Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 158 of 210
Found at i:47799738 original size:20 final size:20
Alignment explanation
Indices: 47799706--47799743 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
47799696 AATTTCAAAC
*
47799706 ATAAATAATAAAATAAATAA
1 ATAAATAATAAAAGAAATAA
47799726 ATAAATAGA-AAAAGAAAT
1 ATAAATA-ATAAAAGAAAT
47799744 TTATCCTCGC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (20 bp):
ATAAATAATAAAAGAAATAA
Found at i:47806603 original size:23 final size:23
Alignment explanation
Indices: 47806519--47806604 Score: 75
Period size: 23 Copynumber: 3.5 Consensus size: 23
47806509 CAAAAATTTG
47806519 TTTTAATTACCCGATTTTACATA
1 TTTTAATTACCCGATTTTACATA
* *
47806542 TTTTACTTACCC-ATTAAACTTGAAATA
1 TTTTAATTACCCGATT----TT-ACATA
* *
47806569 GCTATAATTACCCGATTTTACATA
1 -TTTTAATTACCCGATTTTACATA
47806593 TTTTAATTACCC
1 TTTTAATTACCC
47806605 ATTAAACTTG
Statistics
Matches: 48, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
22 3 0.06
23 21 0.44
24 4 0.08
25 2 0.04
26 2 0.04
27 4 0.08
28 9 0.19
29 3 0.06
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.43
Consensus pattern (23 bp):
TTTTAATTACCCGATTTTACATA
Found at i:47806603 original size:51 final size:51
Alignment explanation
Indices: 47806522--47806628 Score: 196
Period size: 51 Copynumber: 2.1 Consensus size: 51
47806512 AAATTTGTTT
*
47806522 TAATTACCCGATTTTACATATTTTACTTACCCATTAAACTTGAAATAGCTA
1 TAATTACCCGATTTTACATATTTTAATTACCCATTAAACTTGAAATAGCTA
47806573 TAATTACCCGATTTTACATATTTTAATTACCCATTAAACTTGAAATAGCTA
1 TAATTACCCGATTTTACATATTTTAATTACCCATTAAACTTGAAATAGCTA
*
47806624 CAATT
1 TAATT
47806629 CATTACCATA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.39
Consensus pattern (51 bp):
TAATTACCCGATTTTACATATTTTAATTACCCATTAAACTTGAAATAGCTA
Found at i:47806828 original size:51 final size:51
Alignment explanation
Indices: 47806745--47806843 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 51
47806735 ATTCACACAA
* * * *
47806745 GCTTCATACACCCTGTTATCAGCCACCGTACGAACACTCATCAACATACAT
1 GCTTAATACACCATGTTATCAACCACCATACGAACACTCATCAACATACAT
*
47806796 GCTTAATACACCATGTTATCAACTACCATACGAACACTCATCAACATA
1 GCTTAATACACCATGTTATCAACCACCATACGAACACTCATCAACATA
47806844 TTTGTTGTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.35, C:0.32, G:0.08, T:0.24
Consensus pattern (51 bp):
GCTTAATACACCATGTTATCAACCACCATACGAACACTCATCAACATACAT
Found at i:47813462 original size:19 final size:19
Alignment explanation
Indices: 47813417--47813465 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
47813407 AATGGGAGAG
* *
47813417 AAAATGACGTGAGTAGAAGT
1 AAAA-GACGTGAGCAAAAGT
**
47813437 AGGAGACGTGAGCAAAAGT
1 AAAAGACGTGAGCAAAAGT
47813456 AAAAGACGTG
1 AAAAGACGTG
47813466 GACATAAATT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 21 0.91
20 2 0.09
ACGTcount: A:0.45, C:0.08, G:0.33, T:0.14
Consensus pattern (19 bp):
AAAAGACGTGAGCAAAAGT
Found at i:47815068 original size:16 final size:16
Alignment explanation
Indices: 47815047--47815092 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 16
47815037 ATTGAAAATA
47815047 AAAAAATTAAAATTAT
1 AAAAAATTAAAATTAT
47815063 AAAAAA-TAGAAATTAT
1 AAAAAATTA-AAATTAT
47815079 AAAAAATATAAAAT
1 AAAAAAT-TAAAAT
47815093 ATGACAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 2 0.07
16 19 0.70
17 4 0.15
18 2 0.07
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (16 bp):
AAAAAATTAAAATTAT
Found at i:47821379 original size:24 final size:24
Alignment explanation
Indices: 47821340--47821386 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
47821330 GGAATGGGGA
47821340 AGAAAATGAAGAACAA-TGAAGAG
1 AGAAAATGAAGAACAAGTGAAGAG
47821363 AGAAAAGTGAA-AGACAAGTGAAGA
1 AGAAAA-TGAAGA-ACAAGTGAAGA
47821387 ATGAATGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 7 0.33
24 8 0.38
25 6 0.29
ACGTcount: A:0.60, C:0.04, G:0.28, T:0.09
Consensus pattern (24 bp):
AGAAAATGAAGAACAAGTGAAGAG
Found at i:47831866 original size:20 final size:20
Alignment explanation
Indices: 47831823--47831866 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
47831813 ATTTTCCAAG
* * **
47831823 CAGTATCGATACCTCCTTTT
1 CAGTATCGATACCTACGTAA
47831843 CAGTATCGATACCTACGTAA
1 CAGTATCGATACCTACGTAA
47831863 CAGT
1 CAGT
47831867 TTTGGAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (20 bp):
CAGTATCGATACCTACGTAA
Found at i:47832613 original size:5 final size:5
Alignment explanation
Indices: 47832598--47832640 Score: 77
Period size: 5 Copynumber: 8.4 Consensus size: 5
47832588 AGTTGAGATA
47832598 TTATCT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT
1 TTAT-T TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT
47832641 CTCAAAATTC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 33 0.89
6 4 0.11
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:47837285 original size:27 final size:27
Alignment explanation
Indices: 47837255--47837309 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
47837245 GTACAATATA
* *
47837255 TGTGGCAAAGCCACAAGTAATAGTAAT
1 TGTGGCAAAGCCACAAGAAACAGTAAT
* *
47837282 TGTGGCAGAGCCACCAGAAACAGTAAT
1 TGTGGCAAAGCCACAAGAAACAGTAAT
47837309 T
1 T
47837310 CCTCCATAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (27 bp):
TGTGGCAAAGCCACAAGAAACAGTAAT
Found at i:47837478 original size:27 final size:27
Alignment explanation
Indices: 47837447--47837530 Score: 107
Period size: 27 Copynumber: 3.1 Consensus size: 27
47837437 GGGTATTATG
*
47837447 GTAATTTTACCCATTGAGGGTGTTTC-
1 GTAATTTTACCCATTGAGGGTATTTCA
* *
47837473 GATAATTTTACTCATTGGGGGTATTTCA
1 G-TAATTTTACCCATTGAGGGTATTTCA
* *
47837501 GTAAGTTTACCTATTGAGGGTATTTCA
1 GTAATTTTACCCATTGAGGGTATTTCA
47837528 GTA
1 GTA
47837531 TAGTTAACAA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
26 1 0.02
27 47 0.96
28 1 0.02
ACGTcount: A:0.24, C:0.12, G:0.23, T:0.42
Consensus pattern (27 bp):
GTAATTTTACCCATTGAGGGTATTTCA
Found at i:47849217 original size:22 final size:22
Alignment explanation
Indices: 47849192--47849234 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
47849182 TAATTACAAG
47849192 TTTAATTTAGTAT-TAACTATTC
1 TTTAATTTA-TATCTAACTATTC
*
47849214 TTTATTTTATATCTAACTATT
1 TTTAATTTATATCTAACTATT
47849235 GTAATACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.58
Consensus pattern (22 bp):
TTTAATTTATATCTAACTATTC
Found at i:47851184 original size:23 final size:24
Alignment explanation
Indices: 47851136--47851184 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
47851126 CTTTCCCTTT
*
47851136 TGTGCCGCCCAAAGCATCAGAAAG
1 TGTGCCACCCAAAGCATCAGAAAG
47851160 TGTGCCACCCAAAGCAT-AGAAAG
1 TGTGCCACCCAAAGCATCAGAAAG
47851183 TG
1 TG
47851185 GGTTAAATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.35, C:0.27, G:0.24, T:0.14
Consensus pattern (24 bp):
TGTGCCACCCAAAGCATCAGAAAG
Found at i:47853846 original size:15 final size:15
Alignment explanation
Indices: 47853802--47853853 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
47853792 TAATGAGTAC
47853802 TCGTGGTACGTGAGG
1 TCGTGGTACGTGAGG
* *
47853817 TCATGGTA-TTCGAGG
1 TCGTGGTACGT-GAGG
47853832 TCGTGGTACGTGAGG
1 TCGTGGTACGTGAGG
*
47853847 GCGTGGT
1 TCGTGGT
47853854 GGACATCATA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
14 1 0.03
15 28 0.93
16 1 0.03
ACGTcount: A:0.13, C:0.13, G:0.44, T:0.29
Consensus pattern (15 bp):
TCGTGGTACGTGAGG
Found at i:47856983 original size:29 final size:29
Alignment explanation
Indices: 47856941--47857123 Score: 213
Period size: 29 Copynumber: 6.3 Consensus size: 29
47856931 GTGCTAAGCA
** *
47856941 ATGGTCAAAACCATCCCTTTTCATATTTG
1 ATGGTCATCACCATCCCTTTTCATATTCG
*
47856970 ATGGTCATCACCATCCCTTGTCATATTCG
1 ATGGTCATCACCATCCCTTTTCATATTCG
* * * *
47856999 ATAGTCGTCACCAACCCTTTTCATATTCA
1 ATGGTCATCACCATCCCTTTTCATATTCG
**
47857028 ATGGTCAAAACCATCCCTTTTCATATTCG
1 ATGGTCATCACCATCCCTTTTCATATTCG
* *
47857057 ATGGCCGTCACCATCCCTTTTCATATTCG
1 ATGGTCATCACCATCCCTTTTCATATTCG
* * * *
47857086 ATGGTCGTCATCATCTCTTTTCATATTCA
1 ATGGTCATCACCATCCCTTTTCATATTCG
*
47857115 ATGGGCATC
1 ATGGTCATC
47857124 GATACATCGT
Statistics
Matches: 129, Mismatches: 25, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 129 1.00
ACGTcount: A:0.23, C:0.28, G:0.12, T:0.36
Consensus pattern (29 bp):
ATGGTCATCACCATCCCTTTTCATATTCG
Found at i:47857085 original size:87 final size:87
Alignment explanation
Indices: 47856939--47857118 Score: 288
Period size: 87 Copynumber: 2.1 Consensus size: 87
47856929 GTGTGCTAAG
* *
47856939 CAATGGTCAAAACCATCCCTTTTCATATTTGATGGTCATCACCATCCCTTGTCATATTCGATAGT
1 CAATGGTCAAAACCATCCCTTTTCATATTCGATGGCCATCACCATCCCTTGTCATATTCGATAGT
47857004 CGTCACCAACCCTTTTCATATT
66 CGTCACCAACCCTTTTCATATT
* * *
47857026 CAATGGTCAAAACCATCCCTTTTCATATTCGATGGCCGTCACCATCCCTTTTCATATTCGATGGT
1 CAATGGTCAAAACCATCCCTTTTCATATTCGATGGCCATCACCATCCCTTGTCATATTCGATAGT
* * *
47857091 CGTCATCATCTCTTTTCATATT
66 CGTCACCAACCCTTTTCATATT
47857113 CAATGG
1 CAATGG
47857119 GCATCGATAC
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 85 1.00
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (87 bp):
CAATGGTCAAAACCATCCCTTTTCATATTCGATGGCCATCACCATCCCTTGTCATATTCGATAGT
CGTCACCAACCCTTTTCATATT
Found at i:47859043 original size:43 final size:43
Alignment explanation
Indices: 47858988--47859217 Score: 325
Period size: 43 Copynumber: 5.3 Consensus size: 43
47858978 GTTTTTAGAA
* *
47858988 AAAAACGCCGCTAAAGACCAATACCTTTAGCGGTGCTTTTCCC
1 AAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
* *
47859031 AAAAACGCCGCTAAAGACCAAGACTTTTAGCAGCGCTTTTCCC
1 AAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
** *
47859074 ACGAACGCCGCTAAAGACCAAGAACTTTAGCGGCGCTTTTCCC
1 AAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
* *
47859117 GAAAATGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
1 AAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
* * * *
47859160 ACAAACGCCACTGAAGACCAAGAACTTTAGCGGCGCTTTTCCC
1 AAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
* *
47859203 ACAAACGTCGCTAAA
1 AAAAACGCCGCTAAA
47859218 AACATGACTT
Statistics
Matches: 164, Mismatches: 23, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 164 1.00
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
Found at i:47859441 original size:18 final size:18
Alignment explanation
Indices: 47859418--47859477 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
47859408 TTAAAACAAG
47859418 TTACATTCTATATTAGAA
1 TTACATTCTATATTAGAA
*** * *
47859436 TTACATAAGAAAATT-G-T
1 TTACAT-TCTATATTAGAA
47859453 TTACATTCTATATTAGAA
1 TTACATTCTATATTAGAA
47859471 TTACATT
1 TTACATT
47859478 AGTTCTGTTT
Statistics
Matches: 29, Mismatches: 10, Indels: 6
0.64 0.22 0.13
Matches are distributed among these distances:
16 4 0.14
17 7 0.24
18 14 0.48
19 4 0.14
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (18 bp):
TTACATTCTATATTAGAA
Found at i:47862087 original size:21 final size:21
Alignment explanation
Indices: 47862049--47862115 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
47862039 CCCTAACCCG
* *
47862049 ACCCCGAATCTCTAAACCCTAA
1 ACCCCTAA-CTCTTAACCCTAA
* *
47862071 ATCCCTAACTCTTAACCCCAA
1 ACCCCTAACTCTTAACCCTAA
*
47862092 ACCCCTAACAC-TAACCCCTAA
1 ACCCCTAACTCTTAA-CCCTAA
47862113 ACC
1 ACC
47862116 TTATTTAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
20 3 0.08
21 28 0.76
22 6 0.16
ACGTcount: A:0.36, C:0.45, G:0.01, T:0.18
Consensus pattern (21 bp):
ACCCCTAACTCTTAACCCTAA
Found at i:47862359 original size:14 final size:15
Alignment explanation
Indices: 47862342--47862374 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
47862332 CTTAAATCAG
47862342 AATCCCTAA-TTCAT
1 AATCCCTAATTTCAT
47862356 AATCCCTAATTTCAT
1 AATCCCTAATTTCAT
47862371 AATC
1 AATC
47862375 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.27, G:0.00, T:0.36
Consensus pattern (15 bp):
AATCCCTAATTTCAT
Found at i:47863534 original size:41 final size:41
Alignment explanation
Indices: 47863477--47863759 Score: 440
Period size: 41 Copynumber: 6.9 Consensus size: 41
47863467 TTTTATTATT
*
47863477 ATTAGCGGCACTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
* *
47863518 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGTCCTAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
* *
47863559 ATTAGCGGTGCCTTTTCAAAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
*
47863600 ATTGGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
* * *
47863641 ATTGGCGGCGCTTTTTCAAAAACACCGCTAAAGGCTCGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
* *
47863682 ATTAGCGTCGCTTTTTCAAAAACGCAGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
* * *
47863723 ATTAGCGGCGCTTTTTTAAAAACACCGCTAAATGCCC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCC
47863760 CAAAAACTCA
Statistics
Matches: 220, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 220 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.22
Consensus pattern (41 bp):
ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
Found at i:47872224 original size:12 final size:12
Alignment explanation
Indices: 47872209--47872236 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
47872199 GTCTTGAATC
47872209 AAGTCATTCATT
1 AAGTCATTCATT
47872221 AAGTCATTCATT
1 AAGTCATTCATT
47872233 AAGT
1 AAGT
47872237 GTTTTCTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (12 bp):
AAGTCATTCATT
Found at i:47872262 original size:14 final size:13
Alignment explanation
Indices: 47872243--47872359 Score: 73
Period size: 13 Copynumber: 9.1 Consensus size: 13
47872233 AAGTGTTTTC
47872243 TTTCATCAAGTGTT
1 TTTCATCAAGT-TT
47872257 TTTCATCAAGTTCT
1 TTTCATCAAGTT-T
47872271 TTT-ATCAAGTTT
1 TTTCATCAAGTTT
* * *
47872283 TTAATTACCAATTTT
1 TT--TCATCAAGTTT
* *
47872298 TTTTATTAAG-TT
1 TTTCATCAAGTTT
*
47872310 TTGCATCAAGTTT
1 TTTCATCAAGTTT
* *
47872323 TTT--TTAAG-CT
1 TTTCATCAAGTTT
* *
47872333 TTTCGTCAAGTCT
1 TTTCATCAAGTTT
47872346 TTTCATCAAGTTT
1 TTTCATCAAGTTT
47872359 T
1 T
47872360 CCATGGAGTT
Statistics
Matches: 81, Mismatches: 14, Indels: 17
0.72 0.12 0.15
Matches are distributed among these distances:
10 4 0.05
11 4 0.05
12 16 0.20
13 32 0.40
14 16 0.20
15 9 0.11
ACGTcount: A:0.23, C:0.14, G:0.09, T:0.54
Consensus pattern (13 bp):
TTTCATCAAGTTT
Found at i:47872323 original size:23 final size:22
Alignment explanation
Indices: 47872297--47872360 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 22
47872287 TTACCAATTT
47872297 TTTTTATTAAGTTTTGCATCAAG
1 TTTTTATTAAGTTTT-CATCAAG
* *
47872320 TTTTTTTTAAGCTTTTCGTCAAG
1 TTTTTATTAAG-TTTTCATCAAG
*
47872343 TCTTTTCATCAAGTTTTC
1 T-TTTT-ATTAAGTTTTC
47872361 CATGGAGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
23 17 0.50
24 13 0.38
25 4 0.12
ACGTcount: A:0.20, C:0.14, G:0.11, T:0.55
Consensus pattern (22 bp):
TTTTTATTAAGTTTTCATCAAG
Found at i:47874460 original size:115 final size:113
Alignment explanation
Indices: 47874257--47874469 Score: 340
Period size: 115 Copynumber: 1.9 Consensus size: 113
47874247 ATGATCGACT
*
47874257 TAAGGCTGCTTCTAACAGATATAAATCCTACACAGATCTTAAAAGAAGATATTGAGTTTGATGTG
1 TAAGGCTGCTTCTAACAGATATAAATCCTACACAGATCTTAAAAAAAGATATTGAGTTTGATGTG
* * *
47874322 GGGGATCGGATTTTTCTTAAGGTTTTTCCGTGAAAAAAAGTTTTAAGG
66 GGGGATCAGATTTTTCTAAAGGTTTCTCCGTGAAAAAAAGTTTTAAGG
47874370 TAAGGCTGCTTCTAACAGATATAAATCCTAC-CTAGATCTTAAGAGAAAAGATATTGAGTTTGAT
1 TAAGGCTGCTTCTAACAGATATAAATCCTACAC-AGATCTTAA-A-AAAAGATATTGAGTTTGAT
47874434 GTGGGGGATCA-AGTTTTTCTAAAGGTTTCTCCGTGA
63 GTGGGGGATCAGA-TTTTTCTAAAGGTTTCTCCGTGA
47874470 GAAAGGTTTT
Statistics
Matches: 92, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
112 1 0.01
113 40 0.43
114 2 0.02
115 49 0.53
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.33
Consensus pattern (113 bp):
TAAGGCTGCTTCTAACAGATATAAATCCTACACAGATCTTAAAAAAAGATATTGAGTTTGATGTG
GGGGATCAGATTTTTCTAAAGGTTTCTCCGTGAAAAAAAGTTTTAAGG
Found at i:47878054 original size:24 final size:24
Alignment explanation
Indices: 47878024--47878069 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
47878014 TCAATCTTAT
47878024 AAAAATAACTAAAAATA-TATAATA
1 AAAAAT-ACTAAAAATATTATAATA
*
47878048 AAAAATAGTAAAAATATTATAA
1 AAAAATACTAAAAATATTATAA
47878070 AGTTTAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAAATACTAAAAATATTATAATA
Found at i:47885997 original size:18 final size:18
Alignment explanation
Indices: 47885973--47886008 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
47885963 AGAAAAGTAA
47885973 AAAAAAATAACTTTAATTT
1 AAAAAAA-AACTTTAATTT
*
47885992 AAAAAAAAATTTTAATT
1 AAAAAAAAACTTTAATT
47886009 GCTTACGTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAAAAAAACTTTAATTT
Found at i:47891354 original size:2 final size:2
Alignment explanation
Indices: 47891347--47891372 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
47891337 TTTAAATTAT
47891347 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
47891373 AAGATAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47895827 original size:7 final size:7
Alignment explanation
Indices: 47895809--47895850 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
47895799 ACATAAACAA
47895809 ATCATA-
1 ATCATAT
47895815 ATCATAT
1 ATCATAT
47895822 ATCATAT
1 ATCATAT
*
47895829 TTACATAT
1 AT-CATAT
*
47895837 ATCATAA
1 ATCATAT
47895844 ATCATAT
1 ATCATAT
47895851 GGCATACATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 6 0.20
7 18 0.60
8 6 0.20
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.40
Consensus pattern (7 bp):
ATCATAT
Found at i:47902888 original size:22 final size:22
Alignment explanation
Indices: 47902860--47902988 Score: 186
Period size: 22 Copynumber: 5.9 Consensus size: 22
47902850 TTTATTGTTC
*
47902860 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
47902882 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
47902904 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
47902926 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
47902948 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
47902970 AAACATGAGAGCTTAGTAC
1 AAACATGAGAGCTTAGTAC
47902989 TGGTGCCAAG
Statistics
Matches: 96, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 96 1.00
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:47926831 original size:18 final size:19
Alignment explanation
Indices: 47926793--47926831 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
47926783 ATTACAAAAT
* *
47926793 AATTTTAAAATAATTTTTA
1 AATTTCAAAATAATTTATA
47926812 AATTTCAAAAT-ATTTATA
1 AATTTCAAAATAATTTATA
47926830 AA
1 AA
47926832 AATTCTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
AATTTCAAAATAATTTATA
Found at i:47934658 original size:6 final size:6
Alignment explanation
Indices: 47934641--47934688 Score: 69
Period size: 6 Copynumber: 8.0 Consensus size: 6
47934631 ATAGGTTTCA
* * *
47934641 GAAAAT GGAAAT GAAAAT AAAAAT GAAAAT GAAAAT GAAAAT GGAAAT
1 GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT
47934689 AATCCATTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.19, T:0.17
Consensus pattern (6 bp):
GAAAAT
Found at i:47934665 original size:18 final size:18
Alignment explanation
Indices: 47934642--47934688 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
47934632 TAGGTTTCAG
47934642 AAAATGGAAATGAAAATA
1 AAAATGGAAATGAAAATA
* *
47934660 AAAATGAAAATGAAAATG
1 AAAATGGAAATGAAAATA
47934678 AAAATGGAAAT
1 AAAATGGAAAT
47934689 AATCCATTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (18 bp):
AAAATGGAAATGAAAATA
Found at i:47934904 original size:26 final size:26
Alignment explanation
Indices: 47934834--47934908 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 26
47934824 ACATATTTTC
* *
47934834 TCAAAATTTT-CTAGGGGAAAAATCA
1 TCAAAATTTTACTAAGGGTAAAATCA
* *
47934859 TCAAAATTTTACCATA-GGTAAAATCG
1 TCAAAATTTTACTA-AGGGTAAAATCA
*
47934885 TCAAATTTTTACTAAGGGTAAAAT
1 TCAAAATTTTACTAAGGGTAAAAT
47934909 AGGGATGAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
25 11 0.27
26 30 0.73
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (26 bp):
TCAAAATTTTACTAAGGGTAAAATCA
Found at i:47936517 original size:27 final size:27
Alignment explanation
Indices: 47936466--47936518 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
47936456 TCCTAGTTTC
*
47936466 TTTTATAGTAAAATCATCGTCACTTTA
1 TTTTATAGTAAAATCATCATCACTTTA
* *
47936493 TTTTATAGTAAAATCGTCATTACTTT
1 TTTTATAGTAAAATCATCATCACTTT
47936519 GACGGAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (27 bp):
TTTTATAGTAAAATCATCATCACTTTA
Found at i:47936564 original size:16 final size:18
Alignment explanation
Indices: 47936537--47936569 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
47936527 TAGAATTAAG
47936537 TTGAGAAAATT-ATTTAC
1 TTGAGAAAATTAATTTAC
47936554 TTGAG-AAATTAATTTA
1 TTGAGAAAATTAATTTA
47936570 GTTAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAC
Found at i:47938881 original size:58 final size:57
Alignment explanation
Indices: 47938813--47938934 Score: 147
Period size: 57 Copynumber: 2.1 Consensus size: 57
47938803 AGAAATGGTG
*
47938813 AAATGGAGAAAT-AAGAGACATTTGGAAATGATTAAGGTTTTATCCAAAATGAAAATGA
1 AAATGGAGAAATGAA-A-ACATTTGGAAATGAATAAGGTTTTATCCAAAATGAAAATGA
* * ** * * *
47938871 AAATGTAGAAATGAAATCATTTGGAAATGAATGTGGTTTTCTCCAAAATGAAGATGG
1 AAATGGAGAAATGAAAACATTTGGAAATGAATAAGGTTTTATCCAAAATGAAAATGA
47938928 AAATGGA
1 AAATGGA
47938935 AATGGGAATG
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
57 40 0.74
58 12 0.22
59 2 0.04
ACGTcount: A:0.45, C:0.06, G:0.22, T:0.27
Consensus pattern (57 bp):
AAATGGAGAAATGAAAACATTTGGAAATGAATAAGGTTTTATCCAAAATGAAAATGA
Found at i:47952078 original size:20 final size:20
Alignment explanation
Indices: 47952036--47952076 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
47952026 TACAACACAA
*
47952036 TTCAATTTCATATTGAATAT
1 TTCAATTTCATATTCAATAT
*
47952056 TTCAATTT-TTATTCAATAT
1 TTCAATTTCATATTCAATAT
47952075 TT
1 TT
47952077 TCCTAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (20 bp):
TTCAATTTCATATTCAATAT
Found at i:47952570 original size:22 final size:25
Alignment explanation
Indices: 47952545--47952600 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
47952535 CTTTATTTCT
*
47952545 TTTACTTA-T-TTATTTTAT-TATA
1 TTTACTTATTATTATATTATATATA
47952567 TTTACTTTATTATTATATTATATATA
1 TTTAC-TTATTATTATATTATATATA
47952593 TTTACTTA
1 TTTACTTA
47952601 AATATTAAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 5 0.17
23 3 0.10
24 1 0.03
25 11 0.38
26 9 0.31
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.64
Consensus pattern (25 bp):
TTTACTTATTATTATATTATATATA
Found at i:47952592 original size:26 final size:27
Alignment explanation
Indices: 47952545--47952599 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
47952535 CTTTATTTCT
*
47952545 TTTACTTATTTATTTTATTATATTTAC
1 TTTACTTATTTATTATATTATATTTAC
47952572 TTTA-TTATTATATTATA-TATATTTAC
1 TTTACTTATT-TATTATATTATATTTAC
47952598 TT
1 TT
47952600 AAATATTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTACTTATTTATTATATTATATTTAC
Found at i:47952606 original size:26 final size:25
Alignment explanation
Indices: 47952554--47952607 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
47952544 TTTTACTTAT
* * *
47952554 TTATTTTATTATATTTACTTTATTA
1 TTATATTATTATATTTACTTAAATA
47952579 TTATATTATATATATTTACTTAAATA
1 TTATATTAT-TATATTTACTTAAATA
47952605 TTA
1 TTA
47952608 AGCAAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (25 bp):
TTATATTATTATATTTACTTAAATA
Found at i:47953640 original size:18 final size:18
Alignment explanation
Indices: 47953617--47953660 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
47953607 TGAATACGAA
47953617 AAGTCATGTAAAAGCAGG
1 AAGTCATGTAAAAGCAGG
47953635 AAGTCATGTAAAAGCAGG
1 AAGTCATGTAAAAGCAGG
47953653 AAGTCATG
1 AAGTCATG
47953661 ATTATTACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.43, C:0.11, G:0.27, T:0.18
Consensus pattern (18 bp):
AAGTCATGTAAAAGCAGG
Found at i:47961944 original size:52 final size:52
Alignment explanation
Indices: 47961866--47962024 Score: 258
Period size: 52 Copynumber: 3.2 Consensus size: 52
47961856 GCTCACTGAT
47961866 AAATGTTTGAAATGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTG
1 AAATGTTTGAAATGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTG
47961918 AAATGTTTGAAATGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTG
1 AAATGTTTGAAATGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTG
* *
47961970 AAATGTTTGAAATGGTGCTGTT-A----CTACT-TCAACTTTGAATGCTTTG
1 AAATGTTTGAAATGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTG
47962016 AAATGTTTG
1 AAATGTTTG
47962025 CTCACTGATA
Statistics
Matches: 105, Mismatches: 2, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
46 26 0.25
47 4 0.04
51 1 0.01
52 74 0.70
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.43
Consensus pattern (52 bp):
AAATGTTTGAAATGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTG
Found at i:47962061 original size:116 final size:116
Alignment explanation
Indices: 47961918--47962262 Score: 600
Period size: 116 Copynumber: 2.9 Consensus size: 116
47961908 GAATGCTTTG
47961918 AAATGTTTGAAATGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTGAAAT
1 AAATGTTTGAAATGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTGAAAT
47961983 GGTGCTGTTACTACTTCAACTTTGAATGCTTTGAAATGTTTGCTCACTGAT
66 GGTGCTGTTACTACTTCAACTTTGAATGCTTTGAAATGTTTGCTCACTGAT
* *
47962034 AAATGTTTGAAATGGTGCTGATAATTTGGTACTGTTAACTTTGAATGCTTTGAAATTTTTGAAAT
1 AAATGTTTGAAATGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTGAAAT
47962099 GGTGCTGTTACTACTTCAACTTTGAATGCTTTGAAATGTTTGCTCACTGAT
66 GGTGCTGTTACTACTTCAACTTTGAATGCTTTGAAATGTTTGCTCACTGAT
47962150 AAATGTTTGAAATGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTGAAAT
1 AAATGTTTGAAATGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTGAAAT
* *
47962215 GGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTG
66 GGTGCTGTT-A----CTACT-TCAACTTTGAATGCTTTGAAATGTTTG
47962263 AAATGAATTA
Statistics
Matches: 217, Mismatches: 6, Indels: 6
0.95 0.03 0.03
Matches are distributed among these distances:
116 186 0.86
117 1 0.00
121 4 0.02
122 26 0.12
ACGTcount: A:0.26, C:0.10, G:0.21, T:0.43
Consensus pattern (116 bp):
AAATGTTTGAAATGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTGAAAT
GGTGCTGTTACTACTTCAACTTTGAATGCTTTGAAATGTTTGCTCACTGAT
Found at i:47962102 original size:168 final size:162
Alignment explanation
Indices: 47961824--47962140 Score: 535
Period size: 168 Copynumber: 1.9 Consensus size: 162
47961814 AACTGACTTG
* *
47961824 ACTACTTCAACTTTGAATGCTTTGAAATTTTTGCTCACTGATAAATGTTTGAAATGGTGCTGTTA
1 ACTACTTCAACTTTGAATGCTTTGAAATGTTTGCTCACTGATAAATGTTTGAAATGGTGCTGATA
* *
47961889 ATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTGAAATGGTGCTGTTAATTTGGTACTGTT
66 ATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTGAAATGGTGCTGTT-A----CTACT-TC
47961954 AACTTTGAATGCTTTGAAATGTTTGAAATGGTGCTGTT
125 AACTTTGAATGCTTTGAAATGTTTGAAATGGTGCTGTT
47961992 ACTACTTCAACTTTGAATGCTTTGAAATGTTTGCTCACTGATAAATGTTTGAAATGGTGCTGATA
1 ACTACTTCAACTTTGAATGCTTTGAAATGTTTGCTCACTGATAAATGTTTGAAATGGTGCTGATA
*
47962057 ATTTGGTACTGTTAACTTTGAATGCTTTGAAATTTTTGAAATGGTGCTGTTACTACTTCAACTTT
66 ATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTGAAATGGTGCTGTTACTACTTCAACTTT
47962122 GAATGCTTTGAAATGTTTG
131 GAATGCTTTGAAATGTTTG
47962141 CTCACTGATA
Statistics
Matches: 144, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
162 26 0.18
163 4 0.03
167 1 0.01
168 113 0.78
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (162 bp):
ACTACTTCAACTTTGAATGCTTTGAAATGTTTGCTCACTGATAAATGTTTGAAATGGTGCTGATA
ATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTGAAATGGTGCTGTTACTACTTCAACTTT
GAATGCTTTGAAATGTTTGAAATGGTGCTGTT
Found at i:47962228 original size:52 final size:52
Alignment explanation
Indices: 47962150--47962267 Score: 236
Period size: 52 Copynumber: 2.3 Consensus size: 52
47962140 GCTCACTGAT
47962150 AAATGTTTGAAATGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTG
1 AAATGTTTGAAATGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTG
47962202 AAATGTTTGAAATGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTG
1 AAATGTTTGAAATGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTG
47962254 AAATGTTTGAAATG
1 AAATGTTTGAAATG
47962268 AATTAACACC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.27, C:0.07, G:0.23, T:0.43
Consensus pattern (52 bp):
AAATGTTTGAAATGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTG
Found at i:47962471 original size:2 final size:2
Alignment explanation
Indices: 47962464--47962490 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
47962454 CTTATTCGAC
47962464 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 T
47962491 TGAAGTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47965288 original size:91 final size:91
Alignment explanation
Indices: 47965162--47965369 Score: 301
Period size: 91 Copynumber: 2.3 Consensus size: 91
47965152 TTGATTTTAG
* *
47965162 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
* *
47965227 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
* *
47965254 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTATA
47965319 TGTAATAATTATTATTTTAAATTATA
66 TGTAATAATTATTATTTTAAATTATA
* * * *
47965345 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
47965370 GTTATAATTA
Statistics
Matches: 105, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
91 86 0.82
92 19 0.18
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:47965759 original size:45 final size:44
Alignment explanation
Indices: 47965660--47965769 Score: 140
Period size: 45 Copynumber: 2.6 Consensus size: 44
47965650 TTTTCCATTA
47965660 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* ***
47965699 TACTATTACACCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
47965744 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
47965770 CCTCTAATCC
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
39 17 0.28
40 1 0.02
44 16 0.27
45 26 0.43
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.34
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:47965769 original size:16 final size:16
Alignment explanation
Indices: 47965748--47965785 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
47965738 TTGATTTGCT
*
47965748 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
47965764 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
47965780 AATACA
1 ATTACA
47965786 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:47965937 original size:24 final size:24
Alignment explanation
Indices: 47965899--47965950 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
47965889 ATAAACTATG
47965899 CTAATAAATACTAAATATATTATA
1 CTAATAAATACTAAATATATTATA
**
47965923 CTAATAAATGTTAAATATATTATA
1 CTAATAAATACTAAATATATTATA
47965947 CTAA
1 CTAA
47965951 CAAAATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (24 bp):
CTAATAAATACTAAATATATTATA
Found at i:47968525 original size:20 final size:22
Alignment explanation
Indices: 47968500--47968541 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
47968490 GTTATTACTA
47968500 TTATAT-TTATT-TATATATCT
1 TTATATCTTATTATATATATCT
47968520 TTATATCTTATTATATATATCT
1 TTATATCTTATTATATATATCT
47968542 ATNNNNNNNN
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.30
21 5 0.25
22 9 0.45
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (22 bp):
TTATATCTTATTATATATATCT
Found at i:47974859 original size:9 final size:9
Alignment explanation
Indices: 47974838--47974893 Score: 73
Period size: 9 Copynumber: 6.3 Consensus size: 9
47974828 TTCAGACTCA
47974838 AAAAAAATC
1 AAAAAAATC
47974847 --AAAAATC
1 AAAAAAATC
47974854 AAAAAAATC
1 AAAAAAATC
47974863 AAAAAAATC
1 AAAAAAATC
47974872 AAAAAAAAAT-
1 --AAAAAAATC
47974882 AAAAAAATC
1 AAAAAAATC
47974891 AAA
1 AAA
47974894 GTCAAAAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
7 7 0.17
8 8 0.19
9 19 0.45
11 8 0.19
ACGTcount: A:0.80, C:0.09, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAAAATC
Found at i:47974859 original size:16 final size:17
Alignment explanation
Indices: 47974838--47974893 Score: 69
Period size: 16 Copynumber: 3.2 Consensus size: 17
47974828 TTCAGACTCA
47974838 AAAAAAATC-AAAAATC
1 AAAAAAATCAAAAAATC
47974854 AAAAAAATCAAAAAAATC
1 AAAAAAATC-AAAAAATC
*
47974872 AAAAAAAAATAAAAAAATC
1 --AAAAAAATCAAAAAATC
47974891 AAA
1 AAA
47974894 GTCAAAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
16 9 0.26
17 3 0.09
18 7 0.20
19 8 0.23
20 8 0.23
ACGTcount: A:0.80, C:0.09, G:0.00, T:0.11
Consensus pattern (17 bp):
AAAAAAATCAAAAAATC
Found at i:47974860 original size:18 final size:18
Alignment explanation
Indices: 47974837--47974893 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 18
47974827 GTTCAGACTC
47974837 AAAAAAAATCAAAAATC-
1 AAAAAAAATCAAAAATCA
47974854 -AAAAAAATCAAAAAAATCA
1 AAAAAAAATC--AAAAATCA
*
47974873 AAAAAAAATAAAAAAATCA
1 AAAAAAAAT-CAAAAATCA
47974892 AA
1 AA
47974894 GTCAAAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
16 9 0.26
18 7 0.21
19 10 0.29
20 8 0.24
ACGTcount: A:0.81, C:0.09, G:0.00, T:0.11
Consensus pattern (18 bp):
AAAAAAAATCAAAAATCA
Found at i:47974869 original size:19 final size:19
Alignment explanation
Indices: 47974835--47974893 Score: 81
Period size: 18 Copynumber: 3.3 Consensus size: 19
47974825 GAGTTCAGAC
47974835 TCAAAAAAAATC--AAAAA
1 TCAAAAAAAATCAAAAAAA
47974852 TC-AAAAAAATCAAAAAAA
1 TCAAAAAAAATCAAAAAAA
47974870 TCAAAAAAAAAT-AAAAAAA
1 TC-AAAAAAAATCAAAAAAA
47974889 TCAAA
1 TCAAA
47974894 GTCAAAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
16 9 0.24
17 2 0.05
18 10 0.26
19 9 0.24
20 8 0.21
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.12
Consensus pattern (19 bp):
TCAAAAAAAATCAAAAAAA
Found at i:47974885 original size:25 final size:25
Alignment explanation
Indices: 47974838--47974886 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
47974828 TTCAGACTCA
*
47974838 AAAAAAATCAAAAATCAAAAAAATC
1 AAAAAAATCAAAAATAAAAAAAATC
*
47974863 AAAAAAATCAAAAAAAAATAAAAA
1 AAAAAAATCAAAAATAAA-AAAAA
47974887 AATCAAAGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.82, C:0.08, G:0.00, T:0.10
Consensus pattern (25 bp):
AAAAAAATCAAAAATAAAAAAAATC
Found at i:47975785 original size:7 final size:8
Alignment explanation
Indices: 47975768--47975799 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
47975758 TTAAAAAATG
47975768 AATGAAAA
1 AATGAAAA
47975776 AATG-AAA
1 AATGAAAA
47975783 AATGAAAA
1 AATGAAAA
47975791 AATGAAAA
1 AATGAAAA
47975799 A
1 A
47975800 GTAAAAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AATGAAAA
Found at i:47975788 original size:15 final size:15
Alignment explanation
Indices: 47975768--47975808 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
47975758 TTAAAAAATG
47975768 AATGAAAAAATGAAA
1 AATGAAAAAATGAAA
47975783 AATGAAAAAATGAAA
1 AATGAAAAAATGAAA
*
47975798 AA-GTAAAAATG
1 AATGAAAAAATG
47975809 GAGAGGCTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 8 0.32
15 17 0.68
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (15 bp):
AATGAAAAAATGAAA
Found at i:47977137 original size:45 final size:45
Alignment explanation
Indices: 47976999--47977137 Score: 149
Period size: 45 Copynumber: 3.1 Consensus size: 45
47976989 ACAGATCAAT
* * * **
47976999 GAAGATAGCAGATCATGCCTTCCTGTATTGACAGTGAAGCAGATC
1 GAAGATAGCAGATCTTGCCTTTCTGTACTGACAACGAAGCAGATC
* * * * *
47977044 GAAGACACCAG-CCTTG-TTTTCCTGTACTGACAACGGAGCAGAAT-
1 GAAGATAGCAGATCTTGCCTTT-CTGTACTGACAACGAAGCAG-ATC
47977088 GAAGATAGCAGATCTTGCCTTTCTGTACTGACAACGAAGCAGATC
1 GAAGATAGCAGATCTTGCCTTTCTGTACTGACAACGAAGCAGATC
47977133 GAAGA
1 GAAGA
47977138 AACCATAGTT
Statistics
Matches: 74, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
43 2 0.03
44 30 0.41
45 39 0.53
46 3 0.04
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.23
Consensus pattern (45 bp):
GAAGATAGCAGATCTTGCCTTTCTGTACTGACAACGAAGCAGATC
Found at i:47977222 original size:50 final size:50
Alignment explanation
Indices: 47977147--47978340 Score: 1371
Period size: 50 Copynumber: 23.8 Consensus size: 50
47977137 AAACCATAGT
* *
47977147 TTGCAATTAAAAAGATTGAAGCTACAATAGCGGATCTTACTTTCCTAGCA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCA
* * * *
47977197 TTGCAGTGGAATAGATTGAAGCTACAACAGCGGATCTTACTTCCCT-GACA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAG-CA
* *
47977247 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCG
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCA
* * * * * *
47977297 CTGCAGTGGAACAGATTGAAGCTACAATAGCGGATCTTACTTCCCT-GACA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAG-CA
* * *
47977347 TTGCAATTAAGAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCG
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCA
* ** *
47977397 TTGCAGTGGAGCAA-ATTGAAGCTACAACAGCGGATCTTACTTCCCT-GACA
1 TTGCAAT-GAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAG-CA
* * *
47977447 TTGCAATTAAAAAGATTGAAGCTACAACAGCGAATCTTAC-TTCCCAGGCGA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTA-GC-A
* * *
47977498 -TGCAATGGAACAGATTGAAGCTACAACAGCGGATCTTACTTTCCTGGCA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCA
* **
47977547 TTGCAATTAAAAAGATTGAAGCTACAACAATGGATCTTACTTTCCTAGCA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCA
* * * * *
47977597 TTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGGCA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCA
* *
47977647 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCC
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCA
*** * * * * * * * *
47977697 CCCCTA-GCCGAATAGATTGAAGCTACAACCGCTCGCTCTTACTTCCCTGGCA
1 TTGCAATG--AAAAAGATTGAAGCTACAACAGC-GGATCTTACTTTCCTAGCA
* * *
47977749 TTGCACTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCG
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCA
* * * * *
47977799 TTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGGCA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCA
* * * * *
47977849 TTGCAATTAAGAAGATTGAGGCTACAACAGCGGATCTTACTTCCCTGGCA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCA
* *
47977899 TTGCAATTAAAAAAATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCA
* * * * *
47977949 TTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGGCA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCA
* * * * *
47977999 TTGCAATTAAAAAAATTGAAGCTATAATAGTGGATCTTACTTTCCTAGCA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCA
* * * * *
47978049 TTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGGCA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCA
* * *
47978099 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCCTACTTTCCTAGCG
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCA
* * * *
47978149 TTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCT-GACA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAG-CA
* * *
47978199 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTCTCCTAGCG
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCA
* * ** *
47978249 TTGCAGTGGAGCAGATTGAAGCTACAACAGCGGATCTTACTTCCCT-GACA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAG-CA
* *
47978299 TTGCAATTAAAAAGATTGAAGCTACAACAGCGAATCTTACTT
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTT
47978341 CCCAGGCGAT
Statistics
Matches: 948, Mismatches: 177, Indels: 38
0.82 0.15 0.03
Matches are distributed among these distances:
49 12 0.01
50 869 0.92
51 52 0.05
52 15 0.02
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (50 bp):
TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCA
Found at i:47978485 original size:50 final size:50
Alignment explanation
Indices: 47977147--47978478 Score: 1276
Period size: 50 Copynumber: 26.6 Consensus size: 50
47977137 AAACCATAGT
* * *
47977147 TTGCAATTAAAAAGATTGAAGCTACAATAGCGGATCTTACTTTCCTA-GCA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTAC-TTCCCAGGCA
* * * * *
47977197 TTGCAGTGGAATAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCAGGCA
* *
47977247 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGC-
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTAC-TTCCCAG-GCA
* * * * * *
47977298 -TGCAGTGGAACAGATTGAAGCTACAATAGCGGATCTTACTTCCCTGACA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCAGGCA
* * * *
47977347 TTGCAATTAAGAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTA-GCG
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTAC-TTCCCAGGCA
* ** * *
47977397 TTGCAGTGGAGCAA-ATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
1 TTGCAAT-GAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCAGGCA
* *
47977447 TTGCAATTAAAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCAGGCGA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCAGGC-A
* * * *
47977498 -TGCAATGGAACAGATTGAAGCTACAACAGCGGATCTTACTTTCCTGGCA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCAGGCA
* ** *
47977547 TTGCAATTAAAAAGATTGAAGCTACAACAATGGATCTTACTTTCCTA-GCA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTAC-TTCCCAGGCA
* * * *
47977597 TTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGGCA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCAGGCA
* * * *
47977647 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCCCCCC
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTAC-TTCCCAG---GCA
* * * * * * *
47977701 TAGC--CG-AATAGATTGAAGCTACAACCGCTCGCTCTTACTTCCCTGGCA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGC-GGATCTTACTTCCCAGGCA
* * * *
47977749 TTGCACTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTA-GCG
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTAC-TTCCCAGGCA
* * * *
47977799 TTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGGCA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCAGGCA
* * * *
47977849 TTGCAATTAAGAAGATTGAGGCTACAACAGCGGATCTTACTTCCCTGGCA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCAGGCA
* * *
47977899 TTGCAATTAAAAAAATTGAAGCTACAACAGCGGATCTTACTTTCCTA-GCA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTAC-TTCCCAGGCA
* * * *
47977949 TTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGGCA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCAGGCA
* * * * * *
47977999 TTGCAATTAAAAAAATTGAAGCTATAATAGTGGATCTTACTTTCCTA-GCA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTAC-TTCCCAGGCA
* * * *
47978049 TTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGGCA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCAGGCA
* * * *
47978099 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCCTACTTTCCTA-GCG
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTAC-TTCCCAGGCA
* * * * *
47978149 TTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCAGGCA
* * *
47978199 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTCTCCTA-GCG
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACT-TCCCAGGCA
* * ** * *
47978249 TTGCAGTGGAGCAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCAGGCA
* *
47978299 TTGCAATTAAAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCAGGCGA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCAGGC-A
** * ** * * * ** * *
47978350 -TGCAGCGAAATAGATTGAAGCTATGACGGTGAATCTCGCTTCCCCGACA
1 TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCAGGCA
* * * ** *
47978399 TCGCAACT-CAAAAGATTGAAGCCACAATGGCGAATCTTACTTCCCAGGCA
1 TTGCAA-TGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCAGGCA
* ** * *
47978449 ATGCAGCGAAATAGATTGAAGCTACGACAG
1 TTGCAATGAAAAAGATTGAAGCTACAACAG
47978479 TGAATCTCGT
Statistics
Matches: 1025, Mismatches: 222, Indels: 70
0.78 0.17 0.05
Matches are distributed among these distances:
48 5 0.00
49 41 0.04
50 881 0.86
51 86 0.08
52 8 0.01
54 4 0.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (50 bp):
TTGCAATGAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCAGGCA
Found at i:47979024 original size:132 final size:132
Alignment explanation
Indices: 47978786--47979243 Score: 724
Period size: 132 Copynumber: 3.5 Consensus size: 132
47978776 AGCTACGAAT
*
47978786 CAGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATAC
1 CAGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATCTTATCTTCCCAATAC
* *
47978851 AGTGGAGAAGCAGATTTAAGCCACTT-GTCCTATCACTCTAAGCAGTAGTGGAGTAGGTTGAAGA
66 AGTGGAGAAGCAGATTTAAGCCA-TTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTCGAAGA
47978915 TTG
130 TTG
* *
47978918 CAGATTCTGTCACCCTAAGTAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATAC
1 CAGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATCTTATCTTCCCAATAC
*
47978983 AGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGAT
66 AGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTCGAAGAT
*
47979048 GG
131 TG
* *
47979050 CAGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATCTTATCTTCCCAAGAT
1 CAGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATCTTATCTTCCCAATAC
* * * * *
47979115 AGTCGAGAAGCAGATTTGAA-CCATTAGTCCTATCACCCTAAGCAGTAATGGAATGGGTCAAAGA
66 AGTGGAGAAGCAGATTT-AAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTCGAAGA
47979179 TTG
130 TTG
* *
47979182 TAGATTCTGT-ATCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAA
1 CAGATTCTGTCA-CCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATCTTATCTTCCCAA
47979244 GATAGTAGGG
Statistics
Matches: 305, Mismatches: 18, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
131 3 0.01
132 300 0.98
133 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (132 bp):
CAGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATCTTATCTTCCCAATAC
AGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTCGAAGAT
TG
Found at i:47980979 original size:22 final size:22
Alignment explanation
Indices: 47980940--47981001 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
47980930 GTTATTACTA
47980940 TTATAT-TTATT-TATATATCT
1 TTATATCTTATTATATATATCT
47980960 TTATATCTTATTATATATATCT
1 TTATATCTTATTATATATATCT
* *
47980982 ATCTATCTTATTATATATAT
1 TTATATCTTATTATATATAT
47981002 ATGTATATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.16
21 5 0.13
22 27 0.71
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATATCTTATTATATATATCT
Found at i:47982245 original size:6 final size:6
Alignment explanation
Indices: 47982234--47982263 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
47982224 ACTATACCTC
47982234 GTTTAG GTTTAG GTTTAG GTTTAG GTTTAG
1 GTTTAG GTTTAG GTTTAG GTTTAG GTTTAG
47982264 TTATTTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (6 bp):
GTTTAG
Found at i:47986076 original size:34 final size:32
Alignment explanation
Indices: 47985962--47986069 Score: 117
Period size: 34 Copynumber: 3.2 Consensus size: 32
47985952 GTAGGTTTAG
47985962 GGTTTAGGGTTTTTTAAAAAATTAATTAAATTA
1 GGTTTAGGG-TTTTTAAAAAATTAATTAAATTA
* * * *
47985995 AGTTTTGGGGTTTTAAATAAATAAATTAAATTA
1 GGTTTAGGGTTTTTAAA-AAATTAATTAAATTA
* *
47986028 GAGATTAAGGTTTTTAAGAAAATTAATTAAATTA
1 G-GTTTAGGGTTTTTAA-AAAATTAATTAAATTA
47986062 TGGTTTAG
1 -GGTTTAG
47986070 TTTTTTTTAA
Statistics
Matches: 59, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
32 7 0.12
33 21 0.36
34 29 0.49
35 2 0.03
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.43
Consensus pattern (32 bp):
GGTTTAGGGTTTTTAAAAAATTAATTAAATTA
Found at i:47986332 original size:126 final size:126
Alignment explanation
Indices: 47986140--47986404 Score: 365
Period size: 126 Copynumber: 2.1 Consensus size: 126
47986130 TTTTGTTTTT
* *
47986140 TTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAGATAATGTAAAAA
1 TTTTTCTACAGTAGTTCCTAAAAAAATAATTTTGAGAAGACGGTTCTGAAAAGATAATGTAAAAA
* * **
47986205 ATGCTTAAAGCAAG-ATGCATTGTCAGCAAAATT-ACTGAAAATAGCTCCCATGTAGACGTTC
66 ATGCTTAAAGC-AGTATGCACTGTCAGCAAAATTGA-TGAAAAAAGCTCCCATGTAGACACTC
* **
47986266 TTTTTCTACAGTAGTTCCTAAAAAAATAATTTTGAGAAGACGGTTCTGGACAA-ATGGTGTAAAA
1 TTTTTCTACAGTAGTTCCTAAAAAAATAATTTTGAGAAGACGGTTCT-GAAAAGATAATGTAAAA
* * * *
47986330 AATGTTTCAAGCAGTATGCACTGTCAGTAAAATTGATGAAAAAAGCTCCCATGTGGACACTC
65 AATGCTTAAAGCAGTATGCACTGTCAGCAAAATTGATGAAAAAAGCTCCCATGTAGACACTC
47986392 TTTTTCTACAGTA
1 TTTTTCTACAGTA
47986405 TTTCTTGTTT
Statistics
Matches: 123, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
125 2 0.02
126 116 0.94
127 5 0.04
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTCCTAAAAAAATAATTTTGAGAAGACGGTTCTGAAAAGATAATGTAAAAA
ATGCTTAAAGCAGTATGCACTGTCAGCAAAATTGATGAAAAAAGCTCCCATGTAGACACTC
Found at i:47998230 original size:2 final size:2
Alignment explanation
Indices: 47998223--47998263 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
47998213 AGACAAAGGT
47998223 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
47998264 GTTTTTGGGT
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:48004833 original size:17 final size:17
Alignment explanation
Indices: 48004811--48004869 Score: 84
Period size: 17 Copynumber: 3.5 Consensus size: 17
48004801 AAAAAGTATT
48004811 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
**
48004828 TTAAAAA-ATTAAAAAA
1 TTAAAAATATTTTAAAA
48004844 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
*
48004861 TTTAAAATA
1 TTAAAAATA
48004870 AAAAAGTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
16 14 0.39
17 22 0.61
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:48004860 original size:25 final size:24
Alignment explanation
Indices: 48004832--48004885 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
48004822 TTAAAATTAA
*
48004832 AAAATTAAAAAATTAAAAA-TATTTT
1 AAAATT-AAAAATAAAAAAGTA-TTT
*
48004857 AAAATTTAAAATAAAAAAGTATTT
1 AAAATTAAAAATAAAAAAGTATTT
48004881 AAAAT
1 AAAAT
48004886 ATTTAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 18 0.69
25 8 0.31
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (24 bp):
AAAATTAAAAATAAAAAAGTATTT
Found at i:48004863 original size:8 final size:8
Alignment explanation
Indices: 48004824--48004850 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
48004814 AAAATATTTT
48004824 AAAATTAA
1 AAAATTAA
48004832 AAAATTAA
1 AAAATTAA
48004840 AAAATTAA
1 AAAATTAA
48004848 AAA
1 AAA
48004851 TATTTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
AAAATTAA
Found at i:48004873 original size:24 final size:26
Alignment explanation
Indices: 48004840--48004898 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
48004830 AAAAAATTAA
* *
48004840 AAAATTAAAAA-TATTTTAAA-ATTT
1 AAAATAAAAAAGTATTTAAAATATTT
48004864 AAAATAAAAAAGTATTTAAAATATTT
1 AAAATAAAAAAGTATTTAAAATATTT
*
48004890 AAATTAAAA
1 AAAATAAAA
48004899 TTTAAAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 10 0.33
25 8 0.27
26 12 0.40
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (26 bp):
AAAATAAAAAAGTATTTAAAATATTT
Found at i:48004893 original size:25 final size:24
Alignment explanation
Indices: 48004840--48004898 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 24
48004830 AAAAAATTAA
48004840 AAAATTAAAAATATTTTAAAATTT
1 AAAATTAAAAATATTTTAAAATTT
*
48004864 AAAATAAAAAAGTA-TTTAAAATATT
1 AAAATTAAAAA-TATTTTAAAAT-TT
*
48004889 TAAATTAAAA
1 AAAATTAAAA
48004899 TTTAAAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 18 0.60
25 12 0.40
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
AAAATTAAAAATATTTTAAAATTT
Found at i:48004905 original size:33 final size:35
Alignment explanation
Indices: 48004793--48004905 Score: 114
Period size: 33 Copynumber: 3.3 Consensus size: 35
48004783 AATTTATTTT
48004793 AAATATTAAAAAAGTATTTTAAAAATATTTTAAAATTAA
1 AAAT-TTAAAAAAGTA-TTT-AAAATATTTTAAAATT-A
* *
48004832 AAAATT-AAAAA--ATTAAAAATATTTTAAAATTTA
1 AAATTTAAAAAAGTATTTAAAATATTTTAAAA-TTA
48004865 AAA--TAAAAAAGTATTTAAAATA-TTT-AAATTA
1 AAATTTAAAAAAGTATTTAAAATATTTTAAAATTA
48004896 AAATTTAAAA
1 AAATTTAAAA
48004906 TAAATATATT
Statistics
Matches: 65, Mismatches: 3, Indels: 18
0.76 0.03 0.21
Matches are distributed among these distances:
31 7 0.11
32 8 0.12
33 26 0.40
34 13 0.20
35 1 0.02
37 5 0.08
38 2 0.03
39 3 0.05
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (35 bp):
AAATTTAAAAAAGTATTTAAAATATTTTAAAATTA
Found at i:48005205 original size:20 final size:21
Alignment explanation
Indices: 48005167--48005205 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
48005157 AAACAAATAC
48005167 TCATATTTATATAATAAAAAT
1 TCATATTTATATAATAAAAAT
*
48005188 TCATATTT-TATTATAAAA
1 TCATATTTATATAATAAAA
48005206 TATTTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (21 bp):
TCATATTTATATAATAAAAAT
Found at i:48005314 original size:23 final size:23
Alignment explanation
Indices: 48005231--48005314 Score: 57
Period size: 23 Copynumber: 3.6 Consensus size: 23
48005221 TTATAAATTG
48005231 TAATATATATTTATTA-TTAAAATA
1 TAATA-ATA-TTATTATTTAAAATA
* *
48005255 T--TAATATTAATATTTTCAGTAATA
1 TAATAATATTATTA-TTT-A-AAATA
* * *
48005279 TATTAAGAATATTATTTAAAATA
1 TAATAATATTATTATTTAAAATA
48005302 TAATAATATTATT
1 TAATAATATTATT
48005315 GTTAAATTTA
Statistics
Matches: 45, Mismatches: 9, Indels: 13
0.67 0.13 0.19
Matches are distributed among these distances:
20 5 0.11
21 3 0.07
22 4 0.09
23 15 0.33
24 7 0.16
25 3 0.07
26 8 0.18
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (23 bp):
TAATAATATTATTATTTAAAATA
Found at i:48010722 original size:41 final size:41
Alignment explanation
Indices: 48010675--48010821 Score: 206
Period size: 41 Copynumber: 3.6 Consensus size: 41
48010665 CATTGAATGT
* *
48010675 AAGGGGTCGCTAAGTGTAGATTCCCCGAATCATTGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGATCAAA
* *
48010716 AAGGGGTTGCTAAGTGCAGATTCCCAGAATCACTGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGATCAAA
* *
48010757 AAGGGGTTGCTAAGTGCAGATTCCCCGAAAC-TCTGATAAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCAT-TGATCAAA
* *
48010798 AAGGTGTTGCGAAGTGCAGATTCC
1 AAGGGGTTGCTAAGTGCAGATTCC
48010822 TCAAGGGGTT
Statistics
Matches: 95, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
41 95 1.00
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (41 bp):
AAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGATCAAA
Found at i:48010827 original size:26 final size:26
Alignment explanation
Indices: 48010798--48010849 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
48010788 TCTGATAAAA
*
48010798 AAGGTGTTGCGAAGTGCAGATTCCTC
1 AAGGGGTTGCGAAGTGCAGATTCCTC
* **
48010824 AAGGGGTTGCTAAGTGTTGATTCCTC
1 AAGGGGTTGCGAAGTGCAGATTCCTC
48010850 GAATTATTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (26 bp):
AAGGGGTTGCGAAGTGCAGATTCCTC
Found at i:48010972 original size:41 final size:43
Alignment explanation
Indices: 48010865--48010973 Score: 116
Period size: 41 Copynumber: 2.6 Consensus size: 43
48010855 ATTGATTCCA
* * *
48010865 AAGGTGGTTGCTAAGTGCTAATTCCACCGTATCCTTGATTGTG
1 AAGGTGGTTGCTAAGTGCTAATTCCACCGTATCATTGAATATG
* * * * **
48010908 AAAG-GGTTGCTATGTGTTGATTCC-TTGTATCATTGAATAT-
1 AAGGTGGTTGCTAAGTGCTAATTCCACCGTATCATTGAATATG
48010948 AAGGTGGTTGCTAAGTGCTAATTCCA
1 AAGGTGGTTGCTAAGTGCTAATTCCA
48010974 TCGAGTAACG
Statistics
Matches: 51, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
40 3 0.06
41 28 0.55
42 17 0.33
43 3 0.06
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.37
Consensus pattern (43 bp):
AAGGTGGTTGCTAAGTGCTAATTCCACCGTATCATTGAATATG
Found at i:48013961 original size:42 final size:42
Alignment explanation
Indices: 48013869--48013985 Score: 114
Period size: 41 Copynumber: 2.8 Consensus size: 42
48013859 GTTACTCGAT
* * * * *
48013869 GGAATCAACACTTAGCAACCACCTT-ATATTC-AGTGATACGG
1 GGAATCAGCACATAGAAACCACCTTCAAAATCAAG-GATACGG
48013910 GGAATCAGCACATAGAAACC-CCTTCAAAATCAAGGATACGG
1 GGAATCAGCACATAGAAACCACCTTCAAAATCAAGGATACGG
* * * *
48013951 TGGAATCAGCACTTAGCAACCACCTTTAGAATCAA
1 -GGAATCAGCACATAGAAACCACCTTCAAAATCAA
48013986 TAATTTGGGG
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
40 4 0.06
41 28 0.44
42 20 0.32
43 11 0.17
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.21
Consensus pattern (42 bp):
GGAATCAGCACATAGAAACCACCTTCAAAATCAAGGATACGG
Found at i:48013998 original size:42 final size:42
Alignment explanation
Indices: 48013869--48014011 Score: 146
Period size: 42 Copynumber: 3.4 Consensus size: 42
48013859 GTTACTCGAT
* * * *
48013869 GGAATCAACACTTAGCAACCACC-TTATATTCAGTGATACGG
1 GGAATCAGCACTTAGCAACCACCTTTAAAATCAATGATACGG
* * * *
48013910 GGAATCAGCACATAGAAACC-CCTTCAAAATCAAGGATACGG
1 GGAATCAGCACTTAGCAACCACCTTTAAAATCAATGATACGG
* * **
48013951 TGGAATCAGCACTTAGCAACCACCTTTAGAATCAATAATTTGG
1 -GGAATCAGCACTTAGCAACCACCTTTAAAATCAATGATACGG
*
48013994 GGAATCATCACTTAGCAA
1 GGAATCAGCACTTAGCAA
48014012 TCCCTCAGGG
Statistics
Matches: 82, Mismatches: 17, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
40 2 0.02
41 30 0.37
42 35 0.43
43 15 0.18
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.22
Consensus pattern (42 bp):
GGAATCAGCACTTAGCAACCACCTTTAAAATCAATGATACGG
Found at i:48014022 original size:26 final size:26
Alignment explanation
Indices: 48013993--48014042 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
48013983 CAATAATTTG
*
48013993 GGGAATCAT-CACTTAGCAATCCCTCA
1 GGGAATC-TGCACTTAGCAACCCCTCA
48014019 GGGAATCTGCACTTAGCAACCCCT
1 GGGAATCTGCACTTAGCAACCCCT
48014043 TTTTGATCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (26 bp):
GGGAATCTGCACTTAGCAACCCCTCA
Found at i:48014064 original size:41 final size:40
Alignment explanation
Indices: 48014019--48014166 Score: 199
Period size: 41 Copynumber: 3.6 Consensus size: 40
48014009 CAATCCCTCA
48014019 GGGAATCTGCACTTAGCAACCCCTTTTTGATCAAAGTTTCG
1 GGGAATCTGCACTTAGCAACCCCTTTTTGATC-AAGTTTCG
* * * *
48014060 GGGAATCTGCACTTAGCAACTCCTTTTTTATCATTGATTCG
1 GGGAATCTGCACTTAGCAACCCCTTTTTGATCA-AGTTTCG
* *
48014101 GGGAATTTGCACTTAGGAACCCCTTTTTGATC-AGTTATTCG
1 GGGAATCTGCACTTAGCAACCCCTTTTTGATCAAG-T-TTCG
48014142 GGGAATCTGCACTTAGCAACCCCTT
1 GGGAATCTGCACTTAGCAACCCCTT
48014167 ACATTCAATG
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 90 0.98
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.34
Consensus pattern (40 bp):
GGGAATCTGCACTTAGCAACCCCTTTTTGATCAAGTTTCG
Found at i:48014073 original size:67 final size:68
Alignment explanation
Indices: 48013952--48014078 Score: 172
Period size: 67 Copynumber: 1.9 Consensus size: 68
48013942 AGGATACGGT
48013952 GGAATCAGCACTTAGCAACCACCTTTAGAATCAATAATTTGGGGAATCATCACTTAGCAATCCCT
1 GGAATCAGCACTTAGCAACCACCTTTAGAATCAATAATTTGGGGAATCATCACTTAGCAATCCCT
48014017 CAG
66 CAG
* * *
48014020 GGAATCTGCACTTAGCAACC-CCTTTTTG-ATCAA-AGTTTCGGGGAATC-TGCACTTAGCAA
1 GGAATCAGCACTTAGCAACCACC-TTTAGAATCAATAATTT-GGGGAATCAT-CACTTAGCAA
48014079 CTCCTTTTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
66 5 0.09
67 25 0.47
68 23 0.43
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (68 bp):
GGAATCAGCACTTAGCAACCACCTTTAGAATCAATAATTTGGGGAATCATCACTTAGCAATCCCT
CAG
Found at i:48028181 original size:9 final size:9
Alignment explanation
Indices: 48028163--48028238 Score: 91
Period size: 9 Copynumber: 8.4 Consensus size: 9
48028153 TTTGGTTAAA
48028163 AATTAACCG
1 AATTAACCG
*
48028172 AATTACCCG
1 AATTAACCG
48028181 AATTAACCG
1 AATTAACCG
*
48028190 GATT-ACCTG
1 AATTAACC-G
*
48028199 AATTAACTG
1 AATTAACCG
*
48028208 AATTACCCG
1 AATTAACCG
*
48028217 AATTATCCG
1 AATTAACCG
48028226 AATTAACCG
1 AATTAACCG
48028235 AATT
1 AATT
48028239 GAATCACTAC
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
8 3 0.05
9 51 0.91
10 2 0.04
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:48028186 original size:18 final size:18
Alignment explanation
Indices: 48028163--48028238 Score: 107
Period size: 18 Copynumber: 4.2 Consensus size: 18
48028153 TTTGGTTAAA
48028163 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
* *
48028181 AATTAACCGGATTACCTG
1 AATTAACCGAATTACCCG
*
48028199 AATTAACTGAATTACCCG
1 AATTAACCGAATTACCCG
* *
48028217 AATTATCCGAATTAACCG
1 AATTAACCGAATTACCCG
48028235 AATT
1 AATT
48028239 GAATCACTAC
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:48028381 original size:18 final size:18
Alignment explanation
Indices: 48028341--48028384 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
48028331 AATTTTTATG
**
48028341 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
48028359 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
48028377 CTTGGGTT
1 ATTGGGTT
48028385 TGGATTGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:48030079 original size:26 final size:26
Alignment explanation
Indices: 48030049--48030100 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
48030039 GAAGTAAACA
48030049 CCGGATATTTTTTTTACAGAATTGTC
1 CCGGATATTTTTTTTACAGAATTGTC
48030075 CCGGATATTTTTTTTACAGAATTGTC
1 CCGGATATTTTTTTTACAGAATTGTC
48030101 TTATATCATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (26 bp):
CCGGATATTTTTTTTACAGAATTGTC
Found at i:48031250 original size:14 final size:14
Alignment explanation
Indices: 48031227--48031260 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
48031217 TGGTATGAGT
48031227 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
48031240 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
48031254 TTATAGG
1 TTATAGG
48031261 CAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:48032866 original size:57 final size:58
Alignment explanation
Indices: 48032757--48032874 Score: 157
Period size: 57 Copynumber: 2.1 Consensus size: 58
48032747 ATACAAATGG
* * * *
48032757 TGAAAATGGAGAAATGAGAAACATTTGAAAATGATTATAGTTTTTTCTAAAATGAAAA
1 TGAAAATGGAGAAATGAGAAACATTTGAAAATAAATATAGTTTTCTCCAAAATGAAAA
* * * *
48032815 TGAAAATGGAGAAATG-GAATCATTTGGAAATAAATGTGGTTTTCTCCAAAATGAAAA
1 TGAAAATGGAGAAATGAGAAACATTTGAAAATAAATATAGTTTTCTCCAAAATGAAAA
48032872 TGA
1 TGA
48032875 CCTAAGAAGA
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 36 0.69
58 16 0.31
ACGTcount: A:0.46, C:0.05, G:0.19, T:0.30
Consensus pattern (58 bp):
TGAAAATGGAGAAATGAGAAACATTTGAAAATAAATATAGTTTTCTCCAAAATGAAAA
Found at i:48041158 original size:19 final size:20
Alignment explanation
Indices: 48041136--48041179 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
48041126 ATATAAAAAT
48041136 AAAAATATA-AAAAT-TCAGA
1 AAAAATATATAAAATCT-AGA
48041155 AAAAATATATAAAATCTAGA
1 AAAAATATATAAAATCTAGA
48041175 AAAAA
1 AAAAA
48041180 AACATATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.39
20 13 0.57
21 1 0.04
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (20 bp):
AAAAATATATAAAATCTAGA
Found at i:48042873 original size:39 final size:39
Alignment explanation
Indices: 48042735--48042882 Score: 138
Period size: 39 Copynumber: 3.8 Consensus size: 39
48042725 ATATAACTTT
* **
48042735 AGAATATGCAA-ACAAGGCTAGATCTCATTATATTACCTA
1 AGAATTTGCAACA-AAGGCTAGATCTCATTATATTACCCG
* * *
48042774 AGAACTTGCAAC-CAGGTTAGATCTCATTATATTACCCG
1 AGAATTTGCAACAAAGGCTAGATCTCATTATATTACCCG
* ** * * *
48042812 AGAATCTAAAACAAATGATAGATCTCATTACATTACCCG
1 AGAATTTGCAACAAAGGCTAGATCTCATTATATTACCCG
** *
48042851 AGGGTTTGCAACAAAGGCTAGATCTCGTTATA
1 AGAATTTGCAACAAAGGCTAGATCTCATTATA
48042883 ATCTGTACAA
Statistics
Matches: 84, Mismatches: 23, Indels: 4
0.76 0.21 0.04
Matches are distributed among these distances:
38 30 0.36
39 54 0.64
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.28
Consensus pattern (39 bp):
AGAATTTGCAACAAAGGCTAGATCTCATTATATTACCCG
Found at i:48045595 original size:16 final size:16
Alignment explanation
Indices: 48045574--48045624 Score: 84
Period size: 16 Copynumber: 3.2 Consensus size: 16
48045564 TTGGTTCGCT
48045574 GTATTGGAATAGAGGC
1 GTATTGGAATAGAGGC
48045590 GTATTGGAATAGAGGC
1 GTATTGGAATAGAGGC
* *
48045606 GTAATGGAATAGAGAC
1 GTATTGGAATAGAGGC
48045622 GTA
1 GTA
48045625 ATAGCAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.35, C:0.06, G:0.35, T:0.24
Consensus pattern (16 bp):
GTATTGGAATAGAGGC
Found at i:48045886 original size:18 final size:18
Alignment explanation
Indices: 48045856--48045892 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
48045846 TAATTATTAT
48045856 TATATATATTTAATTAAAA
1 TATATATATTTAA-TAAAA
48045875 TATATA-ATTTAATAAAA
1 TATATATATTTAATAAAA
48045892 T
1 T
48045893 TCTTAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 6 0.33
19 6 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TATATATATTTAATAAAA
Found at i:48045999 original size:18 final size:17
Alignment explanation
Indices: 48045976--48046012 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
48045966 AATTATTATT
48045976 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
48045992 AAATATATGATTTAATA
1 AAATATATGATTTAATA
48046009 AAAT
1 AAAT
48046013 TCTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:48046056 original size:120 final size:120
Alignment explanation
Indices: 48045834--48046468 Score: 1087
Period size: 120 Copynumber: 5.3 Consensus size: 120
48045824 ATAATTTAAT
* * *
48045834 TATATTTTAACATAATTATTATTATATATA-TTTAATTAAAATATATAATTTAATAAAATTCTTA
1 TATAATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTA
* *
48045898 ATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAA
66 ATAATCAATATTCTTATATGAATTTACTAAAATTATAATATATGATACTATAAAA
48045953 TATAATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTA
1 TATAATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTA
*
48046018 ATAATCAATATTCTTATATGAATTTACTAAAATTATAATATATGATACTATAAAT
66 ATAATCAATATTCTTATATGAATTTACTAAAATTATAATATATGATACTATAAAA
*
48046073 TATAATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTA
1 TATAATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTA
48046138 ATAATCAATATTCTTATATGAATTTACTAAAATTATAATATATGATACTATAAAA
66 ATAATCAATATTCTTATATGAATTTACTAAAATTATAATATATGATACTATAAAA
*
48046193 TATAATTTGAA-ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTTTT
1 TATAATTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTT
48046257 AATAATCAATATTCTTATATGAATTTACTAAAATTATAATATATGATACTATAAAA
65 AATAATCAATATTCTTATATGAATTTACTAAAATTATAATATATGATACTATAAAA
*
48046313 TATAATTTGAA-ATAATAATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTT
1 TATAATTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTT
* * * *
48046377 AATATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAA
65 AATAATCAATATTCTTATATGAATTTACTAAAATTATAATATATGATACTAT-AAAA
*
48046434 TATAATTTAAAATAATTATTATTAAATATAATTTT
1 TATAATTTAACATAATTATTATTAAATAT-ATTTT
48046469 TCTAAATATA
Statistics
Matches: 494, Mismatches: 17, Indels: 7
0.95 0.03 0.01
Matches are distributed among these distances:
119 28 0.06
120 430 0.87
121 31 0.06
122 5 0.01
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.45
Consensus pattern (120 bp):
TATAATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTA
ATAATCAATATTCTTATATGAATTTACTAAAATTATAATATATGATACTATAAAA
Found at i:48046119 original size:18 final size:17
Alignment explanation
Indices: 48046098--48046132 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
48046088 TTATTATTAA
*
48046098 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
48046116 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
48046133 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:48046239 original size:18 final size:17
Alignment explanation
Indices: 48046216--48046252 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
48046206 AATTATTATT
48046216 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
48046232 AAATATATGATTTAATA
1 AAATATATGATTTAATA
48046249 AAAT
1 AAAT
48046253 TTTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:48046624 original size:45 final size:44
Alignment explanation
Indices: 48046573--48046662 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
48046563 GAACAGAGGC
*
48046573 GTAATGGATTAGAGGCGTAATAGCAAATCAAT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAG-AAATC-ATGTGTTTGGTTGAAT
* *
48046618 GTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAAT
48046662 G
1 G
48046663 GAATAGAGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 18 0.44
45 22 0.54
ACGTcount: A:0.31, C:0.06, G:0.29, T:0.34
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAAT
Found at i:48046844 original size:16 final size:16
Alignment explanation
Indices: 48046807--48046848 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
48046797 TTAATCATAT
*
48046807 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
48046823 TT-AAATATATTATAA
1 TTAAAATATATTATAA
48046838 TTAAAATATAT
1 TTAAAATATAT
48046849 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:48046855 original size:14 final size:15
Alignment explanation
Indices: 48046816--48046857 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
48046806 TTTAAACATA
*
48046816 ATTATTATTAAATAT
1 ATTATAATTAAATAT
48046831 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
48046845 A-TATAATTTAATA
1 ATTATAATTAAATA
48046858 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:48060863 original size:15 final size:16
Alignment explanation
Indices: 48060843--48060880 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
48060833 GTTTAGTCCC
*
48060843 TAGGGTTTTT-TGGTT
1 TAGGGTTTTTAGGGTT
48060858 TAGGGTTTTTAGGGTT
1 TAGGGTTTTTAGGGTT
48060874 TAGGGTT
1 TAGGGTT
48060881 AGAGTTTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.11, C:0.00, G:0.37, T:0.53
Consensus pattern (16 bp):
TAGGGTTTTTAGGGTT
Found at i:48060929 original size:34 final size:34
Alignment explanation
Indices: 48060865--48060956 Score: 114
Period size: 34 Copynumber: 2.6 Consensus size: 34
48060855 GTTTAGGGTT
* * *
48060865 TTTAGGGTTTAGGGTTAGAGTTTTGTTAAAAATAA
1 TTTA-GGTTTAGAGTTAGGGTTTTGATAAAAATAA
48060900 TTTAGGTTTAGAGCTTAGGGTTTT-ATAAAAATAA
1 TTTAGGTTTAGAG-TTAGGGTTTTGATAAAAATAA
*
48060934 TTTTGGTTTAGAGTGTAGGGTTT
1 TTTAGGTTTAGAGT-TAGGGTTT
48060957 AAGAATTTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
33 1 0.02
34 37 0.73
35 13 0.25
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.45
Consensus pattern (34 bp):
TTTAGGTTTAGAGTTAGGGTTTTGATAAAAATAA
Found at i:48061020 original size:34 final size:34
Alignment explanation
Indices: 48060982--48061088 Score: 110
Period size: 34 Copynumber: 3.1 Consensus size: 34
48060972 TAAATGAAGG
**
48060982 TTTAGAGTTTTTTTTAAAATTAATTAAATTAGGT
1 TTTAGAGTTTTTAATAAAATTAATTAAATTAGGT
* * *
48061016 TTTAGAAGTTTTAAAT-AAATAAATAAAATTA-GT
1 TTTAG-AGTTTTTAATAAAATTAATTAAATTAGGT
* * *
48061049 GTTTAGAGTTTTTAAGAAAATTGATTAAATTAGGG
1 -TTTAGAGTTTTTAATAAAATTAATTAAATTAGGT
48061084 TTTAG
1 TTTAG
48061089 TTTTTTTTAA
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
33 10 0.17
34 40 0.69
35 8 0.14
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (34 bp):
TTTAGAGTTTTTAATAAAATTAATTAAATTAGGT
Found at i:48061105 original size:34 final size:33
Alignment explanation
Indices: 48060980--48061104 Score: 99
Period size: 34 Copynumber: 3.7 Consensus size: 33
48060970 AATAAATGAA
*
48060980 GGTTTAGAGTTTTTTTTAA-AATTAATTAAATTAG
1 GGTTTAGA--TTTTTTAAATAATTAATTAAATTAG
* ** * *
48061014 GTTTTAGAAGTTTTAAATAAATAAATAAAATTAG
1 GGTTTAGATTTTTTAAAT-AATTAATTAAATTAG
* * * *
48061048 TGTTTAGAGTTTTTAAGAAAATTGATTAAATTAG
1 GGTTTAGATTTTTTAA-ATAATTAATTAAATTAG
*
48061082 GGTTTAGTTTTTTTTAAATAATT
1 GGTTTAG-ATTTTTTAAATAATT
48061105 GTGTTTAGGT
Statistics
Matches: 69, Mismatches: 18, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
32 6 0.09
34 55 0.80
35 8 0.12
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.47
Consensus pattern (33 bp):
GGTTTAGATTTTTTAAATAATTAATTAAATTAG
Found at i:48061391 original size:126 final size:126
Alignment explanation
Indices: 48061183--48061561 Score: 498
Period size: 126 Copynumber: 3.0 Consensus size: 126
48061173 AATAGTTTTA
* * * * *
48061183 GAAAAATTAATTTTGAGAATACAGTTCTGAA-AAGATAATGTCAAAAATACTTCAAGCAGGATGC
1 GAAAAA-TAATTTTGAGAAGACGGTTCTGAACAA-ATAGTGTAAAAAATGCTTCAAGCAGGATGC
48061247 ACTGTCAGCAAAATTACTGAAAAAAGCTCTCACGTGGACGCTCTTTTTCTACAGTAGTTCCTG
64 ACTGTCAGCAAAATTACTGAAAAAAGCTCTCACGTGGACGCTCTTTTTCTACAGTAGTTCCTG
* *
48061310 GAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTAAAAAATGCTTCAAGTAGGATGCAT
1 GAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTAAAAAATGCTTCAAGCAGGATGCAC
* * *
48061375 TGTCAACAAGAA-TACTGAAAAAAGCTCTCACGTGGACGGTCATTTTCTACAGTAGTTCCTG
66 TGTCAGCAA-AATTACTGAAAAAAGCTCTCACGTGGACGCTCTTTTTCTACAGTAGTTCCTG
* * * * * *
48061436 AAAAAATAATTTTGAGAAGACGTTTTTGAACAAATGGTGTTAAAAGTGCTTCAAGCAGGATGCAC
1 GAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTAAAAAATGCTTCAAGCAGGATGCAC
* * *
48061501 TGTCAGTAAAATTGA-TGAGAAAAA-CT-TCCACGTGGACCCTTTTTTTCTACAGTAGTTCCTG
66 TGTCAGCAAAATT-ACTGA-AAAAAGCTCT-CACGTGGACGCTCTTTTTCTACAGTAGTTCCTG
48061562 TTTGGCCTTA
Statistics
Matches: 222, Mismatches: 24, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
125 3 0.01
126 203 0.91
127 16 0.07
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (126 bp):
GAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTAAAAAATGCTTCAAGCAGGATGCAC
TGTCAGCAAAATTACTGAAAAAAGCTCTCACGTGGACGCTCTTTTTCTACAGTAGTTCCTG
Found at i:48064668 original size:25 final size:25
Alignment explanation
Indices: 48064622--48064669 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
48064612 ACTTCTATTT
*
48064622 TATTAAAAATATAAAAATAATTTAC
1 TATTAAAAATATAAAAAAAATTTAC
*
48064647 TATTAAATAT-TAAAAACAAATTT
1 TATTAAAAATATAAAAA-AAATTT
48064670 TATTTTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (25 bp):
TATTAAAAATATAAAAAAAATTTAC
Found at i:48064673 original size:23 final size:23
Alignment explanation
Indices: 48064618--48064673 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 23
48064608 AAGAACTTCT
*
48064618 ATTTTATTAAAAATATAAAAATA
1 ATTTTATTAAAAATATAAAAAAA
*
48064641 ATTTACTATTAAATAT-TAAAAACAA
1 ATTT--TATTAAAAATATAAAAA-AA
48064666 ATTTTATT
1 ATTTTATT
48064674 TTATTAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
23 8 0.29
24 6 0.21
25 14 0.50
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTTTATTAAAAATATAAAAAAA
Found at i:48065111 original size:18 final size:18
Alignment explanation
Indices: 48065088--48065124 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
48065078 AGAAAATGAA
* *
48065088 ACATATAAGGGTTAGGAT
1 ACATATAAAGGCTAGGAT
48065106 ACATATAAAGGCTAGGAT
1 ACATATAAAGGCTAGGAT
48065124 A
1 A
48065125 TGCACTTGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.08, G:0.24, T:0.24
Consensus pattern (18 bp):
ACATATAAAGGCTAGGAT
Found at i:48066629 original size:25 final size:24
Alignment explanation
Indices: 48066592--48066643 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
48066582 ACTGTTATAA
* *
48066592 AAAATTATAAAAT-AAAAATTAATT
1 AAAATTACAAAATGAAAAAAT-ATT
48066616 AAAATTACATAAATGAAAAAATATT
1 AAAATTACA-AAATGAAAAAATATT
48066641 AAA
1 AAA
48066644 TAATATTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.33
25 10 0.42
26 6 0.25
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (24 bp):
AAAATTACAAAATGAAAAAATATT
Found at i:48070404 original size:19 final size:18
Alignment explanation
Indices: 48070364--48070407 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
48070354 ACAATTCAAA
*
48070364 TATCAATGCAAATTAAGC
1 TATCAATGCAAATCAAGC
* *
48070382 TATCATATGCAAATCATGT
1 TATCA-ATGCAAATCAAGC
48070401 TATCAAT
1 TATCAAT
48070408 TACATAATCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (18 bp):
TATCAATGCAAATCAAGC
Found at i:48072507 original size:68 final size:68
Alignment explanation
Indices: 48072371--48072515 Score: 166
Period size: 68 Copynumber: 2.1 Consensus size: 68
48072361 GTTTGTTAGA
* * * * *
48072371 ACATTAAACATGATATGATATTGTGTAGGACCATAGCTAGAGTATGGCAACATATAGAGTCTATT
1 ACATTAAACATGAGATGATATTGTGTAAGACCATAGCTAGAGTATGGCAACATATAGAGACCACT
48072436 AGG
66 AGG
* * * * * * *
48072439 ACATTAAACATTAGATTATATTGTGTAAGATCATAGCTAG-GATTTGGTAACATATGGAGACCGC
1 ACATTAAACATGAGATGATATTGTGTAAGACCATAGCTAGAG-TATGGCAACATATAGAGACCAC
48072503 TAGG
65 TAGG
48072507 ACATTAAAC
1 ACATTAAAC
48072516 CAGGAGTCCT
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
67 1 0.02
68 63 0.98
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (68 bp):
ACATTAAACATGAGATGATATTGTGTAAGACCATAGCTAGAGTATGGCAACATATAGAGACCACT
AGG
Found at i:48081132 original size:15 final size:15
Alignment explanation
Indices: 48081114--48081172 Score: 59
Period size: 14 Copynumber: 4.0 Consensus size: 15
48081104 TTAAATTTCA
*
48081114 TTTTTTTTGTTA-TT
1 TTTTTTTTGTAATTT
*
48081128 TTTTTTTTGCAATTT
1 TTTTTTTTGTAATTT
*
48081143 GTTTTTTT-TAATTT
1 TTTTTTTTGTAATTT
*
48081157 TTATTTTTTTTAATTT
1 TT-TTTTTTGTAATTT
48081173 ATTACTATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
14 16 0.43
15 15 0.41
16 6 0.16
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.80
Consensus pattern (15 bp):
TTTTTTTTGTAATTT
Found at i:48081173 original size:14 final size:14
Alignment explanation
Indices: 48081100--48081175 Score: 55
Period size: 14 Copynumber: 5.1 Consensus size: 14
48081090 TTGGTCCCCG
*
48081100 TTTTTTAAATTTCATT
1 TTTTTTTAATTT-A-T
*
48081116 TTTTTTGTTATTT-T
1 TTTTTT-TAATTTAT
* *
48081130 TTTTTTGCAATTTGT
1 TTTTTT-TAATTTAT
48081145 TTTTTTTAATTTTTAT
1 TTTTTTTAA--TTTAT
48081161 TTTTTTTAATTTAT
1 TTTTTTTAATTTAT
48081175 T
1 T
48081176 ACTATATTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
14 20 0.40
15 7 0.14
16 19 0.38
17 4 0.08
ACGTcount: A:0.17, C:0.03, G:0.04, T:0.76
Consensus pattern (14 bp):
TTTTTTTAATTTAT
Found at i:48093143 original size:67 final size:67
Alignment explanation
Indices: 48093035--48093165 Score: 235
Period size: 67 Copynumber: 2.0 Consensus size: 67
48093025 TTTCCAATTT
48093035 AGAGAGCACACTCCAGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCAGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
48093100 CA
66 CA
* * *
48093102 AGAGAGCACATTCCCGCGAACCTCATTTCTTACAGCGGGATTACTAGTCCAGGCTAAATCCCCT
1 AGAGAGCACACTCCAGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCT
48093166 ATAATATAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.27, C:0.32, G:0.19, T:0.21
Consensus pattern (67 bp):
AGAGAGCACACTCCAGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
CA
Found at i:48096379 original size:21 final size:21
Alignment explanation
Indices: 48096338--48096380 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
48096328 AAACATGAAG
*
48096338 AAGAGAAGCAAGAGAGTGATA
1 AAGAGAAGAAAGAGAGTGATA
*
48096359 AAGAGGAAGAAAGCGAG-GATA
1 AAGA-GAAGAAAGAGAGTGATA
48096380 A
1 A
48096381 TGAAGGAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.53, C:0.05, G:0.35, T:0.07
Consensus pattern (21 bp):
AAGAGAAGAAAGAGAGTGATA
Found at i:48107736 original size:11 final size:11
Alignment explanation
Indices: 48107720--48107795 Score: 51
Period size: 10 Copynumber: 7.5 Consensus size: 11
48107710 TGTTCAAAAA
48107720 TAATATTATTT
1 TAATATTATTT
48107731 TAATA-TA-TT
1 TAATATTATTT
48107740 TAA-A--A-TT
1 TAATATTATTT
*
48107747 TAAT-TTAATT
1 TAATATTATTT
*
48107757 TAATACTTATCT
1 TAATA-TTATTT
*
48107769 TAATAGTATTT
1 TAATATTATTT
*
48107780 T-ATATTAATT
1 TAATATTATTT
48107790 TAATAT
1 TAATAT
48107796 GAAAGTGATT
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
7 6 0.12
8 1 0.02
9 6 0.12
10 16 0.31
11 14 0.27
12 9 0.17
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (11 bp):
TAATATTATTT
Found at i:48107772 original size:38 final size:37
Alignment explanation
Indices: 48107720--48107793 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 37
48107710 TGTTCAAAAA
*
48107720 TAATATTATTTTAATA-TATTTAAAATTTAATTTAATT
1 TAATATTATCTTAATAGTATTTAAAA-TTAATTTAATT
* *
48107757 TAATACTTATCTTAATAGTATTTTATATTAATTTAAT
1 TAATA-TTATCTTAATAGTATTTAAAATTAATTTAAT
48107794 ATGAAAGTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 5 0.16
38 20 0.62
39 7 0.22
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (37 bp):
TAATATTATCTTAATAGTATTTAAAATTAATTTAATT
Found at i:48110755 original size:14 final size:14
Alignment explanation
Indices: 48110736--48110773 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
48110726 AATCAGAATC
48110736 CTACCCACCAGCCT
1 CTACCCACCAGCCT
48110750 CTACCCACCAGCCT
1 CTACCCACCAGCCT
*
48110764 CTACACACCA
1 CTACCCACCA
48110774 TCTTCGTCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.26, C:0.55, G:0.05, T:0.13
Consensus pattern (14 bp):
CTACCCACCAGCCT
Found at i:48114486 original size:18 final size:18
Alignment explanation
Indices: 48114458--48114540 Score: 78
Period size: 18 Copynumber: 4.6 Consensus size: 18
48114448 AATTTATAAG
*
48114458 AAGCTAGCAAAACATATA
1 AAGCTCGCAAAACATATA
* *
48114476 AAGCTCACAAAACACATA
1 AAGCTCGCAAAACATATA
* *
48114494 GAGCTCGCGAAACACT-TA
1 AAGCTCGCAAAACA-TATA
* * *
48114512 GAGCTTGCAAAACATACA
1 AAGCTCGCAAAACATATA
48114530 AAGCTCGCAAA
1 AAGCTCGCAAA
48114541 TCATGTTCAT
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
17 1 0.02
18 50 0.98
ACGTcount: A:0.47, C:0.24, G:0.14, T:0.14
Consensus pattern (18 bp):
AAGCTCGCAAAACATATA
Done.