AGT-A-GTCAGAAGACTCAACAAAGTAATGTC-TAATAATC-GAGGACC
1 ATTTTGTAACTTTTGA-TAATGT-AGAA-ACTCAACAAAGCAACGTCGT-ATAATCAGA-GACC
1584485 ATTTGTGTA
1 ATTT-TGTA
1584494 CTTCACCCTA
Statistics
Matches: 58, Mismatches: 4, Indels: 11
0.79 0.05 0.15
Matches are distributed among these distances:
57 2 0.03
58 9 0.16
59 43 0.74
60 4 0.07
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.32
Consensus pattern (59 bp):
ATTTTGTAACTTTTGATAATGTAGAAACTCAACAAAGCAACGTCGTATAATCAGAGACC
Found at i:1584941 original size:77 final size:73
Alignment explanation
Indices: 1584842--1584991 Score: 210
Period size: 77 Copynumber: 2.0 Consensus size: 73
1584832 CAAAGCATGT
**
1584842 GCAATAATGTTATTGTAAATAATGGATATTTGGAAATATACAAAACAACAACAAAAATTCAATAA
1 GCAATAATGGCATTGTAAATAATGGATATTTGGAAATAT--AAAA-AA-AACAAAAATTCAATAA
1584907 TTAATTTAGCAA
62 TTAATTTAGCAA
* * * *
1584919 GCAATAATGGCATTTTAGATAATGGATATTTGGAAATATAAAAAAAGCAATAATTCAATAATTAA
1 GCAATAATGGCATTGTAAATAATGGATATTTGGAAATATAAAAAAAACAAAAATTCAATAATTAA
1584984 TTTAGCAA
66 TTTAGCAA
1584992 AAAAAAAATA
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
73 26 0.39
74 2 0.03
75 4 0.06
77 35 0.52
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.31
Consensus pattern (73 bp):
GCAATAATGGCATTGTAAATAATGGATATTTGGAAATATAAAAAAAACAAAAATTCAATAATTAA
TTTAGCAA
Found at i:1585600 original size:15 final size:15
Alignment explanation
Indices: 1585582--1585625 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
1585572 TAAATTTTAT
1585582 ATTTTTAAAAAATAA
1 ATTTTTAAAAAATAA
*
1585597 ATTTTTAAAAAACAA
1 ATTTTTAAAAAATAA
* *
1585612 AATTTTCAAAAATA
1 ATTTTTAAAAAATA
1585626 CTTGAATGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (15 bp):
ATTTTTAAAAAATAA
Found at i:1589092 original size:24 final size:24
Alignment explanation
Indices: 1589065--1589163 Score: 76
Period size: 24 Copynumber: 4.2 Consensus size: 24
1589055 GATATCAAAA
*
1589065 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * * *
1589089 ATCAGAACAAAATCCAGGTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* * *
1589113 ATCAGATCAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* *
1589137 GTCAAAACAGAATTCA-ATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
1589160 ATCA
1 ATCA
1589164 GATAAAATAT
Statistics
Matches: 56, Mismatches: 17, Indels: 5
0.72 0.22 0.06
Matches are distributed among these distances:
23 11 0.20
24 43 0.77
25 2 0.04
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:1591062 original size:36 final size:36
Alignment explanation
Indices: 1591015--1591087 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
1591005 GATAAATTAT
*
1591015 AATCTACATATCCATGGTTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
1591051 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
1591087 A
1 A
1591088 TTCCAGAACT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.42
Consensus pattern (36 bp):
AATCTACATATCCATGGCTGATTCTTTTATCACTTA
Found at i:1595580 original size:36 final size:36
Alignment explanation
Indices: 1595536--1595604 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
1595526 AATTATAATC
* *
1595536 TATATATCCATGGTTGATTCTTTTATCACTTAAATA
1 TATATATCCATGGCTAATTCTTTTATCACTTAAATA
1595572 TATATATCCATGGCTAATTCTTTTATCACTTAA
1 TATATATCCATGGCTAATTCTTTTATCACTTAA
1595605 TTCCAGAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.30, C:0.16, G:0.07, T:0.46
Consensus pattern (36 bp):
TATATATCCATGGCTAATTCTTTTATCACTTAAATA
Found at i:1597899 original size:144 final size:146
Alignment explanation
Indices: 1597615--1597902 Score: 431
Period size: 146 Copynumber: 2.0 Consensus size: 146
1597605 GAAGTAATGT
* ** * ** *
1597615 TCTCCCTAGAGTTCCAGATAACAACCAAACAATGGTTAGAAACCCTCGGGGCCTGGAATTCTACA
1 TCTCCCTAAAGTGACAGACAACAACCAAACAATGGCCAGAAACCCTCAGGGCCTGGAATTCTACA
*
1597680 AAAGACTCTGAAAAAACATCACACCAAATGTCATTCATAAGCACACTGTCAAGTTTCTTAACCAA
66 AAAGACTCTGAAAAAACATCACACCAAATGTCATTCATAAGAACACTGTCAAGTTTCTTAACCAA
1597745 ATATCCCACTTCTTAC
131 ATATCCCACTTCTTAC
*
1597761 TCTCCCTAAAGTGACAGACAACAACCAAACAATGGCCAGAAACCC-CTAGGGCTTGGAATTCTAC
1 TCTCCCTAAAGTGACAGACAACAACCAAACAATGGCCAGAAACCCTC-AGGGCCTGGAATTCTAC
* *
1597825 AAGAGACTCT-AAAAAA-ATCACACCAAATGTCATTCATAAGAAC-CATGTCAAGTTTCTTAGCC
65 AAAAGACTCTGAAAAAACATCACACCAAATGTCATTCATAAGAACAC-TGTCAAGTTTCTTAACC
1597887 AAATATCCCACTTCTT
129 AAATATCCCACTTCTT
1597903 TCTTGTTTGA
Statistics
Matches: 129, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
143 1 0.01
144 58 0.45
145 7 0.05
146 63 0.49
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.23
Consensus pattern (146 bp):
TCTCCCTAAAGTGACAGACAACAACCAAACAATGGCCAGAAACCCTCAGGGCCTGGAATTCTACA
AAAGACTCTGAAAAAACATCACACCAAATGTCATTCATAAGAACACTGTCAAGTTTCTTAACCAA
ATATCCCACTTCTTAC
Found at i:1598518 original size:64 final size:64
Alignment explanation
Indices: 1598442--1598564 Score: 169
Period size: 64 Copynumber: 1.9 Consensus size: 64
1598432 GCATCAATCC
*
1598442 ATGCATCGATGCACCATT-GAATAAATT-GAACATCGAATGCATTTCATGCATCGATGCACTCTC
1 ATGCATCGATGCA-C-TTGGAATAAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCTC
1598505 T
64 T
** **
1598506 ATGCATCGATGCACTTGGGTTTTATTAAAACATCGAATGCATTTCATGCATCGATGCAC
1 ATGCATCGATGCACTTGGAATAAATTAAAACATCGAATGCATTTCATGCATCGATGCAC
1598565 AAGCAATGCA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
62 2 0.04
63 6 0.12
64 44 0.85
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (64 bp):
ATGCATCGATGCACTTGGAATAAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCTCT
Found at i:1598574 original size:64 final size:64
Alignment explanation
Indices: 1598470--1598627 Score: 192
Period size: 64 Copynumber: 2.5 Consensus size: 64
1598460 GAATAAATTG
*** * * * ** * *
1598470 AACATCGAATGCATTTCATGCATCGATGCACTCTCTATGCATCGATGCACT-TGGGTTTTATTAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCACCGATACACTCAAGCTATT-TTAA
*
1598534 AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCACCGATACACTCAAGCTATTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCACCGATACACTCAAGCTATTTTAA
*
1598598 AACATCGAATGCATTTTATGCATCGATGCA
1 AACATCGAATGCATTTCATGCATCGATGCA
1598628 TACTTGGTGC
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
64 77 0.95
65 4 0.05
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCACCGATACACTCAAGCTATTTTAA
Found at i:1612703 original size:16 final size:17
Alignment explanation
Indices: 1612682--1612713 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1612672 AAATAAAATG
1612682 TAAATATATGA-TTTAA
1 TAAATATATGACTTTAA
1612698 TAAATATATGACTTTA
1 TAAATATATGACTTTA
1612714 GCTTTCTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (17 bp):
TAAATATATGACTTTAA
Found at i:1627163 original size:29 final size:29
Alignment explanation
Indices: 1627127--1627197 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
1627117 GTTAAAAAAC
1627127 AACTTTTTATAGTCGGATGACCATTTTGT
1 AACTTTTTATAGTCGGATGACCATTTTGT
1627156 AACTTTTTATAGTCGGATGACCATTTTGT
1 AACTTTTTATAGTCGGATGACCATTTTGT
*
1627185 AACTTTTAATAGT
1 AACTTTTTATAGT
1627198 AATGGACTCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (29 bp):
AACTTTTTATAGTCGGATGACCATTTTGT
Found at i:1627979 original size:24 final size:24
Alignment explanation
Indices: 1627945--1627993 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1627935 TTTGACATTA
* *
1627945 AACATTTAATCACCCTACTATAGC
1 AACATTCAATCAACCTACTATAGC
*
1627969 AACATTCAATCAACCTATTATAGC
1 AACATTCAATCAACCTACTATAGC
1627993 A
1 A
1627994 GCTAGTGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.27, G:0.04, T:0.29
Consensus pattern (24 bp):
AACATTCAATCAACCTACTATAGC
Found at i:1628106 original size:2 final size:2
Alignment explanation
Indices: 1628099--1628159 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1628089 TTACTCAAAT
1628099 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1628141 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
1628160 CATTTTTGTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1630451 original size:41 final size:41
Alignment explanation
Indices: 1630365--1630510 Score: 206
Period size: 41 Copynumber: 3.6 Consensus size: 41
1630355 ACCCATTAAA
* *
1630365 ATTATACATATATGCATAGGATTCATGGATTTAAAATAAAAT
1 ATTATATATATATGCATAGGA-TCATGGGTTTAAAATAAAAT
* *
1630407 ATTATATATATATGCATAGGATCAGGGGTTTAAAATAAGAT
1 ATTATATATATATGCATAGGATCATGGGTTTAAAATAAAAT
* *
1630448 ATTATATATATATGCATAGGATCCATGAGTTTATAATAAAAT
1 ATTATATATATATGCATAGGAT-CATGGGTTTAAAATAAAAT
1630490 A-T-TATATATATGCATAGGATC
1 ATTATATATATATGCATAGGATC
1630511 CAAGTGTTTA
Statistics
Matches: 95, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
39 1 0.01
40 18 0.19
41 40 0.42
42 36 0.38
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.36
Consensus pattern (41 bp):
ATTATATATATATGCATAGGATCATGGGTTTAAAATAAAAT
Found at i:1632564 original size:19 final size:19
Alignment explanation
Indices: 1632540--1632585 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
1632530 ACTTAGACAT
1632540 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTGTTATTTTC
1632559 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTGTTATTTTC
1632578 TTTGCATT
1 TTTGCATT
1632586 CACATTAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTGTTATTTTC
Found at i:1635790 original size:84 final size:84
Alignment explanation
Indices: 1635649--1635856 Score: 285
Period size: 84 Copynumber: 2.5 Consensus size: 84
1635639 CAAACAAACT
* *
1635649 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCACAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACG
1635714 CTCAGCTCCAAGGCATATC
66 CTCAGCTCCAAGGCATATC
* * *
1635733 ATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCACAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACG
*
1635798 CTCAGCTCAACAA--CACATC
66 CTCAGCTC--CAAGGCATATC
* * * * *
1635817 ATTTACAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
1 ATTTGCAGCACAACTTAAGTCGAGAAGGGTTATCTGCCAA
1635857 AGACCCCCGA
Statistics
Matches: 109, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
84 106 0.97
86 3 0.03
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (84 bp):
ATTTGCAGCACAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCATATC
Found at i:1635903 original size:3 final size:3
Alignment explanation
Indices: 1635895--1636059 Score: 240
Period size: 3 Copynumber: 54.7 Consensus size: 3
1635885 TTTATCCATT
* * * *
1635895 TTA TTA TTA TTA TTA TTA ATA TTA ATA TTA TTA TTA TCA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* **
1635943 TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA GCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1635991 TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
*
1636037 ATA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
1636060 TAATAAATAA
Statistics
Matches: 143, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
3 141 0.99
4 2 0.01
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1648803 original size:5 final size:5
Alignment explanation
Indices: 1648793--1648870 Score: 74
Period size: 5 Copynumber: 15.6 Consensus size: 5
1648783 GCTTGAAGAA
1648793 AAAAG AAAAG AAAAAG AAAAG -AAAG AAAAG AAAAAAG AAAAG AAAA-
1 AAAAG AAAAG -AAAAG AAAAG AAAAG AAAAG --AAAAG AAAAG AAAAG
* *
1648839 AATAG AAAATG AAAA- AAAAG AAGA- AAAAG AAA
1 AAAAG AAAA-G AAAAG AAAAG AAAAG AAAAG AAA
1648871 GGGGGTCAAG
Statistics
Matches: 61, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
4 14 0.23
5 32 0.52
6 10 0.16
7 5 0.08
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:1648819 original size:9 final size:9
Alignment explanation
Indices: 1648794--1648871 Score: 65
Period size: 9 Copynumber: 8.4 Consensus size: 9
1648784 CTTGAAGAAA
1648794 AAAGAAAAG
1 AAAGAAAAG
1648803 AAAAAGAAAAG
1 --AAAGAAAAG
1648814 AAAGAAAAG
1 AAAGAAAAG
1648823 -AA-AAAAG
1 AAAGAAAAG
1648830 AAAAGAAAA-
1 -AAAGAAAAG
1648839 AATAGAAAATG
1 AA-AGAAAA-G
*
1648850 AAAAAAAAG
1 AAAGAAAAG
1648859 -AAGAAAAAG
1 AAAG-AAAAG
1648868 AAAG
1 AAAG
1648872 GGGGTCAAGG
Statistics
Matches: 57, Mismatches: 2, Indels: 17
0.75 0.03 0.22
Matches are distributed among these distances:
7 5 0.09
8 6 0.11
9 23 0.40
10 12 0.21
11 11 0.19
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:1648820 original size:27 final size:27
Alignment explanation
Indices: 1648788--1648871 Score: 86
Period size: 27 Copynumber: 3.1 Consensus size: 27
1648778 ATTATGCTTG
1648788 AAGAAAAAAGAAAAGAAAAAGAAAAGA
1 AAGAAAAAAGAAAAGAAAAAGAAAAGA
1648815 AAGAAAAGAA-AAAAG-AAAAGAAAA-A
1 AAGAAAA-AAGAAAAGAAAAAGAAAAGA
* *
1648840 ATAG-AAAATGAAAAAAAAGAAGAAAAAGA
1 A-AGAAAAAAGAAAAGAAA-AAG-AAAAGA
1648869 AAG
1 AAG
1648872 GGGGTCAAGG
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
24 1 0.02
25 9 0.19
26 13 0.27
27 15 0.31
28 8 0.17
29 2 0.04
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (27 bp):
AAGAAAAAAGAAAAGAAAAAGAAAAGA
Found at i:1648829 original size:21 final size:20
Alignment explanation
Indices: 1648794--1648870 Score: 97
Period size: 20 Copynumber: 3.9 Consensus size: 20
1648784 CTTGAAGAAA
1648794 AAAGAAAAGAAAAAGAAAAG
1 AAAGAAAAGAAAAAGAAAAG
1648814 AAAGAAAAGAAAAAAGAAAAG
1 AAAGAAAAG-AAAAAGAAAAG
*
1648835 AAA-AAATAGAAAATGAAAA-
1 AAAGAAA-AGAAAAAGAAAAG
*
1648854 AAA-AGAAGAAAAAGAAA
1 AAAGAAAAGAAAAAGAAA
1648871 GGGGGTCAAG
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
18 10 0.19
19 5 0.10
20 21 0.40
21 16 0.31
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.03
Consensus pattern (20 bp):
AAAGAAAAGAAAAAGAAAAG
Found at i:1650080 original size:82 final size:82
Alignment explanation
Indices: 1649943--1650151 Score: 400
Period size: 82 Copynumber: 2.5 Consensus size: 82
1649933 TTGGACAGAA
*
1649943 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCCGGTTTAACAGAACCAATCAGTGAAT
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAACAGAACCAATCAGTGAAT
1650008 TTAGAAGATGAATTTAT
66 TTAGAAGATGAATTTAT
1650025 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAACAGAACCAATCAGTGAAT
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAACAGAACCAATCAGTGAAT
1650090 TTAGAAGATGAATTTAT
66 TTAGAAGATGAATTTAT
1650107 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1 C-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1650152 GATCAAAACA
Statistics
Matches: 125, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
82 82 0.66
83 43 0.34
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.37
Consensus pattern (82 bp):
CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAACAGAACCAATCAGTGAAT
TTAGAAGATGAATTTAT
Found at i:1650262 original size:52 final size:52
Alignment explanation
Indices: 1650109--1650264 Score: 267
Period size: 52 Copynumber: 3.0 Consensus size: 52
1650099 GAATTTATCA
* *
1650109 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCAAAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAGAAC
* *
1650161 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAGAAC
*
1650213 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAGAAC
1650265 CAATCAGTGA
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 97 1.00
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAGAAC
Found at i:1650300 original size:135 final size:135
Alignment explanation
Indices: 1649859--1650387 Score: 582
Period size: 135 Copynumber: 3.9 Consensus size: 135
1649849 ATATCTTAGT
* * * *
1649859 CCAATCATTGAATTTAGAAGATGAATTTTCTCAATAACCTCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCAGTGAATTTAGAAGATGAA-TTTATCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
*
1649924 CTAATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCCGGTTTA
65 CTAATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTA
1649989 ACAGAA
130 ACAGAA
1649995 CCAATCAGTGAATTTAGAAGATGAATTTATC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCAGTGAATTTAGAAGATGAATTTATCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
* ** * * * * * * *
1650059 TGATCTGGTTTAACAGAACCA-ATCAGTGAATT-TAGAAGATGAATT-TATCAATAGCATCT--T
66 TAATCTGGTTGGACAGAA-CATAGCA-T--CTTCTGGAAG-TG--TTCTTTGAGT--TATCTGAT
** *
1650119 CTGG---AAGTG-T
122 CTGGTTTAACAGAA
* ** * * * ** * *
1650129 TCTTTGAGT-TATCT-G-ATCTG-GTTGATCAAAACATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 CCAATCAGTGAATTTAGAAGATGAATTTATC---A-ATAGCATCTTCTGGAAGTGTTCTTTGAGT
1650190 TATCTAATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGT
62 TATCTAATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGT
1650255 TTAACAGAA
127 TTAACAGAA
1650264 CCAATCAGTGAATTTAGAAGATGAATTTATCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCAGTGAATTTAGAAGATGAATTTATCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1650329 TAATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
66 TAATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1650388 ATTAGACAGA
Statistics
Matches: 315, Mismatches: 51, Indels: 55
0.75 0.12 0.13
Matches are distributed among these distances:
129 4 0.01
130 7 0.02
131 12 0.04
132 5 0.02
133 8 0.03
134 60 0.19
135 159 0.50
136 33 0.10
137 5 0.02
138 11 0.03
139 7 0.02
140 4 0.01
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (135 bp):
CCAATCAGTGAATTTAGAAGATGAATTTATCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
TAATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAA
CAGAA
Found at i:1650351 original size:187 final size:186
Alignment explanation
Indices: 1650025--1650441 Score: 757
Period size: 187 Copynumber: 2.2 Consensus size: 186
1650015 ATGAATTTAT
1650025 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAACAGAACCAATCAGTGAAT
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAACAGAACCAATCAGTGAAT
*
1650090 TTAGAAGATGAATTTATCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAT
66 TTAGAAGATGAATTTATCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGAT
* *
1650155 CAAAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAA
131 CAAAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGATTAGACAG-A
1650212 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAACAGAACCAATCAGTGAAT
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAACAGAACCAATCAGTGAAT
1650277 TTAGAAGATGAATTTATCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGA
66 TTAGAAGATGAATTTATCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTT-GA
* *
1650342 -CAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGA
130 TCAAAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGATTAGACAGA
1650398 -ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1650442 GGTAGGAACT
Statistics
Matches: 224, Mismatches: 5, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
185 44 0.20
186 1 0.00
187 177 0.79
188 2 0.01
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (186 bp):
CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAACAGAACCAATCAGTGAAT
TTAGAAGATGAATTTATCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGAT
CAAAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGATTAGACAGA
Found at i:1650358 original size:52 final size:50
Alignment explanation
Indices: 1650295--1650440 Score: 247
Period size: 52 Copynumber: 2.9 Consensus size: 50
1650285 TGAATTTATC
* *
1650295 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
*
1650345 AACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 -A-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
1650397 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1650441 TGGTAGGAAC
Statistics
Matches: 90, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
50 42 0.47
51 2 0.02
52 46 0.51
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.39
Consensus pattern (50 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
Found at i:1651415 original size:113 final size:113
Alignment explanation
Indices: 1651091--1651651 Score: 843
Period size: 113 Copynumber: 4.9 Consensus size: 113
1651081 GATTCAAATT
* * *
1651091 CATCACTTGATGGATCATCATTACCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
1651156 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATC
* *
1651204 CATCACTTGATGGATCAACATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAG
1 CATCATTTGATGGATCATCATTTCCAGA-GAA-AGTTCATAATGAGAAGAA--C-TCATCTGAAG
*
1651269 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
61 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATC
* *
1651322 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
1651387 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATC
* *
1651435 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *** * *
1651500 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATC
* ** *
1651548 CATCATTTGATGGATCAACATGGCCAAAGAAAGTTCATGAATGAGAAGAACTCATCTGAAGAAGG
1 CATCATTTGATGGATCATCATTTCCAGAGAAAGTTCAT-AATGAGAAGAACTCATCTGAAGAAGG
*
1651613 AAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
1651652 GTTTGATATC
Statistics
Matches: 416, Mismatches: 26, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
113 227 0.55
114 67 0.16
115 17 0.04
116 18 0.04
117 4 0.01
118 83 0.20
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (113 bp):
CATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATC
Found at i:1651956 original size:3 final size:3
Alignment explanation
Indices: 1651948--1652109 Score: 234
Period size: 3 Copynumber: 53.7 Consensus size: 3
1651938 TTTATCCATT
* * * *
1651948 TTA TTA TTA TTA TTA TTA ATA TTA ATA TTA TTA TTA TCA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* **
1651996 TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA GCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
1652044 TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTTA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
1652090 TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
1652110 TAATAAATAA
Statistics
Matches: 140, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
3 138 0.99
4 2 0.01
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1652531 original size:32 final size:32
Alignment explanation
Indices: 1652491--1652552 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 32
1652481 CCAGAGAGAC
1652491 AGAACGAGACA-CAGA-AACAAAAAAAAAAGGA
1 AGAACGAGACACCA-ACAACAAAAAAAAAAGGA
1652522 AGAACCGAGACAGCCAACAACAAAAAAAAAA
1 AGAA-CGAGACA-CCAACAACAAAAAAAAAA
1652553 CAGAGGGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
31 4 0.15
32 7 0.26
33 1 0.04
34 15 0.56
ACGTcount: A:0.66, C:0.18, G:0.16, T:0.00
Consensus pattern (32 bp):
AGAACGAGACACCAACAACAAAAAAAAAAGGA
Found at i:1654206 original size:84 final size:83
Alignment explanation
Indices: 1654061--1655149 Score: 1099
Period size: 84 Copynumber: 13.1 Consensus size: 83
1654051 GGTCACGACA
* * * * * * *
1654061 AGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTAT
1 AGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTAT
*
1654126 CTGTGACCAAAAGATCTTCG
65 CTGTGACC-AAAGACCTTCG
* * * *
1654146 AGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTGAA-TCTAGGAGGGTTGT
1 AGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTT-AAGTCTAGAAGGGTTAT
** *
1654210 CTGCCAACCAAAGACCTTTG
65 CTG-TGACCAAAGACCTTCG
* * * *
1654230 AGTTCGACTACGCTCAGCT-CAACGGCACATCATTTACAGTATAACTTAAGTCGAGAAGGGCTAT
1 AGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTAT
**
1654294 C--TG-CCAAAGACCCCCG
65 CTGTGACCAAAGACCTTCG
* * * * * * *
1654310 AGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTAT
1 AGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTAT
*
1654375 CTGTGACCAAAAGATCTTCG
65 CTGTGACC-AAAGACCTTCG
* * * * * *
1654395 AGTTCAAATACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTGAA-TCTAGGAGGGTTGT
1 AGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTT-AAGTCTAGAAGGGTTAT
** *
1654459 CTGCCAACCAAAGACCTTTG
65 CTG-TGACCAAAGACCTTCG
* * * * *
1654479 AGTTCGACTACGCTCAGCT-CAACGACACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTAT
1 AGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTAT
**
1654543 C--TG-CCAAAGACCCCCG
65 CTGTGACCAAAGACCTTCG
* * * * * * *
1654559 AGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTAT
1 AGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTAT
1654624 CTGTGACCAAAAGACCTTCG
65 CTGTGACC-AAAGACCTTCG
* * * *
1654644 AGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC
1 AGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATC
*
1654709 --TG-CCAAAGACCCTCG
66 TGTGACCAAAGACCTTCG
* * * * * * *
1654724 AGTTCGACTACGTTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTAT
1 AGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTAT
*
1654789 CTGTCACCAAAGACCTTCG
65 CTGTGACCAAAGACCTTCG
* * * *
1654808 AGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCATCACAACTTAAGTCTAGAAGGGTTGTC
1 AGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATC
** * *
1654873 TGCCAACACAAGACCTTTG
66 TGTGACCA-AAGACCTTCG
* * *
1654892 AGTTCGACTACGCTCAACT-CAACGGCACATCATTTGCAGTATAACTTAAGTCGAGAAGGGTTAT
1 AGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTAT
**
1654956 CTGCCAACCAAAGACCTTCG
65 CTG-TGACCAAAGACCTTCG
* * *
1654976 AGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATC
1 AGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATC
* *
1655041 TGTCACCAAAGACCTTGG
66 TGTGACCAAAGACCTTCG
* * * * ** *
1655059 AGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACACAACTTAAGTCGAGAAAAGCTATC
1 AGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATC
* *
1655124 TGTCAACAAAGACCTTTCG
66 TGTGACCAAAGACC-TTCG
1655143 AGTTCGA
1 AGTTCGA
1655150 GTTCGTTCAG
Statistics
Matches: 823, Mismatches: 152, Indels: 59
0.80 0.15 0.06
Matches are distributed among these distances:
80 79 0.10
81 113 0.14
82 4 0.00
83 144 0.17
84 402 0.49
85 81 0.10
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (83 bp):
AGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATC
TGTGACCAAAGACCTTCG
Found at i:1654429 original size:165 final size:164
Alignment explanation
Indices: 1654061--1655149 Score: 1059
Period size: 165 Copynumber: 6.5 Consensus size: 164
1654051 GGTCACGACA
* * * * * * *
1654061 AGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTAT
1 AGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTAT
* * *
1654126 CTGTGACCAAAAGATCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAAC
65 C--TGACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAAC
* * ** *
1654191 TTGAA-TCTAGGAGGGTTGTCTGCCAACCAAAGACCTTTG
127 TT-AAGTCTAGAAGGGTTATCTG-TGACCAAAGACCTTCG
* *
1654230 AGTTCGACTACGCTCAGCT-CAACGGCACATCATTTACAGTATAACTTAAGTCGAGAAGGGCTAT
1 AGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTAT
** * * * * * *
1654294 CTG-CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTC
65 CTGACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTT
* *
1654358 AAGGCTAGAAGGGTTATCTGTGACCAAAAGATCTTCG
129 AAGTCTAGAAGGGTTATCTGTGACC-AAAGACCTTCG
* * * * * * * *
1654395 AGTTCAAATACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTGAA-TCTAGGAGGGTTGT
1 AGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTT-AAGTCGAGAAGGGTTAT
* * * *
1654459 CTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAACGACACATCATTTGCAGTATAG
65 CTG---ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAA
* * **
1654523 CTTAAGTCGAGAAGGGCTATC--TG-CCAAAGACCCCCG
126 CTTAAGTCTAGAAGGGTTATCTGTGACCAAAGACCTTCG
* * * * * * *
1654559 AGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTAT
1 AGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTAT
* *
1654624 CTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGC
65 C--TGACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAAC
* * *
1654689 TTAAGTCGAGAAGGGCTATC--TG-CCAAAGACCCTCG
127 TTAAGTCTAGAAGGGTTATCTGTGACCAAAGACCTTCG
* * * * * * *
1654724 AGTTCGACTACGTTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTAT
1 AGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTAT
* * *
1654789 CTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCATCACAACT
65 CTG--ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
* ** * *
1654854 TAAGTCTAGAAGGGTTGTCTGCCAACACAAGACCTTTG
128 TAAGTCTAGAAGGGTTATCTGTGACCA-AAGACCTTCG
* * *
1654892 AGTTCGACTACGCTCAACT-CAACGGCACATCATTTGCAGTATAACTTAAGTCGAGAAGGGTTAT
1 AGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTAT
*
1654956 CTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAAC
65 CTG---ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAAC
* * * *
1655021 TCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTGG
127 TTAAGTCTAGAAGGGTTATCTGTGACCAAAGACCTTCG
* * * * ** *
1655059 AGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACACAACTTAAGTCGAGAAAAGCTATC
1 AGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATC
*
1655124 TGTCAACAAAGACCTTTCGAGTTCGA
66 TG--ACCAAAGACC-TTCGAGTTCGA
1655150 GTTCGTTCAG
Statistics
Matches: 771, Mismatches: 122, Indels: 56
0.81 0.13 0.06
Matches are distributed among these distances:
163 2 0.00
164 125 0.16
165 283 0.37
166 21 0.03
167 120 0.16
168 178 0.23
169 42 0.05
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (164 bp):
AGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATC
TGACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAA
GTCTAGAAGGGTTATCTGTGACCAAAGACCTTCG
Found at i:1654499 original size:249 final size:249
Alignment explanation
Indices: 1654061--1655042 Score: 1316
Period size: 249 Copynumber: 3.9 Consensus size: 249
1654051 GGTCACGACA
1654061 AGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTAT
1 AGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTAT
* *
1654126 CTGTGACCAAAAGATCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAAC
66 CTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCACAAC
* * * *
1654191 TTGAA-TCTAGGAGGGTTGTCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGG
131 TT-AAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCAACGG
* * *
1654255 CACATCATTTACAGTATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCG
195 CACATCATTTACAGCATAACTCAAGGCGAGAAGGGCTATCTGCCAAAGACCCCCG
1654310 AGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTAT
1 AGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTAT
* * * *
1654375 CTGTGACCAAAAGATCTTCGAGTTCAAATACGCTCAGCTCCAAGGCATATCATTTGCAGCACAAC
66 CTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCACAAC
* * * * *
1654440 TTGAA-TCTAGGAGGGTTGTCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGA
131 TT-AAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCAACGG
* * * * *
1654504 CACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCG
195 CACATCATTTACAGCATAACTCAAGGCGAGAAGGGCTATCTGCCAAAGACCCCCG
1654559 AGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTAT
1 AGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTAT
* * *
1654624 CTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGC
66 CTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCACAAC
* * * * *
1654689 TTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAGGG
131 TTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCAACGG
* * * **
1654750 CATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCG
195 CACATCATTTACAGCATAACTCAAGGCGAGAAGGGCTATCTG---CCAAAGACCCCCG
* * * * * * * * * * *
1654808 AGTTCGACTACGCTCAGC-TCCAAGGCATATCATTTGCATCACAACTTAAGTCTAGAAGGGTTGT
1 AGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTAT
** * * * * * *
1654872 CTGCCAACACAAGACCTTTGAGTTCGACTACGCTCAACT-CAACGGCACATCATTTGCAGTATAA
66 CTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCACAA
1654936 CTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-G
130 CTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCT-CAACG
* *
1655000 GCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG
194 GCACATCATTTACAGCATAACTCAAGGCGAGAAGGGCTATCTG
1655043 TCACCAAAGA
Statistics
Matches: 665, Mismatches: 57, Indels: 20
0.90 0.08 0.03
Matches are distributed among these distances:
245 28 0.04
246 38 0.06
247 2 0.00
248 113 0.17
249 409 0.62
251 44 0.07
252 31 0.05
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.24
Consensus pattern (249 bp):
AGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTAT
CTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCACAAC
TTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCAACGGC
ACATCATTTACAGCATAACTCAAGGCGAGAAGGGCTATCTGCCAAAGACCCCCG
Found at i:1656659 original size:42 final size:39
Alignment explanation
Indices: 1656502--1656640 Score: 190
Period size: 40 Copynumber: 3.5 Consensus size: 39
1656492 AAAATTATAC
*
1656502 ATATATGCATAGGATTCATGGATTTAAAATAAAATATTATAT
1 ATATATGCATAGGATCCATGG-TTTAAAATAAAATA-T-TAT
* *
1656544 ATATATGCATAGGAT-CAGGGGTTTAAAATAAGATATTAT
1 ATATATGCATAGGATCCA-TGGTTTAAAATAAAATATTAT
*
1656583 ATATATGCATAGGATCCATGAGTTTATAATAAAATATTAT
1 ATATATGCATAGGATCCATG-GTTTAAAATAAAATATTAT
1656623 ATATATGCATAGGATCCA
1 ATATATGCATAGGATCCA
1656641 AGTGTTTAGA
Statistics
Matches: 89, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
39 19 0.21
40 38 0.43
41 15 0.17
42 17 0.19
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.35
Consensus pattern (39 bp):
ATATATGCATAGGATCCATGGTTTAAAATAAAATATTAT
Found at i:1657941 original size:289 final size:289
Alignment explanation
Indices: 1657422--1658000 Score: 1149
Period size: 289 Copynumber: 2.0 Consensus size: 289
1657412 GGGATTCCCG
1657422 ACGAACTTCTCTCTGATTCAGCCTCGTCGGTGCCACAAGGTAACACGATCAATGGTTTATCAAAT
1 ACGAACTTCTCTCTGATTCAGCCTCGTCGGTGCCACAAGGTAACACGATCAATGGTTTATCAAAT
*
1657487 ATTGGTTTGCAAGTCACCTATCGGTTGAATATGGGCGGGCCGATGATCACTCCGAAAAACGATAC
66 ATTGGTTTGCAAGTCACCTATCAGTTGAATATGGGCGGGCCGATGATCACTCCGAAAAACGATAC
1657552 ATTGGGGAGAACATGGGCTCCGGATGTACCATACAACACGTTTCCCCAATGAACCGAGGTCGTCA
131 ATTGGGGAGAACATGGGCTCCGGATGTACCATACAACACGTTTCCCCAATGAACCGAGGTCGTCA
1657617 CGGGTAAAAACATCAAGTACCGACCGGAGAATAAGATGACTCGGTTGGTCGAGCCGAAGATGGTT
196 CGGGTAAAAACATCAAGTACCGACCGGAGAATAAGATGACTCGGTTGGTCGAGCCGAAGATGGTT
1657682 TATGAGACGGCGGATCGGATGATGTCCGA
261 TATGAGACGGCGGATCGGATGATGTCCGA
1657711 ACGAACTTCTCTCTGATTCAGCCTCGTCGGTGCCACAAGGTAACACGATCAATGGTTTATCAAAT
1 ACGAACTTCTCTCTGATTCAGCCTCGTCGGTGCCACAAGGTAACACGATCAATGGTTTATCAAAT
1657776 ATTGGTTTGCAAGTCACCTATCAGTTGAATATGGGCGGGCCGATGATCACTCCGAAAAACGATAC
66 ATTGGTTTGCAAGTCACCTATCAGTTGAATATGGGCGGGCCGATGATCACTCCGAAAAACGATAC
1657841 ATTGGGGAGAACATGGGCTCCGGATGTACCATACAACACGTTTCCCCAATGAACCGAGGTCGTCA
131 ATTGGGGAGAACATGGGCTCCGGATGTACCATACAACACGTTTCCCCAATGAACCGAGGTCGTCA
1657906 CGGGTAAAAACATCAAGTACCGACCGGAGAATAAGATGACTCGGTTGGTCGAGCCGAAGATGGTT
196 CGGGTAAAAACATCAAGTACCGACCGGAGAATAAGATGACTCGGTTGGTCGAGCCGAAGATGGTT
1657971 TATGAGACGGCGGATCGGATGATGTCCGA
261 TATGAGACGGCGGATCGGATGATGTCCGA
1658000 A
1 A
1658001 GCGTATGCTC
Statistics
Matches: 289, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
289 289 1.00
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.22
Consensus pattern (289 bp):
ACGAACTTCTCTCTGATTCAGCCTCGTCGGTGCCACAAGGTAACACGATCAATGGTTTATCAAAT
ATTGGTTTGCAAGTCACCTATCAGTTGAATATGGGCGGGCCGATGATCACTCCGAAAAACGATAC
ATTGGGGAGAACATGGGCTCCGGATGTACCATACAACACGTTTCCCCAATGAACCGAGGTCGTCA
CGGGTAAAAACATCAAGTACCGACCGGAGAATAAGATGACTCGGTTGGTCGAGCCGAAGATGGTT
TATGAGACGGCGGATCGGATGATGTCCGA
Found at i:1661032 original size:60 final size:59
Alignment explanation
Indices: 1660939--1661082 Score: 157
Period size: 60 Copynumber: 2.4 Consensus size: 59
1660929 TAGAATATTC
* * * * *
1660939 AAAAGTTTAGGGACTAATTTAGAAA-GATAGTCATAGTTT-AGGGATGAATTTATAATGCTT
1 AAAAGTTTAAGGACTAATTTA-AAATGAGAGTCATAATTTGA-GGAT-AAATTATAATACTT
*
1660999 AAAAGTTTAAGGACTAATTTAAAATGAGAGTCATAATTTGAGGATAAATTATAATATTT
1 AAAAGTTTAAGGACTAATTTAAAATGAGAGTCATAATTTGAGGATAAATTATAATACTT
* ** *
1661058 AAAAGTTCAAAAACCAATTTAAAAT
1 AAAAGTTTAAGGACTAATTTAAAAT
1661083 AAAAATTATA
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
59 35 0.49
60 36 0.50
61 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (59 bp):
AAAAGTTTAAGGACTAATTTAAAATGAGAGTCATAATTTGAGGATAAATTATAATACTT
Found at i:1670412 original size:2 final size:2
Alignment explanation
Indices: 1670405--1670440 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1670395 TTTTTACCAA
1670405 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
1670441 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1671435 original size:16 final size:17
Alignment explanation
Indices: 1671373--1671428 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
1671363 TTAAGAAATA
* *
1671373 AAAATATATTATGA-TT
1 AAAATATATAATAATTT
*
1671389 AAAA-ATACAATAAATTTT
1 AAAATATATAAT-AA-TTT
1671407 AAAATATATAATAATTT
1 AAAATATATAATAATTT
1671424 AAAAT
1 AAAAT
1671429 TTTAATAGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
15 5 0.16
16 5 0.16
17 8 0.25
18 8 0.25
19 6 0.19
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (17 bp):
AAAATATATAATAATTT
Found at i:1671758 original size:42 final size:43
Alignment explanation
Indices: 1671698--1671911 Score: 190
Period size: 43 Copynumber: 5.0 Consensus size: 43
1671688 AAACTTATAC
1671698 TTTTTTAATCTCACTTTTTACCTTTATAATTGAGACCCCTAAT
1 TTTTTTAATCTCACTTTTTACCTTTATAATTGAGACCCCTAAT
* * * * *
1671741 TTTTTTAATCTCATTTTTTA-C-TCATAATTTAGGCCCAT-AT
1 TTTTTTAATCTCACTTTTTACCTTTATAATTGAGACCCCTAAT
* * *
1671781 TTATTTTAATCTCACTTTTTACCTATAAAATTAATGA-CCCT-AT
1 TT-TTTTAATCTCACTTTTTACCTTTATAATTGA-GACCCCTAAT
* * * **
1671824 TTTTTTAATATCACTTTTTATCTTTATAATTGGGGTCCCTAAT
1 TTTTTTAATCTCACTTTTTACCTTTATAATTGAGACCCCTAAT
* * * *
1671867 TTTTTCAATCAT-ACTTTTTACTTTTATAGTTTA-AGCCCCTAAT
1 TTTTTTAATC-TCACTTTTTACCTTTATAATTGAGA-CCCCTAAT
1671910 TT
1 TT
1671912 AATCATTTTT
Statistics
Matches: 135, Mismatches: 28, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
40 4 0.03
41 31 0.23
42 31 0.23
43 67 0.50
44 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.05, T:0.51
Consensus pattern (43 bp):
TTTTTTAATCTCACTTTTTACCTTTATAATTGAGACCCCTAAT
Found at i:1672474 original size:30 final size:30
Alignment explanation
Indices: 1672438--1672499 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
1672428 AAATTCTTTG
1672438 ATTTTAAAAA-TATTAAATATTT-ATATTTAT
1 ATTTTAAAAAGT-TTAAATATTTAAT-TTTAT
*
1672468 ATTTTAAAAAGTTTTAATATTTAATTTTAT
1 ATTTTAAAAAGTTTAAATATTTAATTTTAT
1672498 AT
1 AT
1672500 AAACTTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 26 0.90
31 3 0.10
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (30 bp):
ATTTTAAAAAGTTTAAATATTTAATTTTAT
Found at i:1676198 original size:19 final size:18
Alignment explanation
Indices: 1676174--1676227 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 18
1676164 AATCTAATTA
1676174 ATTATTTATTTGAAATAAT
1 ATTATTTATTT-AAATAAT
*
1676193 ATTA-TT-TTTAAATTAT
1 ATTATTTATTTAAATAAT
1676209 ATT-TTTAATTTTAAATAAT
1 ATTATTT-A-TTTAAATAAT
1676228 TAAATTCAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
16 11 0.38
17 3 0.10
18 2 0.07
19 13 0.45
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
ATTATTTATTTAAATAAT
Found at i:1677849 original size:14 final size:14
Alignment explanation
Indices: 1677830--1677860 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1677820 ATGAATTACA
1677830 TTTCTGGAAAACGT
1 TTTCTGGAAAACGT
*
1677844 TTTCTGGAAAATGT
1 TTTCTGGAAAACGT
1677858 TTT
1 TTT
1677861 TCGTAAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.10, G:0.19, T:0.45
Consensus pattern (14 bp):
TTTCTGGAAAACGT
Found at i:1678060 original size:20 final size:20
Alignment explanation
Indices: 1678037--1678076 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1678027 ATTTTTAAAA
1678037 TATTAAA-ATAATTTCTTTAT
1 TATTAAATATAATTT-TTTAT
*
1678057 TATTAAATATTATTTTTTAT
1 TATTAAATATAATTTTTTAT
1678077 AATTTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTAAATATAATTTTTTAT
Found at i:1678097 original size:30 final size:31
Alignment explanation
Indices: 1678061--1678133 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 31
1678051 CTTTATTATT
**
1678061 AAATATTAT-TTTTTATAATTTTATT-AATAA
1 AAATATTATATTGGTAT-ATTTTATTAAATAA
1678091 AAATATTAATATTGGTATATTTTATTGAAATAA
1 AAATATT-ATATTGGTATATTTTATT-AAATAA
1678124 AAATATTATA
1 AAATATTATA
1678134 AATTATATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
30 7 0.19
31 10 0.27
32 8 0.22
33 12 0.32
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (31 bp):
AAATATTATATTGGTATATTTTATTAAATAA
Done.