Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2552
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: 81852
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:862 original size:28 final size:27
Alignment explanation
Indices: 804--876 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 27
794 GAAAAAGTTA
* * *
804 AAAGAAAAAGTACAAAAAAAGAAACACC
1 AAAGAAAAAAT-CAAAAAAAAAAAAACC
*
832 AAAGAAAAAATGCAAAAAAAAAAAAAGC
1 AAAGAAAAAAT-CAAAAAAAAAAAAACC
**
860 AAAGGCAAAATCAAAAA
1 AAAGAAAAAATCAAAAA
877 GAGGGAACAA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 6 0.16
28 32 0.84
ACGTcount: A:0.74, C:0.11, G:0.11, T:0.04
Consensus pattern (27 bp):
AAAGAAAAAATCAAAAAAAAAAAAACC
Found at i:3147 original size:55 final size:55
Alignment explanation
Indices: 3087--3207 Score: 170
Period size: 55 Copynumber: 2.2 Consensus size: 55
3077 CAAGTCAAAA
* * * * *
3087 ACTTTTGTCAAAATCTTTAAGTCCAGTGTTGCTAGCTTTGATTTAGCACATTGAC
1 ACTTTTGTCAAAATCTCTAAGTCCAATGTTGCTAGCCTTGAATTAGCACATCGAC
*
3142 ACTTTTGTCAAAATCTCTAAGTCCAATGTTGCTGGCCTTGAATTAGCACATCGAC
1 ACTTTTGTCAAAATCTCTAAGTCCAATGTTGCTAGCCTTGAATTAGCACATCGAC
**
3197 ACCCTTGTCAA
1 ACTTTTGTCAA
3208 TCTTTTTCAA
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (55 bp):
ACTTTTGTCAAAATCTCTAAGTCCAATGTTGCTAGCCTTGAATTAGCACATCGAC
Found at i:3309 original size:36 final size:34
Alignment explanation
Indices: 3269--3750 Score: 251
Period size: 36 Copynumber: 14.0 Consensus size: 34
3259 ATACAAGTCA
*
3269 GTGGCAACCAAACATTTTTAAAGTCCACACGAGTTG
1 GTGGCAACCAAACA--TTCAAAGTCCACACGAGTTG
* * *
3305 GTGGCATCC---CAGTT-AAATTCCATA-GTAGTTG
1 GTGGCAACCAAACA-TTCAAAGTCCACACG-AGTTG
* * *
3336 GTGGC-ACC--CCATTCAAAGTCCACACAAATTG
1 GTGGCAACCAAACATTCAAAGTCCACACGAGTTG
* **
3367 GTGGCAACCAAACCCATTCAAAGTTCACACGAGTCA
1 GTGGCAACCAAA--CATTCAAAGTCCACACGAGTTG
* * *
3403 GTGGCAACCAAAGCCATTCAAAGTCAACACAAATTG
1 GTGGCAACCAAA--CATTCAAAGTCCACACGAGTTG
* * *
3439 GTGGCAACCAAACCTTTTCAAAGTCCACATGAGGTG
1 GTGGCAACCAAA-C-ATTCAAAGTCCACACGAGTTG
* *
3475 GTGGCATCC---CAGTT-AAAGTCCACACAAGTTG
1 GTGGCAACCAAACA-TTCAAAGTCCACACGAGTTG
* *
3506 GTGGC-ACC---CGATTCAAAGTCCACATGAGTTA
1 GTGGCAACCAAAC-ATTCAAAGTCCACACGAGTTG
* * **
3537 GTGGCAACCAAACCTTTCCAAAGTCCACACAAGTCA
1 GTGGCAACCAAA-CATT-CAAAGTCCACACGAGTTG
*** * * * * *
3573 AAAGCAACCACACCTTTTC-AACTCCACACAAGTCG
1 GTGGCAACCA-AAC-ATTCAAAGTCCACACGAGTTG
*
3608 GTGGCAACCAAACCTATTCAAAGTCCACACGAGTCG
1 GTGGCAACCAAA-C-ATTCAAAGTCCACACGAGTTG
* * **
3644 GTGGCAACCAAACCTATTCAAAGTCTACACAAGTCA
1 GTGGCAACCAAA-C-ATTCAAAGTCCACACGAGTTG
* * *
3680 GTGGCAACCAAATCCATTAAAAGTCCACAAGAGTCG
1 GTGGCAACCAAA--CATTCAAAGTCCACACGAGTTG
* *
3716 GTGGCAACCAAACCTTTTCAAAGTCCACATGAGTT
1 GTGGCAACCAAA-C-ATTCAAAGTCCACACGAGTT
3751 TATGGCATCC
Statistics
Matches: 355, Mismatches: 66, Indels: 50
0.75 0.14 0.11
Matches are distributed among these distances:
30 10 0.03
31 76 0.21
32 11 0.03
33 2 0.01
34 1 0.00
35 32 0.09
36 217 0.61
37 6 0.02
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.21
Consensus pattern (34 bp):
GTGGCAACCAAACATTCAAAGTCCACACGAGTTG
Found at i:3368 original size:31 final size:31
Alignment explanation
Indices: 3288--4140 Score: 232
Period size: 31 Copynumber: 25.7 Consensus size: 31
3278 AAACATTTTT
* *
3288 AAAGTCCACACGAGTTGGTGGCATCCCAGTT-
1 AAAGTCCACACAAGTTGGTGGCACCCCA-TTC
* * **
3319 AAATTCCATAGTAGTTGGTGGCACCCCATTC
1 AAAGTCCACACAAGTTGGTGGCACCCCATTC
*
3350 AAAGTCCACACAAATTGGTGGCAACCAAACCCATTC
1 AAAGTCCACACAAGTTGGTGGC-A-C---CCCATTC
* * **
3386 AAAGTTCACACGAGTCAGTGGCAACCAAAGCCATTC
1 AAAGTCCACACAAGTTGGTGGC-ACC----CCATTC
* * *
3422 AAAGTCAACACAAATTGGTGGCAACCAAACCTTTTC
1 AAAGTCCACACAAGTTGGTGGC-ACC---CC-ATTC
** * *
3458 AAAGTCCACATGAGGTGGTGGCATCCCAGTT-
1 AAAGTCCACACAAGTTGGTGGCACCCCA-TTC
*
3489 AAAGTCCACACAAGTTGGTGGCACCCGATTC
1 AAAGTCCACACAAGTTGGTGGCACCCCATTC
** * *
3520 AAAGTCCACATGAGTTAGTGGCAACCAAACCTTTCC
1 AAAGTCCACACAAGTTGGTGGC-ACC---CCATT-C
***** *
3556 AAAGTCCACACAAGTCAAAAGCAACCACACCTTTTC
1 AAAGTCCACACAAGTTGGTGGC-A-C-C-CC-ATTC
* *
3592 -AACTCCACACAAGTCGGTGGCAACCAAACCTATTC
1 AAAGTCCACACAAGTTGGTGGC-ACC---CC-ATTC
* *
3627 AAAGTCCACACGAGTCGGTGGCAACCAAACCTATTC
1 AAAGTCCACACAAGTTGGTGGC-ACC---CC-ATTC
* ** *
3663 AAAGTCTACACAAGTCAGTGGCAACCAAATCCATTA
1 AAAGTCCACACAAGTTGGTGGC-ACC----CCATTC
* *
3699 AAAGTCCACA-AGAGTCGGTGGCAACCAAACCTTTTC
1 AAAGTCCACACA-AGTTGGTGGC-ACC---CC-ATTC
** ** *
3735 AAAGTCCACATGAGTTTATGGCATCCCAGTT-
1 AAAGTCCACACAAGTTGGTGGCACCCCA-TTC
* ** *
3766 AAAGCCCACAGGAGTCGGTGGCACCCCATTC
1 AAAGTCCACACAAGTTGGTGGCACCCCATTC
* * * *
3797 AAAGTCCACACAAATTGATGGTAGCCAAACCTTTCC
1 AAAGTCCACACAAGTTGGTGGCA-CC---CCATT-C
* * * *
3833 AAAGTCCACCCAAGCTGGTGGCA-TCCTTTCC
1 AAAGTCCACACAAGTTGGTGGCACCCCATT-C
* * * *
3864 AAAGTCCATACAAGCTGGTGGCA-TCCTTTCC
1 AAAGTCCACACAAGTTGGTGGCACCCCATT-C
* * *
3895 AAAGTCCACACAAGCTGGTGGCA-TCCTTTCC
1 AAAGTCCACACAAGTTGGTGGCACCCCATT-C
* * * *
3926 AAAGTCCACACAAATCGATGGCACAATCCCAGTC
1 AAAGTCCACACAAGTTGGTGGCAC---CCCATTC
* * ***
3960 AAAGTCCACACGAGTTGGTGGCAACATTTTC
1 AAAGTCCACACAAGTTGGTGGCACCCCATTC
** ***
3991 AAAGTCCACATGAGTTGGTGGCACAATAGTT-
1 AAAGTCCACACAAGTTGGTGGCACCCCA-TTC
* * **
4022 AAAGTCCACACGAGTTGGTGGCATCCTTTTC
1 AAAGTCCACACAAGTTGGTGGCACCCCATTC
* * * *
4053 AAAGTCCACACAAGCTGATGGCA-TCCTTTC
1 AAAGTCCACACAAGTTGGTGGCACCCCATTC
* ** * **
4083 TAAAGTCTACACAAGTCAGTGGAACAAACCTTTTC
1 -AAAGTCCACACAAGTTGGTGG--C-ACCCCATTC
4118 AAAGTCCACACAAGTTGGTGGCA
1 AAAGTCCACACAAGTTGGTGGCA
4141 ACCAAACCTT
Statistics
Matches: 643, Mismatches: 133, Indels: 92
0.74 0.15 0.11
Matches are distributed among these distances:
30 13 0.02
31 292 0.45
32 18 0.03
33 3 0.00
34 40 0.06
35 54 0.08
36 214 0.33
37 8 0.01
38 1 0.00
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (31 bp):
AAAGTCCACACAAGTTGGTGGCACCCCATTC
Found at i:3507 original size:170 final size:169
Alignment explanation
Indices: 3269--3649 Score: 471
Period size: 170 Copynumber: 2.2 Consensus size: 169
3259 ATACAAGTCA
* * * * * **
3269 GTGGCAACCAAACATTTTTAAAGTCCACACGAGTTGGTGGCATCCCAGTTAAATTCCATAGTAGT
1 GTGGCAACCAAACCTTTTCAAAGTCCACACGAGGTGGTGGCATCCCAGTTAAAGTCCACACAAGT
* * *
3334 TGGTGGCACCCCATTCAAAGTCCACACAAATTGGTGGCAACCAAACCCATT-CAAAGTTCACACG
66 TGGTGGCACCCCATTCAAAGTCCACACAAATTAGTGGCAACCAAA-CCATTCCAAAGTCCACACA
*** * *
3398 AGTCAGTGGCAACCAAAGCC-ATTCAAAGTCAACACAAATTG
130 AGTCAAAAGCAACCAAA-CCTATTC-AACTCAACACAAATCG
*
3439 GTGGCAACCAAACCTTTTCAAAGTCCACATGAGGTGGTGGCATCCCAGTTAAAGTCCACACAAGT
1 GTGGCAACCAAACCTTTTCAAAGTCCACACGAGGTGGTGGCATCCCAGTTAAAGTCCACACAAGT
* ** * *
3504 TGGTGGCACCCGATTCAAAGTCCACATGAGTTAGTGGCAACCAAACCTTTCCAAAGTCCACACAA
66 TGGTGGCACCCCATTCAAAGTCCACACAAATTAGTGGCAACCAAACCATTCCAAAGTCCACACAA
* * * *
3569 GTCAAAAGCAACCACACCTTTTCAACTCCACACAAGTCG
131 GTCAAAAGCAACCAAACCTATTCAACTCAACACAAATCG
*
3608 GTGGCAACCAAACCTATTCAAAGTCCACACGA-GTCGGTGGCA
1 GTGGCAACCAAACCTTTTCAAAGTCCACACGAGGT-GGTGGCA
3650 ACCAAACCTA
Statistics
Matches: 181, Mismatches: 27, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
168 2 0.01
169 55 0.30
170 124 0.69
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.20
Consensus pattern (169 bp):
GTGGCAACCAAACCTTTTCAAAGTCCACACGAGGTGGTGGCATCCCAGTTAAAGTCCACACAAGT
TGGTGGCACCCCATTCAAAGTCCACACAAATTAGTGGCAACCAAACCATTCCAAAGTCCACACAA
GTCAAAAGCAACCAAACCTATTCAACTCAACACAAATCG
Found at i:3648 original size:107 final size:108
Alignment explanation
Indices: 3516--3749 Score: 312
Period size: 107 Copynumber: 2.2 Consensus size: 108
3506 GTGGCACCCG
*
3516 ATTCAAAGTCCACATGAGTTAGTGGCAACCAAACCT-TTCCAAAGTCCACACAAGTCAAAAGCAA
1 ATTCAAAGTCCACATGAGTCAGTGGCAACCAAACCTATT-CAAAGTCCACACAAGTCAAAAGCAA
* * **
3580 CCACA-CCTTTTCAACTCCACACA-AGTCGGTGGCAACCAAACCT
65 CCAAATCCATTAAAACTCCACA-AGAGTCGGTGGCAACCAAACCT
* * * ***
3623 ATTCAAAGTCCACACGAGTCGGTGGCAACCAAACCTATTCAAAGTCTACACAAGTCAGTGGCAAC
1 ATTCAAAGTCCACATGAGTCAGTGGCAACCAAACCTATTCAAAGTCCACACAAGTCAAAAGCAAC
*
3688 CAAATCCATTAAAAGTCCACAAGAGTCGGTGGCAACCAAACCT
66 CAAATCCATTAAAACTCCACAAGAGTCGGTGGCAACCAAACCT
*
3731 TTTCAAAGTCCACATGAGT
1 ATTCAAAGTCCACATGAGT
3750 TTATGGCATC
Statistics
Matches: 110, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
107 59 0.54
108 51 0.46
ACGTcount: A:0.36, C:0.29, G:0.15, T:0.19
Consensus pattern (108 bp):
ATTCAAAGTCCACATGAGTCAGTGGCAACCAAACCTATTCAAAGTCCACACAAGTCAAAAGCAAC
CAAATCCATTAAAACTCCACAAGAGTCGGTGGCAACCAAACCT
Found at i:3757 original size:36 final size:36
Alignment explanation
Indices: 3346--3749 Score: 261
Period size: 36 Copynumber: 11.5 Consensus size: 36
3336 GTGGCACCCC
* * * * *
3346 ATTCAAAGTCCACACAAATTGGTGGCAACCAAACCC
1 ATTCAAAGTCCACACGAGTCGATGGCAACCAAACCT
*
3382 ATTCAAAGTTCACACGAGTC-AGTGGCAACCAAAGCC-
1 ATTCAAAGTCCACACGAGTCGA-TGGCAACCAAA-CCT
* * * * *
3418 ATTCAAAGTCAACACAAATTGGTGGCAACCAAACCT
1 ATTCAAAGTCCACACGAGTCGATGGCAACCAAACCT
* * * *
3454 TTTCAAAGTCCACATGAGGT-GGTGGC-ATC---CC-
1 ATTCAAAGTCCACACGA-GTCGATGGCAACCAAACCT
* * * *
3485 AGTT-AAAGTCCACACAAGTTGGTGGC-A-C---CCG
1 A-TTCAAAGTCCACACGAGTCGATGGCAACCAAACCT
* *
3516 ATTCAAAGTCCACATGAGT-TAGTGGCAACCAAACCT
1 ATTCAAAGTCCACACGAGTCGA-TGGCAACCAAACCT
* * ** *
3552 -TTCCAAAGTCCACACAAGTCAAAAGCAACCACACCT
1 ATT-CAAAGTCCACACGAGTCGATGGCAACCAAACCT
* * * *
3588 TTTC-AACTCCACACAAGTCGGTGGCAACCAAACCT
1 ATTCAAAGTCCACACGAGTCGATGGCAACCAAACCT
*
3623 ATTCAAAGTCCACACGAGTCGGTGGCAACCAAACCT
1 ATTCAAAGTCCACACGAGTCGATGGCAACCAAACCT
* *
3659 ATTCAAAGTCTACACAAGTC-AGTGGCAACCAAATCC-
1 ATTCAAAGTCCACACGAGTCGA-TGGCAACCAAA-CCT
* * *
3695 ATTAAAAGTCCACAAGAGTCGGTGGCAACCAAACCT
1 ATTCAAAGTCCACACGAGTCGATGGCAACCAAACCT
* *
3731 TTTCAAAGTCCACATGAGT
1 ATTCAAAGTCCACACGAGT
3750 TTATGGCATC
Statistics
Matches: 294, Mismatches: 51, Indels: 46
0.75 0.13 0.12
Matches are distributed among these distances:
30 7 0.02
31 36 0.12
32 5 0.02
33 1 0.00
35 36 0.12
36 201 0.68
37 8 0.03
ACGTcount: A:0.35, C:0.28, G:0.17, T:0.19
Consensus pattern (36 bp):
ATTCAAAGTCCACACGAGTCGATGGCAACCAAACCT
Found at i:3757 original size:72 final size:71
Alignment explanation
Indices: 3344--3749 Score: 379
Period size: 72 Copynumber: 5.8 Consensus size: 71
3334 TGGTGGCACC
* * * *
3344 CCATTCAAAGTCCACACAAATTGGTGGCAACCAAACCCATTCAAAGTTCACACGAGTCAGTGGCA
1 CCATTCAAAGTCCACACAAGTCGGTGGCAACCAAACCTATTCAAAGTCCACACGAGTCAGTGGCA
3409 ACCAAA
66 ACCAAA
* * * * * *
3415 GCCATTCAAAGTCAACACAAATTGGTGGCAACCAAACCTTTTCAAAGTCCACATGAGGT-GGTGG
1 -CCATTCAAAGTCCACACAAGTCGGTGGCAACCAAACCTATTCAAAGTCCACACGA-GTCAGTGG
*
3479 C-ATC---
64 CAACCAAA
* * * *
3483 CCAGTT-AAAGTCCACACAAGTTGGTGGC-A-C---CCGATTCAAAGTCCACATGAGTTAGTGGC
1 CCA-TTCAAAGTCCACACAAGTCGGTGGCAACCAAACCTATTCAAAGTCCACACGAGTCAGTGGC
3542 AACCAAA
65 AACCAAA
* **** * * * * *
3549 CCTTTCCAAAGTCCACACAAGTCAAAAGCAACCACACCTTTTC-AACTCCACACAAGTCGGTGGC
1 CCATT-CAAAGTCCACACAAGTCGGTGGCAACCAAACCTATTCAAAGTCCACACGAGTCAGTGGC
3613 AACCAAA
65 AACCAAA
* * *
3620 CCTATTCAAAGTCCACACGAGTCGGTGGCAACCAAACCTATTCAAAGTCTACACAAGTCAGTGGC
1 CC-ATTCAAAGTCCACACAAGTCGGTGGCAACCAAACCTATTCAAAGTCCACACGAGTCAGTGGC
3685 AACCAAA
65 AACCAAA
* * *
3692 TCCATTAAAAGTCCACA-AGAGTCGGTGGCAACCAAACCTTTTCAAAGTCCACATGAGT
1 -CCATTCAAAGTCCACACA-AGTCGGTGGCAACCAAACCTATTCAAAGTCCACACGAGT
3750 TTATGGCATC
Statistics
Matches: 273, Mismatches: 43, Indels: 36
0.78 0.12 0.10
Matches are distributed among these distances:
61 2 0.01
62 23 0.08
63 2 0.01
65 3 0.01
66 3 0.01
67 40 0.15
68 3 0.01
69 1 0.00
71 57 0.21
72 135 0.49
73 4 0.01
ACGTcount: A:0.35, C:0.29, G:0.17, T:0.19
Consensus pattern (71 bp):
CCATTCAAAGTCCACACAAGTCGGTGGCAACCAAACCTATTCAAAGTCCACACGAGTCAGTGGCA
ACCAAA
Found at i:3840 original size:277 final size:276
Alignment explanation
Indices: 3346--3846 Score: 738
Period size: 277 Copynumber: 1.8 Consensus size: 276
3336 GTGGCACCCC
* *
3346 ATTCAAAGTCCACACAAATTGGTGGCAACCAAACCCATTCAAAGTTCACACGAGTCAGTGGCAAC
1 ATTCAAAGTCCACACAAATCGGTGGCAACCAAACCCATTCAAAGTTCACACAAGTCAGTGGCAAC
* * *
3411 CAAAGCCATTCAAAGTCAACACAAATTGGTGGCAACCAAACCTTTTCAAAGTCCACATGAGGTGG
66 CAAAGCCATTAAAAGTC-ACACAAATCGGTGGCAACCAAACCTTTTCAAAGTCCACATGAGGTGA
* * * ** *
3476 TGGCATCCCAGTTAAAGTCCACACAAGTTGGTGGCACCCGATTCAAAGTCCACATGAGTTAGTGG
130 TGGCATCCCAGTTAAAGCCCACACAAGTCGGTGGCACCCCATTCAAAGTCCACACAAATTAGTGG
3541 CAACCAAACCTTTCCAAAGTCCACACAAGTCAAAAGCAACCACACCTTTTCAACTCCACACAAGT
195 CAACCAAACCTTTCCAAAGTCCACACAAGTCAAAAGCAACCACACCTTTTCAACTCCACACAAGT
3606 CGGTGGCAACCAAACCT
260 CGGTGGCAACCAAACCT
* * *
3623 ATTCAAAGTCCACACGAGTCGGTGGCAACCAAACCTATTCAAAG-TCTACACAAGTCAGTGGCAA
1 ATTCAAAGTCCACACAAATCGGTGGCAACCAAACCCATTCAAAGTTC-ACACAAGTCAGTGGCAA
* *
3687 CCAAATCCATTAAAAGTC-CACAAGAGTCGGTGGCAACCAAACCTTTTCAAAGTCCACATGAGTT
65 CCAAAGCCATTAAAAGTCACACAA-A-TCGGTGGCAACCAAACCTTTTCAAAGTCCACATGAGGT
* **
3751 TATGGCATCCCAGTTAAAGCCCACAGGAGTCGGTGGCACCCCATTCAAAGTCCACACAAATT-GA
128 GATGGCATCCCAGTTAAAGCCCACACAAGTCGGTGGCACCCCATTCAAAGTCCACACAAATTAG-
* * *
3815 TGGTAGCCAAACCTTTCCAAAGTCCACCCAAG
192 TGGCAACCAAACCTTTCCAAAGTCCACACAAG
3847 CTGGTGGCAT
Statistics
Matches: 198, Mismatches: 22, Indels: 8
0.87 0.10 0.04
Matches are distributed among these distances:
275 5 0.03
276 4 0.02
277 189 0.95
ACGTcount: A:0.35, C:0.29, G:0.17, T:0.19
Consensus pattern (276 bp):
ATTCAAAGTCCACACAAATCGGTGGCAACCAAACCCATTCAAAGTTCACACAAGTCAGTGGCAAC
CAAAGCCATTAAAAGTCACACAAATCGGTGGCAACCAAACCTTTTCAAAGTCCACATGAGGTGAT
GGCATCCCAGTTAAAGCCCACACAAGTCGGTGGCACCCCATTCAAAGTCCACACAAATTAGTGGC
AACCAAACCTTTCCAAAGTCCACACAAGTCAAAAGCAACCACACCTTTTCAACTCCACACAAGTC
GGTGGCAACCAAACCT
Found at i:3903 original size:62 final size:62
Alignment explanation
Indices: 3826--4190 Score: 274
Period size: 62 Copynumber: 5.7 Consensus size: 62
3816 GGTAGCCAAA
* *
3826 CCTTTCCAAAGTCCACCCAAGCTGGTGGCATCCTTTCCAAAGTCCATACAAGCTGGTGGCAT
1 CCTTTCCAAAGTCCACACAAGCTGGTGGCATCCTTTCCAAAGTCCACACAAGCTGGTGGCAT
* *
3888 CCTTTCCAAAGTCCACACAAGCTGGTGGCATCCTTTCCAAAGTCCACACAA-ATCGATGGCACAA
1 CCTTTCCAAAGTCCACACAAGCTGGTGGCATCCTTTCCAAAGTCCACACAAGCT-GGTGG--C-A
3952 T
62 T
** * * * * * ** *
3953 CCCAGT-CAAAGTCCACACGAGTTGGTGGCAACATTTTCAAAGTCCACATGAGTTGGTGGCA-
1 -CCTTTCCAAAGTCCACACAAGCTGGTGGCATCCTTTCCAAAGTCCACACAAGCTGGTGGCAT
* * * * *
4014 CAATAGTT--AAAGTCCACACGAGTTGGTGGCATCCTTTTCAAAGTCCACACAAGCTGATGGCAT
1 C-CT--TTCCAAAGTCCACACAAGCTGGTGGCATCCTTTCCAAAGTCCACACAAGCTGGTGGCAT
* * * * * *
4077 CCTTTCTAAAGTCTACACAAG-TCAGTGGAACAAACCTTTTCAAAGTCCACACAAGTTGGTGGCA
1 CCTTTCCAAAGTCCACACAAGCT-GGTGG--C-ATCCTTTCCAAAGTCCACACAAGCTGGTGG--
*
4141 ACCAAA
60 --C-AT
*
4147 CCTTTCTCAAATTCCACACAAGCTGGTGGCATCCTTTCTCAAAG
1 CCTTTC-CAAAGTCCACACAAGCTGGTGGCATCCTTTC-CAAAG
4191 CTTGCATAAG
Statistics
Matches: 241, Mismatches: 38, Indels: 41
0.75 0.12 0.13
Matches are distributed among these distances:
60 3 0.01
61 2 0.01
62 119 0.49
63 3 0.01
64 2 0.01
65 71 0.29
66 4 0.02
68 6 0.02
69 7 0.03
70 7 0.03
71 16 0.07
72 1 0.00
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.24
Consensus pattern (62 bp):
CCTTTCCAAAGTCCACACAAGCTGGTGGCATCCTTTCCAAAGTCCACACAAGCTGGTGGCAT
Found at i:4117 original size:127 final size:126
Alignment explanation
Indices: 3895--4190 Score: 296
Period size: 127 Copynumber: 2.3 Consensus size: 126
3885 CATCCTTTCC
3895 AAAGTCCACACAAGCTGGTGGCATCCTTTCCAAAGTCCACACAAATCGATGGCACAATCCCAGTC
1 AAAGTCCACACAAGCTGGTGGCATCCTTTCCAAAGTCCACACAAATCGATGG-ACAATCCCAGTC
* ** **
3960 AAAGTCCACACGAGTTGGTGGCAACATTTTCAAAGTCCACATGAGTTGGTGGCACAATAGTT
65 AAAGTCCACACAAGTCAGTGGCAACATTTTCAAAGTCCACACAAGTTGGTGGCACAATAGTT
* * * * **
4022 AAAGTCCACACGAGTTGGTGGCATCCTTTTCAAAGTCCACAC-AAGCTGATGG-C-AT-CCTTTC
1 AAAGTCCACACAAGCTGGTGGCATCCTTTCCAAAGTCCACACAAATC-GATGGACAATCCCAGTC
* *
4083 TAAAGTCTACACAAGTCAGTGGAACAAACCTTTTCAAAGTCCACACAAGTTGGTGGCAACCAA-A
65 -AAAGTCCACACAAGTCAGTGG--C-AACATTTTCAAAGTCCACACAAGTTGGTGGC-A-CAATA
*
4147 CCTTTCT
124 ---GT-T
*
4154 CAAATTCCACACAAGCTGGTGGCATCCTTTCTCAAAG
1 -AAAGTCCACACAAGCTGGTGGCATCCTTTC-CAAAG
4191 CTTGCATAAG
Statistics
Matches: 138, Mismatches: 18, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
123 4 0.03
124 19 0.14
125 1 0.01
126 4 0.03
127 72 0.52
128 2 0.01
129 3 0.02
131 1 0.01
132 1 0.01
133 26 0.19
134 5 0.04
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.24
Consensus pattern (126 bp):
AAAGTCCACACAAGCTGGTGGCATCCTTTCCAAAGTCCACACAAATCGATGGACAATCCCAGTCA
AAGTCCACACAAGTCAGTGGCAACATTTTCAAAGTCCACACAAGTTGGTGGCACAATAGTT
Found at i:4122 original size:34 final size:36
Alignment explanation
Indices: 4079--4168 Score: 112
Period size: 34 Copynumber: 2.5 Consensus size: 36
4069 GATGGCATCC
*
4079 TTTCTAAAGTCTACACAAGTCAGTGG-AA-CAAACCT
1 TTTC-AAAGTCCACACAAGTCAGTGGCAACCAAACCT
**
4114 TTTCAAAGTCCACACAAGTTGGTGGCAACCAAACCT
1 TTTCAAAGTCCACACAAGTCAGTGGCAACCAAACCT
*
4150 TTCTCAAATTCCACACAAG
1 TT-TCAAAGTCCACACAAG
4169 CTGGTGGCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
34 18 0.38
35 6 0.12
36 9 0.19
37 15 0.31
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (36 bp):
TTTCAAAGTCCACACAAGTCAGTGGCAACCAAACCT
Found at i:4163 original size:37 final size:36
Alignment explanation
Indices: 3348--4177 Score: 242
Period size: 36 Copynumber: 24.7 Consensus size: 36
3338 GGCACCCCAT
* **
3348 TCAAAGTCCACACAAATTGGTGGCAACCAAACCCAT-
1 TCAAAGTCCACACAAGTTGGTGGCAA-CAAACCTTTC
* * ** *
3384 TCAAAGTTCACACGAGTCAGTGGCAACCAAAGCC-AT-
1 TCAAAGTCCACACAAGTTGGTGGCAA-CAAA-CCTTTC
* *
3420 TCAAAGTCAACACAAATTGGTGGCAACCAAACCTTT-
1 TCAAAGTCCACACAAGTTGGTGGCAA-CAAACCTTTC
** * * **
3456 TCAAAGTCCACATGAGGTGGTGGCATC---CCAGT-
1 TCAAAGTCCACACAAGTTGGTGGCAACAAACCTTTC
**
3488 T-AAAGTCCACACAAGTTGGTGGC-AC---CCGAT-
1 TCAAAGTCCACACAAGTTGGTGGCAACAAACCTTTC
** *
3518 TCAAAGTCCACATGAGTTAGTGGCAACCAAACCTTTC
1 TCAAAGTCCACACAAGTTGGTGGCAA-CAAACCTTTC
***** *
3555 -CAAAGTCCACACAAGTCAAAAGCAACCACACCTTT-
1 TCAAAGTCCACACAAGTTGGTGGCAA-CAAACCTTTC
* * *
3590 TC-AACTCCACACAAGTCGGTGGCAACCAAACCTAT-
1 TCAAAGTCCACACAAGTTGGTGGCAA-CAAACCTTTC
* * *
3625 TCAAAGTCCACACGAGTCGGTGGCAACCAAACCTAT-
1 TCAAAGTCCACACAAGTTGGTGGCAA-CAAACCTTTC
* ** *
3661 TCAAAGTCTACACAAGTCAGTGGCAACCAAATCC-AT-
1 TCAAAGTCCACACAAGTTGGTGGCAA-CAAA-CCTTTC
* *
3697 TAAAAGTCCACA-AGAGTCGGTGGCAACCAAACCTTT-
1 TCAAAGTCCACACA-AGTTGGTGGCAA-CAAACCTTTC
** ** * **
3733 TCAAAGTCCACATGAGTTTATGGCATC---CCAGT-
1 TCAAAGTCCACACAAGTTGGTGGCAACAAACCTTTC
* ** * **
3765 T-AAAGCCCACAGGAGTCGGTGGC-AC---CCCAT-
1 TCAAAGTCCACACAAGTTGGTGGCAACAAACCTTTC
* * * *
3795 TCAAAGTCCACACAAATTGATGGTAGCCAAACCTTTC
1 TCAAAGTCCACACAAGTTGGTGGCA-ACAAACCTTTC
* * *
3832 -CAAAGTCCACCCAAGCTGGTGG---C-ATCCTTTC
1 TCAAAGTCCACACAAGTTGGTGGCAACAAACCTTTC
* * *
3863 -CAAAGTCCATACAAGCTGGTGG---C-ATCCTTTC
1 TCAAAGTCCACACAAGTTGGTGGCAACAAACCTTTC
* *
3894 -CAAAGTCCACACAAGCTGGTGG---C-ATCCTTTC
1 TCAAAGTCCACACAAGTTGGTGGCAACAAACCTTTC
* * * * ***
3925 -CAAAGTCCACACAAATCGATGGC-ACAATCC-CAG
1 TCAAAGTCCACACAAGTTGGTGGCAACAAACCTTTC
*
3958 TCAAAGTCCACACGAGTTGGTGGCAAC--A--TTT-
1 TCAAAGTCCACACAAGTTGGTGGCAACAAACCTTTC
** *
3989 TCAAAGTCCACATGAGTTGGTGGC-AC-AA--TAGT-
1 TCAAAGTCCACACAAGTTGGTGGCAACAAACCT-TTC
* *
4021 T-AAAGTCCACACGAGTTGGTGG---C-ATCCTTT-
1 TCAAAGTCCACACAAGTTGGTGGCAACAAACCTTTC
* * *
4051 TCAAAGTCCACACAAGCTGATGG---C-ATCCTTTC
1 TCAAAGTCCACACAAGTTGGTGGCAACAAACCTTTC
* **
4083 T-AAAGTCTACACAAGTCAGTGG-AACAAACCTTT-
1 TCAAAGTCCACACAAGTTGGTGGCAACAAACCTTTC
4116 TCAAAGTCCACACAAGTTGGTGGCAACCAAACCTTTC
1 TCAAAGTCCACACAAGTTGGTGGCAA-CAAACCTTTC
* *
4153 TCAAATTCCACACAAGCTGGTGGCA
1 TCAAAGTCCACACAAGTTGGTGGCA
4178 TCCTTTCTCA
Statistics
Matches: 632, Mismatches: 121, Indels: 81
0.76 0.15 0.10
Matches are distributed among these distances:
29 2 0.00
30 14 0.02
31 242 0.38
32 13 0.02
33 5 0.01
34 47 0.07
35 39 0.06
36 243 0.38
37 27 0.04
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (36 bp):
TCAAAGTCCACACAAGTTGGTGGCAACAAACCTTTC
Found at i:4529 original size:79 final size:79
Alignment explanation
Indices: 4375--4544 Score: 196
Period size: 79 Copynumber: 2.2 Consensus size: 79
4365 CTGATGTTAT
* * * * *
4375 CTCCTTCCAAGCCTAATATCATTGGCCTTGAATTAGCACATTAGCATTCTACCCTAGTCATACAG
1 CTCCTTCTAAGCCTAATATCACTGGCCTTAAATCAGCACATTAGCATTCTACCCTAGTCAGACAG
* *
4440 CATTTTTCAAAACC
66 AATTTGTCAAAACC
* * * * * * * *
4454 TTCCTTCTAAGCCTAATGTCACTGGCCTTAAATCAGCACATTGGCATTTTGCCTTAGTTAGGCAG
1 CTCCTTCTAAGCCTAATATCACTGGCCTTAAATCAGCACATTAGCATTCTACCCTAGTCAGACAG
4519 AATTTGTCAAAACC
66 AATTTGTCAAAACC
*
4533 CTCTTTCTAAGC
1 CTCCTTCTAAGC
4545 TAGTGTTGCT
Statistics
Matches: 74, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
79 74 1.00
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (79 bp):
CTCCTTCTAAGCCTAATATCACTGGCCTTAAATCAGCACATTAGCATTCTACCCTAGTCAGACAG
AATTTGTCAAAACC
Found at i:4634 original size:78 final size:80
Alignment explanation
Indices: 4548--4695 Score: 210
Period size: 81 Copynumber: 1.9 Consensus size: 80
4538 TCTAAGCTAG
* * * *
4548 TGTTGCTAGCCTTGGATTA-CATTGGCACCTTGCCCTAAGTCATGTGGCATCTGTC-AAATCTTC
1 TGTTGCTAGCCTTGAATTACCATTAGCACCTTCCCCTAAGTCATGCGGCATCTGTCTAAATCTTC
4611 TTCACTAAAGCCCAA
66 TTCACTAAAGCCCAA
* *
4626 TGTTGCTAGCCTTGAATTAGCTCATTAGCACCTTCCCCTGAGTCATGCGGCGTCTGTCTAAATCT
1 TGTTGCTAGCCTTGAATTA-C-CATTAGCACCTTCCCCTAAGTCATGCGGCATCTGTCTAAATCT
4691 TCTTC
64 TCTTC
4696 TCAAGCTTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
78 18 0.30
81 31 0.52
82 11 0.18
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (80 bp):
TGTTGCTAGCCTTGAATTACCATTAGCACCTTCCCCTAAGTCATGCGGCATCTGTCTAAATCTTC
TTCACTAAAGCCCAA
Found at i:10349 original size:27 final size:27
Alignment explanation
Indices: 10311--10374 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
10301 TTTGGAAAGC
* *
10311 GGGTTGGAGTGTTCCCTTGAA-GAGGTG
1 GGGTTGGAGTGTTCCC-TCAAGGAGCTG
10338 GGGTTGGAGTGTTCCCTCAAGGAGCTG
1 GGGTTGGAGTGTTCCCTCAAGGAGCTG
10365 GGGTTGGAGT
1 GGGTTGGAGT
10375 ATCCCTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 3 0.09
27 31 0.91
ACGTcount: A:0.14, C:0.12, G:0.45, T:0.28
Consensus pattern (27 bp):
GGGTTGGAGTGTTCCCTCAAGGAGCTG
Found at i:13349 original size:28 final size:29
Alignment explanation
Indices: 13318--13375 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
13308 TACCATGGAT
*
13318 TTGTAGGCTTGAA-A-AGGGTGCCACTAAC
1 TTGTAGGCTT-AAGAGAGGATGCCACTAAC
*
13346 TTGTGGGCTTAAGAGAGGATGCCACTAAC
1 TTGTAGGCTTAAGAGAGGATGCCACTAAC
13375 T
1 T
13376 CGTGGACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 2 0.08
28 10 0.38
29 14 0.54
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (29 bp):
TTGTAGGCTTAAGAGAGGATGCCACTAAC
Found at i:20260 original size:20 final size:21
Alignment explanation
Indices: 20235--20282 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
20225 AAATTATATC
20235 GATACATGAGTG-AATGTATT
1 GATACATGAGTGTAATGTATT
**
20255 GATACATGCTTGTAATGTATT
1 GATACATGAGTGTAATGTATT
20276 GATACAT
1 GATACAT
20283 CACTCATTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (21 bp):
GATACATGAGTGTAATGTATT
Found at i:23681 original size:16 final size:16
Alignment explanation
Indices: 23648--23798 Score: 144
Period size: 16 Copynumber: 9.4 Consensus size: 16
23638 AAAGTCAACA
*
23648 ACCCGAATCC-AAACTG
1 ACCCGAACCCGAAA-TG
*
23664 ACCCAAACCCGAAATG
1 ACCCGAACCCGAAATG
*
23680 ACTCGAACCCGAAATG
1 ACCCGAACCCGAAATG
*
23696 ACCCGAATCC-AGAATG
1 ACCCGAACCCGA-AATG
*
23712 ACCCAAACCCGAAATG
1 ACCCGAACCCGAAATG
* * *
23728 ACCTGAATCCAAAATG
1 ACCCGAACCCGAAATG
* *
23744 ACCTGAACCCGAGATG
1 ACCCGAACCCGAAATG
* *
23760 ACCCGAATCTGAAATG
1 ACCCGAACCCGAAATG
* *
23776 ACCCAAACCAGAAATG
1 ACCCGAACCCGAAATG
23792 ACCCGAA
1 ACCCGAA
23799 TAATTAACTC
Statistics
Matches: 109, Mismatches: 23, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
15 1 0.01
16 104 0.95
17 4 0.04
ACGTcount: A:0.40, C:0.32, G:0.16, T:0.11
Consensus pattern (16 bp):
ACCCGAACCCGAAATG
Found at i:23702 original size:48 final size:46
Alignment explanation
Indices: 23648--23799 Score: 160
Period size: 48 Copynumber: 3.2 Consensus size: 46
23638 AAAGTCAACA
23648 ACCCGAATCCAAACTGACCCAAACCCGAAATGACTCGAACCCGAAATG
1 ACCCGAATCCAAA-TGACCCAAACCCGAAATGAC-CGAACCCGAAATG
* *
23696 ACCCGAATCCAGAATGACCCAAACCCGAAATGACCTGAATCCAAAATG
1 ACCCGAATCCA-AATGACCCAAACCCGAAATGACC-GAACCCGAAATG
* * * * * * * *
23744 ACCTGAACCCGAGATGACCCGAATCTGAAATGACCCAAACCAGAAATG
1 ACCCGAATCC-AAATGACCCAAACCCGAAATGA-CCGAACCCGAAATG
23792 ACCCGAAT
1 ACCCGAAT
23800 AATTAACTCA
Statistics
Matches: 86, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
47 1 0.01
48 80 0.93
49 5 0.06
ACGTcount: A:0.40, C:0.32, G:0.16, T:0.12
Consensus pattern (46 bp):
ACCCGAATCCAAATGACCCAAACCCGAAATGACCGAACCCGAAATG
Found at i:24759 original size:22 final size:21
Alignment explanation
Indices: 24734--24774 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
24724 TAAACCTGAT
24734 TGACTCAAACCTAAATTTAAAA
1 TGACTCAAACCT-AATTTAAAA
**
24756 TGACTTGAACCTAATTTAA
1 TGACTCAAACCTAATTTAA
24775 CCCGAATGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.32
Consensus pattern (21 bp):
TGACTCAAACCTAATTTAAAA
Found at i:24855 original size:16 final size:16
Alignment explanation
Indices: 24832--24906 Score: 105
Period size: 16 Copynumber: 4.6 Consensus size: 16
24822 GAAACAACCT
24832 GAACCCAAAATGACCC
1 GAACCCAAAATGACCC
* *
24848 GAATCCAAAATGACCT
1 GAACCCAAAATGACCC
*
24864 GAACCCGAAATGACCC
1 GAACCCAAAATGACCC
*
24880 GAACCCAAAATGACTC
1 GAACCCAAAATGACCC
24896 GAACCCGAAAA
1 GAACCC-AAAA
24907 CAACCCAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
16 47 0.92
17 4 0.08
ACGTcount: A:0.44, C:0.32, G:0.15, T:0.09
Consensus pattern (16 bp):
GAACCCAAAATGACCC
Found at i:24948 original size:15 final size:15
Alignment explanation
Indices: 24925--24959 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
24915 AAATTTTATA
*
24925 AACCAGAAATAAACC
1 AACCCGAAATAAACC
*
24940 AACCCGAAATAATCC
1 AACCCGAAATAAACC
24955 AACCC
1 AACCC
24960 AAAACCAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.51, C:0.34, G:0.06, T:0.09
Consensus pattern (15 bp):
AACCCGAAATAAACC
Found at i:38002 original size:11 final size:9
Alignment explanation
Indices: 37977--38037 Score: 59
Period size: 9 Copynumber: 6.1 Consensus size: 9
37967 CGATGATAGG
37977 AGGAGAGAT
1 AGGAGAGAT
37986 AGGAGAGAT
1 AGGAGAGAT
*
37995 AGTAGAGAT
1 AGGAGAGAT
38004 AGGAGGGATGAT
1 AGGA--GA-GAT
38016 AGGAGGAAAGAT
1 AGGA-G--AGAT
38028 AGGAGAGAT
1 AGGAGAGAT
38037 A
1 A
38038 ATAGAGAGAG
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
9 25 0.56
11 5 0.11
12 14 0.31
13 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.43, T:0.13
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:38006 original size:42 final size:42
Alignment explanation
Indices: 37960--38066 Score: 169
Period size: 42 Copynumber: 2.5 Consensus size: 42
37950 GAAAGAAGAT
* *
37960 ATAGGAGCGATGATAGGAGGAGAGATAGGAGAGATAGTAGAG
1 ATAGGAGGGATGATAGGAGGAGAGATAGGAGAGATAATAGAG
*
38002 ATAGGAGGGATGATAGGAGGAAAGATAGGAGAGATAATAGAG
1 ATAGGAGGGATGATAGGAGGAGAGATAGGAGAGATAATAGAG
* *
38044 AGAGGAGGGATGACAGGAGGAGA
1 ATAGGAGGGATGATAGGAGGAGA
38067 AAAGAAAAAG
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.42, C:0.02, G:0.44, T:0.12
Consensus pattern (42 bp):
ATAGGAGGGATGATAGGAGGAGAGATAGGAGAGATAATAGAG
Found at i:51043 original size:18 final size:18
Alignment explanation
Indices: 51022--51092 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
51012 CCTGTCATCC
51022 CTCCTCTCTCTATTATCT
1 CTCCTCTCTCTATTATCT
*
51040 CTCCTGTCTCTCCTACTATCATCC
1 CTCC--TCTCT-CTA-T-T-ATCT
* *
51064 CTCCTATCTCTACTATCT
1 CTCCTCTCTCTATTATCT
*
51082 CTCCTGTCTCT
1 CTCCTCTCTCT
51093 CCTCCTATCA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
18 17 0.40
19 1 0.02
20 5 0.12
21 6 0.14
22 5 0.12
23 1 0.02
24 7 0.17
ACGTcount: A:0.11, C:0.42, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTCTCTCTATTATCT
Found at i:51062 original size:42 final size:42
Alignment explanation
Indices: 51007--51125 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
50997 TTCTTCTCTC
* *
51007 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
51049 CTCCTACTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
51091 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
51126 TTGAGGGCTA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.09, C:0.45, G:0.03, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:51067 original size:24 final size:24
Alignment explanation
Indices: 51031--51116 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
51021 CCTCCTCTCT
* *
51031 CTATTATCTCTCCTGTCTCTCCTA
1 CTATCATCCCTCCTGTCTCTCCTA
*
51055 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTA
*
51076 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTA
*
51097 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
51117 TCTTTCTCTT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 15 0.30
22 5 0.10
24 21 0.42
ACGTcount: A:0.12, C:0.44, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTA
Found at i:51091 original size:9 final size:9
Alignment explanation
Indices: 51035--51095 Score: 56
Period size: 9 Copynumber: 7.1 Consensus size: 9
51025 CTCTCTCTAT
51035 TATCTCTCC
1 TATCTCTCC
*
51044 TGTCTCTCC
1 TATCTCTCC
*
51053 TA-CTAT-C
1 TATCTCTCC
*
51060 -ATCCCTCC
1 TATCTCTCC
*
51068 TATCTCTAC
1 TATCTCTCC
51077 TATCTCTCC
1 TATCTCTCC
*
51086 TGTCTCTCC
1 TATCTCTCC
51095 T
1 T
51096 CCTATCATCC
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
6 1 0.03
7 3 0.08
8 4 0.10
9 32 0.80
ACGTcount: A:0.11, C:0.43, G:0.03, T:0.43
Consensus pattern (9 bp):
TATCTCTCC
Found at i:55854 original size:165 final size:166
Alignment explanation
Indices: 55576--56032 Score: 643
Period size: 165 Copynumber: 2.8 Consensus size: 166
55566 GCCAAACACC
55576 AGGGATTAAATAGCAAATTTTAGTTTTTAAAGGTAAAATCATCATTTTAGTCATTTTTAAAGATT
1 AGGGATTAAATAGCAAATTTTAGTTTTTAAAGGTAAAATCATCATTTTAGTCATTTTTAAAGATT
* * *
55641 TCTATTATTCCTATGGCCTTCCGTAGGGGTACAA-AAATTTTCAAAACTTTTCATATCCTCTCAG
66 TCTATTATTCCTATGGCCTTCCGTAAGGGTA-AAGAAATTTTCAAAACTTTTCGTATCCTCTCAA
** * *
55705 TTTTCTGTTAAGTACA-AAATGAAATTTTTAAAAGTTT
130 TTTTCCATCAAGTA-AGAAATGAAATTTTCAAAAGTTT
* * * * *
55742 AGGGATTAAATACCAAATTTTAG-TTTTAAAGATAAAATCAACATTTTAGTCATTTATAATGATT
1 AGGGATTAAATAGCAAATTTTAGTTTTTAAAGGTAAAATCATCATTTTAGTCATTTTTAAAGATT
* * * *
55806 TCTATTATTCCTATGGCCTTTCGTAAGGATAAAGAAATTTTTAAAACTTTTCGTATCTTCTCAAT
66 TCTATTATTCCTATGGCCTTCCGTAAGGGTAAAGAAATTTTCAAAACTTTTCGTATCCTCTCAAT
**
55871 TTTCCATCGGGTAAGAAATGAAATTTTCAAAAGTTT
131 TTTCCATCAAGTAAGAAATGAAATTTTCAAAAGTTT
* *
55907 AAGGATTAAATAGCAAATTTTAGTTTTTAGAGGTAAAATCATCATTTTAGTCATTTTTAAAGATT
1 AGGGATTAAATAGCAAATTTTAGTTTTTAAAGGTAAAATCATCATTTTAGTCATTTTTAAAGATT
* * * *
55972 TCTATTATT-CTCATGGCCTTCCATAAGGGTATAGAAATTTTCAAGACTCTTCGTATCCTCT
66 TCTATTATTCCT-ATGGCCTTCCGTAAGGGTAAAGAAATTTTCAAAACTTTTCGTATCCTCT
56033 TGGTTTTTCA
Statistics
Matches: 254, Mismatches: 33, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
164 3 0.01
165 143 0.56
166 108 0.43
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (166 bp):
AGGGATTAAATAGCAAATTTTAGTTTTTAAAGGTAAAATCATCATTTTAGTCATTTTTAAAGATT
TCTATTATTCCTATGGCCTTCCGTAAGGGTAAAGAAATTTTCAAAACTTTTCGTATCCTCTCAAT
TTTCCATCAAGTAAGAAATGAAATTTTCAAAAGTTT
Found at i:59233 original size:12 final size:11
Alignment explanation
Indices: 59211--59286 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
59201 AGAGAAAGAA
*
59211 GAGAGAGGAGG
1 GAGATAGGAGG
59222 GATGATAGGAGG
1 GA-GATAGGAGG
*
59234 AGAGACAGGA--
1 -GAGATAGGAGG
*
59244 GAGATAGTA--
1 GAGATAGGAGG
59253 GAGATAGGAGG
1 GAGATAGGAGG
59264 GATGATAGGAGG
1 GA-GATAGGAGG
*
59276 AGAGACAGGAG
1 -GAGATAGGAG
59287 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:59243 original size:24 final size:24
Alignment explanation
Indices: 59210--59295 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
59200 AAGAGAAAGA
*
59210 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
59234 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
59252 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
59276 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
59296 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:59262 original size:42 final size:42
Alignment explanation
Indices: 59201--59319 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
59191 TAGCCCTCAA
* *
59201 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
59243 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
59285 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
59320 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:70055 original size:29 final size:28
Alignment explanation
Indices: 69998--70087 Score: 92
Period size: 29 Copynumber: 3.1 Consensus size: 28
69988 TGCCATGGAT
*
69998 TTGTGGGCTTGAA-AAGGGTGCCATTAAC
1 TTGTGGGCTT-AAGAAGGGTGCCACTAAC
*
70026 TTGTGGGCTTAAGAGAGGATGCCACTAAC
1 TTGTGGGCTTAAGA-AGGGTGCCACTAAC
* ** *
70055 TTGTGGACTTTTGAAAGGGTGTCACTAAC
1 TTGTGGGCTTAAG-AAGGGTGCCACTAAC
70084 TTGT
1 TTGT
70088 AGACTTTTGA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 2 0.04
28 11 0.21
29 38 0.73
30 1 0.02
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.31
Consensus pattern (28 bp):
TTGTGGGCTTAAGAAGGGTGCCACTAAC
Found at i:70092 original size:29 final size:29
Alignment explanation
Indices: 70048--70104 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
70038 GAGAGGATGC
*
70048 CACTAACTTGTGGACTTTTGAAAGGGTGT
1 CACTAACTTGTAGACTTTTGAAAGGGTGT
70077 CACTAACTTGTAGACTTTTGAAAGGGTG
1 CACTAACTTGTAGACTTTTGAAAGGGTG
70105 CCAGTGACGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.33
Consensus pattern (29 bp):
CACTAACTTGTAGACTTTTGAAAGGGTGT
Found at i:70244 original size:28 final size:29
Alignment explanation
Indices: 70208--70338 Score: 133
Period size: 29 Copynumber: 4.5 Consensus size: 29
70198 CTAGCTAGTG
*
70208 TGGGCTTT-AAAGAGG-TGCCACTGACTCA
1 TGGGCTTTGAAA-AGGATGCCACTGACTTA
*
70236 TGGGCTTT-AAAAGGATGCCACTGACTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTA
* * * *
70264 TGGGTTTTGAAAAGGGTGCAACGGACTTA
1 TGGGCTTTGAAAAGGATGCCACTGACTTA
** *
70293 TGGGCTTTGAAAAGGATGCCACCAACTAA
1 TGGGCTTTGAAAAGGATGCCACTGACTTA
70322 TGTGGACTTTGAAAAGG
1 TG-GG-CTTTGAAAAGG
70339 TTTGGTTGCC
Statistics
Matches: 86, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
27 3 0.03
28 29 0.34
29 41 0.48
30 2 0.02
31 11 0.13
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (29 bp):
TGGGCTTTGAAAAGGATGCCACTGACTTA
Found at i:70335 original size:31 final size:30
Alignment explanation
Indices: 70297--70566 Score: 155
Period size: 31 Copynumber: 8.3 Consensus size: 30
70287 GACTTATGGG
**
70297 CTTTGAAAAGGATGCCACCAACTAATGTGGA
1 CTTTGAAAAGG-TGCCACCAACTTGTGTGGA
* **
70328 CTTTGAAAAGGTTTGGTTGCCACTAACTTGTGTAAA
1 CTTTGAAAA-----GG-TGCCACCAACTTGTGTGGA
**
70364 CTTTGAATGGGGTGCCACCAACTTGTGTGGA
1 CTTTGAA-AAGGTGCCACCAACTTGTGTGGA
* * **
70395 -TTTTAACTATGGTGCCACCAACTCCTGTGGA
1 CTTTGAA--AAGGTGCCACCAACTTGTGTGGA
**
70426 CTTTGAAAAGGTTGCCACCAACTCATGTGGA
1 CTTTGAAAAGG-TGCCACCAACTTGTGTGGA
** *
70457 CTTTGACTGAGGTTCCACCAACTTGTGTGGA
1 CTTTGA-AAAGGTGCCACCAACTTGTGTGGA
**
70488 CTTTGAAAAGGATTGTGCCACTGACTTGTGTGGA
1 CTTTGAAAA-G---GTGCCACCAACTTGTGTGGA
*
70522 CTTTGAAAAAGGTTAAGTGCCACCGACTTGTGTGGA
1 CTTTG-AAAA-G----GTGCCACCAACTTGTGTGGA
*
70558 CTTTAAAAA
1 CTTTGAAAA
70567 TGATTTGGTT
Statistics
Matches: 189, Mismatches: 34, Indels: 28
0.75 0.14 0.11
Matches are distributed among these distances:
30 9 0.05
31 92 0.49
32 10 0.05
34 22 0.12
35 10 0.05
36 46 0.24
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (30 bp):
CTTTGAAAAGGTGCCACCAACTTGTGTGGA
Found at i:70442 original size:62 final size:64
Alignment explanation
Indices: 70375--70525 Score: 182
Period size: 62 Copynumber: 2.4 Consensus size: 64
70365 TTTGAATGGG
*
70375 GTGCCACCAACTTGTGTGGATTTTAACT-ATGGTGCCACCAACTCCTGTGGACTTTGAAAAGG-T
1 GTGCCACCAACTTGTGTGGACTTTAACTGA-GGTGCCACCAACTCCTGTGGACTTTGAAAAGGAT
** * * **
70438 -TGCCACCAACTCATGTGGACTTTGACTGAGGTTCCACCAACTTGTGTGGACTTTGAAAAGGATT
1 GTGCCACCAACTTGTGTGGACTTTAACTGAGGTGCCACCAACTCCTGTGGACTTTGAAAAGGA-T
**
70502 GTGCCACTGACTTGTGTGGACTTT
1 GTGCCACCAACTTGTGTGGACTTT
70526 GAAAAAGGTT
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
62 52 0.71
63 1 0.01
64 1 0.01
65 19 0.26
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.31
Consensus pattern (64 bp):
GTGCCACCAACTTGTGTGGACTTTAACTGAGGTGCCACCAACTCCTGTGGACTTTGAAAAGGAT
Found at i:70484 original size:93 final size:94
Alignment explanation
Indices: 70309--70487 Score: 225
Period size: 93 Copynumber: 1.9 Consensus size: 94
70299 TTGAAAAGGA
* ** *
70309 TGCCACCAACTAATGTGGACTTTGAAAAGGTTTGGTTGCCACTAACTTGTGTAAACTTTGAATGG
1 TGCCACCAACTAATGTGGACTTTGAAAA----TGGTTGCCACCAACTCATGTAAACTTTGAATGA
70374 GGTGCCACCAACTTGTGTGGATTTTAACTATGG
62 GGTGCCACCAACTTGTGTGGATTTTAACTATGG
** ** * *
70407 TGCCACCAACTCCTGTGGACTTTGAAAA-GGTTGCCACCAACTCATGTGGACTTTGACTGAGGTT
1 TGCCACCAACTAATGTGGACTTTGAAAATGGTTGCCACCAACTCATGTAAACTTTGAATGAGGTG
70471 CCACCAACTTGTGTGGA
66 CCACCAACTTGTGTGGA
70488 CTTTGAAAAG
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
93 45 0.63
98 26 0.37
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (94 bp):
TGCCACCAACTAATGTGGACTTTGAAAATGGTTGCCACCAACTCATGTAAACTTTGAATGAGGTG
CCACCAACTTGTGTGGATTTTAACTATGG
Found at i:70520 original size:34 final size:35
Alignment explanation
Indices: 70471--70598 Score: 134
Period size: 36 Copynumber: 3.6 Consensus size: 35
70461 GACTGAGGTT
*
70471 CCACCAACTTGTGTGGACTTTGAAAAGGATT-GTG
1 CCACCGACTTGTGTGGACTTTGAAAAGGATTAGTG
*
70505 CCACTGACTTGTGTGGACTTTGAAAAAGG-TTAAGTG
1 CCACCGACTTGTGTGGACTTTG-AAAAGGATT-AGTG
* * *
70541 CCACCGACTTGTGTGGACTTTAAAAATGATTTGGTTG
1 CCACCGACTTGTGTGGACTTTGAAAAGGA-TTAG-TG
* * *
70578 GCATCAACTTGTGTGGACTTT
1 CCACCGACTTGTGTGGACTTT
70599 AAGTGCCACC
Statistics
Matches: 79, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
34 22 0.28
35 11 0.14
36 24 0.30
37 22 0.28
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (35 bp):
CCACCGACTTGTGTGGACTTTGAAAAGGATTAGTG
Found at i:78410 original size:42 final size:42
Alignment explanation
Indices: 78363--78481 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
78353 TTCTTTTCTC
* *
78363 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
78405 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
78447 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
78482 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.08, C:0.46, G:0.03, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:78422 original size:12 final size:11
Alignment explanation
Indices: 78396--78471 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
78386 TCTATTATCT
*
78396 CTCCTGTCTCTC
1 CTCCTATCTC-C
78408 CTCCTATCATCC
1 CTCCTATC-TCC
78420 CTCCTATCT--
1 CTCCTATCTCC
*
78429 CTACTATCT--
1 CTCCTATCTCC
*
78438 CTCCTGTCTCTC
1 CTCCTATCTC-C
78450 CTCCTATCATCC
1 CTCCTATC-TCC
*
78462 CTCCTCTCTC
1 CTCCTATCTC
78472 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:78423 original size:24 final size:24
Alignment explanation
Indices: 78387--78472 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
78377 CCTCCTCTCT
* *
78387 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
78411 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
78432 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
78453 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
78473 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:78447 original size:18 final size:18
Alignment explanation
Indices: 78378--78448 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
78368 CCTGTCATCC
* *
78378 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
78396 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
78418 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
78438 CTCCTGTCTCT
1 CTCCTGTCTCT
78449 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Done.